Progress Updates

Welcome to the PLOS Progress Update 2011-2012, aimed at keeping our authors, reviewers, editors, and supporters fully apprised of our developments and activities over the past year.

Download the Progress Update – low-resolution or high-resolution – or scroll down to read it on this page. Our complete 2011 financial disclosure is also available. For a fuller historical picture of how far we have come, read the Progress Updates from 2008, 2009, and 2010, or download our 2010 financial disclosure.

A Transformation in Scientific Communication

PLOS is a nonprofit organization founded to accelerate progress in science and medicine by leading a transformation in research communication.

From the Chairman and CEO

We mark another year of progress toward our mission of transforming research communication. This transformation can be realized only when the results of research itself are fully open. As the scientific community and public increasingly embrace open access, we continue to gain momentum. Our progress and the growth of additional open-access organizations and publishers are signs that publishing unrestricted, peer-reviewed research that is available to everyone is a viable model.

PLOS began publishing journals to demonstrate that high-quality, open-access research can flourish without the barriers imposed by subscription fees. Today, our publishing model sustains our journals and enables us to invest in innovations and outreach that are changing the scientific communication landscape. Technology is improving the way articles are used. Governments and academic institutions are increasing support for the open-access movement. Growing numbers of scientists are submitting articles to PLOS, choosing to make their research open.

This Progress Update outlines our investments in infrastructure to support our growth; outreach activities that promote open access; innovations that focus on article reach; and journal publications that impact the scientific community. We are grateful to our authors, readers, reviewers, editors, advisors, and staff for all that we have accomplished in the past year and for supporting our ongoing mission.

Gary Ward, Chairman of the Board
Peter Jerram, Chief Executive Officer

Sharing Scientific Research

PLOS supports open access to make scientific articles immediately and freely available to anyone, anywhere, to download, print, distribute, read, and reuse without charge or other restrictions, with proper attribution of the authors and original source. Open access fuels discovery by freeing research from its barriers. Scientists can more rapidly build on the work of others in their field. Librarians can enable wider dissemination. Funders can maximize their return on investment in the research they fund. Entrepreneurs can access articles to develop new technologies. And the public can benefit from scientific and medical advances.

“The beauty of PLOS’ open access model ripples out far beyond the individual journals. Under the Creative Commons license, PLOS content can be easily distributed with appropriate attribution.”
-Craig Dalton, Public Health Physician at Hunter New England Health, Conjoint Senior Lecturer, School of Medicine and Public Health, University of Newcastle, Australia

A New Platform
To optimally share our articles, we migrated them to a new platform that scales to accommodate the publishing growth of PLOS journals. The platform can store any type of data, runs on a private cloud, and is designed to minimize downtime, simplify development and implementation of new features, and speed website access. After migration to the new platform, the average load time of a sample article fell from four seconds to 0.8 seconds. Work is ongoing to redesign the appearance and usability of our websites to update look and feel. We have optimized article figure images for online viewing by increasing resolution and interactivity.

Supporting Community

PLOS is part of a larger community that contributes to and raises awareness of open access. We collaborate with many groups of researchers, educators, students, developers, and librarians at the forefront of the open-access movement. PLOS served on the Budapest Open Access Initiative’s 10-year anniversary steering committee. PLOS staff has been involved with organizations that develop open-access policies, including the UK Open Access Implementation Group and the United Nations Educational, Scientific, and Cultural Organization (UNESCO). We remain integrally involved in International Open Access Week, as a founding advisory committee member. Open Access Week 2011 included thousands of participants from more than 92 countries. We sponsored a webinar with Healthcare Information for All (HIFA) 2015, which comprises more than 5,000 individuals, representing 2,000 organizations in 167 countries. Webinar participants met online and discussed how open access can save lives by advancing healthcare knowledge. We participated at the Berlin 9 Open Access 2011 conference in Washington, DC, to continue engaging organizations and institutions in support of the Berlin Declaration on Open Access.

The open-access community has made great strides over the past year. Our institutional membership has grown to more than 130 organizations. We launched the Article-Level Metrics (ALM) Technical Working Group to help steer ongoing development of these measurements. We piloted open access Hackathons, bringing together 20 developers and five technology- and advocacy-based organizations to share expertise and develop applications that encourage the adoption of open access. The goal of developing these applications is to help organize and empower the open-access community.

