Plos

Progress and Challenges for Neglected Tropical Diseases: An Anniversary Assessment

This year PLOS celebrates the 10th anniversary of PLOS Neglected Tropical Diseases (PLOS NTDs). The festivities are off to an impressive start with a strong presence at the 2017 NTD Summit in Geneva, Switzerland, a 10th Anniversary Collection, a blog post outlining anniversary launch activities and a PLOS NTDS 10th Anniversary landing page that will be updated throughout the celebration.

But what, exactly, are NTDs? They are a diverse group of communicable diseases that flourish in tropical and subtropical conditions in 149 countries, costing developing economies billions of dollars every year, according to the World Health Organization (WHO). NTDs mainly affect populations living in poverty, without adequate sanitation and in close contact with infectious vectors, domestic animals and livestock. In addition to causing mortality, NTDs remain an impediment to poverty reduction and socioeconomic development (WHO). Approximately 1.2 billion people globally have their quality of life and economic productivity diminished by NTDs.

In this context, however, there has been tremendous progress in the past five years. “For some diseases we’re ahead of our 2020 targets,” says Dirk Engels, Director, WHO Department of Control of Neglected Tropical Diseases. WHO, Uniting to Combat NTDs and the NTD community collaborated to host the recent 2017 NTD Summit celebrating the 5th year since the signing of the London Declaration, a collaborative disease eradication program inspired by the WHO 2020 roadmap to eradicate or negate transmission for at least ten NTDs.

Partnering with summit organizers and the Bill and Melinda Gates Foundation, PLOS NTDs – on the occasion of its 10th anniversary – co-hosted a uniting to combat NTDs panel at the summit with PLOS NTDs co-Editor-in-Chief Peter Hotez and PLOS Executive Editor Veronique Kiermer as moderators. The panel brought together experts on lymphatic filariasis, soil-transmitted helminth infection and schistosomiasis. Panelists from the National Institute for Medical Research, United Republic of Tanzania; University of Kelaniya, Sri Lanka; and the National Institute of Parasitic Diseases, Center for Disease Control and Prevention, People’s Republic of China participated in an engaging discussion of science and operational research in disease-endemic countries.

Published in parallel with the panel, the Symposium article “Partnering to Promote Research Where It Matters” focuses on capacity-building efforts and the positive impact of Open Access scientific literature for those working in disease-endemic countries. In China, “We work together on issues like health education, behavior change, and communication skills,” says panelist Xiao-Nong Zhou, Director of the National Institute of Parasitic Diseases at the Chinese Center for Disease Control and Prevention. “Our university could only afford a very restricted number of titles,” says Nilanthi de Silva, parasitologist at the University of Kelaniya in Sri Lanka. PLOS NTDs (and other Open Access journals publishing NTD-related research) offers an essential venue for researchers in low- and middle-income countries. Of the papers published to date, 25% have at least one author from Africa and 23% have an author from South America.

It is possible that nearly half of the current NTDs could be eliminated, eradicated or show significant gains in these directions within the decade. That would take continued dedication, and funding. “The last decade has seen a mixed picture when it comes to success stories in the progress to control or eliminate the world’s NTDs,” acknowledge PLOS NTDs Editors-in-Chief Serap Aksoy and Peter Hotez. According to David Molyneux, Emeritus Professor Liverpool School of Tropical Medicine and lead of their overarching Neglected Tropical Diseases program, “The future is going to be about building capacity for NTDs and recognizing that we’re talking about a broader problem of sustainable development.”

In the Tenth Anniversary Collection, Editorial Board members examine this progress in 20 of the major NTDs over the last decade. Those familiar with these diseases, those wanting a comprehensive overview or those wanting to focus on a specific disease will find in the collection reflections on significant lessons and successes as well as remaining challenges. The collection lays out a roadmap for future research priorities and identifies key opportunities for further progress in disease elimination. The Editorial by Aksoy and Hotez, “PLOS NTDS: Ten Years of Progress in Neglected Tropical Disease Control and Elimination…More or Less, provides an excellent introduction to the PLOS NTDs Tenth Anniversary Collection.

PLOS NTDs was founded to represent the needs of a community of scientists, public health experts and global advocates working on diseases of the poor and simultaneously to be a capacity-building tool for disease experts living and working in Africa and other disease-endemic regions of the world. Since founding, the journal has published over 4,700 articles (Research Articles, Editorials, Viewpoints, Policy Platforms, From Innovation to Application articles and more) written by more than 8,000 authors. Currently 40% of the journal’s 255 editorial board members are from disease-endemic countries. For more details of the journal’s history and impact over the past ten years, see the Editorial, “The PLOS Neglected Tropical Diseases Decade.”

Journal editors and staff have worked diligently on its dual mission to build capacity and encourage the submission and publication of the work of authors living and conducting research in disease-endemic countries. Editors have hosted 26 writing workshops in affected countries around the globe and provide training on best practices to ensure robust peer review, avoid plagiarism, handle data management and address other issues of research integrity. They also cover tips on crafting comments to authors and editing decision letters. These activities build a strong NTDs community to ensure ongoing success of the journal and scientific endeavors related to NTDs research.

So bookmark the 10th Anniversary landing page, browse the 10th Anniversary Collection and celebrate 10 years of advancing research, policy and progress in combatting NTDs. There’s more work to be done!

 

Image Credit:

Emma Burns, A Ray of Hope

Open Data Projects Win Wellcome Trust, NIH and HHMI Open Science Prize

“Scientists can do much more with their own data if things are shared publicly and shared publicly quickly in order to have potential for real world impact.” -Trevor Bedford, lead of the Open Science Prize winning team.

The Open Science Prize, a new initiative from the US National Institutes of Health (NIH), Howard Hughes Medical Institute (HHMI) and the Wellcome Trust, encourages and supports open science approaches that generate benefit to society, advance research and spur innovation. An integral component of the selection process is demonstrated use and generation of open data, so PLOS is proud that this year’s winner of the Open Science Prize is PLOS author and evolutionary, computational biologist Trevor Bedford of the Fred Hutchinson Cancer Research Center in Seattle, Washington. Finalists for the prize are also PLOS authors, including Michael Bamshed’s team, featured in a blog post for Rare Disease Day; Aurel Lazar’s and Ann-Shyn Chiang’s team, for the Fruit Fly Brain Observatory and Ben Goldacre’s team, for OpenTrialsFDA.

These scientists and their teams are making sure that open content – from publications, datasets, code and other research outputs – are discovered, accessed and reused. Bedford and his team won the prize for development of nextstrain.org, a website that integrates shared, open sequence data from global research teams into a model for real-time tracking of virus evolution. This provides the larger community a powerful graphic tool to facilitate pathogen surveillance and epidemiological investigations.

Open Data Tool Accelerates Policy and Research

In an interview discussing the value of open science approaches, Bedford spoke about open data, attribution, licensing and his experience in using preprints to support a publication strategy that releases data quickly while providing peer-reviewed citations for himself, his international collaborators and his postdocs and students.

One of the three final criteria in judging for the award is the level of demand and utility demonstrated by the proposed service or tool. This criterion worked in favor for nextstrain.org, as the team works with viral sequence data, made publicly available, to infer transmission patterns and evolutionary dynamics. Over the course of the last 15 years, according to Bedford, methods have gotten to a good place. Most recently, “fast genomic turnaround times means more actionable information is possible. This has created a powerful situation during outbreaks, where context is needed for robust conclusions, so investigators are willing to share data,” says Bedford. “We need to put datasets together for comprehensive inferences about what is going on,” he continues.

In creating the nextstrain.org website, Bedford wanted to do something useful that wouldn’t be construed as scooping other people’s data for a publication. He sees the website as a good way to provide value to the community and work with other labs’ data, yet not be perceived as wanting to make a claim of ownership in the same way as a preprint or published paper would. Those involved in the project are committed to use and reuse of properly attributed pre- and post-publication data that is out there and referenceable.

What gives Bedford’s collaborators their intellectual property claim? “I admit this is a wild west at the moment for sequence data,” he says. Many researchers deposit sequences in GenBank before publication “but fear that it is not clear this is prepublication data,” he adds (GenBank doesn’t have these type of settings). Scientists also post data to lab websites or GitHub with caveats that the data is prepublication; his website uses all these sources. Sequences posted with GitHub are immediately incorporated with sources notified of data use.

When asked if everyone is a believer in open data and if there were instances when he encountered resistance or hesitancy to share data, Bedford replied they use whatever people want to share. He has noticed a positive trend in the sharing ethos, however. During the time of the Ebola outbreak there was a significant lag that by the time of Zika was less so. The publisher agreement, signed by PLOS and others, to make data rapidly and openly available helped in this area, he believes. “The requirement for sequence data to be deposited in GenBank or otherwise made publicly available at the time of manuscript submission, not publication, contributes to research reproducibility,” says Bedford. PLOS, through its own sequence deposition policies and partnerships for enhanced methods reporting, continually works to strengthen these issues.

