Public Library of Science

PLOS Supports Net Neutrality to Ensure Global Access to the Scientific Literature

PLOS — Wed, 12 Jul 2017 05:00:37 +0000

PLOS works to remove barriers to public access of scientific research. Typically, these barriers are considered in terms of copyrights and journal subscriptions, but unfettered access to network infrastructure also contributes to supporting readers’ access to scientific literature. In simple terms, unencumbered dissemination of scientific research depends on a fair Internet. The provision of a fair and open Internet lies in the hands of Internet Service Providers (ISPs) and government agencies that regulate these providers. PLOS supported the July 12, 2017 Day of Action in the United States, led by Battle for the Net, aimed at publicizing the issues surrounding Open Internet Rules and their critical role in maintaining Internet freedoms as currently in place.

In February 2015, the US Federal Communication Commission (FCC) reclassified broadband providers as common carriers rather than information providers under Title II of the Communications Act of 1934, the law that continues to regulate modern communication modes such as the Internet. This gave the FCC authority to ensure that established, large corporations including AT&T, Comcast and Verizon can’t block, slow (throttle) or otherwise interfere with Internet traffic. Innovations in online businesses and services, including those of PLOS, have thrived under Title II regulations. Importantly, these regulations in the US provide each and every user of the Internet a guarantee that ISPs and government regulators treat all data on the Internet the same, without discriminating against or charging differentially by user, content, website, platform, application, type of equipment or mode of communication (see https://en.wikipedia.org/wiki/Net_neutrality). These protections are known as net neutrality; scientists and those working to support the scientific endeavor rely on net neutrality for unprejudiced access to databases, the literature and information services.

Allowing ISPs to sort traffic based on content, sender and receiver opens the door for corporate and government censorship which would greatly hinder access to scientific information around the globe.

To protect against this type of restriction in information flow, the first EU-wide Net Neutrality rules were adopted in October 2015 with public guidelines released by the Body of European Regulators for Electronic Communications in late 2016.

In the US, the current FCC Commissioner wants to weaken these protections and this could have consequences for all scientists, not just those in the US: access to information around the world could become pay to play without these protections. Services provided by publishers such as PLOS and other providers could be restricted for all our users around the world, unless we pay for priority access to our content. This will affect any Internet traffic that routes through the US, from services relying on servers located in the US to requests that are routed through the US. For instance, most of the Domain Name Server (DNS) requests for South America, Central America and the Carribbean are routed by servers located in Florida.

July 12, 2017, was a Day of Action in support of a fair and open Internet. Visitors to the PLOS.org homepage (www.plos.org) and active PLOS staff blogs (The Official PLOS Blog, EveryONE, PLOS Biologue, Speaking of Medicine, PLOS Channels and Collections, PLOS Tech and PLOS Podcasts) saw a message of explanation and letter of support for net neutrality in the form of a pop up window. This message appeared only on July 12, once per site, per device. Visitors to these web pages could choose to either immediately close the pop up by clicking on the x in the upper right or fill in the four boxes to send a message to the FCC in support of its current Open Internet Rules and the efforts to dissuade FCC Chairman Ajit Varadaraj Pai from his plan to roll back these rules. Public comment continues for an additional 60 days following the Day of Action. Form letters or personalized comments may be sent directly from https://www.battleforthenet.com/.

PLOS purposefully did not place this notice on any journal content or information pages, so that access to our content was not impeded in any way.

To learn more about net neutrality around the globe, visit https://www.thisisnetneutrality.org/; to learn more about the Day of Action visit https://www.battleforthenet.com/july12/.

This post was edited slightly on July 13, 2017 to indicate past tense for the Day of Action.

Immediate and Lasting Impact: Top Ten New Species of 2017

Sheryl P. Denker — Mon, 19 Jun 2017 08:00:24 +0000

0000-0001-7318-5892

The unique morphology of the spiny ant, uncovered with the use of an advanced form of 3D microscopy known as 3D X-ray microtomography, garnered this species a place this year among the Top 10 New Species of 2017. The Top 10 New Species list honors the legacy of Swedish botanist Carolus Linnaeus, known for his pioneering work on the hierarchical classification of plants and animals that developed beyond genus and species into modern taxonomy. The list is compiled by the International Institute for Species Exploration (IISE) working with a panel of international scientists as selection committee members.

SUNY-ESF President Quentin Wheeler. (Photos for SUNY-ESF by M.J. Okoniewski)

PLOS spoke with Quentin Wheeler, founding director of IISE and president of the College of Environmental Science and Forestry in Syracuse, New York, on assessing research impact, the purpose and influence of this list and the impact of climate change on species diversity.

