PLOS 2013/2014 PROGRESS UPDATE 2 From the Chair and CEO

PLOS has been dedicated to leading a transformation in scientific research communication since its inception. The organization begins its second decade as a publisher by rededicating itself to creating and promoting the most effective means of scientific communication possible.

In an age of constant and rapid change, PLOS believes that research assessment is in need of reinvention. One-time pre-publication review must be replaced by continual assessment that offers findings without unnecessary delay and fosters the evolution of scientific ideas over time. PLOS has taken important steps toward this ideal with open evaluation to explore alternative assessments of research outcomes, assessment of impact at the article level rather than by journal and by augmenting the depth of Article-Level Metrics through crowdsourcing of media coverage.

Traditional publishing models and the static PDF are insufficient for 21 st century scientific communication. Integral to its effort to move beyond the article, PLOS implemented a new Data Policy that encourages scientific dialogue by ensuring access to the data that underlies the research findings. This in turn advances research through corollary improvements in quality, reproducibility and appropriate credit.

Fortunately, growing momentum in Open Access research and policies frees scientific outputs from the constraints of traditional publishing models, accelerates dissemination of knowledge and engages communities in active dialogue and participation.

PLOS exists because of the vital contributions of authors, readers, reviewers, editors, advisors, funders, librarians, policy advocates and staff. The active support of this extended community is critical to continue driving research communication towards its full potential.

PLOS honors its commitment to foster a culture of innovation, embrace and facilitate change, and liberate scientific knowledge to provide rapid and effective communication and assessment of scientific ideas, results and discoveries for the public good.

Gary Ward, Chair Elizabeth Marincola, Chief Executive Officer

3 Capturing Impact for Better Assessment Innovative Forms of Peer Evaluation Allow Continual Assessment PLOS believes that research assessment needs to be timely, continual and inclusive. In collaboration with experienced scientists and 200 PLOS ONE Academic Editors, PLOS piloted an open evaluation approach to research assessment that complements existing PLOS Highlights peer review practices. In open evaluation, at any time, members of the science community can rapidly evaluate one another’s work by providing open, structured feedback on the scientific merit of published articles and on their presentation and importance. If widely % adopted, continual assessment will facilitate evolving scientific consensus and track 100 evolution over time to more accurately reflect article impact than current practices. Open Access Monitoring the Scholarly Record Improves Accuracy To communicate the reliability of PLOS content, for both initial publications and updates, PLOS participates in CrossRef’s CrossMark program. This service provides researchers 204 a consistent way to be informed about changes to the scholarly record, including updates, Staff corrections, errata, retractions and withdrawals. The functionality is in place for every (As of June 30, 2014) PLOS article page on the journal sites – over ten years of publishing that translates into approximately 110,000 articles and over 3,000 migrated corrections – and on the + downloadable PDFs for all newly-published articles going forward. 10 Article-Level Metrics Developments Ease Scale and Reporting Years as a leader in Article-Level Metrics (ALMs) paint the evolving picture of a published work over time to Open Access publishing provide a deeper understanding of the impact and influence of individual scholarly works. Development work has extended the robustness and scale of the ALM application for use by the publishing industry: CrossRef Labs has indexed 748,254 articles with PLOS’ ALM application to use as a test index during technical improvement; enhanced ALM Reports 7 better support the wide breadth of reporting needs by the research, funding, policy and Journals institutional communities; and the PLOS ALM suite of academic and social sources now includes PubMedCentral Europe and PubMedCentral Europe Database links. 22 Crowdsourcing Captures Media Coverage Blogs The Media Curation Tool enhancement to PLOS article pages enables researchers, journalists, funders, institution administrators and authors to submit links to and access media stories from individual article pages. Crowdsourcing of additional media coverage, in combination with curation by PLOS staff, provides a more comprehensive view of media coverage without compromise to the reliability of sources. The information is 18 broadly organized into three groups – news media coverage, blog coverage and related Collections launched resources – and the community is encouraged to submit newly discovered content. (July 2013 - July 2014)

4 ALMs Highlight Articles and their Backstory The ALM Article Feature series highlights articles across the PLOS journals with substantial ALMs and presents the article together with an interesting backstory. This brings a deeper understanding of both ALMs and the breadth of ways in which PLOS research articles influence scholarly research and the broader world beyond. The community is invited to join the conversation and suggest future articles for the series.

Knowledge Sharing Advances ALMs and Tools To strengthen the community of ALM producers and consumers across the research ecosystem, PLOS hosts an annual ALM conference funded by the Alfred P. Sloan Social Media Highlights Foundation. Participants represent the research, publishing, funding and technology industries in Europe, Canada and the United States. As a pioneer in the development of ALM applications and an Open Access advocate, PLOS encourages others to develop + tools through its shared application program interface (API), recognized this year as a top API of the week for “unusually rich access to their collection’s usage metrics” by 150,000 ProgrammableWeb, the online journal of the API community. Twitter followers (Through July 2014) Article Versioning Updates Knowledge PLOS Currents published its first versioned article in May 2014 [1]. Following the original March publication on forecasting West Nile Virus incidence, the authors gathered data on predictions for 2014 that were not available at the time of the original publication. The new data was incorporated into the manuscript and a second edition was published. The ability to publish versions is a special feature of this rapid publication, where readers also have the early ability to access the original version of the article.