Gaining Momentum

In 2011-2012 there has been a surge of support for open-access publication from the scientific community. PLOS and other open-access publishers saw an acceleration of growth in submissions and published articles. We applaud Harvard University; the University of California, San Francisco; UNESCO; the Wellcome Trust; Research Councils UK; and the World Bank for issuing open-access statements and policies during the past year. Recently, the Finch Report recommended adopting open-access publishing for publicly funded research and the UK government has committed to making all publicly funded research accessible. The major UK government funding bodies have issued a policy recommending the use of open-access journals and requiring a Creative Commons Attribution License (CC-BY) where a publication fee is paid. Following the announcement of the UK policy, the European Commission ruled as a “general principle” that recipients of the commission’s research grants publish in open-access journals.

The America COMPETES Reauthorization Act, signed by President Obama in 2011, prompted the US Office of Science and Technology Policy to release two Requests for Information (RFIs) on policies for federally funded peer-reviewed scholarly articles. RFI comments reflected the position that public access to research enables economic growth. Alongside ACCESS2RESEARCH, we helped mobilize the open-access community by building grassroots support for a recent White House petition, requesting free access to articles arising from taxpayer-funded research. The Research Works Act (RWA), which threatened to enforce restrictive copyrights for publishers while negating the NIH Public Access Policy, was retracted by its original sponsors. The Federal Research Public Access Act (FRPAA), which PLOS supports, remains before Congress.

Publishing Research Responsibly

Maintaining integrity in the communication of science remains one of the most critical functions of scholarly publishing. Each PLOS journal is peer-reviewed and employs rigorous ethical and quality control checkpoints throughout the publishing process, including a clear policy on competing interests and financial disclosures. PLOS staff is part of the leadership of the Committee on Publication Ethics (COPE) council, the World Association of Medical Editors (WAME), and OASPA. We have published extensively on the issue of ghostwriting, when one or more unacknowledged authors substantially contribute to a manuscript. We recently formed an advisory committee to develop a policy on “dual-use” research, which can potentially be used for harm. PLOS Medicine, PLOS Biology, and PLOS ONE will not publish papers in which any of the research costs or author salaries have been funded, in whole or in part, by a tobacco company.

PLOS staff has participated in the development of reporting guidelines, and has published a number of them. These guidelines are tools that help authors prepare manuscripts that accurately and completely report the research. They help peer reviewers better assess manuscripts and readers understand them, with the ultimate aim of improving the quality of published research. In the past, PLOS Medicine published the revision to the Consolidated Standards of Reporting Trials (CONSORT) and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. More recently, PLOS Medicine published guidelines on the Strengthening the Reporting of Observational Studies in Epidemiology – Molecular Epidemiology (STROBE-ME) statements, and the guidelines on Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK), while PLOS Biology published the Animals in Research: Reporting In Vivo Experiments (ARRIVE) guidelines.

Advancing Scholarly Publishing

PLOS is working to evolve the scientific article from a static publication event into a more dynamic, living form of communication. Our authors’ contributions to open repositories, such as Dryad, enable other scientists to validate, explore, and repurpose data for research questions not anticipated by the original authors. PLOS is a contributing member of Open Researcher & Contributor ID (ORCID, Inc.), which aims to standardize author disambiguation. Our innovative publishing approach to advance speed, flexibility, and revision capabilities, PLOS Currents, was recently migrated onto a new platform, allowing for growth and experimentation toward more rapid communication of scientific and medical information.

PLOS remains at the center of efforts to reimagine the tools for discovering and assessing research articles. Article-Level Metrics (ALMs), including usage and citation data, are available for every PLOS article, from the first one published to the most recent. These provide a suite of measures that can help researchers, institutions, and funders track the use and reach of their articles. We continue to develop the quantity, quality, and usefulness of these measures. Increasingly, ALMs help readers find the article most relevant to their needs and understand the larger context of the work.