Policies and Purpose

Research reporting these new species is published in a variety of journal types, from subscription to Open Access. When asked if there are considerations of access to research when the members of the international selection committee evaluate nominations, Wheeler states that “the selection committee is encouraged to focus on the organisms rather than where they were published.” This de-emphasis on journal choice is a hallmark of the IISE selection process; work that is posted on a preprint server, rather than published in a peer-reviewed journal, may also be eligible for consideration. “What matters is compliance with the international codes of (botanical and zoological) nomenclature which requires publication that can now include electronic publication. So long as the requirements of the code were met during the previous calendar year, a species is eligible for consideration,” he says.

In an era of continued global extinction of animals, plants and microbes, Wheeler hopes the Top 10 New Species list brings research outcomes to the public to help convey the acute relevance of climate change. “Our goal is to increase awareness of the loss of species in the biodiversity crisis and the important roles played by taxonomy and natural history museums in biodiversity exploration and conservation. The wide media attention gained by the Top 10 [and this year’s PLOS ONE article] has hopefully played a role toward that goal,” he says. While he is not aware of specific policies shaped directly by the list, the hope is that it “keeps the importance of species exploration in the minds of those making such policies.”

Valuing Work, Not Impact Factor

Over the past 10 years of generating this list, one notable detail is that selected work is published in journals with impact factors ranging from less than one to greater than 20. When asked what this says to him and the scientific community about the value and relevance of evaluating a work based on its own merit, rather than on the journal in which it appears, Wheeler is quite direct.

“As a scientist and scholar, I like to think that science is a meritocracy of ideas and that their value derives from the quality of the work and its impact rather than the impact factor of the journal overall. Taxonomy is a very special case that is not at all served well by impact factors as they are today calculated.”

He explains this concept more fully. “First, the best taxonomic work is comprehensive and comparative in the form of lengthy taxonomic revisions and monographs. Such long works are not accepted by most journals with high impact factors. Second, even the best taxonomic work is rarely cited because once species are known they are typically identified by field biologists through secondary literature (field guides, etc.). Even the secondary literature is often omitted from citations by ecologists and others, and the primary literature is only rarely cited outside of other taxonomy papers.” Due to the long-term nature of taxonomy work, “we routinely consult papers from 1758 forward,” says Wheeler. “Thus the true impact of the work is measured over generations which is quite different from most experimental fields where papers are outdated in just a few years.”

Last year two species on the list made their debuts in PLOS ONE: the description of a new Galapagos giant tortoise species and a new genus, species and subfamily of isopod crustacean. Together with this year’s winner and the four PLOS ONE articles describing top species in 2014, this cohort of articles has collectively received over 290,000 views, 3,500 shares and broad media coverage since publication, indicating their influence and interest for taxonomists and the public at large.

Connectivity and Credit

As with other scientific disciplines, innovation and modernization are a must in taxonomy, and Wheeler is in favor of such policy shifts. First, he recommends mandating a “central deposition of all nomenclatural acts, including descriptions of new species” as it now takes several years to track down all new species named in any given year. He also believes “the actual technical description of species should be open access, even in journals that are not. The descriptive material should be intellectual property of humankind and available to everyone.”

Further modernization, according to Wheeler, would establish electronic connectivity between published work and the central repository. “That central repository, likely IPNI for botany and ZooBank for zoology,” he says, “ought to be connected via hyperlink to every scientific name published. Were this done it would be a service to editors by assuring the correct scientific name is being used and spelled correctly. Also by virtue of that link we could electronically track the usage of scientific names and give “impact” measure of the use of the names as credit to the taxonomists.”

PLOS encourages scientists making these discoveries to publish the entire research article, not just the technical data, in fully Open Access journals and repositories to ensure the work has maximum visibility and reach. ORCID iDs can help in linking taxonomy descriptions, datasets, published work and grants to individual researchers for maximum credit and recognition. Those interested in learning more about the biodiversity crisis can watch a brief interview with Quentin Wheeler and those interested in learning more about new species and biodiversity can browse this selection of PLOS articles.

****************

Quentin Wheeler is founding director of the International Institute for Species Exploration and president of the College of Environmental Science and Forestry (ESF) in Syracuse, New York. He was previously vice president and dean of the College of Liberal Arts and Sciences at Arizona State University, chair of entomology and director of the Liberty Hyde Bailey Hortorium at Cornell University, Head of Entomology at the Natural History Museum in London and Director of the Division of Environmental Biology at the National Science Foundation.

Hero Image Credit: ESF

Getting the Impact Factor Genie Back in the Box

Sheryl P. Denker — Mon, 05 Jun 2017 07:00:01 +0000

0000-0001-7318-5892

On occasion The Official PLOS Blog presents Thought Leadership interviews with scientists leading the way on issues integral to the transformation of science communication and advancement of Open Science. Previous interviewees include Bruce Alberts and Trevor Bedford. Here we present our conversation with Sandra Schmid from University of Texas Southwestern Medical Center.