PLOS ONE – Measuring Article Impact

0.08 13,797 articles published in 2011 10% of articles 23 citations CALCULATED CITATION FREQUENCY 0.00 0.02 0.04 0.06 0 10 20 30 40 50 60 SCOPUS CITATIONS

Courtesy Martin Fenner. Scopus citation counts as of August 10, 2014 for PLOS ONE papers published in 2011

5 Advancing Usability and Discovery Collaboration Encourages Data Reuse PLOS continues its collaboration with Dryad to help authors improve the reuse and accessibility of their data by providing a permanent Open Access repository and assigning unique Digital Object Identifiers (DOIs) for all the data associated with a single Author Highlights published article. Integration of the Dryad data repository into the publication process for PLOS Biology and PLOS Genetics allows authors to connect their data with the manuscript at time of submission and links data and manuscript throughout peer % review to final publication, so that confidential access to data is an intrinsic part of the 93 scientific publishing process. Other PLOS journals link data housed in Dryad to the accepted, published article. Of authors likely to publish with PLOS again (Author Survey 2013) Collaboration Brings Rich Data Building on the ability to enhance articles with supporting information files through figshare, PLOS readers can access recommendations of additional figures, datasets, media, code, software, filesets and scripts that are relevant to the article and published 53 in PLOS. These expanded figshare capabilities help respond to a critical need for tools Nobel laureates that facilitate discovery of the full breadth of research content, increasing the value of as authors the research beyond the article itself. (through 2013) Collaboration Accelerates Discovery The ability to connect bibliographic references among articles as structured metadata accelerates discovery. Rich citations are an improved data format for bibliographic references because they contain structured metadata from the primary article and the cited article, thus enabling discovery of relationships between them. PLOS built an overlay for its articles using rich citation data; this makes the list of references a research tool in itself, demonstrating the advantages of structured citation metadata. PLOS is engaged with other publishers to encourage wide-scale adoption of rich citations.

6 Global Media Extends Article Reach and Impact

“Y Chromosome is not Doomed to Shrivel Away to Nothing, say Researchers” January 9, 2014

PLOS Genetics “This Dirty Little Weed May Have “Watch out for Climate ‘Surprises,’ Cleaned Up Ancient Teeth” Scientists Warn” July 16, 2014 December 4, 2013 PLOS ONE PLOS ONE

“Toxin Wipes Out Persistent HIV” January 10, 2014 PLOS Pathogens “‘Milestone’ for Child Malaria Vaccine” July 29, 2014 PLOS Medicine

“Video: Inside Look at Insect Flight” “Sleeping Sickness and Tsetse Flies” March 25, 2014 June 1, 2014 PLOS Biology PLOS Neglected Tropical Diseases

“A New Mathematical Model Can Cut Jet-Lagged Time in Half, Study Says” “Bank Voles Provide Clue to Prion April 11, 2014 Disease Susceptibility” PLOS Computational Biology April 4, 2014 PLOS Pathogens

7 Publishing Research Responsibly Reporting Guidelines Toolbox Supports Quality Outcomes The Reporting Guidelines Collection [2] is an essential toolbox of 27 articles for authors to help ensure clarity in the reporting of their findings and maximize the impact of their research. The collection gathers in one place the growing number Article Highlights* of reporting, presentation and evaluation resources published in PLOS journals and includes guidance, commentary and research on these topics. PLOS authored “Open Science and Reporting Animal Studies: Who’s Accountable?” [3]; contributions + to the collection from the global research community include a use case analysis of guidelines created for writing abstracts of systematic reviews [4] from Australia 34,000 and a review of published methods and reporting on the use of expert panels in Articles published diagnostic research [5] from The Netherlands, each with more than 6,000 views in the first six months after publication.

+ Rigorous Review Ensures Scientific Integrity 9 PLOS ONE convened a Human Research Advisory Group following the model of the journal’s Animal Research Advisory Group. These international experts guide Million policy to ensure that PLOS ONE upholds the highest international standards for Monthly article views integrity in animal and clinical research. The journal also developed a new approach to handling meta-analyses. Authors of these studies, which hold the potential to influence clinical diagnosis and care, must demonstrate the validity of the + research design before submission can proceed to review. 1.7 Million Monthly article downloads

*2013

8 Moving Beyond the Article New Data Policy Enables Reproducibility PLOS believes that sharing data and making data available to the entire scientific community promotes new discovery, replication and validation, meta-analysis, and larger, more widely distributed outcomes for funders, institutions and researchers. Blog Highlights In March, PLOS launched its new Data Policy to establish an early commitment from authors to make their data available and ensure availability of supporting data + to authors, peer reviewers, editors and readers. The policy requires authors to make 1.126 all data underlying the findings described in a manuscript fully available without restriction, with exception and consideration granted in selected cases of human Million subjects, intellectual property, and/or other ethical or legal concerns. When submitting Visitors to PLOS Blogs a manuscript online, authors must provide a Data Availability Statement describing (through 2014) where data is housed, when it is shared and how access is provided. This information is published with the article.

Experience Educates the Next Generation “It is simply a matter of common To share knowledge about lab organization and scientific management the new sense that data associated with PLOS Computational Biology collection “About My Lab” was developed [6]. Each a publication be made available article represents an interview with a Principal Investigator who shares his or her to the community – it is fantastic experience of running a lab by discussing selected topics in an informal style. that PLOS is taking a leadership Building on the success of the personal format of the “Ten Simple Rules” series, role with their Data Policy, and I About My Lab launched with an editorial [7] by journal Founding Editor-in-Chief expect the other publishers will Philip E. Bourne and collection Editor Theodore Alexandrov, accompanying an follow suit.” article featuring interviews [8] with early-career Principal Investigators. Joseph DeRisi Howard Hughes Medical Mini-reviews Provide Lessons that Last Investigator, Professor and Chair, Department of “Pearls,” published in PLOS Pathogens, are educational mini-reviews that address Biochemistry & Biophysics, important and wide-ranging topics in pathogenesis. These short articles bring out University of California, the significance of the selected topic, making it clear and compelling to a general San Francisco readership while offering accessible and accurate insight at a graduate student level. Pearls cover the emergence of MERS coronavirus [9], the origin of the 2010 Haitian cholera outbreak [10] and the teaching of Leishmania cell biology with animations [11]. A Pearl by Anthony Fauci and David Morens reviews the impact of emerging infectious diseases on human health and global stability [12]. To celebrate the 200 th Pearl and the collection’s Fifth Anniversary, the collection was launched on Flipboard where it is followed by more than 2,000 readers.

