Public Library Of Science Research Articles

Sharing Science: Enabling Global Access to the Scientific Literature

Peer-reviewed literature is the formal channel of communication for the scientific community. Through it, scientists convey their discoveries to one another across distance and time. Providing both a broadcast system and an archive, it is pivotal to the collaborative effort that is modern science. Without access to it, a scientist cannot keep up with develop-ments, has nowhere to contribute findings, and is pretty much out of the loop. One traditional problem of access to the literature faced by researchers and academics in developing countries has been the inability of their institutions to afford journal subscriptions, which can run into the thousands of dollars per publication. But things have been changing, with the last 10 years having seen important efforts to make the world’s peer-reviewed scientific journals available to these members of the research community either free or at a much-reduced price. Top-flight open-access journals have also come into being, theoretically making the papers they contain free for all to use. But is purchase price the only obstacle hindering the entry of the developing world’s researchers into international scientific dialogue?

Crimea 2011 International Conference: Libraries and Information Resources in the Modern World of Science, Culture, Education and Business

PurposeThe purpose of this paper is to provide a conference report of Crimea 2011 that the author attended in June 2011. The conference is held in Sudak, Crimea, Ukraine, each year and is organized by the Russian National Public Library of Science and Technology.Design/methodology/approachThe author attended the conference and compiled a report.FindingsThe Crimea Conference has a special relationship with IFLA and highlights library developments in Russia and the former Soviet Union countries.Originality/valueThis is an original review of the conference, which is the premiere annual library conference for Russian and Ukrainian librarians, as well as librarians from the former Soviet Union countries. For librarians with a focus on Russian area studies and Eastern Europe, the Crimea is an event not to be missed.

Article Commentary: Screening for cardiovascular disease using age alone: reflections on a paper Peer-Reviewed as both ‘radical’ and ‘unsurprising’

Article Commentary: Screening for cardiovascular disease using age alone: reflections on a paper Peer-Reviewed as both ‘radical’ and ‘unsurprising’

Finances of the publishers of the most highly cited US medical journals

The open access model, defined here as free access to scholarly publishing, has emerged alongside the traditional, subscription-based model for publishing medical journals [1–3]. The open access model was developed largely in response to rapidly rising subscription prices [4, 5], which raised concerns about access to scientific research, especially that funded by public entities [2]. In 2003, Public Library of Science (PLoS) launched a nonprofit scientific and publishing venture producing open access journals with no charge for access and, other than appropriate citation, no restrictions on use [6]. Funders of biomedical research, including the National Institutes of Health (NIH), also pushed for open access to research they support. In 2007, the NIH public access policy was signed into law, requiring that all investigators funded by NIH have an electronic version of their final manuscripts publicly available within twelve months of publication [2]. Despite the emergence of open access, knowledge of the finances of medical journal publishers is limited [4]. Published reports have surveyed open access journals, described their business models, and reported their finances [1, 7] but have been limited by their scope or have been disproportionately weighted away from for-profit publishers [1]. This study therefore sought to increase understanding of the finances of the publishers of the most highly cited US general and internal medicine journals by examining the tax status, revenue, expenses, and operating margins in order to inform public debate and policy.

Has the revolution in scholarly communication lived up to its promise?

AbstractEditor's SummaryIn the late 1990s the need for an overhaul in the approach to scholarly publishing was recognized. A drastic change would revise the economic model on which publishing was based, give authors rights to their own works in open access repositories and enable consumers across the world to access scholarly materials, building a flow of valuable information for the common good. The revolution has yet to materialize, though small but welcome achievements have been made. The open access business model has gained a foothold with the Public Library of Science (PLoS), and scientists receiving grants through the National Institutes of Health must submit manuscripts to the PubMed Central digital archive. Several universities mandate that faculty members deposit their scholarly articles in institutional repositories, and the Compact for Open Access Publishing Equity promotes open publishing by supporting authors. Librarians are both part of the problem and part of the solution. Instead of worrying about paying rising subscription fees, they could use their position to influence authors to take advantage of open access channels despite publish‐or‐perish pressures. Recent legislative and presidential initiatives, geared to disseminating publicly funded research, may be effective in moving open access closer to transforming the traditional system of scholarly communication.