PLOS encourages others to use our content and data by providing application programming interfaces (APIs) for ALM data and a Search API, both of which enable outside developers to create applications. To date, 160 developers have used the PLOS APIs to determine, for example, the total impact of articles using aggregated data from multiple sources. We encouraged further development of PLOS APIs by cosponsoring the PLOS/Mendeley Binary Battle. Grand prize winner openSNP developed an application that shares personal genome data and accesses the latest relevant research, helping scientists to discover new genetic associations. PLOS also made its ALM application available as open source so that other platforms and publishers may offer these metrics to their users.

“PLOS not only publishes open access articles, but actively measures the reach and reuse of those articles using innovations that themselves are open to reuse.”
-Heather Piwowar, co-founder of total-impact, ALM Technical Working Group member, postdoc with Duke University at NESCent and the Department of Zoology at University of British Columbia, Vancouver, Canada

Our goal is not only to measure but to extend the reach of articles. Through open-access publishing, we promote article reuse in projects such as PLOSable Biology, which provides interactive learning opportunities to invite public involvement in science. When research results are reused in novel ways, it contributes to discovery. Advances in computational biology research, for example, require openly accessible methods and computational resources, including databases and software that implement a specific procedure or algorithm. PLOS Computational Biology is requesting articles for a new software section that features outstanding open-source software, supports reproducibility, distinguishes rigorous work, and promotes new hypotheses and observations. Seven articles have been accepted to date on software shown to provide significant biological insight and meet stringent documentation requirements. The collection will formally launch in late 2012.

Highlighting Our Journals

The seven open-access journals published by PLOS are each rigorously peer reviewed. Everything that we publish is freely available online for anyone to access. Here are some articles published over the past year that have generated significant attention and interest.

PLOS Biology, the first journal published by PLOS, covers all aspects of biology. Highlights from the past year include the Open Access Collection, with an illuminating perspective focusing on important benchmarks and advantages of open access, covering copyright and licensing attributes.

A study assessing the number of species in Earth’s biosphere predicted that there are about 8.7 million (±1.3 million) species globally. If true, 86% of the species on Earth have yet to be discovered. The study received more than 73,000 views and significant press coverage.

A study that revisited analyses from the nineteenth and twentieth centuries showed that the scientific method can shield results from cultural bias, in contrast to Stephen Jay Gould’s analysis of George Morton’s work on human skulls and the nature of variation among human populations. The article has been viewed more than 32,000 times and generated much buzz.

Research into the internal clock of blind cavefish that live in perpetual darkness showed that they retain a circadian rhythm—albeit one of nearly 47 hours—nearly twice as long as most animals. The fish’s clock is not affected by introducing light into its environment, but could be regulated by a feeding schedule. The findings were widely covered, including in The New York Times.

A study of neural speech processing suggested it may be possible to determine intended speech by measuring brain activity. The article received over 60,000 views and was described in the PBS video series Science Bytes (episode 4), and a podcast.

Investigation of the first deep-sea hydrothermal vent communities discovered in the Antarctic suggested that the environmental conditions of the Southern Ocean may act as a barrier to some vent animals. The article has been viewed more than 38,000 times and was broadly covered in the press.

PLOS Medicine is the leading open-access medical journal, providing an innovative and influential venue for primary research and analysis on the major challenges to human health worldwide. Article highlights include a study by researchers from World Health Organization (WHO) and Save the Children, providing estimates of newborn mortality rates for all WHO member states over 20 years. Picked up by international media and publicized widely by WHO and Save the Children, the study has been accessed more than 24,000 times and has led to further estimations of global child mortality.

Research on rural Kenyan district hospitals and a related cost-effectiveness analysis showed that an intervention involving physician training and feedback leads to improved care for sick children. Scaling up the intervention is as cost-effective as accepted approaches, such as insecticide-treated bed nets. The intervention strategy is being funded by the UK government and rolled out in several East African countries.

An unprecedented analysis on conflicts of interest among funders of global health showed that many foundations have associations with and investments in private food and pharmaceutical corporations that benefit from foundation grants. The authors recommend several strategies for mitigating these conflicts of interest.