9 Interactive Articles Engage Community To engage the broader genetics community through shared interests and discussion around the wide array of topics encompassed by this field, PLOS Genetics commenced an interactive article series, “Deep Reads” [13]. This annual column kicked off with Jane Gitschier introducing readers to her favorite memoirs, biographies, nonfiction and fiction related to genetics and science. Readers are encouraged to offer postings of their own. The inaugural Deep Reads column received over 20,000 views in its first six months.

Rapid Publication Fosters Timely Action PLOS Currents: Outbreaks provides a service to the community in times of crisis by Global Reach Highlights* rapidly posting work in any area of research and public health relevant to infectious diseases outbreaks or pandemics. An exemplar of actionable information occurred in the case of Ebola hemorrhagic fever, following an April announcement by the Guinea + Ministry of Health of suspected and confirmed cases. In May, within five days of receiving a submission on the topic, PLOS Currents published a research article [14] providing 245 evidence that – at that time – Guinea was likely under siege by the same, rather than Countries with readers divergent strain, of Ebola involved in previous outbreaks in the Democratic Republic of the Congo, the Republic of the Congo and Gabon. Rapid and repeated mutation of the virus further emphasizes the need for rapid publication forums to disseminate information. + 200 Countries with contributing authors Engaging Communities for Continual Assessment

PLOS community sites invite scientists to engage in the dialogue of science, *Through July 2014 gain exposure to interesting field-specific content that might otherwise be difficult to discover and keep up to date with important research and analysis while putting what’s new and significant in context.

Through blogging, commentary and discussion the community site model is one platform that facilitates continual assessment, and through crowdsourcing elevates topics deemed important by those engaged on the site. Additional content includes practical information in areas such as data sharing, Open Access policies and funding opportunities – all essential to keep today’s researchers operating optimally and to help accelerate discovery.

The PLOS Neuroscience Community and the PLOS Synthetic Biology Community feature posts covering topics and trends in these fields and highlight significant research articles, along with their ALMs, to showcase the article’s academic and social impact.

These online communities are under the leadership of practicing researchers working in synthetic biology and neuroscience, and engage the broad community as site editors and Contributing Editors. In the first two months online, more than 10,000 viewers visited the sites.

“Nice to see a scientist talk critically about their work with a perspective beyond just daily research and funding.” David Konerding, Senior Engineer, Google PLOS Synthetic Biology community site reader comment

10 Accelerating Science through Open Access Robust Open Access Environment Increases Publication The rise in Open Access policies from institutions, funders, foundations and government agencies around the world has brought foundational change to the way scientific research is published and disseminated. More than 80 funders and 180 academic Published Article Highlights institutions worldwide have Open Access policies, contributing to an 180% increase in Open Access journals listed in the Directory of Open Access Journals from 2008 – 2013. In the US, dedicated resources for Open Access publication from institutions and funders + are increasingly available and in 2012 the Research Councils UK (RCUK) announced it will provide nearly £37 million (approximately $47 million) for Open Access publishing through 100,000 2015. According to the Open Access Scholarly Publishers Association (OASPA) over Articles published (Through 2013) 117,000 articles were published by Science, Technology and Medicine publishers in 2013 using the licensing access standard adopted by PLOS (CC BY).

Policies Improve Access PLOS advocacy includes collaboration with the Open Access community to educate lawmakers and the public about policies that impact dissemination of scientific research outputs. In the UK, PLOS engaged in parliamentary committee enquiries shaping the framework of ongoing Open Access implementation and brought attention to Open Access barriers, including author fees and embargoes, through evidence submitted to the Business, Innovation and Skills Select Committee. Additional community efforts include the review of RCUK’s implementation of its Gold Open Access mandate and the European Expert Group Report on Copyright Reform.

PLOS supports The Taxpayer Access to Publicly Funded Research – California State Assembly Bill AB609 – that requires researchers with California Department of Public Health grants to make their papers publicly available no later than 12 months after publication. The bill has passed the California State Assembly and is awaiting the Governor’s signature.

Growth in Published Open Access Articles 120,000

100,000

80,000

60,000

40,000

20,000 NUMBER OF ARTICLES

2001 2003 2005 2007 2009 2011 2013 YEAR

Data from OASPA includes BMC, Copernicus, Ecancermedicalscience, eLife, Frontiers, Hindawi, JMIR Publications, MDPI, PeerJ, PLOS, Springer Open

11 Usage Data Captures Impact Metrics and usage data provide granularity to research assessment by capturing the impact of research outcomes at the article rather than journal level. Usage data must be openly available for analysis, reuse and critique. PLOS submitted evidence to the Higher Education Funding Council for England (HEFCE) on the value of both metrics in research assessment and the creation of a data and analysis environment where usage data is openly available. HEFCE oversees UK’s Research Excellence Framework through which institutional block grant research funds are distributed based on research assessment.