Article title type and its relation with the number of downloads and citations

Title of an article can be descriptive, declarative or a question. It plays important role in both marketing and findability of article. We investigate the impact of the type of article titles on the number of citations and downloads articles receive. Number of downloads and citations for all articles published in six of PLoS (Public Library of Science) journals (2,172 articles) were obtained from PLoS and type of each article's title (including descriptive, indicative and question) was determined as well as the number of substantive words in title (title length). Statistical difference and correlation tests were carried out. The findings showed that differences exist between articles with different types of titles in terms of downloads and citations, especially articles with question titles tended to be downloaded more but cited less than the others. Articles with longer titles were downloaded slightly less than the articles with shorter titles. Titles with colon tended to be longer and receive fewer downloads and citations. As expected, number of downloads and citations were positively correlated.

On the Path to Global Open Access: A Few More Miles to Go

The PLoS Medicine Editors' individual competing interests are at http://www.plosmedicine.org/static/editorsInterests.action. PLoS is funded partly through manuscript publication charges, but the PLoS Medicine Editors are paid a fixed salary (their salary is not linked to the number of papers published in the journal). The PLoS Medicine Editors are each paid a salary by the Public Library of Science, and they wrote this editorial during their salaried time. No specific funding was received for this paper. Provenance: Written by editorial staff; not externally peer reviewed.

Open access journals: Why are we not there yet? (!)

Open access journals: Why are we not there yet? (!)

Searching for common ground: public access policy and the Scholarly Publishing Roundtable

The Scholarly Publishing Roundtable, which convened in June 2009 and issued its report the following January, was perhaps as notable for the range of backgrounds and experiences represented as it was for the resulting report. The members were drawn from: academic administration (three provosts and an association executive) and from academic libraries (three librarians), publishers of scientific journals (two from learned societies, one from an established commercial house offering a range of business models, and one from an innovative and successful open access start-up), and three researchers in the domains of library and information science. [1] Our charge was to come to a consensus on how best to provide public access to the peer-reviewed results of federally funded research. We didn't quite get there, but we accomplished a great deal. It would have been a singular achievement indeed to have arrived at complete consensus on the part of all members. On the other hand, the thoughtful dissents of YS Chi, vice chairman and managing director of global academic and customer relations, Elsevier, and Mark Patterson, director of publishing, Public Library of Science (PLoS), serve to set the outer boundaries of much of the discussion that still swirls around these issues [2, 3]. By highlighting those boundaries, the lack of complete agreement may actually have been for the best. We did come to consensus on many issues: We all agreed on the key principles and most of the recommendations. There was no dissent about the need for expanding public access to the results of federally funded research and a clear consensus on the importance of the stewarded version of record. We agreed that peer review must be protected, that the need for interoperability among repositories needs to get greater attention, and that it is absolutely crucial to address long-term preservation issues. What the dissents came down to was a matter of control and the role of government. I hope it is not a caricature of the dissents to say that, in the end, Patterson, coming from his experience with the most successful open access publisher to date, felt that the report did not call strongly enough for a firm government hand in moving expeditiously toward full open access. He believes that it is time. Informed by his experience in leadership with the most successful commercial science, technology, and medicine publisher in the world, Chi ultimately felt that the report allowed for too much government interference in achieving the public access goal. The disagreement was not over the necessity of expanded access, but over how fast to move and how strong a role the government should be allowed to take. This is an important discussion to have. The full report and the dissents speak for themselves. What I would like to relate here is my personal experience with the roundtable and my reflections on what I think we accomplished.

Free Journals Grow Amid Ongoing Debate

Ten years ago, a few scientists started an ‘open access’ campaign for free journals funded by author fees. Their flagship, the Public Library of Science, is expected to break even soon—but remains controversial.

What Do I Want from the Publisher of the Future?

