Public Library of Science - PLoS Neglected Tropical Diseases

PLoS Author Surveys 2009 – Summary Presentation

Mark Patterson — Wed, 23 Dec 2009 02:45:25 -0800

Earlier this year, PLoS sent out a series of surveys to authors whose work was considered by our journals in 2008. We wanted to find out what authors think about all aspects of our services – from submission and peer review, through to publication and the functionality of the PLoS journal web sites.

We have learned a lot from the surveys, primarily that levels of satisfaction amongst authors are generally very good. We also identified areas where services can be improved, and we’ve adjusted our services in a number ways during 2009.

We have now summarized the results of the surveys along with how we have responded to some of the suggestions during 2009 in a short presentation, which is publicly available. We feel it’s important to share these results in particular with the authors who were kind enough to complete the questionnaires, and we would like to express our thanks to the hundreds of authors who took part. We are planning to repeat the surveys next year, so that we can monitor how views have changed and can respond to suggestions for further improvements.

Meanwhile, we welcome feedback from anyone who is using our services, as an author, reviewer, editor or reader.

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PLoS at ASTMH 2009 - Booth 501

Shabnam Sigman — Fri, 30 Oct 2009 14:20:32 -0700

PLoS is getting ready for this year's ASTMH meeting (Washington, D. C., November 18–22), where you’ll find us at Booth 501 in the exhibition hall.

Meet editorial team members from PLoS Neglected Tropical Diseases and PLoS Pathogens who will be on hand to answer questions about publishing your work with PLoS, open access, and article-level metrics.

Editors-in-Chief Peter Hotez and Serap Aksoy (PLoS Neglected Tropical Diseases) and Kasturi Haldar (PLoS Pathogens) will be at the booth at selected times along with other journal editors and PLoS staff members Shabnam Sigman (Publications Manager, PLoS Neglected Tropical Diseases) and Mary Kohut (Publications Manager, PLoS Pathogens). Visit Booth 501 for the schedule.

Pick up some great giveaways:

T-Shirts—for delegates who sign up to receive free e-mail content alerts. This year’s shirt, with its unique design, is available only at this event, so be sure to stop by, sign up, and claim yours while supplies last.
Buttons/Badges—designed for our authors, Editorial Board members, readers, and supporters.
Fact Sheets—that showcase the Editorial Boards and top papers.
Postcards— to remind yourself and your colleagues why you should publish with PLoS.

We look forward to welcoming ASTMH 2009 delegates to our booth!

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PLoS NTDs: Providing Access to Innovation for the World's Poor

Shabnam Sigman — Wed, 29 Jul 2009 18:56:15 -0700

This month’s editorial in PLoS Neglected Tropical Diseases introduces Serap Aksoy, who steps up as Editor-in-Chief alongside Peter Hotez. Together they examine the articles being submitted to the journal, and the different ways in which the impact and quality of the journal can be measured.

Here’s an excerpt:

… It is clear that our community journal is moving in the right direction and in some cases has already achieved some of its goals. Article submissions to the journal have been steadily increasing from throughout the world, with roughly one-half from “the North,” i.e., the United States, Canada, and Europe (and also Australia), and the other half from “the South,” i.e. Latin America and the Caribbean, Africa, and Asia.

… The observation that almost one-half of our article submissions come from the NTD-endemic countries is especially gratifying. Brazil now accounts for the second largest number of article submissions, behind the United States. Submissions from Brazil have been extremely high in quality and cover a wide range of topics, from molecular pathogenesis and clinical aspects to epidemiology and policy.

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PLoS Journals – measuring impact where it matters

Mark Patterson — Mon, 13 Jul 2009 05:22:00 -0700

In 2009, in this online world, how do most scientists and medics find the articles they need to read? The answer for the content published by PLoS (and no doubt by many other publishers) is via one of the now ubiquitous search engines, be it one that only searches the scientific literature, or more likely, one that searches the entire web. Given that readers tend to navigate directly to the articles that are relevant to them, regardless of the journal they were published in, why then do researchers and their paymasters remain wedded to assessing individual articles by using a metric (the impact factor) that attempts to measure the average citations to a whole journal? We’d argue that it’s primarily because there has been no strong alternative. But now alternatives are beginning to emerge.