For some, the Open Access, Open Science community needs to do a better job of showcasing the value of this more transparent and open way of doing science, from bench to publication and beyond. Thus far there has been positive engagement with the World Health Organization for influenza vaccine strain selection via the related tool, nextflu.org (eventually slated to migrate to the nextstrain website).  Bedford envisions three audiences that would make practical use of his team’s open data tool:

  • Those performing viral sequencing or using sequence data, as a useful platform to compare and share data
  • Those involved in outbreak responses, as a tool to understand data, transmission patterns and strain evolution
  • Researchers or others interested in characterization of mutants and the ability to look at historical mutations
Publishing and License Choice

Bedford has an integrated publication strategy for his lab and work that best uses the various venues available. He publishes in a mix of Open Access and paywalled journals, creates webtools, deposits datasets and posts preprints. One strategy is to publish a statistical model or methods article, develop the model into a website or webtool and link to the website in published articles (rather than embedding JavaScript for the tool directly into the article).

He likes the pattern of building an ecosystem around a work: post a preprint with links to published/released genomes, update the preprint with new data or analysis and then submit that paper for publication to a peer-reviewed journal. This allows his team to capture the whole chain of research and progress, establishing provenance of credit along the way. Concerns of datasets posted on GitHub or GenBank getting scooped are similar to the scooping concerns surrounding the preprint server conversation. Helping people understand they’re putting an intellectual claim on their data (or paper) with posting has ameliorated, but not eliminated, those concerns.

Those using source code to develop tools for Open Science have several choices in licensing. For smaller projects, Bedford prefers the MIT license (also used for code developed at PLOS that is released as Open Source) which provides free and unlimited use and reuse rights, provided attribution is made clear. Other projects of his, including nextstrain.org, are released to the public under a GNU General Public License (GPL). This license provides that anyone using the source code to generate a derived product must, in turn, make that product open source. In other words, if a commercial entity adopts his open source code, that company must provide their code open source as well. The license status is essentially inherited and passed down to the next generation of product together with the code. One benefit of choosing the less restrictive MIT license, similar to CC BY for published articles, is maximum reuse without restriction.

Congratulations to all finalists of the Open Science Prize, sharing their work and data for the benefit of basic science, translational research and global public health.

 

Image Credits: The Open Science Prize, nextstrain

Protocols.io Tools for PLOS Authors: Reproducibility and Recognition

Solutions to the challenges of reproducibility in experimental science should be as diverse as the challenges themselves. Inconsistent reagents, barriers to the open sharing of supporting data, experimental variation that goes unrecorded and researcher’s concerns for lack of recognition and credit for novel and meticulously created experimental methods all contribute to the challenges of reproducibility in biomedical research.

PLOS now partners directly with protocols.io to provide authors better ways to share methodological details about their work, practical tools to reduce wasted research efforts and persistent, citable identifiers for laboratory methods. For PLOS, this is a step forward on commitments to address reproducibility and provide improved recognition and credit for all contributions to a work.

“We are delighted to be associated with a like-minded partner such as PLOS,” says protocols.io CEO Lenny Teytelman. “We are aligned in our Open Access ethos, and we strive to facilitate the communication of research in an effective, accessible and reusable way.”

This new offering complements PLOS’ already robust data availability policy, requiring that data underlying the conclusions of an article be made available at the time of publication. Since the strengthening of this policy in 2014, about 60,000 articles have been published that contain a Data Availability Statement.

“We are excited to engage with protocols.io,” says PLOS Executive Editor Veronique Kiermer. “This is another step towards Open Science, facilitating access not only to the data but now also to the laboratory methodology that generated these data.”

How It Works

Researchers are encouraged, at their discretion, to deposit their laboratory protocols on the protocols.io site, obtain a unique DOI and link directly to these from the Methods section of their articles. The unique link allows reviewers and editors access to the protocols during peer review. At the time of publication, the partnership between PLOS and protocols.io ensures that links to and from the published article are established and protocols are automatically made publicly available under a CC BY license for anyone to access, use and cite.

DOI: 10.1371/journal.pbio.1002538

 

Archived and linked permanently to and from the article, protocols become part of the scientific record. The protocols.io application allows scientists to create, copy, modify and evolve laboratory protocols, describing the critical details of experimental procedures that are often overlooked in articles Methods sections. While detailed steps in a protocol may evolve and improve over time, the version that relates to the published article remains accessible to help explain experimental nuances.

“Methods sections that describe laboratory experiments are narratives that tend to omit subtle variations that may affect the experiments,” says Kiermer. “I hope that scientists will take up the opportunity to describe their methods in a way that is much more useful to others.”

Nuanced methodological details can be shared in new ways, that in time can integrate seamlessly into the research cycle, from bench to publication and back. “It is not merely a tool for publication,” says Teytelman, “it can be useful as a lab tool, at the bench, for record keeping and for sharing expertise within and outside a laboratory.”

Engaged commenting on the protocols.io website allows interested readers to clarify and discuss deeper with others using an article’s methodology. “This partnership will improve reproducibility of published research while fostering scientists’ collaborative engagement with our content,” adds Kiermer.

A DOI for methods, citable by others, provides more granular credit to those individuals contributing to methodological development. It also enables researchers to compare methodological details between laboratories pursuing similar approaches or between published experimental methods and those subtly revised by users. In this respect, protocols.io helps bridge an information gap between published experimental methods and methods refined over time.

PLOS looks forward to authors’ participation in this novel approach to enhancing Methods sections—an Open Access tool to record and share detailed protocols. We hope you try it and let us know your experience via comment below or email to communications@plos.org.

 

Hero image inset credit (CC BY): Bandage plot of transcripts assembled by J. Mamrot

Early Career Researchers and Forbes 30 Under 30 Innovators Have What It Takes

This post is part one of a two-part blog series. Visit the PLOS ECR Community for part two.

In advance of the third Early Career Researcher Travel Award Program launching today, PLOS reached out to recipients of Forbes 30 Under 30 in Healthcare and Science who were also PLOS authors at the time of the awards (scroll down on the Forbes pages to see individual honorees). Five leading Early Career Researchers (ECRs) working in genetics, pathogens, virology and the intersection of medicine and policy shared their views with PLOS on Open Access, open data and communicating scientific results. Below are their responses that we hope will inspire and motivate ECRs in all disciplines. At the end of this post, PLOS Medicine Chief Editor Larry Peiperl specifically responds to the importance of data sharing and publishing all valid results.

When asked, “Do you and your colleagues discuss publishing in Open Access journals, or making data openly available?” these stellar scientists replied:

As a computational group, we rely almost exclusively on publicly available datasets. Making data openly available is critical to moving science forward, and it’s really frustrating that it is still far from ubiquitous. But I think we need to go even a step forward, and make all parts of publications, including the code and pipelines, easily available as well. I have been actively involved in discussions about why and how to do this. Luckily, I think the field of human genomics has been quite pioneering in moving toward a more “open” culture. Among my colleagues, it is just assumed that everyone puts their papers on preprint servers as soon as they’re submitted. We give people a hard time if their data is not available. Increasingly, software is getting posted on github or similar repositories. Unfortunately, this is not the case in every field. —Melissa Gymrek, Assistant Professor, UC San Diego. Read Gymrek’s work in PLOS ONE.

 

It’s incredibly important for data to be shared in a way that promotes collaboration and the advancement of knowledge. I think in general the more diverse ways you can examine a problem, or a data set, the more likely you are to reach surprising and meaningful conclusions. As biomedical researchers, our major goal should always be to improve human health, and open access seems to be an essential part of that effort. —Carrie Cowardin, Postdoctoral fellow, Washington University. Read Cowardin’s work in PLOS Neglected Tropical Diseases.

 

 

Making data openly available is an approach we highlight and discuss in our recent analysis of alternative mechanisms of research and development on our Re:route microsite. Open data platforms are one way we can make biomedical R&D help more people, by increasing scientific discovery output, sharing negative results, increasing competition and decreasing the cost of medicines, vaccines and diagnostics. This model is already being used to some extent by Drugs for Neglected Diseases initiative (DNDi) and Medicines for Malaria Venture (MMV), among others. But it is not enough. This has to be implemented more broadly. —Gloria Tavera, President of the board, Universities Allied for Essential Medicines. Read Tavera’s work in PLOS Neglected Tropical Diseases.

When asked, as one of the new generation of influencers in their respective fields, what changes do they foresee or would like to see related to the way research findings make their way to the greater scientific community, these innovators described preprints, linked data and code, the role of politics in the direction of scientific research and new forms of media as communication tools.

 

One of the many things I’d like to see in the future is to get the science spread to the general public more often. As a scientist, we’ve more often just focused on exchanging our ideas or findings within our close circle, while the general public have little idea of what we are doing. I think it will be really great for the next generation of scientists to become better communicators, and try to bridge what we know to the others, and with the use of new forms of media, I am pretty sure there will be many endeavors taken pretty soon. —Jiang He, Postdoctoral fellow, Massachusetts Institute of Technology. Read He’s work in PLOS Pathogens.

 

If current trends continue, the most recent scientific developments will continue to be communicated to the greater scientific community digitally, through many different open access platforms. The advantage is that this information can reach a wider audience than we could have ever imagined. However, we need to make sure that this dissemination mitigates sensationalism and only communicates good, accurate science. We will need well-trained science journalists and editors to lead these changes. —Srilakshmi Raj, Postdoctoral fellow, Cornell University. Read Raj’s work published in PLOS ONE.