When I took on the role of Editor-in-Chief of this open-access journal, I began,for the first time, to think about scholarlycommunication beyond submitting my pa-pers and getting them published. Thisthinking led to previous Perspectives [1–3],all of which shared an underlying theme—there are many opportunities to achievebetter dissemination and comprehension ofour science, and as producers of that outputI believe authors have a responsibility to seeit used in the best possible way.No need to take my word regarding theopportunities that exist to improve schol-arly communication and comprehension. Irecommend reading ‘‘Part 4: ScholarlyCommunication’’ from the free onlinebook the Fourth Paradigm: Data Intensive Scien-tific Discovery [4] (http://research.microsoft.com/en-us/collaboration/fourthparadigm/),which is a tribute to the late Turing Awardwinner Jim Gray. Jim, and many of theauthors who pay homage to his vision, havethought deeply about the subject of scholarlycommunication. They conclude that dataand knowledge-driven computation is indeeda fourth wave, as computation has impactedscience to the point where every aspect of itis touched by computation (hence the nameeScience), including dissemination and com-prehension. These visionaries recognize thatwe are at a tipping point at which scholarlycommunication will change from a tradi-tional print-oriented medium (albeit an on-line version of the print journal) to somethingelse. That something else begins to transformtoday’s research article as we realize thepower of the medium, establish new forms ofknowledge discovery, and measure theimpact of scholarly contributions in newways. For all that vision, these luminaries donot address the question that I have beenpondering, and which I would like to raisehere. Assuming all this innovation takesplace, what will the publisher of the futurelook like, and as a contributor and consumerof a publisher’s services in this new era, whatdo I want from the publisher of the future?Recently, at gatherings of publisherswhere I have been invited to speak, I havebeen trying to pose and then answer thisquestion. Unfortunately, I fear that what Ipropose appears so radical as to be greetedwitheitherblankstaresorlooksof getreal.LetmetryheretodoabetterjobatstatingwhatI want from my publisher in the future.Many of you are undoubtedly thinkingthat just accepting your papers will beenough, but bear with me. Presumably,publishing will continue in the life sciences(unless we go over completely to anArXiv.org or similar model where articlesare simply deposited without peer reviewand impact measured by how much theyare accessed), and if so, will continue to beoverseen by the publishers we, as scientists,work with today. A few new and innova-tive publishers like the Public Library ofScience (PLoS) will continue to emerge asbusiness models and practices change, butexisting publishers will probably adapt inthis new era. I anticipate similarities toearlier phases of the Internet revolution.Amazon.com emerged as a new and majoronline-only shopping entity, but Sears,Wal-Mart, Harrods, etc., while beingslower in adopting the new medium, dideventually successfully support onlineshopping and a range of new services. Bycomparison, a few innovators have hadsome impact on scholarly communication,but traditional science, technology, andmedical (STM) publishers will continue todominate the conservative and relativelyslow-moving market. These pioneeringpublishers are now experimenting withinteractive PDFs, ‘‘articles of the future,’’semantic tagging, data integration withresearch articles, incorporating rich media(video and podcasts), and so on. Mostlikely, at some point these innovations willbecome mainstream through increasedintroduction by traditional publishers, butthen what? Stated another way, if wefinally move away from the traditionalPDF to something more dynamic thatintegrates data, rich media, and includesinteractive access, what do I as a scientistwant from publishers at that point?To answer this question, let us start withwhere we are today. As authors, we put anenormous amount of effort into producingapublishablemanuscript.Atsomepointwepass it over to the publisher without asecondthought.Subsequently,wewillputalarge amount of effort into a revision orrebuttal letter, but again, there is nothought on what will happen to our workafterithasbeenacceptedbeyondthedateitwill be published and appear in PubMed.There is an enormous amount of trust inour publisher that our creations will behandled in the best possible way and, whenpublished, that they will be disseminated toallwhowanttoreadourwork.Openaccessintroduced a hairline fracture in this trustwith some scientists realizing that perhapstheir work was notbeingaswidely accessedaspossible.Nevertheless,mostscientistsstilldo not think seriously about limited accessand signing away the copyright. After alloureffortsatproducingapaper,veryfewofus have asked the question, is journal xpresenting my work in a way that maxi-mizes the understanding of what has beendone, providing the means to ensuremaximum reproducibility of what has beendone, and maximizing the outreach of mywork? I would suggest that now is the timenottojusttossthepaperoverahighbarrierto the journal and forget about it, but tobreak down the barrier and have a newform of interaction and dialog with apublisher who is prepared to embrace achanging publishing model and cananswerthe question in a satisfactory manner. Inother words, we have an interaction withthe publisher that does not begin when thescientific process ends, but begins at thebeginning of the scientific process itself.Perhaps you are beginning to see why Iget so many blank stares when I raise thisissue with scientists (producers and consum-