A few months ago, PLoS initiated a program to provide a series of metrics on the individual articles published in all the PLoS Journals. You can see some examples here, here, here and here. There are two complementary benefits to the new approach.

First, we are focusing on articles rather than journals. The dominant paradigm for judging the worth of an article is to rely on the name and the impact factor of the journal in which the work is published. But it’s well known that there is a strong skew in the distribution of citations within a journal – typically, around 80% of the citations accrue to 20% of the articles. So the impact factor is a very poor predictor of how many citations any individual article will obtain, and in any case, journal editors and peer reviewers don’t always make the right decision. Indicators at the article level circumvent these limitations, allowing articles to be judged on their own scientific merits.

Second, we are not confining article-level metrics to a single indicator. As summarized by Michael Jensen, and discussed by many others including recently over at the Scholarly Kitchen, there’s a lot more to scientific impact than citations in the selection of journals covered by the Web of Science – the proprietary source of data that provides the impact factor calculation. Citations can be counted more broadly, along with web usage, blog and media coverage, social bookmarks, expert/community comments and ratings, and so on. Our own efforts are so far confined to citations (as measured by Scopus and PubMed Central), social bookmarks (as made by users of Connotea and CiteULike), and blog coverage (as recorded by Bloglines, Postgenomic and Nature Blogs), and these metrics will be improved and expanded over the coming months. The good news is that many of these indicators can be collated automatically, using openly available web tools that constantly update information on the article itself.

The presentation of a comprehensive array of this data is an enticing prospect. When an article has been published, we have tended to regard that as the end of the story (barring corrections or the occasional retraction). But if, as frequently happens, a very good article has been published in a specialist journal after being rejected from a highly selective one, it would be great to indicate to a user that this article is actually looking pretty significant, and show how its influence develops over the months and years.

Rather than basing judgments on the importance of research on the opinions of two or three reviewers and editors, article-level metrics will attempt to capture the actions and opinions of entire communities of readers to give a rich and sophisticated picture of research impact that will be helpful to authors and readers alike. Readers may then frame that picture in the context of their particular field and their own work.

To realize the vision for article-level metrics there are still some significant hurdles to clear: it won’t be enough simply to provide indicators without some context or guidance on how to interpret them; some indicators (particularly citations) take months to build up limiting their value as early indicators of impact; and standards will need to be developed so that the indicators are reliable and as free as possible from gaming and manipulation.

A clear editorial selection process will always have a place before publication in a scholarly journal. But a reduction in the reliance on the impact factor for so many aspects of research assessment could be massively liberating. PLoS Medicine, to cite an example close to home, has recently restated its mission – focusing on the diseases and risk factors that have the most profound impacts on global health. By carefully selecting articles that are likely to have the biggest influence on global health and using innovative and diverse approaches to assess and indicate that influence, PLoS Medicine will be a greater force, regardless of how many citations an average article accrues

Looking towards other modes of publishing, PLoS ONE is predicated on the notion that judgements about impact and relevance can be left almost entirely to the period after publication. By peer-reviewing submissions purely for scientific rigour, ethical conduct and proper reporting before publication, articles can be assessed and published rapidly. Once articles have joined the published literature, the impact and relevance of the article can then be determined on the basis of the activity of the research community as a whole. Article-level metrics and indicators, along with other post-publication features are part and parcel of the PLoS ONE approach, and could help readers to filter and sort literature after it is published. Ultimately, the aim of adding value to articles after publication is to improve the whole process of scientific communication and accelerate research progress itself. You can read more about article-level metrics in the context of PLoS ONE, and a talk is also available online from Pete Binfield (Managing Editor of PLoS ONE).

Article-level metrics and indicators will become powerful additions to the tools for the assessment and filtering of research outputs, and we look forward to working with the research community, publishers, funders and institutions to develop and hone these ideas. As for the impact factor, the 2008 numbers were released last month. But rather than updating the PLoS Journal sites with the new numbers, we’ve decided to stop promoting journal impact factors on our sites all together. It’s time to move on, and focus efforts on more sophisticated, flexible and meaningful measures.