 

Preprints and open access will become the norm.…I am particularly inspired by the ATGU’s eloquent publication policy. They sum it up: “We believe that it is only a matter of time before the concept of restricted access to the products of scientific research becomes an anachronism.” …In principle, a publication should include everything needed to reproduce the main findings of the study. That has to include software as well! I am frustrated with how many times I have to reinvent the wheel by redoing an analysis that was already done in another paper. My dream is that every figure, table, and result in a paper will be linked directly to the code and data used to produce them. —Melissa

We live in an interconnected world, and as technology advances, it becomes ever more pressing to share data openly and in an expedient way. The methods put in place by the WHO for sharing data on Zika virus come to mind. It’s incredibly important to maintain the quality of work we do while improving our ability to share it with others, and part of that means timely publication of results. I also hope for more acceptance of negative data, which can be just as important to be aware of as interesting positive results. Better communication and recognition of negative results would make current research much more efficient and productive. —Carrie

PLOS Medicine Chief Editor Larry Pieperl responds:

Encouraging data sharing became a priority for many during the West Africa Ebola outbreak 2-3 years ago. WHO called a consultation on data sharing and invited several journal editors to join the researchers and funding agencies for discussions in Geneva. The evidence presented there included an analysis that showed most of the research from the 2003 SARS outbreaks were not even submitted for publication until after the crisis was over.

I think some people had the idea that editors presented a barrier by refusing to publish research if the data had been previously shared, and wanted us to account for ourselves. What happened may have surprised them: journal editors had no problem endorsing data sharing in public health emergencies. This statement of editorial policy turned out to be timely, as the first studies on Zika came soon after, and data sharing quickly became an expectation. Of course, many of us believe that data sharing shouldn’t require an international emergency. Requirements by major funding agencies that researchers share data as a condition of their grant award are an interesting recent development.

Regarding negative results, they may not win awards, but their publication is unquestionably a contribution to the research community. Think of a forest where a few well-known paths appear on a published map, but most paths are not marked at all, even though some of them have already been explored for long distances only to find they lead nowhere. Surely a signpost should be added to keep others from wasting time and resources. In clinical research, a conclusive negative result can have the immediate benefit of preventing futile, costly or hazardous interventions in subsequent patients.

Now PLOS invites all ECRs who meet the PLOS Early Career Researcher Travel Award guidelines to share their views. For an opportunity to obtain support to attend a professional meeting, let us know your thoughts on the below:

Considering new and modern ways of communicating science, describe the role the community can play in changing the way science is judged and assessed to accelerate science and discovery.

We look forward to hearing your vision of the future. For more on the Forbes 30 Under 30 honorees, their backgrounds, greatest challenges and advice for success, head to the PLOS ECR Community for the second part of this two-part blog.

NYT: Why Trump’s N.I.H. Cuts Should Worry Us, by PLOS Co-Founder Harold Varmus

PLOS is pleased to highlight here an important Op-Ed written by PLOS Co-Founder Harold Varmus, published in The New York Times on March 22, 2017.

Source: Why Trump’s N.I.H. Cuts Should Worry Us – The New York Times [Featured image: Thoka Maer]

Last week I was in London to participate in a scientific symposium. During coffee breaks, many British colleagues asked me and other American visitors to explain the bewildering news that President Trump had announced his intention to cut the budget for the National Institutes of Health by 18.3 percent, about $5.8 billion.

My answer to “What is going on?” did include some consoling reminders. A presidential budget request is a proposal, not a done deal. The actual fiscal year 2018 appropriation for the N.I.H. will be determined by Congress, which has historically provided enthusiastic bipartisan support for biomedical research. Although the N.I.H. has lost a substantial amount of its spending power gradually over the past decade, it has only rarely experienced a sharp decline in actual dollars and never of this magnitude. Furthermore, strong nonpartisan opposition to Mr. Trump’s proposal will come from many quarters, including advocates of research on specific diseases.

But it would be a mistake to be complacent about the president’s proposal, because it is likely to have real consequences. Yes, some have said that the proposed cut to the N.I.H. will be dead on arrival in Congress. But the president’s budget proposal is still important: The administration’s representatives will need to defend it at hearings, and it could be the starting point for negotiations among appropriators. It is not difficult to imagine a compromise in which the N.I.H. suffers a steep reduction.

David Knutson, speaking for PLOS, offered this comment on the New York Times Op-Ed by Harold Varmus.

To understand just how devastating a cut of less than 20 percent of an agency’s budget would be requires some understanding of how the N.I.H. operates. Very little of its typical annual budget is spent on the agency’s administration: The industrious, underpaid government scientists who manage the funding of the N.I.H.’s research programs consume less than 5 percent of its budget. Only a bit more, about 10 percent, supports the work of government scientists. In sharp contrast, over 80 percent of its resources are devoted to competitively reviewed biomedical research projects, training programs and science centers, affecting nearly every district in the country.

The N.I.H. awards multiyear grants and contracts, but receives annual appropriations that must be spent that year. This means that at the start of each year most of its dollars are already committed to recipients of awards from prior years. A budget cut of the size that is proposed would effectively prevent the awarding of new grants or the renewal of any that have reached the end of a multiyear commitment. Junior scientists, already struggling in a highly competitive atmosphere, may not get a chance to have an academic career. Senior investigators might need to lay off staff, disrupting research teams and leaving projects unfinished.

A substantial N.I.H. budget cut would undermine the fiscal stability of universities and medical schools, many of which depend on N.I.H. funding; it would erode America’s leadership in medical research; and it would diminish opportunities to discover new ways to prevent and treat diseases.

Read the complete Op-Ed by Harold Varmus in the New York Times, March 22, 2017

Harold Varmus, a professor at Weill Cornell Medicine and a co-recipient of the 1989 Nobel Prize in Physiology or Medicine, was the director of the National Institutes of Health from 1993 to 1999 and of the National Cancer Institute from 2010 to 2015. He co-founded the Public Library of Science (PLOS) in 2000 with Patrick O. Brown and Michael B. Eisen.

A Sincere Thank You from PLOS

2017 marks the third year that PLOS formally acknowledges our community of reviewers and editors with a public thank you published as a citable journal article. We do this to honor the dedicated service and substantial contributions made by working scientists – scientists with day jobs – who graciously provide their time and expertise to our organization. Thank you journal articles provide reviewers and editors the academic citation and recognition for their valuable service to colleagues, institutions, funders and the public.

It takes a global network of more than 78,000 reviewers and 7,000 editors to ensure that articles, perspectives, editorials and more achieve the highest quality possible. The more than 12 million article views per month (on average) this past year shows that PLOS reviewers and editors are up to the task of vetting the science, the ethics, the reporting guidelines and journal publication criteria presented in the more than 27,000 research articles published in 2016.

For the first time we are including in each of the seven journals’ thank you articles the number of newly submitted and published research articles brought to the public in 2016. We are confident that this data, in real terms, supports our ongoing commitment to increased transparency surrounding the publishing process.

We are also confident that readers will appreciate the workload required of reviewers and editors to support these publication numbers. In addition, contributors to PLOS Biology were tasked with fine-tuning Aperta™, our new submission system, as they reviewed, discussed and moved submissions through the publication process.

As they shepherd papers and provide feedback so authors may improve manuscripts and refine experimental work, it is more than quality that our contributor community champions. Reviewers, Editors and Editorial Board members who choose to do so also communicate the mission of Open Access, the value of Open Data and the relevance of Open Science to society at large.

These individuals serve as ambassadors not just for PLOS but for all of science. Public access to rigorous peer-reviewed research, the role of journals in communicating the work of our communities and the enthusiasm of our own staff are all sustained by this extensive pool of inspired and dedicated scientists.

To all of our Reviewers, Academic Editors, Guest Editors and Editorial Board members, thank you! Those wanting to explore deeper will find every reviewer’s and editor’s name in the Supporting Information of each journal’s published article; links to these articles are below.

Channel Your Community’s Research

At PLOS, we aim to support academic communities in communicating their research in open and accessible ways. The first of the PLOS Channels, a new way for specialist communities to communicate, find and read research content, launch this week.

Channels provide an innovative way of curating and presenting published research relevant to a scholarly community. Each is curated by a small group of Channel Editors, themselves researchers, who continuously bring together and showcase recently published research content selected from the broad scope of PLOS journals. Importantly, Channel Editors can point to resources, news and commentary from many online sources, including articles published in other journals.

PLOS developed Channels for communities to drive according to their own content priorities, without limitation to any particular journal.

With experts at the helm, and content selected by researchers for researchers, we hope to create online venues that become a preferred destination for research communities. To this end, the Channels concept was designed with researchers’ input to adapt to various needs. Channels can be adopted as a resource by researchers in a specialist area, or bring together researchers from different academic backgrounds working towards a common aim. The first three Channels to launch illustrate a variety of applications.

 

The Veteran Disability & Rehabilitation Research Channel was born from a collaboration with the US Department of Veterans Affairs Rehabilitation Research and Development Service, as a new home for the community previously served by the Journal of Rehabilitation Research & Development (JRRD) which ceased publication in 2017. The new Channel, with an expanded international focus, features multidisciplinary research for a global community of researchers and care providers working with veterans.