A systematic review of eHealth technologies challenges assumptions about the effectiveness of digital solutions to enhance healthcare delivery. The study showed a lack of evidence for eHealth to improve patient outcomes and for their cost-effectiveness. The article has been viewed more than 32,000 times.

An investigation of medical complicity in torture at Guantánamo Bay drew on case records, documenting for perhaps the first time that health providers assigned to the US Department of Defense at Guantánamo Bay neglected and/or concealed medical evidence of intentional harm.

PLOS Medicine also published an editorial to accompany the study. Together, the editorial and the study have been viewed more than 22,000 times.

A study on forced human trafficking and health and a related editorial show that trafficking for sexual exploitation was associated with violence and serious subsequent health problems. The study received substantial press coverage in numerous languages and countries.

The trafficking article was included in the PLOS Medicine Migration & Health Collection. Another groundbreaking series, the Ghostwriting Collection, included a recent article on challenging ghostwriting in the courts that has received more than 11,000 views so far this year.

PLOS ONE is the world’s largest peer-reviewed open-access scientific journal. It is known as an innovator in scholarly publishing for pioneering the replacement of subjective evaluation measures with objective criteria that focus on technical quality. The journal publishes primary research from over 50 diverse science and biomedical disciplines. PLOS ONE articles have more than 53 million page views.

In addition to being recognized as a Scholarly Publishing and Academic Resources Coalition (SPARC) Innovator, the journal was acknowledged by The American Heart Association Council on Functional Genomics and Translational Biology for publishing research that was considered to be one of the top advances in 2011. The International Society for Environmental Epidemiology honored a PLOS ONE article with the Best Environmental Epidemiology Paper Award of 2011.

A recent article on genomic features of a Drosophila lineage, reared in a dark environment for 57 years (1,400 generations), suggested a list of genes involved in environmental adaptation. The article received more than 194,000 views and significant press coverage. Another important study in 2011 described a new antiviral therapy that selectively kills mammalian cells containing viral dsRNA. The article was viewed more than 114,000 times and widely cited in the press.

A study sampling metagenomic data from the Atlantic, Pacific, and Indian Oceans indicated a possible fourth domain of life—a potential shift from the canonical eukaryotic, prokaryotic, and archaeal domains. The article received more than 40,000 views and significant press coverage.

Firmly in the eukaryotic domain, a new species of Yeti crab was discovered in a study that describes the crabs waving their bristly claws to farm symbiotic bacteria for food. This research also received substantial attention in the press.

PLOS Genetics publishes new research in genetic and genomic biology. A recent editorial on genome-wide association studies clarified the journal’s policy for this type of study and emphasized the importance of open access for data. The journal’s most-viewed article in 2011 was a phylogenetic analysis to determine the origin, evolution, patterns of speciation, and unique features in genomic divergence among primate lineages. The article was viewed more than 21,000 times and received attention in the press.

Articles on the legality and safety of traditional Chinese medicines; the genetics underlying the phenotype depicted in Vincent van Gogh’s Sunflowers; and the potential for a non-hormonal contraceptive for men also received widespread public and press attention.

The first study of a genome-wide association of habitual caffeine intake, involving over 40,000 participants, revealed two loci or genetic variants associated with habitual caffeine consumption. The article was viewed more than 14,000 times and received significant press coverage.

Perspective articles, each highlighting a research article in 1,000 words or less, have also featured prominently recently, with 17 Perspectives published during the past year. One notable Perspective on germline selection in human males was written by the population geneticist James F. Crow.

PLOS Pathogens publishes original research and a variety of commentary articles on the biology of pathogens and host-pathogen interactions. A study that showed a tumor cell marker is a receptor for measles virus was the journal’s top-cited paper last year, receiving significant press attention. The study suggested the possible approach using the measles virus for fighting cancer.

A potentially groundbreaking study, Innate Sensing of HIV-Infected Cells, described a new cytoplasmic pathway of detection of HIV-infected lymphocytes that acts independently of the well-studied endosomal TL7 pathway.

A study on malaria showed that Plasmodium knowlesi infections are not new to humans in Southeast Asia and suggested that the pathogen’s preferred host could shift from macaques to humans, due to population growth and deforestation.