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Creative Re-Use Demonstrates Power of Semantic Enhancement

Shabnam Sigman — Thu, 16 Apr 2009 15:44:17 -0700

A Review article published today in PLoS Computational Biology describes the process of semantically enhancing a research article to enrich content, providing a striking example of how open-access content can be re-used and how scientific articles might take much greater advantage of the online medium in future.

Dr. David Shotton and his team from Oxford University spent about ten weeks enriching the content of an article published in PLoS Neglected Tropical Diseases, the results of which can be seen online here.

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.

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 (obtains background from, confirms, extends, shares authors with, uses method in). The group has also provided interactive versions of some of the figures: compare the original, static Figure 3 to the moveable, overlaying, enhanced version.

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. These developments significantly enrich the content of a paper, and also demonstrate some of the potential that open-access provides by removing any barriers on the re-use of content. 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. 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, either as a comment to this post, or on the article itself.

By Evie Browne, Publication Manager, PLoS Computational Biology

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International Trachoma Initiative and Task Force for Child Survival and Development Announce New Merger

Shabnam Sigman — Mon, 23 Mar 2009 12:25:58 -0700

Partnership aims to eliminate blinding trachoma and scale up the fight against other neglected tropical diseases

Guest blog by Ibrahim Jabr, President, International Trachoma Initiative

This week has seen a significant development in the fight against blinding trachoma. As president of the International Trachoma Initiative (ITI), I was pleased to announce on March 18 that we are joining forces with The Task Force for Child Survival and Development (the Task Force) to significantly scale up efforts and leverage additional resources for eliminating trachoma, a neglected tropical disease (NTD) that is the world’s leading cause of preventable blindness.

All of us at ITI are excited by the enormous potential that this merger brings to the Global Elimination of Blinding Trachoma by the year 2020 (GET 2020). We realized in 2006 that to meet this WHO goal, we would need a new partner. The ITI board and executive team engaged in an extensive, year-long search for an organization that could help us scale up and increase the impact of our efforts. We are confident that the Task Force is that partner.

ITI selected the Task Force because of its capacity in program development and implementation, fundraising, and advocacy. CARE USA has expressed interest in working with the Task Force as a partner in trachoma elimination, along with other NGOs.

Particularly important to all our work is the implementation of the World Health Assembly (WHA)-endorsed SAFE strategy that combines public health education, improved hygiene, sight-saving surgery, and treatment with antibiotics donated to ITI by Pfizer Inc. (SAFE stands for Surgery, Antibiotics, Facial cleanliness, and Environmental improvements.) The Task Force, working with CARE USA, provides a forum for sharing knowledge and expertise in these four program areas, especially in the area of integration of mass drug administration with the global goals of sanitation and safe water.

As many in the field know, ITI was created through a public-private partnership of the Edna McConnell Clark Foundation and Pfizer in 1998. At the time of our announcement, Jeffrey B. Kindler, Chairman and CEO of Pfizer said: "Pfizer is confident that the merger between ITI and the Task Force is a positive step forward in ridding the world of blinding trachoma … We look forward to continuing our support and working through ITI and its Trachoma Expert Committee to provide the Zithromax that will be needed to eliminate blinding trachoma by 2020 and restore the health and well-being of families now and generations to come."

I feel that ITI’s merger with the Task Force will not only improve our efficiency and impact but also allow us to take full advantage of a unique synchronicity in approaching NTDs. The Task Force currently houses programs that are successfully addressing three NTDs: onchocerciasis, lymphatic filariasis, and intestinal worms. The ITI merger with the Task Force will allow us to take full advantage of our combined momentum and together increase the impact of our joint efforts worldwide.

Disclaimer: ITI receives funding and donation of Zithromax from Pfizer Inc.

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A reminder: PLoS will reject unregistered trials

Gavin Yamey — Sun, 01 Mar 2009 12:43:31 -0800

Last week, the PLoS Neglected Tropical Diseases editors rejected a clinical trial, without even sending it for peer review, because the trial had been initiated after July 1 2005 and yet the authors had failed to prospectively register it in a clinical trials registry.