 

The Open Source Toolkit Channel showcases research from a diverse group of fields that have in common the description of innovative open source software and hardware applications that can be used in research and education. This Channel aims not to serve a specific scientific discipline but to create bridges between vibrant communities that build tools to support democratization and reproducibility of research.

 

The Tuberculosis Channel, led by Academic Editors from PLOS ONE and PLOS Medicine, will launch on World TB Day, March 24th, 2017. This Channel will draw from PLOS journal content covering all aspects of TB from mycobacteriology to computational epidemiologic models, clinical diagnosis and treatment. By integrating these reports with content from a variety of external sources, Channel Editors aim to provide an accessible resource of interest to TB researchers around the world.

We are grateful to the Channel Editors who have stepped up enthusiastically to pioneer the use of this new tool for their communities. More PLOS Channels will follow later this year—some are already in preparation. If you have interest in becoming a Channel Editor or see an unmet need in your community for this tool, we welcome your thoughts. We look forward to working with many more communities to help disseminate their work, create useful resources and foster collaboration within and across specialist communities.

Stay tuned!

 

Optimism on Rare Disease Day: With Research, Possibilities are Limitless

Since 2008 in Europe and 2009 in the US, the last day of February is marked as Rare Disease Day. In less than 10 years, Rare Disease Day (and #RareDiseaseDay) has grown from a centralized effort to bring attention to these disorders by patient organizations in Europe to an international awareness and action day that includes patients, legislators, research funders, scientists and clinicians.

It is estimated that 350 million people worldwide suffer from rare diseases, defined regionally according to prevalence. In the European Union a rare disease is one that affects less than 1 in 2,000 patients while in the United Kingdom the qualification is less than 50,000 patients and in the United States the classification is less than 200,000 patients. Regardless, rare diseases usually have a genetic basis and are frequently progressive, disabling and with time, life-threatening. There are currently more than 7,000 different types of rare diseases and disorders, according to the rare disease patient advocacy organization Global Genes.

Those interested in general concepts related to rare disease and treatments or drug development can look to recent PLOS articles covering “Clinical Practice Guidelines for Rare Diseases: The Orphanet Database,” “Profitability and Market Value of Orphan Drug Companies: A Retrospective, Propensity-Matched Case-Control Study” and “Access to Orphan Drugs: A Comprehensive Review of Legislations, Regulations and Policies in 35 Countries.”

Research is the theme of Rare Disease Day 2017 with the slogan “With research, possibilities are limitless.”

Research published in PLOS journals is a testament to the dedication of scientists working on these diseases that often have less funding and attention than other biomedical issues, and the willingness of these scientists to go beyond publishing Open Access to make their data available for the rare disease community is critical to accelerate a path forward to uncover treatments and cures.

Image Credit: Michael Bamshad et. al.; video frame

Coincidentally, one of this year’s finalists for the Open Science Prize, given for unique insights developed from shared data, is described in this video “MyGene2: Accelerating Gene Discovery with Radically Open Data Sharing.” Researchers at the University of Washington created the web portal MyGene2 as a place for people with rare genetic mutations to connect with others that share the condition and with researchers interested in their particular mutation. Michael Bamshad, PLOS author and professor and chief of the Division of Genetic Medicine in the Department of Pediatrics at the University of Washington & Seattle Children’s Hospital, describes this Open Science resource in a RARECast podcast interview, “Helping Patients with the Same Undiagnosed Genetic Condition Find Each Other.” Research from Bamshad’s group also includes PLOS ONE articles on the implications of fine-scale patterns of population ancestry on rare variant genome-wide association studies, genetic variation and risk for symptomatic West Nile Virus infection and disease progression and the PLOS Genetics article discussing mutations and a rare-disease inheritance model applied to congenital heart disease.

In addition to data sharing, opportunities to improve diagnoses stem from genetic sequencing advances, as described in improving the identification of cancer-associated genes and co-occurrence of rare diseases and resolution of a complex phenotype by next-gen sequencing.

Rare Disease Day is a chance to draw attention to the research and policies needed to advance understanding of these disorders that challenge the lives of so many. This year’s theme, “with research, possibilities are limitless” meshes well with the community PLOS serves as a science, technology and medicine Open Access publisher. A small sample of new research on rare diseases from PLOS authors is highlighted below:

Friedreich’s Ataxia

Progeria

Gaucher’s disease

Mitochondrial diseases

 

A Year of Open for Discovery

Every year, PLOS releases an Annual Update of milestones and highlights. We do this for more than just archival purposes of notable research; we do this to bring to light foundational work of the many teams that help make us ONE PLOS. PLOS is unique among other Open Access publishers in that the work of our teams serves authors and the greater community—we are active collaborators on advocacy and technology initiatives that increase access, discovery and use of the scientific literature. The Annual Update provides a centralized resource for those looking to understand more about who we are and what we do.

We hope readers will find work of interest to use, reuse and remix from one or more of the sections including:

  • Letter from the Chairman and Interim CEO
  • Research and Global Media Highlights
  • A Modern Technical Framework to Accelerate Innovation
  • Moving Beyond the Article to Expand Author Opportunities
  • Updated Policies and Practices to Address Reproducibility, Discovery and Author Recognition
  • Multifaceted Approach to Advance Open Data and Open Science

Readers will notice several changes from previous updates: a more concise report to enable easier browsing through the year’s achievements, more links to quickly access key research and a selection of news interviews to hear directly from PLOS authors. This year’s update also marks a shift to calendar year reporting to consolidate internal data-gathering activities, allowing us to focus more on getting important research out to the public as quickly as possible.

2016 PLOS BY THE NUMBERS

While you’ll find all the details of the above infographic inside the 2016 PLOS Annual Update, we are full-steam ahead into 2017 as PLOS engaged with a record number of new Twitter followers in January (more than 7,000) who discovered and shared exciting research.

Today, we announce the open source release of Ambra™, our journal and collections publishing platform.

In providing Ambra to the community, we live up to our commitment to make software developed at PLOS available open source once we are confident of the code’s scalability. Assigning the open source MIT license to Ambra follows our 2014 MIT licensing of PLOS ALMs as Lagotto. Read “Ambra, the PLOS Journal Publishing Platform, is Open Again” by Patrick Polischuk, Senior Product Manager, Product Development, for a brief history of Ambra and details on this release.

Stand Up for Science

“You look at science (or at least talk of it) as some sort of demoralizing invention of man, something apart from real life, and which must be cautiously guarded and kept separate from everyday existence. But science and everyday life cannot and should not be separated.” -Rosalind Franklin

In this current political climate, facts matter more than ever. With responsibility as a leading Open Access publisher, a beacon of positive change to archaic systems, PLOS loudly stands up for science and scientists around the world in their efforts to improve the health and well-being of societies and explain the wonder of the world around and beyond us.

Back in the 17th and 18th centuries, enlightenment thinkers advanced politics, philosophy, science and communication; they supported equality and human dignity, and opposed superstition, intolerance and bigotry. Scientific thinking and the scientific method was a critical shaper of the enlightenment. As we look at the world around us, we must ask, what has the scientific method brought to our world, and to our world view? To answer this question, we must let the data speak for itself. Your data. My data. And the data of every geologist, atmospheric scientist, evolutionary biologist, geneticist, physicist, engineer, software developer and physician scientist. This is a position PLOS has exemplified through its Open Data policy and we strongly support the Office of Science and Technology Policy’s guidance, provided most recently in its January 6, 2017 memo, on this important area.

Science in Action

But how can this data speak when science communication is blocked from reaching the public and the scientists themselves are prevented from reaching their labs, their communities, their places of work? Access to information, access to research and data enables better policy decisions. In turn, policies informed by publicly and privately funded data and created by enlightened governments, academic communities, patient advocacy groups and global coalitions all power improvements in our world. Climate change, vaccine safety and animal welfare are among the many areas where we support the scientific endeavor to inform the debate with data-based evidence, and organizations like the Center for Disease Control and the World Health Organization rely on data-based evidence to foster human health both in the US and around the world.

It is impossible for PLOS to know how many of our global network of nearly 7,000 editors, more than 78,000 reviewers and authors from more than 190 countries are on any particular type of visa. We do know science is, and has been for generations, an international endeavor. Scientists collaborate and travel for post-doctoral fellowships, conferences, review panels, sabbaticals and speaking engagements. Conceptual understanding, testable hypothesis, well-designed studies, observational methods and sufficient replication are the tenets of science discussed during these meetings, as well as during routine days in the lab. These tenets of science are upheld by all researchers, regardless of nationality, religion, race, gender, sexual orientation, career stage or professional stature. Immigration restrictions inhibit that free exchange of knowledge.

As a nonprofit publisher, innovator and advocacy organization founded to accelerate progress in science communication, we must advocate for what we know to be true: PLOS must not only liberate science communication from the constraints of traditional publishing, we must stand up for science to ensure the liberation of scientific facts, intelligent discourse and conclusions based on data. Given that PLOS’ primary mission is the elimination of barriers to the open dissemination of scientific research, we’re naturally against policies and practices that increase, rather than decrease, obstacles.