Accelerating Science Awards Restrictive Licenses Receive Push Back Program Highlights PLOS joined a coalition of funders, institutions, publishers, curators and users of public resources that called on the International Association of Scientific, Technical and Medical + Publishers to withdraw new model licenses for research articles that would make licensing 200 of the research literature incompatible with millions of Creative Commons-licensed resources. Demonstrating unity in the desire for established, standardized and proven legal Nominees tools to enable the sharing and reuse of scholarly content, PLOS, Creative Commons, the Scholarly Publishing and Academic Resources Coalition (SPARC), the Association + of Research Libraries (ARL) and the Wikimedia Foundation joined forces to advocate for 30 withdrawal of restrictive licenses. Ninety-three signatories joined in support. Nominated countries Awards Program Recognizes Innovations in Open Access Reuse The Accelerating Science Awards Program (ASAP) recognizes individuals who use, apply and/or remix scientific research – published through Open Access – to advance science, 6 medicine, business and/or technology, and therefore, society as a whole. PLOS joined Finalists with dozens of co-sponsors, including Wellcome Trust and Google, who value the transformative impact of Open Access to attract over 200 nominations from more than 30 countries.

3 The top awardees received $30,000 each. A celebration of the selected work was Awardees sponsored by PLOS, SPARC and the World Bank during Open Access Week 2013 in Washington, DC.

HIV Self-Test Empowers Patients A private and inexpensive strategy for self-screening of HIV with a “What I think is exciting is that smartphone application and a HIV self-test help circumvent the burden they’ve shown the value of of testing in a healthcare facility and increase HIV screening, counseling Open Access from an actual and treatment rates for individuals in low- and middle-income countries. true real result, not just it’s good because it’s good but it’s good Global Collaboration to Fight Malaria because it comes out in value Scientists worldwide in The Open Source Malaria Consortium accelerate for the world.” anti-malaria drug discovery through crowdsourcing and real-time Gregg Gordon interactions involving Open Access laboratory notebooks and social President and Chief Executive media in a cost effective model of collaborative, open discovery. Officer, Social Science Research Network Visualizing Complex Science To enhance readers’ understanding of scientific research through visual content, the Open Access Media Importer crawls scholarly publication databases for sharable audio and video files and uploads them to Wiki- media Commons for easy reuse, revision, remixing and redistribution.

12 PLOS Opens Blog Advances Open Access To connect with and provide a forum for those interested in advancing Open Access, the “PLOS Opens” blog launched with commentary and a call to readers to deliberate the future of scholarly communication. The blog contains “The Opens Roundup,” a feature highlighting recent initiatives and announcements related to Open Access. Guest bloggers from the community, together with PLOS staff, address relevant topics around harnessing the potential of the Internet to advance science for the greater public good. The blog attracted 160,000 visitors in its first six months.

Guide Increases Global Understanding of Open Access “Important research remains The pocket-sized “HowOpenIsIt?®” Open Access Spectrum clarifies what makes a journal inaccessible to the vast majority more or less open, helping authors to make informed decisions about where to publish. of the world. Unlocking Users include authors, libraries, research funders, government agencies and others. knowledge on the frontier of Community volunteers have translated the guide from English into Spanish, Chinese, understanding accelerates progress, enables innovation, Italian and Portuguese. and ultimately grows the world economy.”

Alex Kozak Senior Policy Analyst, Google Public Policy

13 Aggregating Content For Deeper Understanding: Collections

Open Access Benefits Education Collaboration Advances Climate Socioeconomic Disparity Research The Marine Megafauna Collection [15] Change Research Accessible to Everyone presents a broad survey of research The broad range of papers within the Socioeconomic disparity is a major and on marine organisms and systems Ecological Impacts of Climate Change growing determinant of health for at-risk and provides core materials for marine Collection [16] emphasize not only the populations, with neglected tropical science educators seeking to increase multifaceted impacts of climate change diseases and non-communicable the engagement of students through use on ecological and human systems, but diseases disproportionately affecting not of compelling examples. The collection also the breadth and depth of research only those in low- and middle-income was created in collaboration with The on these subjects being reported in countries but also poorer people living Johnston Lab of Habitat, Climate and PLOS journals. Curated by PLOS ONE in high-income countries. The Blue Marine Wilderness at Duke University Academic Editor Ben Bond-Lamberty, Marble Health Collection [19] was created and provides the primary reading list for the collection is accompanied by a to highlight this recognition in global the Marine Megafauna Massive Open blog series. Since the launch, PLOS health. The collection, a collaboration Online Course (MOOC), in which over has further committed to the science of between PLOS Medicine and PLOS 14,000 people worldwide have enrolled. climate change by calling for papers that Neglected Tropical Diseases, launched constructively respond to its impact with with a Viewpoints article “NTDs V.2.0: attempts to mitigate the effects. This ‘Blue Marble Health’– Neglected Tropical resulted in a collection, Responding to Disease Control and Elimination in a Climate Change [17], featuring a review Shifting Health Policy Landscape” by [18] by James Hansen and colleagues, Peter Hotez [20] and “Poor Health in “Assessing Dangerous Climate Change: Rich Countries: A Role for Open Access Required Reduction of Carbon Emissions Journals,” Larry Peiperl’s first editorial to Protect Young People, Future [21] as Chief Editor of PLOS Medicine. Generations and Nature.” Professionals working in the field are encouraged to submit to Open Access journals works that address health disparities.

14 PLOS Journals

PLOS publishes a suite of influential journals from disparate areas of science and medicine that contain rigorously peer reviewed Open Access research articles, together with expert comment and analysis. Major milestones include: PLOS Biology’s ten-year anniversary [22] of its first issue, PLOS Computational Biology’s “Ten Simple Rules” [23] series of editorials on professional development, which surpassed one million page views, and a PLOS Medicine essay originally published in 2005, “Why Most Published Research Findings Are False” [24] reaching one million page views, becoming the most viewed paper in PLOS Medicine’s ten-year history. In 2013 PLOS ONE averaged one million article downloads every month.

15 PLOS Biology PLOS Biology features research articles of exceptional significance in all areas of biological science, from molecules to ecosystems.

The journal celebrated its first ten years by publishing the Tenth Anniversary PLOS Biology Collection [22] showcasing ten research articles chosen by PLOS Biology Editors and Editorial Board members and accompanied by a series of ten blog posts on “PLOS Biologue.”