We want to remind all authors again of our position on clinical trial registration, a position made explicit in our guidance to authors:

“PLoS supports the position of the International Committee of Medical Journal Editors (ICMJE) on trial registration. All trials initiated after 1 July 2005 must be registered prospectively in a publicly accessible registry (i.e., before patient recruitment has begun), or they will not be considered for publication. For trials initiated before 1 July 2005, all trials must be registered before submission to our journals. See the ICMJE faq on trial registration for further details. The WHO's list of approved registries is listed here.”

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Guest Blog: Call for Scale-up of R&D for Neglected Diseases

Shabnam Sigman — Mon, 23 Feb 2009 16:46:38 -0800

By Oliver Yun, Medical Editor, Doctors Without Borders/Médecins Sans Frontières, New York, NY

Doctors Without Borders/Médecins Sans Frontières (MSF) and the Drugs for Neglected Diseases initiative (DNDi) issued a call today for ramping up funding and governmental support for R&D to combat neglected diseases. Related research appears in PLoS Neglected Tropical Diseases, among other journals, and we applaud such publications for bringing much-needed attention to these overlooked diseases, which primarily affect the world’s poor and neglected populations.

In the field, MSF faces numerous neglected diseases, both endemically, such as sleeping sickness (human African trypanosomiasis), kala azar (visceral leishmaniasis), and Chagas disease; and epidemically, including cholera, meningitis, and measles. Developing and improving the tools to diagnose, treat, and prevent these diseases require numerous resources, not the least of which is financial. The first three diseases alone put more than 500 million people at risk of infection.

Two recent reports estimated global and US funding at $2.5 billion and $366 million, respectively, for neglected-disease R&D: the February 2009 George Institute for International Health’s Global Funding of Innovation for Neglected Diseases (G-FINDER) study, financed by the Gates Foundation and published in part in PLoS Medicine; and the December 2008 Families USA report “The World Can’t Wait: More Funding Needed for Research on Neglected Infectious Diseases,” which focused on eight diseases and four US government agencies.

These highly informative yet troubling reports, coupled with today’s call to action, serve as stark reminders for the urgent need for increased funding into R&D for the world’s most neglected diseases. Without action, these diseases will continue to exact their silent, devastating toll.

You can read the full MSF/DNDi press release here: http://doctorswithoutborders.org/press/release.cfm?id=3429&cat=press-release

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PLoS Neglected Tropical Diseases at ASTMH 2008

Liz Allen — Fri, 21 Nov 2008 12:17:25 -0800

PLoS Neglected Tropical Diseases, is getting ready for this year's ASTMH meeting (New Orleans, Dec 7-11), where you’ll find us at Booth 101 in the exhibition hall.

Here are examples of recent research articles that received media attention that should be of interest to those attending this meeting:

The Burden of Trachoma in Ayod County of Southern Sudan by King JD et al.
Tribendimidine and Albendazole for Treating Soil-Transmitted Helminths, Strongyloides stercoralis and Taenia spp.: Open-Label Randomized Trial by Steinmann P et al.
The Global Programme to Eliminate Lymphatic Filariasis: Health Impact after 8 Years by Ottesen EA et al.
Acute Schistosoma mansoni Infection Increases Susceptibility to Systemic SHIV Clade C Infection in Rhesus Macaques after Mucosal Virus Exposure by Chenine A-L et al.
Relationship between Transmission Intensity and Incidence of Dengue Hemorrhagic Fever in Thailand by Thammapalo S et al.

Visiting us at Booth 101 at ASTMH provides a nice opportunity to meet the team—PLoS Neglected Tropical Diseases Editor-in-Chief Peter Hotez and the journal’s Deputy Editors will be at the booth at selected times (posted at the booth) to answer questions about PLoS, open access, the NIH Public Access Policy, and publishing your work in PLoS Neglected Tropical Diseases. PLoS staff members Shab Sigman (Publications Manager) and Vanessa Tomlinson (Publications Assistant) will also be on hand to answer your questions.