In a world that abruptly and forcefully presents challenges of accessibility, accountability and discovery, a rigorous commitment to our core principles and mission to transform how research results are communicated is even more critical. A growing international community of readers, educators, policy makers, scientists and entrepreneurs share, reuse and remix Open Access research article content without restriction—advancing the innovation economy and the health of communities around the world.

We continue to support the scientific community from which we were founded and to be vocal in pushing the continued expansion of open science. We support, and will be represented at, the March for Science in Washington—now scheduled for Earth Day April 22nd! We look forward to seeing you there.

To reach The Official PLOS Blog team, email communications@plos.org or leave a comment below.

 

Image Credit: Shahee Ilyas

Imaging Active Cells for Insights, Education and Reward

Effective science communication engages readers through use of multiple formats, from written text to visual images. In recognition of the long-standing importance of microscopy and increasing use of video for understanding cell biological processes, PLOS sponsored the 2016 American Society for Cell Biology Celldance video contest. With support from ASCB, the “Tell Your Own Cell Story” videos document membrane remodeling during cell migration, invasion and metastasis; dendritic cell migration during the immune response and chromosome movement during cell division. Through these videos attendees at the ASCB meeting were able to see the personal, creative side of scientists not typically presented to a wide audience.  PLOS interviewed these scientists by email following the conference.

Daniela Cimini’s lab at Virginia Tech University studies the molecules and structures during mitosis that ensure accurate chromosome segregation during cell division. Related work of the Cimini group addresses the causes and consequences of abnormal chromosome numbers in normal and cancer cells, including kinetochore-microtubule attachment and chromosome segregation irregularities. She has a long-standing interest in use of video to describe the dynamic nature of mitosis and considers video microscopy “particularly important for disseminating ideas to non-scientists or scientists that are not expert in a particular field, which may include funders and policymakers.” In creating the videos, scientists in Cimini’s lab – comfortable giving lectures or presenting work to colleagues – experienced how difficult it was to present their work in front of a camera. During production, scientists, writers and videographer interacted to plan and execute the project, said Cimini. “It was very interesting to see all these different perspectives and areas of expertise come together.” Cimini has been publishing with PLOS since 2009.

Cimini lab with Jagesh Shah (left) for ASCB Celldance

Roberto Weigert’s lab at the National Institutes of Health focuses on unraveling basic molecular mechanisms regulating trafficking events in mammalian tissues, with a particular emphasis on membrane remodeling. The lab pioneered a new technique to image these processes live in multicellular organisms and to investigate membrane dynamics during endocytosis, tumor progression, invasion and metastasis. The work in their Celldance video highlights this technique but also the collaborative use of new technologies to enhance research discussions among lab members. For Weigert’s team, while the most difficult part in making the video was “avoiding the use of jargon and other technical terms that are part of our daily life,” the experience provided them an exciting opportunity “to talk about the overall theme of our research rather than focusing on a single project.” Wiegert personally thinks scientists play an important role in direct dissemination of research findings. “I find that when scientific messages are disseminated more widely by an intermediary, there is a loss in translation. Hearing the voice of the scientists that are doing the job is a more compelling and direct way to communicate the messages.”

Weigert lab with Jagesh Shah (left) for ASCB Celldance

Matthieu Piel’s lab at the Institut Curie, National Center for Scientific Research (CNRS) is fascinated by how cells determine front and back – cell polarity – in the context of cell migration and cell division. Members of the Piel lab documented through video that when dendritic cells – key participants of the immune response responsible for presenting antigens to T cells – migrate through narrow passages they can be squeezed so hard that nuclear proteins leak out of and cytosolic proteins leak into the nucleus. This has serious implications for cell survival. For Piel, the most challenging part of creating the video was not what to show or how to show it, “I knew which movies I wanted to show and I wrote in a way that included them all,” he says, but how to tell this dynamic story in five minutes. Piel often watches short science videos and thinks there is a need for more of this forum for communicating science—kids especially should watch more of them, he says. When asked about funders and policy makers, however, he is less certain. “Maybe they would be more interested to know about scientists. The few I know are usually more interested about people.” Piel has been publishing with PLOS since 2008; his early work examined structural proteins involved in membrane ruffling. In addition to basic research, the lab uses nano- and micro-fabrication techniques to develop (and patent) tools to study cell polarity through control and modulation of key physical and chemical parameters of the cell microenvironment.

Piel lab with Jagesh Shah (left) for ASCB Celldance

All three labs embraced the challenge of presenting complex science in a visually engaging yet comprehensible way that is also representative of dynamic cellular movements observed in response to environmental stimuli. Watch the videos and see for yourself that all three labs lived up to the challenge; read more from the author interviews in the coming days on PLOS Biologue to find out what motivated these scientists to submit their work for an ASCB Celldance 2016 Award and leave a comment here to let us know what you think.

 

 

Image credit:
Daniela Cimini
https://vimeo.com/193753945/38c3a4a14a

Ten Years of Advancing Science as ONE

This special blog post in celebration of the journal’s tenth anniversary is authored by Joerg Heber, PLOS ONE Editor-in-Chief.

Ten years ago on this day, PLOS ONE published its first papers, thus embarking on its stated mission to be an open public venue for all rigorous scientific research from every discipline: a journal that promotes open science and access to the peer-reviewed literature for all.

Being designed to be a home for all research, PLOS ONE always had the potential to be a large journal. Yet who would have foreseen the publication of more than 165,000 papers in its first decade? This enormous success would not have been possible without the support of the academic community submitting these papers, the efforts of the editorial board, the peer reviewers assessing submitted papers, and last but not least the staff at the journal, past and present. Thank you all! An appreciation of PLOS ONE’s history and its achievements is the topic of a separate post on the EveryONE blog here.

As the newly-appointed Editor-in-Chief of PLOS ONE, I am privileged and very lucky indeed to be leading this great journal into its second decade. The environment that we are operating in has changed significantly during the past decade, stimulated to a degree by our own success. Other journals are now using similar publishing models, which is a welcome development. The more Open Access journals operating without any subjective selection criteria of their published output beyond scientific validity, the better it is for science. At PLOS ONE, we continue to be a home to all research, whether it is a stepwise advance, a replication, a negative result, or a study that fundamentally changes the thinking in a field.

We cannot rest there, and PLOS ONE needs to continue its mission to facilitate and drive open science. Making scientific papers open to read, to utilize them, and to distribute them is only one facet of the scientific process. Opening this process further promises significant advances. An example is the sharing of primary research data, which in many instances can stimulate follow-up studies by others. Already we have a strong data availability policy in place, and we will continue to refine its implementation and will continue to drive further efforts towards rewarding those scientists who do share their primary data.

Sharing scientific results and conclusions more broadly also needs to take place earlier in the process, so that others can build on new findings as soon as possible. At PLOS, we are strong supporters of preprint servers to communicate research. PLOS ONE is an ideal partner for such efforts, given our mission to publish all rigorous scientific conclusions. Embedding preprints into the publishing process, as we have already done with bioRxiv, increases its transparency. Going forward, we need to strive to also open our peer review process, lending strong support to the wider adoption of this model.

Other publishers and journals are working on similar themes, and we applaud this. While these initiatives mean a faster and larger increase in the global number of open articles published and available globally to the scientific community, the submissions to PLOS ONE have decreased, posing the question of our continuing unique value in this market. There will be challenges, but irrespective of our size, PLOS ONE will always play an important role towards PLOS’ broader mission as a not-for profit organization to support and advocate open science.

We are driven by the belief that open science benefits everyone involved in the scientific process, which thrives best in an environment of collaboration. We are driven by serving the community and not by the need for the high profit margins made elsewhere in publishing, so that funding resources in the sciences are used in the most productive way — to conduct scientific research. And at PLOS ONE in particular we are driven to publish a journal that serves communication among scientists from all the natural sciences and engineering, from medical research, as well as from the related social sciences and humanities. Our strong board of academic editors from all disciplines enables the entire scientific community to come together, making PLOS ONE their journal.

As part of this mission, PLOS ONE has the opportunity as well as the obligation to play its role in addressing the challenges science and society are facing. We can and need to assume a strong role promoting scientifically rigorous, open, fact-based debates that facilitate solutions to these challenges. As we advance towards this goal, we all at PLOS ONE are truly grateful for the continuing, strong support of the scientific community, and building on this we are confident that we can be as successful going into our second decade as we have been these past ten years.

Image Credit: Gerd Altmann

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Join us in celebrating PLOS ONE‘s Tenth Anniversary – here are some ways to get involved:

 

 

 

 

Author Credit: 2016 Roundup

In previous blog posts we’ve talked about PLOS’ efforts to improve recognition for authors and increase transparency around individuals’ contributions to published research. In today’s post, we review our 2016 accomplishments in this area and the progress we’ve made toward our goals.

ORCID Implementation

In January, PLOS, eLife, the Royal Society and other major publishers developed and signed an Open Letter committing to follow best practices when collecting, processing and displaying ORCID iDs. Signatories further agreed to begin requiring by year end that each corresponding author associate their name with an ORCID iD and 15 signatories have already implemented this policy. As of December 7 this is now also PLOS policy—corresponding authors on manuscripts coming in to either of our submission systems (Editorial Manager or Aperta™) must provide an authenticated ORCID iD.