Image Credit: University of Texas Southwestern Medical Center

Over the years, Sandra Schmid has gained a reputation for academic strength and leadership, most recently as Professor and Chairman of the cell biology department at University of Texas Southwestern (UTSW) Medical Center. She’s also gained a reputation for her honesty regarding varied issues, including the position of post-docs, “if it were a job, we’d pay you better and give you retirement benefits,” the training of faculty, “few of us as mentors, as Principal Investigators, were ever taught how to run a lab or how to mentor individuals” and how she participates in open discussion of research before publication “mostly over beers.”

Schmid has been particularly vocal about the misuse of journal impact factors (JIFs) as a way to evaluate researchers and, as she claims, “the unfortunate consequences to the scientific community of their misuse.” At UTSW, Schmid’s home institution, there has been no overt discussion among the leadership regarding JIFs and where faculty should choose to publish. There is no formalized preference for high impact journals. “In fact, we celebrated the founding of eLIFE [a journal which rejects the use of JIFs] and have faculty on the Editorial Board of the journal,” says Schmid. The JIF was “never intended to and indeed does not measure the quality or impact of the individual papers in a journal,” says Schmid. It was originally developed and commercialized by Eugene Garfield to help librarians decide on which journals they should spend their subscription dollars.

“Individuals and institutions are being spuriously judged – by other scientists, funders, governing bodies and administrators – based indirectly on JIF, rather than directly on the quality and impact of their work,” Schmid wrote in “Negative Consequences of the Misuse of Journal Impact Factors for Scientific Assessment” as part of the 8th Forum on the Internationalization of Sciences and Humanities.

Flawed Statistics

The JIF is a statistic calculated based on the average citations of a selection of papers in a given journal. One major problem with the JIF is that citations are highly skewed, with most articles receiving fewer citations. Since citation distributions are skewed, averages are meaningless. “Indeed,” writes Schmid, there are journals that “flaunt their JIF in marketing material to authors that would ironically not accept papers reporting such flawed statistics.” This skewed distribution was clearly demonstrated last year through a collaboration between multiple publishers, including Université de Montréal, Imperial College London, PLOS, eLife, EMBO Journal, The Royal Society, Nature and Science (see Measuring Up: Impact Factors Do Not Reflect Article Citation Rates). The analysis, posted on bioRxiv, showed that citation distributions of journals with clearly distinct impact factors greatly overlap—in other words that all journals publish many papers with similar lower numbers of citations, and few highly cited papers.

A Better Option: Citation Distributions

The authors of the bioRxiv analysis call for publishers to make publicly available the actual citation distributions of their journal’s articles, rather than rely on irrelevant and misleading JIFs. Since journals use many different techniques to artificially increase their impact factor, including publication of review articles (which are often more highly cited than the original research papers they review) and front matter, including commentary and mini-review articles (that generate citations but are not counted as “citable” content) comparison across journals is problematic. It is hoped that public disclosure of article citation distributions will lead to more granular comparisons and better informed decisions by authors on where to submit their work.

Then and Now

From the perspective of a senior investigator with a long-established career and history of publishing quality work at all tiers of influence, what has changed for Schmid when deciding where to publish is that in the past, “journals had different purposes and different scopes” and that was good. Before there was the JIF there was an understanding of what journal went with what type of data. “We sent our best biochemistry to Journal of Biological Chemistry; our best cell biology to Journal of Cell Biology. If we happened upon a new and potentially important discovery, even before we understood mechanism, we’d communicate it rapidly in Science and Nature because they were three figure papers.” Before the advent of supplemental materials, more meaty, in-depth studies were published in non-page limited, subject-specific journals.

When asked in the post-print era, how do researchers decide where to publish, Schmid replies, “That is the unfortunate part.” A lot of the decisions are being made by postdocs telling her about impact factors, although she cautions that “publishing in high impact factor journals doesn’t mean it’s high quality work.” Early career researchers are looking at numbers as a distinguisher between journals, says Schmid, so her efforts are focused on getting these scientists to think more broadly. Her response and recommendation? First and foremost is to choose the journal where the work will get in front of the audience that matters the most. Schmid is crystal clear when outlining her main considerations for deciding where to publish her work and the work from her lab:

Are the people who handle my paper able to identify qualified referees?
Are the editors going to understand the discussion and criticisms and be helpful in handling my papers; do they understand my field?
Do my peers read and respect the content in this journal?