Open access initiatives in life, biological and medical sciences: an investigative outlook

Published scientific discoveries and ideas are the foundation for future progress in science and medicine. The more widely and freely accessible the literature is, the greater its value to scientists, researchers, doctors, students and the general public. Unfettered access to research literature will allow scientists, physicians, educators, students, and the general public to find and read the latest scientific and medical discoveries. Authors have discussed various open access initiatives in this article include OpenWetWare (OWW), The Public Library of Science (PLoS), Protocol Online, PubMed and PubMed Central (PMC), Directory of Open Access Journals (DOAJ) and 3 QUARKS Daily.

Reframing Critical Needs in Vector Biology and Management of Vector-Borne Disease

Reframing Critical Needs in Vector Biology and Management of Vector-Borne Disease

New Law May Be Having Some Effect on Publication Bias

P ositive trials get reported more often than negative trials, according to many studies. And despite efforts in the past decade to combat publication bias, it remains a substantial problem, according to two articles published last fall. One found that results had been published from fewer than half of the trials registered in the federal database, clinicaltrials.gov. The second article found that approximately one-third of the trials eventually published in journals changed the trial endpoint prior to publication. Despite the disconcerting results, experts are cautiously optimistic that a federal law may be having an effect. The law requires not only registration of trials but also that researchers enter results into the database. Journal policies had previously encouraged trial registration, but the new law adds clout. “The only way trial registration was going to have an effect was if someone was going to enforce it, and this is the enforcement that is needed. I think it could well address publication bias,” said Virginia Barbour, M.D., chief editor of the open-access journal PLoS Medicine, in the Public Library of Science in London. Although experts look forward to evaluating the infl uence of the law, no one — including Barbour — expects that it can entirely cure the problem. Other efforts are needed, experts say, including increased scrutiny of trial protocols and registration information during the peer-review process.

Profitable failure: antidepressant drugs and the triumph of flawed experiments

Drawing on an analysis of Irving Kirsch and colleagues' controversial 2008 article in "PLoS [Public Library of Science] Magazine" on the efficacy of SSRI antidepressant drugs such as Prozac, I examine flaws within the methodologies of randomized controlled trials (RCTs) that have made it difficult for regulators, clinicians and patients to determine the therapeutic value of this class of drug. I then argue, drawing analogies to work by Pierre Bourdieu and Michael Power, that it is the very limitations of RCTs -- their inadequacies in producing reliable evidence of clinical effects -- that help to strengthen assumptions of their superiority as methodological tools. Finally, I suggest that the case of RCTs helps to explore the question of why failure is often useful in consolidating the authority of those who have presided over that failure, and why systems widely recognized to be ineffective tend to assume greater authority at the very moment when people speak of their malfunction.