In preparing for the launch of this requirement, we tackled both technical and operational hurdles. But there were – and still are – behavioral changes needed. PLOS began capturing ORCID iDs in Editorial Manager in 2014. By the beginning of 2016 there were more than 27,000 authenticated iDs in our database. Throughout this year, we have actively engaged with our authors, editors and reviewers to encourage sign-ups; in addition to email campaigns and messaging in the submission system we have posted an informational page on our web site, updated our author instructions and provided how-to videos to assist our contributors.

As of this week, we have upwards of 54,000 authenticated ORCID iDs, more than doubling the count in less than a year. We still have a long way to go, however, as there are many more in our database who have yet to register!

How PLOS Uses ORCID IDs

From early 2016, we have been passing authors’ iDs on published articles through to Crossref with our metadata deposits. Crossref, in turn, communicates that information to ORCID; if the author has agreed to allow for updates their ORCID profile is enhanced to include the new publication. This auto-update function makes it possible for authors to maintain their records going forward without having to take action. It’s vitally important that authors provide their permission for this process to work.

Are you an author who’s provided an ORCID iD to us and published a PLOS article during 2016? Are you wondering why credit isn’t showing up in your ORCID profile? Watch our short video to see how to ensure you’ve given the needed permission.

CRediT Implementation

While ORCID allows us to know and unambiguously credit WHO participated in published articles, CRediT goes a step further and allows us to provide attribution for WHAT those individuals did in relation to the articles. Such attribution improves the ability of institutions and funders to more accurately evaluate researchers based on their actual contributions to published works, rather than by the journals in which those articles appear.

While PLOS has for many years required contributions for each of the named authors to any submitted work, in 2016 we adopted the CRediT taxonomy of contributions. CRediT is a community-developed open standard intended to replace over time the many disparate lists – or free-text – that publishers have been using for this purpose. More information is provided in our instructions for authors.

We are gathering data on how the CRediT taxonomy is being used by our authors and will be analyzing and sharing that out in 2017.

Looking Ahead

Progress in these two areas – uniquely identifying and crediting authors and gathering standardized author contributions – are major steps along the path of providing improved attribution and transparency in scholarly publishing. PLOS will continue to provide or adopt new tools and services that help accelerate the pace and transparency of scientific research and will continue to collaborate with others to establish ways to speed publication, improve the author experience and advance standards for reporting and reproducing research.

A PLOS Response to Open in Action with Open Science

With the theme of Open in Action, International Open Access Week 2016 served as a call for researchers, policymakers, funders and publishers around the globe to take “concrete steps to open up research and scholarship.” In direct response to this call, PLOS thought carefully about Open Science and what it means for us.

Reflections on Open Science at PLOS

PLOS has proven that making quality research openly available for anyone to read, download and reuse is a viable business model. Our collaborative efforts with like-minded organizations have inspired others – from individual researchers to the larger publishing industry – to move toward a more open ethos. In this environment, Open Access is no longer constrained to free access to research, it’s also about open data and a more open way of working together. Examples of this at PLOS include our pioneering a forward-thinking data policy at scale and contributions to the community-developed open-standard taxonomy of contributions – the CRediT Project – that provides specific and comprehensive attribution on research articles for all who participate in generating a published work.

We are proud to be Open in Action collaborators with other publishers including The Royal Society, eLife, Science journals and EMBO Press in making a public commitment to implement persistent identifiers such as ORCID iDs by year end. These iDs enable researchers to receive credit for a wide range of research outputs in addition to publications (for example blog posts at PLOS) and we are well on the way to meeting this goal. With many of these same collaborators (The Royal Society, eLife, ScienceEMBO Journal, Nature and Professor of Structural Biology Stephen Curry and Associate Professor of Information Science Vincent Larivière) we committed to publish citation distributions of our journals to demonstrate a key flaw with impact factors—they simply do not reflect article citation rates. In publishing this data, PLOS hopes to “strengthen a call for action originally voiced by Stephen Curry, one of the authors, and to encourage other journals to follow suit.” The original paper and dataset are posted on bioRxiv for all to access.

Open Policies and Open Research

Data sharing and Open Access are a matter of course for PLOS authors, providing open and rapid dissemination of their original research in all areas of science. PLOS supports authors who wish to share early versions of their research manuscripts to receive feedback before – or in parallel to – formal peer review, and encourages researchers to share via preprint servers either before or after submission to a PLOS journal. PLOS has a long-standing policy of accepting manuscripts previously posted to preprint servers, however we have eased the process for authors for this rapid dissemination vehicle that also brings transparency to the review process. Authors can now use bioRxiv’s direct transfer to journal service drop-down menu to submit directly to PLOS.

We have exemplified Open in Action as the first publisher to react to the Zika outbreak with a Call for Research and The Zika Collection. This placed PLOS on the map for rapid dissemination and discovery of results during the outbreak. As a result, work of authors who published with PLOS caught the attention of legislators: The US Capitol called PLOS to ask for additional information regarding the PLOS Currents: Outbreaks article, “Travel Volume to the United States from Countries and U.S. Territories with Local Zika Virus Transmission” as they were considering this information for use in upcoming legislation.

The practical impact of Open Access and open data may not always be immediate. The International Union for Conservation of Nature (IUCN), publishers of the IUCN Red List of Threatened Species, voted in September 2016 to adopt the Environmental Impact Classification for Alien Taxa (EICAT) for classifying invasive species, work originally published in PLOS Biology in 2014. Author Tim Blackburn stated “IUCN has approved the motion on our method for classifying alien species impacts…The adopted text requires a consultation before EICAT becomes an IUCN standard… [but] it is an extremely positive development… Getting the paper published somewhere so high profile (and open) really made a difference, so thank you!”

Actionable knowledge on an international scale extends beyond conservation efforts to inform human health and disease initiatives. The WHO Estimates of Foodborne Disease Collection reports the first estimates by the World Health Organization (WHO) Foodborne Disease Burden Epidemiology Reference Group of the incidence, mortality and disease burden caused by 31 foodborne hazards. Outcomes reported in the Collection – from PLOS, WHO and F1000Research authors – can contribute to improvements in food safety throughout the food chain when incorporated into policy development at regional, national and international levels.

If you choose to be Open in Action with PLOS, you can also have a bit of intellectual fun. The PLOS Paleo Community held a competition for the paleontology research community for the Top 10 Open Access Fossil Vertebrates of the year, to honor researchers that have thought long and worked hard to provide our community quality research that is openly available to all. Articles represent the vertebrate diversity published in Open Access journals, from PLOS ONE to PeerJ, Science Advances and Paleontologia Electronica.

Encouraging the Next Generation of Open

PLOS supports the growth of Early Career Researchers (ECRs) as they build skills in science communication, become champions of Open Science and develop into ambassadors of change for a future where all research is freely available, all work is evaluated fairly and all members of the scientific community have opportunity to participate in the dialogue of and about science. To support the efforts of ECRs, we are continuing to offer our Early Career Researcher Travel Award (ECRTA) program, launched in 2015. For its first round in 2016, applicants were asked to describe characteristics of the optimal peer review process and how they might build this in a way that makes science more transparent and research more rapidly available. Winners were profiled and we’ve now completed a second award round asking what ECRs consider to be the value of a preprint server and how its broad adoption might benefit the scientific community and society.

As a participant in OpenCon 2016, a conference focused on educating and empowering the next generation in the areas of Open Access, Open Education and Open Data, PLOS will have the opportunity to hear directly from participants regarding their desires and concerns for the future of science communication. In a video welcoming address, Publisher Louise Page acknowledges the inspiration provided by this annual gathering of Open Science thinkers and presents highlights of the past year at PLOS that reflect how the organization is Open in Action.

“PLOS was founded with the researcher foremost in our minds and we want to work with you to continue our journey from Open Access to Open Data, Open Source and ultimately to Open Science,” says Page.

The brief video is an introduction to an OpenCon Community Webcast with Peter Suber, Director of the Harvard Office for Scholarly Communication. You can also listen to the OpenCon 2015 video address by PLOS Executive Editor Véronique Kiermer on The Future of Science Communication.

Open Access Is Open in Action

In an increasingly vibrant research world where multimedia data, new types of research outputs and real-time online discussions are altering the way the community works, communicates and cooperates, Open Access is more than ever Open in Action. PLOS is proud that our founding core principles exemplify Open in Action. What makes us notable among other publishers is that we were Open in Action from the start: 24/7, 52 weeks a year.

Our View of Open Science As a leading Open Access publisher, PLOS pursues a publishing strategy that optimizes the openness and integrity of the publication process by aiming to ensure that research outcomes are discoverable, accessible and available for discussion and that science communication is constructive, transparent and verifiable. We strive to implement policies and innovations that promote reproducibility, credit and accountability, as these priorities support establishment of an Open Science culture, with open data, early sharing of work and clear contributor recognition. We see the benefit of Open Access content in relation to future advances in machine-readable formats and text and data mining.

We look forward to hearing your Open Science stories and the outcomes, large or small, that you have achieved. Leave a comment here or email to communications@plos.org.