The RON2-AMA1 protein-protein interaction is a critical step in host cell invasion by Apicomplexan parasites, according to a study that opened the way for possible new approaches to interfere with the functions of Toxoplasma gondii and Plasmodium falciparum.

A study on Pseudomonas aeruginosa showed that the polysaccharide Pel is crucial for biofilm integrity for some strains of the bacteria, and suggested that Pel enhances resistance to antibiotics.

PLOS Neglected Tropical Diseases is devoted to the study of helminth, bacterial, viral, protozoan, and fungal infections endemic to tropical regions. The Genetically Modified Insect Collection featured articles that described the technological advances, regulatory framework, and societal dialogue necessary for the wide-scale application of this controversial approach to disease control.

An article in the Sleeping Sickness Collection reports WHO findings that showed new cases of human African trypanosomiasis (HAT), more familiarly known as sleeping sickness, fell below 10,000 in 2009. The accompanying editorial suggests that this result may signal a possible end to the latest epidemic cycle.

Another recent collection focused on the control and elimination of human helminthiases. An editorial described the WHO Disease Reference Group on Helminth Infections (DRG4), which put forward a series of eight reviews. Together, the reviews outlined a compelling approach for the control and elimination of six of the major helminth diseases affecting humans.

A joint statement by an international team of scientists argued for a comprehensive, integrated cholera response in Haiti in the wake of the January 12, 2010 earthquake. The resulting humanitarian crisis coupled with long-standing problems with healthcare, water, and sanitation, and the observed virulence of the El Tor hybrid strain, necessitate control and preventative approaches to solve the crisis.

PLOS Neglected Tropical Diseases coordinated the launch of a new Google.org tool to track dengue outbreaks by publishing the methodology behind the tool. An expert commentary accompanied the article and provided an alternative perspective to the approach used by the researchers at Google Inc. and Harvard University who developed the tracking tool.

PLOS Computational Biology is a society journal, aligned with the International Society for Computational Biology (ISCB), that publishes new research in all areas of biology using computational methods. In 2011 more than 553,000 unique visitors were documented on the journal website from 211 countries. The journal’s highlights from 2011 included an analysis of gene regulation focusing on cell-to-cell variability in transcriptional output. The research has more than 10,500 views.

One article described the imaging of 354 rat whiskers to create a three-dimensional model of a rat face. The analysis helped researchers understand how rats translate whisker bending into sensory perception. More than 2,800 people viewed the article, which was widely covered in the press, including on NPR’s Talk of the Nation and Science Friday.

The most highly viewed article in the journal during 2011 was an editorial that outlined 10 tips for building and maintaining a scientific reputation. Part of the journal’s Ten Simple Rules Collection, the article provided a starting point to quantify scientific reputation and challenged researchers to contribute to the description. The editorial was viewed more than 19,600 times.

The Bioinformatics: Starting Early Collection was introduced during the past year to support teaching the discipline in secondary schools. The collection affirmed the journal’s relationship with ISCB and suggested a place for bioinformatics in high school curricula.

The Editors’ Outlook Collection featured diverse mini-reviews from members of the PLOS Editorial Board on their research areas, and included discussions of new and future developments. The collection formed a record of what computational biology has achieved and what it can hope to achieve in the near term.

Financials: Achieving Sustainability and Investing in Open-Access Advancement

PLOS posted an increase in net assets of $3.95 million in 2011, the second straight year of sustainability. Gross revenue grew 49% to $24.7 million—the result of publishing nearly twice as many research articles as in 2010—while expenses (inclusive of publication fee assistance) grew by 51% to $20.8 million, resulting in a modest improvement in our financial performance of net assets over 2010. The key contributor to our growth was PLOS ONE, now the largest journal in the world, which had the biggest absolute increase in volume. Our growth and revenues validate open access as a viable and sustainable publishing model, and enable us to invest in our mission by scaling up our infrastructure and removing barriers through increased open access and innovation.

Investing in Our Mission
To meet the growing needs of our authors and expand our capacity to meet the increased volume in submissions and published articles, PLOS has invested substantially over the past year in our operational infrastructure. We have improved our tools, processes, and systems, added staff to meet increased volume demands, and expanded our facilities. In addition, we have built up operational reserves to enable future investments in our mission and to provide a buffer against unforeseen changes.