Further reflections on open access

The round table in last month’s Bulletin stated that “it is only through removing the barriers to access to global research that health improvements can be accelerated”.1 Similar thinking inspired the founding publishers and WHO to establish the Health Access to Research programme (HINARI) in 2001. I agree with the round table’s authors that the topic is a critical reminder for policy-makers as the world continues to struggle with those barriers. HINARI is a public–private partnership and our main concern is to make research available to developing countries. The partnership focuses on that goal and does not attempt to evaluate the relative advantages of any particular publishing model. I would like to correct a few small errors in the way HINARI is described in this round table. HINARI is portrayed as a means for developing country institutions to have access to commercial publisher journals. However, in addition to commercial publishers, HINARI has a wide range of open access and local publishing partners such as MedKnow, the Public Library of Science (PLoS) and Bioline International, with which two of the authors of this round table are affiliated. The authors state the importance of exposing research “from both research communities in developing countries as well as from ‘international’ research”.1 In fact, HINARI and its related programmes – Access to Global Online Research in Agriculture (AGORA) and Online Access to Research in the Environment (OARE) – currently have 127 publishers that usually charge subscription fees and 89 publishers that distribute their content without subscription fees. All three programmes do more than just providing access to published research. The programmes also supply training on how to search the scientific literature and use its resources to inform decisions. Another important function of HINARI, AGORA and OARE is to collaborate with other international agencies and partners to build the technological infrastructure that institutions need to access information. I am puzzled by the concern expressed by the authors that selection of content for HINARI is not driven by science (i.e. contents are determined by whatever publishers wish to donate). The content initially offered by each publisher is further expanded and refined through ongoing feedback from the programme and users with a view to including all that is relevant – for HINARI this is biomedical and related social sciences literature. Such an inclusive policy aligns with the open access goal of providing access to what is published and letting the reader decide what is of most interest. The authors state that access is available only from registered libraries and on provision of a password controlled by libraries. This is not quite accurate. HINARI registers many tiny research institutes, very few of which actually have a library and some of which are research institutes of only one or two people. Passwords are provided to directors of institutions and librarians, if there is a library. If there is no library, the director may designate another person to assist in the password distribution. In this way, even the smallest AIDS research station can have the benefit of the information access and HINARI becomes their library. The authors quote a letter to PLoS Medicine noting an analysis done at Universidad Peruana Cayetano Heredia on access to HINARI in April 2007.2 This letter mentions that one possibility for a drop in HINARI users was an increase in users of commercial content aggregations like ProQuest and Ebsco. Further studies are needed: both to capture the complex picture of information access in developing countries as people gain more access to the world’s research output and to design the spectrum of responses that are required to address their needs. HINARI, AGORA and OARE review their activities on a regular basis and use the results to ensure the achievement of objectives and improve the quality of service. HINARI is only one way to lower the barriers to information access and there are many others. It is unlikely that any one solution will meet everyone’s needs. The key is to develop and perfect many overlapping solutions and methods, so that all researchers can access the scientific information published globally by their predecessors and contemporaries, however that access is provided. ■

Proposal of a new editorial policy for EHPM and Nippon Eiseigaku Zasshi

Proposal of a new editorial policy for EHPM and Nippon Eiseigaku Zasshi

Websites of note

Websites of note

A reflection on open-access, citation counts, and the future of scientific publishing

In the new era of wide dissemination of information, the opportunities to communicate and share the results of scientific research are immense. The consequences of this change are, however, somewhat unpredictable. For one thing, the more people have access to information and ideas, the more ideas we will have and, in theory, scientific knowledge may expand to levels never seen before. Nevertheless, one may wondered whether this expansion of knowledge will have beneficial or harmful effects. The widespread diffusion of erroneous ideas, whether from scientists or laymen, has the potential to do substantial damage due to the pervasive influence of the Internet. However, this same ubiquity will, surely, ensure that mistaken ideas or theories, at least those propounded by reputable scientists, will also be discussed and refuted where necessary. In the field of scientific publishing, the scrutiny of ideas and results, i.e. peer review, appears to have worked quite well until the arrival of the World Wide Web. Moreover, science is largely a self-correcting process. It is also true that the mechanisms used by scientific journals to communicate new scientific data have contributed greatly to the present state of things. But it is also easy to imagine that scientific knowledge could spread much faster in the new information age than hitherto. It is thus understandable that the open-access movement has received such overwhelming support from many sectors. For scientists, open access implies not only immediate access to the full written article, but also to data and metadata that can be used for re-analysis. It also means major visibility; in other words, if someone is looking for a paper and does not have access through the Internet, they may simply disregard it unless they really need it. However, it is also understandable that traditional publishers, who no doubt have been those mainly responsible for and the guarantors of the transmission of most scientific discoveries for the betterment of society so far, are reluctant to accept the new system. Although the true cost of scientific publishing has not been determined, many journals are profitable to their owners. Journals owned by for-profit companies may well contend that they are conducting sound business, while revenue from publications is used by not-for-profit organizations to further advance the cause of the organization (DeAngelis and Musacchio 2004). In addition, publishers can always argue that they took the initial financial risk in starting journals and are entitled to a return on their investment. Much has been written on the topic of open access over the last few years, especially since the launch of the Public Library of Science (PLoS) in October 2003. Richard Smith, former editor of the BMJ, has perhaps too radically compared the business of publishing to theft, where publishers make money by preventing ideas from breeding more ideas and stopping the expansion of knowledge (Smith 2007). Smith, who was BMJ’s chief editor for 25 years, suggested that journals should bid for the best papers, rather than researchers transferring their copyright to journals for free. The traditional system of scholarly publishing certainly reveals some striking ironies. A reviewer who has worked to shape an article and has refereed the article for free may have no access to the final version of the published article if they or their institution has no subscription to the journal. At the other end of the spectrum are those who argue that we are inundated by information but lack the time to evaluate it and that open access worsens this situation by opening the gates to increasing amounts of unfiltered information (Esposito 2007), which is, in my opinion, sometimes really junk information. There are also concerns about whether reputational incentives will 2009 Arch. Immunol. Ther. Exp., 2009, 57, 91–93 PL ISSN 0004-069X DOI 10.1007/s00005-009-0016-y VARIA