 

Image Credit: SPARC

The Best of Both Worlds: Preprints and Journals

For some time now PLOS has discussed new initiatives designed to accelerate research communication, from development of Aperta™, our streamlined manuscript submission system that facilitates a faster time to first decision to our Content Management System that allows for rapid creation of curated PLOS Collections. These efforts span the range of ways we are accelerating access to discovery of not just the final publication but the entire research life cycle.

Stake a Claim

An additional strategy – early posting of articles before formal peer review through the use of preprints – can also advance science faster, more openly and with broader participation. In posting preprints, authors are able to make their findings immediately available to the scientific community and to receive feedback on draft manuscripts before they are submitted to journals. The benefit extends beyond making early work openly and freely available prior to or during consideration at a journal; in posting a preprint, an author or author group stakes an intellectual claim to methods, results and ideas contained within that paper. This can be especially important for scientists looking to change the focus of their research and connect with engaged colleagues in new fields; for those on the job market needing to show the status of their current research, their collaborative nature and their ability to embrace change for a more open way of doing science; and for early career researchers who may find opportunity to interact with new contacts interested in their work.

PLOS supports authors who wish to share early versions of their research manuscripts to receive feedback before – or in parallel to – formal peer review, and encourages researchers to share via preprint servers either before or after submission to a PLOS journal. Preprints are an excellent way to:

  • Establish intellectual precedence for ideas, methods, results
  • Receive early feedback from engaged colleagues
  • Obtain and document citations to a work before publication in a peer-reviewed journal
  • Contribute to accelerating scientific discovery and increasing research efficiency

PLOS has a long-standing policy of accepting manuscripts previously posted to preprint servers, however we recently collaborated with bioRxiv to ease the process as a reflection of the importance we assign to this rapid dissemination vehicle for authors that also brings transparency to the review process. Authors can now use bioRxiv’s direct transfer to journal service drop-down menu to submit directly to PLOS. While authors posting to bioRxiv can choose the reuse options under which to make their article available (various CC BY options or no reuse), licensing terms of PLOS content has not changed. To inform authors and the public of the current and more seamless arrangement with bioRxiv we have updated our preprint policy on all journal ethical publishing practice and related manuscript sections as well as the Wikipedia page that describes the landscape of publisher’s preprint policies.

Researchers First

With preprints, authors – not publishers – are in control of when they publicly timestamp their intellectual property as well as when they want it to go for review. They decide when their research paper is ready to post and when they’re ready to submit their paper for formal peer review. In an open environment, the community can evaluate what any individual scientist’s standards are for their work and their online interaction with colleagues. By posting work and commenting on the posted work of others, authors are more in control of their own reputations. In essence, the use of preprints is analogous, in a very public and large-scale version, to the more intimate practice of sending a complete manuscript draft to a colleague to get their opinion with potential to improve the manuscript before submitting to a journal. Some have likened it to going public with a conference abstract or presentation.

How it Works

In the same way that not all Open Access is created equal, not all preprint servers work the same way. Launched in 2013 by Cold Spring Harbor Laboratory, bioRxiv is now in its third year with more than 5,000 preprints posted to the site and more than 1 million article views each month. At bioRxiv, all posted research papers receive a digital object identifier (DOI) that remains associated with the original preprint. When a manuscript is transferred to PLOS from bioRxiv, PLOS stores the preprint DOI; if that manuscript is accepted for publication it then receives a PLOS DOI and we deposit both the preprint and the final article DOI to CrossRef so the two works can be associated with each other.

Importantly, whether posting a preprint or submitting to a journal, authors can help themselves ensure full recognition for both the preprint and the final article by including their ORCID iD at all times.

At PLOS, preprints are acceptable resources for inclusion in the reference section of an article. Should anyone follow a link from an article citation to a preprint that has subsequently been peer reviewed and published, they would be directed from the preprint to the article on the PLOS journal website.

DOI: 10.1371/journal.pone.0164504

 

Value Perspective

Preprints do not diminish the need for reputable peer-reviewed journals. In fact, the combination provides scientists the best of both worlds; preprints accelerate making work public and provide an opportunity for early feedback for those willing to share their work whereas journals provide a mechanism for formal assessment, curation and dissemination. Journals reinforce standards for ethical and reporting guidelines, plagiarism checks, conflicts of interest and work with organizations such as CrossRef to ensure seamless and complete metadata transfer. Publishing in journals has the added benefits of validating the quality of work through rigorous peer review; placing work in context through perspectives, editorials and incorporation into collections; providing opportunities for online dialogue with authors through PLOS Science Wednesday AMAs and tracking article influence through Article-Level Metrics. Our current work with bioRxiv is one more example of how we are putting researchers at the center of science communication and placing authors in control of their manuscripts. In the future, expansion of Aperta to the full suite of PLOS journals and incorporating aspects of community review to our processes will place PLOS in the space necessary to accelerate dissemination of research results and conversation surrounding a scholarly work.

Those wanting an objective look at the value of preprints might find Breaking Down Pros and Cons of Preprints in Biomedicine of interest; for a detailed discussion of preprints by one active participant listen to the PLOScast with James Fraser, Associate Professor at UCSF and a founding member of ASAPbio, an initiative of the biology community to encourage use of preprints. When you’re ready, go ahead, post that paper, place your results and ideas in the mix and we’ll advance science forward faster, together.

 

Image Credit: Lisa Ann Yount

Jenny Machida Appointed to PLOS Board of Directors

PLOS is pleased to announce that Jenny Machida has joined the PLOS Board of Directors, effective October 21, 2016. “Jenny’s deep business knowledge with a focus on strategy, growth and organization performance will greatly contribute to PLOS as we strive to build a better publishing experience for authors in 2017 and beyond,” said Board Chairman Gary Ward.  “We are delighted that she is joining our Board of Directors and look forward to benefiting from her depth and breadth of experience.”

Machida received her BA summa cum laude from Yale University and earned an MBA from the University of California at Berkeley. Machida is currently a Managing Director at IMB Development Corporation, a private equity investment and operating firm. Prior to IMB, she co-founded and led business development at a medical technology start-up company called Sevident and helped to build out an academic research and advisory center at Columbia University focused on advancing diversity in higher education. Machida was also a Principal at Booz & Co. and a Principal and Co-founder of the Healthcare and Diversity & Inclusion practice areas at Katzenbach Partners.

Open Access Week 2016 – Open in Action

Now in its ninth year, Open Access Week celebrates progress and promotes awareness to help make Open Access – the founding principle of PLOS – the new norm in scholarship and research globally. Join PLOS in celebrating Open Access Week by being Open in Action.

 

  • Register for an ORCiD ID – distinguish yourself and create a record of your scholarly contributions.
  • Join the conversation about Open Access Tools with PLOS authors Lenny Teytelman and Hilda Bastian on 10/26 10am PT for a special OA week edition of PLOS Science Wednesday – the Ask Me Anything (AMA) series on redditscience.
  • Get a sneak peak of PLOS’ upcoming projects with PLOS Publisher Louise Page in this OpenCon 2016 Community Webcast.
  • Listen to a special episode of PLOScast – a podcast focused on science, academia and the future of scholarship – featuring UCSF’s James Fraser discussing the use of preprints in the life sciences.
  • Meet PLOS staff and editors at SVP or iGEM – stop by the booth, learn more about Open Access publishing and pick up a giveaway.
  • Browse the Open Highlights Collection, with research from across PLOS journals and the wider Open Access literature curated by staff editors to provide depth of coverage on select topics.

Have a great Open Access Week!

Influential Work from PLOS Authors Garners Lasker Awards

The Lasker Awards recognize the contributions of scientists, physicians and public servants who have made major advances in the understanding, diagnosis, treatment and prevention of human disease. Each year since 1945, dedicated scientists benefit from the mission of the Albert and Mary Lasker Foundation to recognize research excellence, public education and advocacy.

As a champion of biomedical research, Mary Lasker worked to increase public appreciation for and government funding of medical sciences. As a result of her advocacy efforts, several NIH Institutes were newly created, including the National Heart Institute, the National Institute of Mental Health and the (originally named) National Institute of Neurological Diseases and Blindness. Lasker helped change the biomedical research landscape in the United States and the scientific community to this day benefits from her dedication.

PLOS is proud that six of this year’s seven Lasker awardees have published research or an interview with PLOS, and we are fortunate to benefit from the expertise of Charles M. Rice of The Rockefeller University in his role as an Academic Editor for PLOS Pathogens.

Here are the 2016 Lasker Award honorees with a summary of their PLOS research and interviews, spanning five journals and The PLOS Blog Network, for a collective total of 38 articles and two interviews. Oxygen sensing—an essential process for survival:

Gregg L. Semenza’s three PLOS ONE articles cover the role of NADPH oxidase in Hypoxia Inducible Factor-1α (HIF-1α) activation, the dependency on tumor suppressor p53 for macrophage migration inhibitory factor’s effect on HIF-1 activation, and the ability of HIF-1α to regulate the expression of cell adhesion molecule CD44.