The protease inhibitor cystatin NtCYS and Accompanying the anniversary collection is a video of PLOS co-founder Michael its target, the protease NtCP14, regulate Eisen and long-time PLOS Biology Editorial and Advisory Board member Jonathan organ programmed cell death during Eisen discussing the history and future of the journal and its relation to the larger plant embryogenesis. Open Access movement.

On the Community Page, Greg Wilson of the Mozilla Foundation in Toronto and colleagues outline a set of best practices [25] for writing scientific code, designed to improve the productivity of scientists and the reliability of their software. These “Best Practices for Scientific Computing” received over 50,000 views and over 1,000 shares in the first six months of publication.

A research study [26] on viral evasion, “Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein,” was awarded the Omenn Prize for the best paper in evolution, medicine and public health for 2013 by The Evolution, Medicine, & Public Health foundation. A feature on author Ann Demogines, from the University of Texas at Austin, is published in PLOS Biologue.

A research article [27] that received considerable media attention revealed a phenomenon known as the ‘blue wave of death’ that can be seen to sweep across a laboratory worm in its dying moments. This cascade generates a wave of endogenous blue anthranilate fluorescence, allowing death to be visualized directly from degradation of a naturally occurring amino acid.

Research by Adam Eyre-Walker and Nina Stoletzki [28] shows that scientists are unreliable judges of the importance of other researchers’ publications. These conclusions and their implications for research assessment are discussed in an accompanying editorial [29] by Senior Advocacy Manager and PLOS ONE Consulting Editor, Catriona MacCallum and colleagues.

A study [30] with 31,000 views in its first month of publication which was widely covered features an X-ray movie of a blowfly in flight. New imaging research led by scientists from the University of Oxford reveals how the astonishing flight maneuverability of blowflies occurs. The research is discussed in a primer [31] by editorial board member Anders Hedenström and on PLOS Biologue.

PLOS Biology published The Promise of Plant Translational Research, a collection [32] supported by the Bill & Melinda Gates Foundation. Technical advances highlighted in the collection exemplify how basic research discoveries translate into methods to develop and improve important crop traits and address the pressing need for plant research to contribute solutions to improve food security in a sustainable and safe way.

16 PLOS Medicine PLOS Medicine is the leading Open Access medical journal for research and comment on the major challenges to human health worldwide, publishing articles across all areas of medical science with potential to directly and substantially inform clinical practice and/or health policy, or to provide substantial, novel mechanistic insights into disease processes.

Implementation of mass vaccination campaign The most highly cited and accessed articles include a systematic review [33] on financial with oral cholera vaccine in response to conflicts of interest and reporting bias on research into the association between sugar- outbreak in Guinea. sweetened beverages and weight gain; a study [34] of mortality rates in Iraq, suggesting that around half a million people died there between 2003 and 2011 as a result of the war and subsequent occupation; a study [35] of the global disease burden of depressive disorders; and a study [36] of the expanding definitions of diseases in guidelines from authors with ties to industries that benefit from those expanded definitions.

Virginia Barbour’s final editorial [37] as Chief Editor of PLOS Medicine in 2013 celebrates the journal’s history of publishing disruptive articles and encouraging debate. She highlights a case study [38] on alcohol industry claims made to the Scottish Government consultation in which the industry used research evidence to advocate policies in line with their commercial interests.

The journal continued in this tradition after Larry Peiperl joined as Chief Editor in September 2013, publishing a review [39] of transnational tobacco companies’ submissions to the UK government on standardized packaging that concluded that industry critique of evidence in favor of standardized packaging was highly misleading. The study was cited in the UK Government’s Independent Review into the plain packaging of tobacco.

PLOS Medicine continues the partnership [40] initiated in 2011 with Harvard’s Maternal Health Task Force and released a new collection [41], Maternal Health is Women’s Health, which highlights how the health of women and girls before pregnancy affects their ongoing health as mothers. The Measuring Coverage in Maternal, Newborn and Child Health Collection presents innovative assessments of the validity of measuring coverage of health interventions for mothers, newborns and infants [42].

The PLOS Pediatric Medicine Collection [43], launched to highlight PLOS Medicine’s 10th Anniversary, includes key research and commentary relating to the health of children and was published in PLOS Medicine and PLOS Neglected Tropical Diseases. The collection covers the main conditions affecting children worldwide, of all ages and socioeconomic levels. Unsurprisingly, HIV and malaria feature prominently. One study [44] shows that young HIV-positive, antiretroviral therapy-naive children can achieve high CD4 counts in later life, provided therapy is initiated as recommended by the World Health Organization. A systematic review [45] of 29 controlled clinical studies supports the delivery of psychosocial interventions to children with autism and learning difficulties by non-specialist providers, making access to treatment a possibility for all children.

Médecins Sans Frontières blogged for “Speaking of Medicine” on the availability of treatments for snakebites, tetanus and rabies in low- and middle-income countries.

17 PLOS ONE PLOS ONE is the original, and the world’s largest, journal dedicated to publishing all technically sound work across all scientific disciplines. Research highlights in the past year range in scope from population biology to video game training.

The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone offers macromolecular modeling, prediction and design software supported by

Diversity of fluorescent patterns and colors in a large developer community, enjoying a diverse user base. The collection [46] highlights marine fishes. new scientific developments within the Rosetta developer community and provides a reproducible workflow for each protocol.

PLOS ONE published 15 articles as part of the collection [47] Sauropod Gigantism: A Cross-Disciplinary Approach, which details efforts by evolutionary biologists and paleontologists to understand sauropods as living animals, and to explain their evolutionary success and gigantic body size. The articles address these questions from the viewpoints of ecology, engineering, functional morphology, animal nutrition and paleontology.