A Review of 2008 for PLoS Computational Biology

A very Happy New Year to all our authors, readers, editors, and reviewers from everyone at the Public Library of Science! 2008 was a remarkable year for PLoS Computational Biology; which saw 50% more submissions than in 2007 (900 full articles and 175 presubmission inquiries), more than 260 high-quality research articles published, and regular contributions of Editorials, Reviews and Perspectives, and Education and Society pages. This growth and maturity of content leaves no doubt that our Journal has become a leading reference for the field of computational biology and a trusted place to publish. Such success has come through the hard work of our Editors, not only from our Editorial Board but also from the anonymous reviewers and Guest Editors who expend so much time and energy in the assessment of submitted manuscripts (each averaging 2.8 reviews and 1 to 2 rounds of revisions), and from the attention to detail and care taken over the content. Peer review by external experts is essential to ensuring that the work published in PLoS Computational Biology is of the very highest quality, and we are grateful to all of our reviewers for their thoughtful and informed comments. Guest Editors are those who step in to edit one particular paper that describes work in an area of research that falls outside the expertise of the more than 50 volunteer Editors on our Board. The flexibility and availability of these Guest Editors is invaluable in our being able to provide a high level of review, as well as playing an important role in maintaining the broad appeal and vibrancy of the Journal. Their names can be found together in Table S1 as an acknowledgment of the good work they do and the time they donate to improve the body of scientific literature and knowledge. In 2008, our pool of reviewers included approximately 1,300 scientists in 36 countries, including Vietnam, Mexico, Brazil, and Afghanistan, as well as in countries such as Israel, Germany, and Japan, where the Journal is better-known. This impressive geographical spread indicates that we are reaching the best of the best across the scientific world, something only a well-respected journal of quality is able to accomplish. Organic growth requires that we constantly assess both the kinds of papers we accept and the standards of research they represent. We have revised our scope statement to reflect slight changes in our focus (see http://www.ploscompbiol.org/static/information.action), and we constantly refine our Editorial Board (http://www.ploscompbiol.org/static/edboard.action) to handle the number and types of papers we are encouraging. Experiencing solid growth can come at a price to the speed of our Editorial processes, however, and while we aim to provide a decision to our authors within 35 days, some papers defy this time limit. We are confident, however, that with your continued help and support, we will reach our targets more consistently this year. As authors, you appreciate a swift response time, and as reviewers you can help us achieve this by making a commitment in 2009 to return reviews within two weeks. Looking ahead in 2009, you can expect to see not only more great research, but also greater connectivity between content found in different PLoS journals and among members of your community. As an example of the former, PLoS Computational Biology will be working with PLoS ONE to feature developments in software important to our discipline. For the latter, the community can read and participate in discussions that start when readers post a comment or rating on a published article. As we have done since our launch, we welcome your feedback on how we're doing and what we should be doing going forward. This is your Journal, and our open philosophy encourages your engagement in it. By working together, we can further establish the importance of our science to our understanding of living systems and make a positive contribution to moving it forward even in these uncertain times. Once again, many thanks to all of you for your support and commitment to making 2008 a successful year for PLoS Computational Biology and to ensuring that we are able to achieve even more in the upcoming year.