Peter J. Ratcliffe published two PLOS ONE articles and one each in PLOS Biology and PLOS Medicine. Some of this work examines the relationship between the von Hippel-Lindau (VHL) tumor suppressor gene, HIF-1 and extracellular matrix in C. elegans, the role of VHL-HIF pathway in human cardiopulmonary physiology and function at standard and high altitudes, and most recently the investigation of compounds that inhibit the hypoxia sensors of the HIF system, the HIF prolyl-hydroxylases, with implications for therapeutic treatment of stroke or other diseases of cerebral ischemia.

DOI: 10.1371/journal.pbio.0020289

 

 

 

 

 

 

William G. Kaelin’s PLOS Biology article – published in the journal’s inaugural year – explores the relationship between inactivation of the VHL gene, subsequent HIF2α activity and renal carcinoma tumor formation.

Hepatitis C replicon system and drug development:

Charles M. Rice has eight articles with PLOS; three in PLOS ONE and five with PLOS Pathogens. His virology research – while primarily focused on hepatitis C virus (HCV) – also addresses arthropod-transmitted viruses in the Flaviviridae family, such as yellow fever virus, and natural inhibitors of HIV identified from simulation screening of the pan-African Natural Product Library followed by cell-based testing. A subset of Rice’s HCV work published in PLOS Pathogens covers direct deregulation of the cell cycle in HCV infection as a contributor to liver disease, host cell protein and lipid mapping to uncover temporal and global changes as a result of HCV infection and a mutational structural analysis of the p7 protein revealing positions important for particle assembly and infectivity.

DOI: 10.1371/journal.ppat.1000719 DOI: 10.1371/journal.ppat.1005297

 

 

 

 

 

 

Ralf Bartenschlager tops the PLOS list with 27 articles; 20 in PLOS Pathogens and seven in PLOS ONE. Select key early work on HCV includes the role of cyclophilin A in HCV replication and polyprotein processing, the role of HCV p7 protein as a membrane pore involved in production and release of infectious virions and the dependence of HCV envelope glycoprotein secretion on assembly of triglyceride rich lipoproteins.

Bartenschlager’s team also determined the nonstructural protein 5A (NS5A), a component of the viral RNA replication machinery, as a key factor for the formation of infectious HCV particles through an assembly determinant domain and lipid droplets. Bartenschlager’s seminal microscopy work on the intracellular membranes of HCV infected cells is visually stunning and included in the PLOS Pathogens 10th Anniversary Collection.

More recent articles describe use of a yeast two-hybrid screening strategy to generate an interactome of cellular proteins that may function with influenza virus non-structural proteins NS1 and NS2, potentially informing therapeutic interventions, and work on Dengue virus that provides a genetic map of determinants involved in viral RNA replication and extends the list of functions ascribed to the enigmatic nonstructural protein 1.

DOI: 10.1371/journal.ppat.1005277 DOI: 10.1371/journal.ppat.1003056

 

 

 

Discoveries in DNA replication and leadership in science and education:

In 2012, PLOS GeneticsJane Gitschier Interviews turned to this year’s Lasker-Koshland Special Achievement Award in Medical Science awardee Bruce Alberts for his memories of how he got into science and his thoughts on learning from failure and getting committees to reach consensus. More recently Alberts shared with PLOS his insights into issues facing scientists today, such as journal impact factors, new forms of recognition for contributions to the scientific publication process and the role of senior as well as junior researchers in changing the culture of science.

For those wanting more information on the significance of the work of this year’s winners and the award in general, The Lasker Foundation and Cell provide coverage.  Cell has also curated Collections dedicated to Hypoxia-Inducible Factors and virus infections. Much, but not all, of the content is Open Access.

PLOS has previously profiled author recipients of the 2016 Breakthrough Prize in Life Sciencesso bookmark The Official PLOS Blog and visit this site as future scientific prizes are awarded.

 

Image credit: The Lasker Foundation

PLOS appoints Dr. Joerg Heber Editor-in-Chief of PLOS ONE

PLOS announced today that after an extensive search, Dr. Joerg Heber has been appointed Editor-in-Chief of PLOS ONE. Heber will be responsible for setting the editorial course of the journal and continue its mission of improving scholarly communication. His appointment is effective November 21, 2016.

“Joerg’s deep understanding of scholarly publishing and his passion for Open Access will be tremendous assets to me and our editorial staff, and most importantly to PLOS ONE’s 6,000 Academic Editors and our authors,” said Veronique Kiermer, Executive Editor of PLOS. “PLOS ONE has been a driver of changes in scientific communication since its launch ten years ago. It is an enormous responsibility and I am entirely confident in Joerg’s ability to lead the journal through its next phase, to further develop its mission and meet the needs of the scientific community.”

“I am delighted to be joining PLOS” said Heber. “PLOS’ commitment to Open Access and to innovation has been transformative, and PLOS ONE is ideally placed to support Open Access and open science with continued advancements in scholarly communication. I’m excited to work with the PLOS ONE team to serve science as a whole.”

Prior to joining PLOS, Heber was Executive Editor of Nature Communications. In this role Heber had responsibility for the journal’s overall editorial strategy. He was instrumental in Nature Communications transparent peer review initiative, implementing its Data Availability Statements and contributed to the journal’s move to full Open Access publishing. Heber also worked as a Senior Editor for Nature Materials and his previous experience includes a visiting professorship at the University of Tokyo and lecturer at Philipps-University Marburg, Germany.

Heber obtained his PhD in semiconductor physics at Imperial College London, UK, and did post-doctoral work at Bell Labs, New Jersey.

Riding A Wave Towards Improved Truth in Science Communication

It is an exciting time in scientific publishing. Initiatives such as digital identifiers for authors through ORCID, more granular recognition of collaborative work with standardized language for specific roles with CRedIT, and more competition in the Open Access publishing world benefit researchers and move the scientific endeavor toward a more transparent and accountable future.

Yet, the write up and publication of results is one of the most challenging aspects of the endeavor, with peer review and reproducibility at the heart of this stage of the research lifecycle. We have previously acknowledged on The Official PLOS Blog that the public

“relies on the belief that content published in peer-reviewed journals is trustworthy, despite the fact that this is too often not the case.”

We have also acknowledged that we must do better: all stakeholders, including publishers, are accountable. Although the overall concept of peer review is an accepted form of quality control and valued by the scientific community, in practice it suffers from imperfections that prevent it from achieving that one great thing: advancing research communication.

In a thoughtful consideration of Truth in Science Publishing: A Personal Perspective, Thomas Sudhof eloquently describes peer review and reproducibility as flawed checkpoints that impair the “validity of published scientific results” and impede trust in science.

As a recipient of both the Nobel Prize and the Lasker Award for his work on synaptic transmission, Sudhof brings perspective and integrity to his thought leadership. Highlighting hidden conflicts of interest, too little accountability for journals and reviewers, and lack of competition between journals as three problems with peer review that have “corrupted the process, decreasing its value,” Sudhof endorses more transparency in the peer review process to reduce bias.

At PLOS there are a range of ways to improve the process without diminishing those aspects that the community values. Current tools and systems that address these limitations include the posting of research to preprint servers before formal publication, to enable researchers to improve their work and share it earlier. There is an opportunity to improve review forms that may be cumbersome or insufficient to provide thoughtful and constructive feedback to authors. Appropriate and rigorous reviewer and editor training can help to mitigate potential reviewer bias and mentor early career researchers. With improved technologies and processes, publishers have an opportunity to improve efficiencies, quality, trustworthiness and authenticity of the process.

As for reproducibility, Sudhof outlines increasingly complex experiments that are impossible to reproduce, “tweaked or selected” results that do not hold up with repetition, lack of validation of reagents and methods, and the “near impossibility” of publishing negative results as contributors to the problem.

Providing opportunity to showcase peer-reviewed articles that address the reproducibility issue is an important value of PLOS and PLOS ONE; the journal welcomes submission of negative, null and inconclusive results. PLOS Biology’s Meta-Research section welcomes experimental, observational, modeling and meta-analyses that address research design, methods, reporting, verification or evaluation.

PLOS Biology and PLOS Genetics authors can contribute to the reproducibility effort by identifying model organisms, antibodies or tools with a unique Research Resource Identifier (RRID). PLOS is a part of the Research Resource Identification Initiative, a cross-publisher effort to promote reproducibility in science and enable effective tracking of the use of particular research resources across the biomedical literature.

PLOS works toward a future where research is published without unnecessary delays, and continual assessment and commentary is provided by a robust and ethical system of visible, engaged pre- and post-publication peer review. We strive to engage a global editorial and reviewer contributor community, appropriately trained, recognized and incentivized. With regard to journal-facilitated peer review, rigorous input from experts in a relevant field of research is highly valued by both authors and readers, and contributes to trust of research results for working scientists, clinicians, patient advocates, policymakers and educators.

Addressing the issues and challenges that perversely incentivize unreliable research or prevent peer review from achieving its scholarly ideal will not be easy or quick. The challenges are substantial and the solutions must be as well, and satisfy a diverse researcher and stakeholder community. Broader adoption of reproducibility efforts and better recognition for the range of contributions made by researchers and reviewers will not be enough without the engagement of early career researchers, junior investigators and senior leadership with the power to influence change.

 

Image credit: one-vibe, pixabay.com

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