The most highly cited and accessed articles include a study [48] assessing crop yields that suggests current trends are insufficient to keep up with rising demand; a new approach [49] to resolving the phylogeny of birds, based on 1500 collected genetic loci; the application [50] of droplet digital PCR to improve detection of HIV-1 proviral DNA; an article [51] on the gene expression profile and blood test that may help detect impending preterm birth; and review [18] by James Hansen and colleagues that assesses the current state of climate change and suggests reductions to restore Earth’s energy balance.

Studies attracting significant media attention include a description of cancer [52] in a Neanderthal from 120,000 years ago; deformable joints in dinosaurs [53] and their role in gigantism; and a new super-predator [54] larger than T. rex. Also widely read were several language-related studies, from an investigation into the universality of the expression “Huh?” [55] and a phylogeny [56] of the tale of Little Red Riding Hood to the largest study [57] to date of language and personality. An analysis [58] of four ice sections from sub-glacial Lake Vostok; the characterization of a newly named shape, the hemihelix [59]; the earliest hominin footprints [60] found in the UK; a new water filtration method [61] using plant xylem; an examination of how scientific impact [62] affects funding and the increase in cognitive functions through video game training [63] were all highly featured.

The most popular posts on the “EveryONE” blog feature research detailing how fiction may affect empathy, musical microbes, interspecies sharing, new species, imaging methods, falcon physics, yeast genetic diversity and Black Death.

18 PLOS Computational Biology PLOS Computational Biology publishes research that provides substantial new insight into living systems at all scales, from the nano to the macro, and across multiple disciplines, from molecular science, neuroscience and physiology to ecology and population biology, through the application of computational methods.

The journal is an official journal of the International Society for Computational Biology Free energy surface for benzocaine in the (ISCB) and publishes research articles and sections on Software and Methods. PLOS bacterial voltage gated sodium channel. Computational Biology engages with the community through innovative projects and collections.

An article [64] on social behavior in dogs appeared in the New Scientist, while TIME reported on a study [65] that explores the effect of environmental and state-level factors on autism incidence. An article [66] presenting a model for dealing with the effects of jet lag was covered by the New Scientist, and research [67] by David J. McIver and John S. Brownstein that estimates levels of influenza in America by monitoring Internet traffic on specific Wikipedia articles was featured in The Huffington Post.

Philip Bourne, Founding Editor-in-Chief, looked back in PLOS Biologue over the history of the “Ten Simple Rules” series. Bourne describes the series as “one of the unexpected surprises and pleasures” arising from this community journal. “Writing a Literature Review” [68] attracted more than 100,000 views; “Good Poster Presentations” [69] and “Making Good Oral Presentations” [70] had more than 200,000 views each. PLOS Computational Biology offers a collection [71] of articles by the ISCB Student Council, “Stories from the Road.”

Fran Lewitter stepped down after eight years as Education Editor, succeeded by Francis Ouellette and Joanne Fox. PLOS Genetics PLOS Genetics publishes new research in genetic and genomic biology. The journal seeks to reflect the interests of a broad genetics community by highlighting studies with significant biological insight across a wide range of systems and fields.

Many of the 800 research articles published last year received media and public attention. Research [72] showing that a six-month exercise intervention influences DNA methylation, likely altering fat cell metabolism, received over 70,000 page views in the 12 The sexually dimorphic stag beetle. months after publication, as well as over 15 citations and 900 social media shares. Also of interest was a study [73] that used genome sequencing to understand the evolutionary history of dogs and to show that dogs and wolves diverged between 11,000 and 16,000 years ago. This article was highlighted by an accompanying perspective [74] and featured by blogs and the press.

19 Particular interest also surrounded research on the population genetic history of the Caribbean peoples [75], Y chromosome evolution [76], diet–gene interactions affecting risk of colorectal cancer [77], stresses and telomere length [78] and how the envelope [79] surrounding Gram-negative bacteria may be disrupted to treat infection. Pleuni Pennings produced a video about selective sweeps in the evolution of drug resistance [80] in HIV.

PLOS Genetics also offers a lively front section of interview, review, viewpoints and perspective articles. Interviews [81] feature New York lawyer Barry Scheck [82], a specialist in DNA evidence; the BRCA1 geneticist Mary-Claire King [83]; and the author of In Pursuit of the Gene, James Schwartz [84]. The 38 interviews are also available on Flipboard. A review [85] on single cell genomics and a Viewpoints article [86] on the case for “junk DNA” also attracted significant interest.

PLOS Genetics is now fully integrated with Dryad, allowing authors to deposit their underlying data easily upon submission or acceptance. Dryad data may be confidentially shared with editors and peer reviewers, and upon publication is discoverable, freely reusable and citable. PLOS Neglected Tropical Diseases PLOS Neglected Tropical Diseases (PLOS NTDs) is the first Open Access journal dedicated to the advancement of research on the world’s most neglected tropical diseases, including elephantiasis, river blindness, leprosy, hookworm, schistosomiasis and African sleeping sickness. Leading research and commentary is published on the scientific, medical, political and public health aspects of these forgotten diseases affecting the world’s most neglected people. Community health workers visit rural Haitian villages with oral cholera vaccine and health and hygiene education messages. PLOS NTDs published the first of the Historical Profiles and Perspectives Collection [87] in honor of the journal’s Fifth Anniversary in 2012, a collection that currently includes over a dozen articles. In April 2014 the journal published the Tsetse Genome Biology Collection [88], consisting of historical profiles, perspectives and editorial, together with research articles from PLOS Genetics and PLOS ONE. The collection received global media coverage, including Scientific American and Science Africa.