We'll also have some great giveaways for those of you who come and visit us:

T-Shirts—We will be giving our 2008 t-shirt to delegates who sign up to receive free e-mail content alerts. This year’s shirt, with its unique design, is available at only this event, so be sure to stop by, sign up, and claim yours while stocks last.
Buttons/Badges designed for our authors, Editorial Board members, readers, and supporters.
Fact Sheets that showcase the Editorial Board and top papers.
Postcards to remind yourself and your colleagues why you should publish in PLoS Neglected Tropical Diseases.

We look forward to welcoming ASTMH 2008 delegates to our booth.

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Low-Hanging Fruit: An Anti-Parasitic Drug Database

Shabnam Sigman — Tue, 28 Oct 2008 09:30:08 -0700

A guest blog by Michelle Arkin and James McKerrow at The Sandler Center for Research in Parasitic Diseases and the Small Molecule Discovery Center, University of California, San Francisco

Neglected tropical diseases (NTDs) affect hundreds of millions of people worldwide, but are largely ignored by the biopharmaceutical industry because the afflicted are usually poor people in poor regions of the world. As a result, the drug development pipeline for these diseases is largely empty. Furthermore, drugs currently used to treat these diseases may have frequent and severe side effects, efficacy limited to certain stages of the disease, or efficacy only in certain geographical regions. Target-directed drug development for NTDs is one logical approach to fill the pipeline.

A second and very cost-effective approach is “diversity” or “phenotypic” screens where drug libraries are tested directly against parasites in culture without regard to known or validated targets. In one variation of this approach, we searched for previously unrecognized antiparasitics among the drugs currently approved for clinical use. Such hits would be “low-hanging fruit”, with the advantages of proven human safety, and known dosing schedules and pharmacokinetics. Chris Lipinski has estimated there are approximately 2,000 such drugs (www.collaborativedrug.com/register/FDA - register, log in, and go to “data sets”), and an analysis by Chong et al. at Johns Hopkins University puts the number at 3,400 (Chong CR et al. Nat Chem Biol 2: 415-16, 2006). Some of these drugs can be obtained commercially or through material transfer agreements (Microsource, NINDS, Johns Hopkins Clinical Compound Library [JHCCL]). Additionally, Iconix Biosciences has donated to the Sandler Center its proprietary collection, which contains ~1,000 compounds, 218 of which are not found in the Microsource or JHCCL collections (P. Phuan, unpublished data). Close to 30 other companies have donated proprietary libraries to the Sandler Center for screening.

Two years ago, the first screen of the Microsource Spectrum Collection (1,995 compounds) against Trypanosoma brucei was published (Mackey ZB et al. Chem Biol Drug Design 67: 355-63, 2006). Since then, similar screens have been run for Leishmania donovani and Plasmodium falciparum (Weisman JL et al. Chem Biol Drug Des, 2006). The Low-Hanging Fruit site provides a portal by which the community can view hits from these screens and make decisions on which compounds represent the most suitable leads to take to the next step in the drug development pipeline. We have now carried out screens for T. brucei, L. donovani, Entamoeba histolytica, and Schistosoma mansoni using the Spectrum Collection. We are in the process of expanding our dataset using the Iconix library, and we will post this data in the coming months.

The apples on the tree at the website represent links to data for the parasites indicated. In some cases, this data is a simple list of hits to be viewed by those individuals and agencies interested in rapid follow-up. In other instances, a more complete database can be accessed under “protocols and statistics” as compiled by Pipeline Pilot (Accelrys) software.

We view this website as both a resource and a challenge. Through Low-Hanging Fruit, we provide our data on an open-source basis to the antiparasitic drug development community at large. We hope this encourages others to pursue these hits, either as potential drug leads or for target discovery and validation studies. We expect that some of the drug hits will interest researchers with expertise in particular biochemical pathways. We also challenge the community at large to provide their data in a similar open-source manner to encourage new collaborations and follow-up. We envision that this website may serve as one component of a larger community database “hub”, linking global efforts in all stages of the antiparasitic drug development pipeline to initiate new collaborations and minimize redundancy of effort.

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