PLOS is also investing in research and development (R&D) by establishing new and innovative ways to publish, disseminate, and share scientific research. Our efforts in developing ALMs as a way to comprehensively measure the impact of articles continued throughout 2011. We made progress on PLOS Currents to innovate and accelerate the communication of research within specific fields of science and medicine. PLOS Hubs continues to serve the research community as our expert curators add and enrich the most compelling open-access content to the hub.

We continue to work on innovations to encourage post-publication activity, advance data interactivity through rich media, create new functionality with the ALM application, increase navigability and discoverability, and connect people to content by showcasing authors and other scientists. We are investing in ways to reduce the time between the completion of research and the sharing of results, including new authoring tools and channels.

In 2011, PLOS reaffirmed its commitment to removing cost as a barrier to authors. We provided $2.5 million in publication fee assistance, which included waivers ($2.2 million) for authors unable to pay all or part of their publication fees and institutional discounts ($0.3 million). For the third consecutive year we have not raised publication fees. In 2012 PLOS plans to provide even more publication fee assistance for authors.

2011 Expenses

Thanking Our Supporters
PLOS thanks the following foundations and sponsors for their support.

Grants
Alfred P. Sloan Foundation
The John D. and Catherine T. MacArthur Foundation
William K. Bowes, Jr. Foundation
Open Society Foundations

Sponsorships
Harvard School of Public Health
Imperial College
Parent Project Muscular Dystrophy
UNAIDS and PEPFAR

PLOS Board of Directors and Management as of August 2012

PLOS Board
Gary E. Ward, PLOS Chairman of the Board
Professor of Microbiology and Molecular Genetics and Co-Director of the Vermont Center for Immunology and Infectious Diseases, University of Vermont

Patrick O. Brown, PLOS Co-founder Stanford University School of Medicine, Howard Hughes Medical Institute

Michael B. Eisen, PLOS Co-founder
Assistant Professor of Genetics, Genomics and Development, Department of Molecular and Cell Biology, University of California, Berkeley

Heather Joseph, Executive Director, SPARC

David Liddle, Venture Partner, US Venture Partners

Robin Lovell-Badge, Head of the Division of Stem Cell Biology and Developmental Genetics, MRC National Institute for Medical Research, London

Rosalind L. Smyth, Director of the Institute of Child Health, UCL, London

Marty Tenenbaum, Chairman and Founder, CommerceNet

Beth Weil, Former Head Librarian, Marian Koshland Bioscience and Natural Resources Library, University of California, Berkeley

Senior Staff
Peter Jerram, Chief Executive Officer
Steve Borostyan, Chief Financial Officer
Kristen Ratan, Chief Products Officer
Darlene Yaplee, Chief Marketing Officer
Liz Allen, Director of Marketing and Business Development
Susan Au, Director of Finance
Virginia Barbour, Chief Editor, PLOS Medicine; Medicine Editorial Director
Theodora Bloom, Chief Editor, PLOS Biology; Biology Editorial Director
Paula Carter, Director of Project Management
Richard Cave, Director of IT & Computer Operations
John Chodacki, Director of Product Management
Cameron Neylon, Director of Advocacy
Damian Pattinson, Executive Editor, PLOS ONE
Tracy Pelon, Director of Production Operations
Paul Raskin, Director of Customer Experience
Katie Sharabati, Director of Human Resources

Editorial Boards
PLOS Biology: (view Editorial Board)
PLOS Medicine: (view Editorial Board)
PLOS Computational Biology: Philip E. Bourne, Editor-in-Chief and Ruth Nussinov, Editor-in-Chief (view Editorial Board)
PLOS Genetics: Gregory S. Barsh and Gregory P. Copenhaver, Editors-in-Chief (view Editorial Board)
PLOS Pathogens: Kasturi Haldar, Editor-in-Chief (view Editorial Board)
PLOS Neglected Tropical Diseases: Peter Hotez and Serap Aksoy, Editors-in-Chief (view Editorial Board)
PLOS ONE: (view Editorial Board)