One of the journal’s most impactful policy statements, published in 2009, continues to receive considerable attention. The proposal, by Peter Hotez, Alan Fenwick and Eyrun Kjetland [89], “Africa’s 32 Cents Solution for HIV/AIDS,” was recently featured as a vital consideration for HIV/AIDS control in Africa. Also this year, The Web of Science recognized PLOS NTDs as a ‘Rising Star’ in the field of immunology.

A policy platform [90] on the elimination of lymphatic filariasis in Togo attracted coverage in the New York Times Opinion Pages and other media outlets around the world.

PLOS NTDs supported a writing workshop designed to provide guidance to young researchers in disease-endemic countries. Notes are available to the community in PLOS NTDs in English and Spanish.

20 PLOS Pathogens PLOS Pathogens publishes primary research, analysis and educational content that significantly advances the understanding of bacteria, fungi, parasites, prions and viruses, and how these pathogens interact with their host organisms.

On World AIDS Day 2013, 165,000 readers visited an article [91] reporting that an engineered enzyme able to excise integrated HIV from host cell chromosomes showed Scanning electron micrograph shows significant antiviral activity in mice genetically modified to develop a functional human macropinocytic uptake of mycobacteria immune system. in activated macrophages. A study [92] using the Lyme disease bacterium, B. burgdorferi, demonstrated that the capacity to evolve is itself the object of natural selection. The research received an Omenn Prize honorable mention from the Evolution, Medicine, & Public Health Foundation and was discussed in Popular Science and Nature news. A study [93] covered in Science news, analyzing the oral mycobiome of HIV-infected patients, identified that the fungi Pichia can suppress oral candidiasis.

New strategies to control malaria by interrupting the parasite lifecycle in its mosquito host were reported. One study [94] identifies molecules derived from wasp and bee venoms that are toxic to the parasite but not to mosquitoes. A second [95] reports the development of a decoy molecule that mimics structures on the mosquito gut surface and interferes with infection.

The first three-dimensional ultrastructural study [96] of HIV infection in vivo revealed how the virus hides within intestinal tissue and was covered in New Scientist and Popular Science. A new inhibitor of membrane-bound viral RNA synthesis was reported [97] to exhibit potent antiviral activity against SARS and MERS coronaviruses in the cells that line human airways. An article [98] reporting that New World bats harbor a diverse reservoir of Influenza A viruses accumulated over 50 citations.

In anticipation of the May 2014 World Health Assembly vote to eliminate the last live stores of the smallpox virus Variola, PLOS Pathogens published an opinion [99] calling for further research to address crucial scientific questions and unmet public health goals. This sparked a substantive discussion by national and international press, including Science Friday, NPR, Smithsonian Magazine, The Hindu and Le Monde.

In October 2013, Deputy Editor Grant McFadden joined Kasturi Haldar as co-Editor-in-Chief.

21 Reinvesting to Advance Science The 2013 financial year was marked by record revenues and the fourth consecutive year of sustainability for PLOS. Gross revenue and support grew 31% to $50.8 million (2012: $38.8 million), of which the increase in net assets was $9.87 million (2012: $7.15 million). Expenses grew by 35% to $37 million (2012: $27.4 million), driven by investments in two key areas:

• Building a sustainable organization and scalable infrastructure to support the growth in publishing operations

• Laying a foundation to support the pursuit of the PLOS vision to provide rapid and effective communication and assessment of scientific ideas, results and discoveries for the public good

PLOS grew from 176 employees to over 200 during assistance in 2013 totaling $3.4 million to authors the year, with corresponding expansion of office (2012: $3.8 million) and $500,000 to institutions (the footprints in both the US and the UK. PLOS particularly same in 2012), for a total of $3.9 million in publication makes significant investments in human resources for fee assistance. The PLOS Global Participation platform development. Initiative assistance to authors who are funded by low- and middle-income countries is included in the PLOS enters its second decade as a leading publisher publication fee assistance amounts reported. PLOS in a robust Open Access environment. PLOS published also expanded its institutional program through which over 34,000 research articles in 2013, an increase of 33% PLOS administers payment of full or partial fees for over 2012, bringing the total number of Open Access authors at participating institutions. articles published by PLOS to more than 100,000.

PLOS continues to support those who are unable to pay all or part of their publication fees, with

22 Statement of Activities ($000’s) 10% Revenue and Support 2013 Contributions 132 1% Publication fee 48,956 Membership fee 313 18% Advertising and other 1,363 Total gross revenue and support 50,765 Less: Publication Fee Assistance 3,889

Total net revenue and support 46,876

Expenses 71% Publishing 29,611 General and administrative 7,393 Total expenses 37,004

Increase in net assets 9,872

Total Expenses Plus Publication Fee Assistance $40.9 Million Balance Sheet ($000’s)

assets 2013 71% Publishing Current Assets Efforts related to editorial and Cash and cash equivalents 1,407 production operations and Program and accounts receivable, net 1,314 advocacy, including staffing, Prepaid expenses, loan receivable and other 708 productivity tools and platform Total current assets 3,430 development Noncurrent Assets 10% Publication Fee Assistance Investments 26,040 Fee assistance provided by PLOS Property and equipment, net 2,350 to authors unable to pay all or part Deposits 8 of their article publication fees, Total noncurrent assets 28,399 including those qualifying under the PLOS Global Participation Initiative Total assets 31,829

1% Research and Development liabilities and net assets 2013 Efforts include innovations, PLOS Current Liabilities Article-Level Metrics (ALMs) Accounts payable 1,736 improvements and PLOS Accrued liabilities 1,332 Currents enhancements Deferred revenue 2,620 Total current liabilities 5,687 18% General & Administrative Deferred rent liability 404 non-publishing costs that support staff and outsourced services in Total liabilities 6,091 human resources, legal and accounting; also includes rent Net Assets and bank fees Unrestricted 24,846 Temporarily restricted 892 Total net assets 25,737

Total liabilities and net assets 31,829

23 PLOS SUPPORTERS

PLOS thanks the following foundations and sponsors for their support in 2013:

Grants

Alfred P. Sloan Foundation Open Society Foundations

Bill & Melinda Gates Foundation William K. Bowes, Jr. Foundation

Sponsorships

The United States Fund of UNICEF Jisc

Copernicus Publications Max Planck Society for the Advancement of Science

Doris Duke Charitable Foundation Microsoft Research

eLife Research Councils UK

Google Research Libraries UK

Howard Hughes Medical Institute Social Science Research Network

Hindawi Publishing Corporation Scholarly Publishing and Academic Resources Coalition

Jhpiego Corporation Wellcome Trust

24 PLOS BOARD OF DIRECTORS AND MANAGEMENT ( As of August 2014 )

Board of Directors

Patrick O. Brown Heather Joseph Elizabeth Marincola Stanford University School Scholarly Publishing and Academic Chief Executive Officer of Medicine Resources Coalition (SPARC) Rosalind L. Smyth Michael W. Carroll David Liddle Institute of Child Health, American University US Venture Partners University College London Washington College of Law Robin Lovell-Badge Gary E. Ward Michael B. Eisen Medical Research Council, Chair University of California, Berkeley National Institute for Medical University of Vermont Howard Hughes Medical Institute Research, UK

Senior Staff

Elizabeth Marincola Katie Sharabati John Chodacki Chief Executive Officer Director of Human Resources Product Director Richard Hewitt Helen Atkins Jonathan Dugan Chief Financial Officer Director of Publishing Services Director of PLOS Labs Kristen Ratan Susan Au Cameron Neylon Publisher Director of Finance & Accounting Advocacy Director CJ Rayhill Virginia Barbour Damian Pattinson Chief Technology Officer Medicine and Biology Editorial Director, PLOS ONE Editorial Director Darlene Yaplee Larry Peiperl Chief Marketing Officer Paula Carter Chief Editor, PLOS Medicine Director of Project Ray Campbell Debbie Woo Management Office General Counsel & Secretary Director of Product Marketing

Editorial Boards

PLOS Biology PLOS Computational Biology PLOS Neglected Tropical Diseases plosbiology.org/static/edboard Ruth Nussinov Peter J. Hotez and Serap Aksoy, Editor-in-Chief Editors-in-Chief PLOS Medicine ploscompbiol.org/static/edboard plosntds.org/static/edboard plosmedicine.org/static/edboard PLOS Genetics PLOS Pathogens PLOS ONE Gregory S. Barsh and Kasturi Haldar and Grant McFadden, plosone.org/static/edboard Gregory P. Copenhaver, Editors-in-Chief Editors-in-Chief plospathogens.org/static/edboard plosgenetics.org/static/edboard

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29 IMAGE CREDITS

Cover: followtheseinstructions, Flickr.com. Cover, page 8: Frederico Pedraja. PLOS Computational PLOS Medicine. 2014. 11(7) Biology. 2014. 10(7)

Cover, page 9: HyonJin Jeon. PLOS Neglected Tropical Cover, page 15, page 18: Sparks JS, Schelly RC, Smith Diseases. 2014. 8(2) WL, Davis MP, Tchernov D, et al. PLOS ONE. 2014. DOI: 10.1371/journal.pone.0083259 Cover, page 4: School of Natural Resources. Flickr.com. PLOS Medicine. 2013. 10(7) Page 5: Gaber ZB, Butler SJ and Novitch BG. PLOS Biology. 2013. 11(10) Cover, page 15, page 19: Hiroki Gotoh. PLOS Genetics. 2014. 10(1) Page 6: Andreas Bunten and clix. PLOS Computational Biology. 2013. 9(12) Cover, page 11: Melkani GC, Trujillo AS, Ramos R, Bodmer R, Bernstein SI, et al. PLOS Genetics. 2013. 9(12) Page 12: Gerald S. Wilkinson. PLOS Genetics. 2014. 10(5)

Cover, page 15, page 17: Ciglenecki I, Sakoba K, Luque- Page 13: Rodríguez JM, Chichón FJ, Martín-Forero E, ro FJ, Heile M, Itama C, et al. PLOS Medicine. 2013. 10(9) González-Camacho F, Carrascosa JL, et al. PLOS Pathogens. 2014. 10(5) Cover, page 15, page 21: Somdeb BoseDasgupta and Jean Pieters in collaboration with the Center for Page 13: Yasser. Flickr.com Microscopy, University of Basel. PLOS Pathogens. 2014. 10(1) Page 13: PLOS. 2013

von Beeren C, Schulz S, Hashim R, Witte V. Cover: Adrian H Elcock. PLOS Computational Biology. Page 13: 2010. 6(3) BMC Ecology. 2011. DOI:10.1186/1472-6785-11-30

David W. Johnston. PLOS Marine Cover, page 10: Marlene Andersson. PLOS Biology. Page 14: 2014. 12(8) Megafauna Collection

Matt Rudge, Flickr.com; Vik Walker, Flickr.com; Cover: Richard Retallick. PLOS Biology. 2004. 2(11) Page 14: Vera Kratochvil, PublicDomainPictures.net; NASA Cover: Cristian Cañestro. PLOS Genetics. 2009. 5(5) Goddard Space Flight Center. PLOS Responding to Climate Change Collection Cover, page 15, page 19: Lewis J. Martin and Ben Corry. PLOS Computational Biology. 2014. 10(7) Page 14: Fdecomite. Flickr.com. PLOS Blue Marble Health Collection Cover, page 15, page 20: Jonathan Lascher. PLOS Neglected Tropical Diseases. 2013. 7(11) Page 15, page 16: Peng Zhao and Meng-xiang Sun. PLOS Biology. 2013. 11(9)

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