Unintended Consequences

The real question for Schmid is how to get the “impact factor genie” as she calls it, “back in the box.” Why is this so important? Scientists and publishers often focus on the limitations of JIFs and the benefits of evaluating work at the article rather than journal level. However, there are more than just limitations to the JIF. According to Schmid there are very “specific and unintended consequences of the abuse of JIF as a tool for individual and institutional assessment.” Many of these, she notes, are direct; others are subtle, downstream ramifications:

Deferred communication of discoveries that might launch new fields as reviewers and editors demand more information per paper
Discouraged follow-up or augmentative studies to verify results due to over-interpretation of findings for the purpose of artificially inflating a work’s value
Misguided evaluation of graduate students, postdoctoral fellows and junior faculty by their individual papers rather than the combinatorial impact of their work in context
Wasted time and resources spent satisfying unnecessary demands of reviewers and editors in high-impact journals
Demoralized early career researchers forced to package an entire thesis or postdoctoral project into one comprehensive paper

A Better Option: Article-Level Metrics

Perhaps wanting to get that impact factor genie back in the box was more than a mistaken mixing of two idioms. The difficulty of reverting to a situation that formerly existed (putting the genie back in the bottle) combined with the repercussions of doing something that causes unexpected and unintended negative consequences (opening a Pandora’s box) does describe the situation the scientific community has with JIFs. Fortunately, this is not an impossible situation to remedy. Article-Level Metrics were developed by PLOS as a better means to assess research value in an electronically networked world. They are gaining acceptance across a broad swath of the scientific community, from scientists to funders and more, since they provide granularity, breadth and proximity (PLOS ALMs are updated daily to monthly, depending on source and age of the individual article). ALMs also allow different scholarly research outputs to be tracked, such as policy impact, datasets, software and code. Schmid also recommends simply using PubMed as a portal for assessing the influence of an article, stating, “from title to abstract to download is a good metric,” although not as complete as a suite of ALMs.

Leadership in Practice

In 2013 as Schmid took up the position of Chair of the Department of Cell Biology at UTSW, she offered an employer’s manifesto (published as a Science Careers column) on the approach her department would take in hiring new assistant professors. This manifesto promised “a better job of screening applicants—and to avoid inappropriate criteria such as journal impact factors.” The idea was to encourage applications from qualified candidates who “might feel sidelined because their paper has yet to be, or perhaps won’t be, published in a high-impact journal.” Schmid closed her column with an enthusiastic “Let’s run this experiment!” Four years later, she shared some of the results with PLOS. Using their Academic Jobs portal the entire faculty is engaged in viewing applicants and every candidate that has piqued the interest of even one faculty member is interviewed via Skype, removing the need for reaching a ‘consensus’ that might rely more on JIFs. Those few candidates whose programs are most likely to thrive in the department’s specific environment are invited to campus to visit. Since taking this approach “our new faculty are indeed thriving,” says Schmid.

This approach suggests that a reduction on emphasis of JIFs in favor of more constructive and meaningful measures of evaluation, both quantitative and qualitative, fosters an assessment program that is both fair and thoughtful. This is how science should be; if it works for people it can work for research outputs as well.

*************

Sandra Schmid is Cecil H. Green Distinguished Chair in Cellular and Molecular Biology, Professor and Chairman, Department of Cell Biology at the University of Texas Southwestern Medical Center. She was co-founding editor of Traffic, Editor-in-Chief of Molecular Biology of the Cell and president of the American Society for Cell Biology. Schmid was elected fellow of the American Association for the Advancement of Science and Vice-Chair of the European Molecular Biology Laboratory Scientific Advisory Committee.

PLOS Appoints Alison Mudditt Chief Executive Officer

PLOS — Thu, 18 May 2017 11:00:13 +0000

PLOS is pleased to announce the appointment of Alison Mudditt as its Chief Executive Officer, effective June 19, 2017. For the past six years Mudditt served as Director of University of California Press (UC Press) where she ushered in new strategies to lead the company into the digital age, including the innovative journal and monograph Open Access programs Collabra and Luminos. Prior to UC Press, Mudditt was Executive Vice President at SAGE Publications, Inc., leading publishing programs across books, journals and digital platforms. Her 25 plus years in the publishing industry include leadership positions at Blackwell Publishers in Oxford, UK and Taylor & Francis Inc., in Philadelphia, US. Mudditt received her Bachelor of Arts degree from the University of Bath and her Master of Business Administration from The Open University.

“PLOS is truly privileged to bring on board a person of Alison’s caliber whose extensive experience in and deep knowledge of academic publishing will invigorate a renewed focus on our mission—transforming research communication to better serve authors, readers and the public,” said Gary Ward, Chairman of the Board at PLOS. “Her history and accomplishments as a leader, coalition builder and strategic thinker for organizations experiencing change is impressive and will prove very valuable to PLOS in the years ahead.”

“I am delighted to join a like-minded publisher in PLOS, which fully embraces the Open Access principles that drive its mission,” said Mudditt. “PLOS’ long-held reputation as a change agent in this industry provides a tremendously gratifying challenge as we continue to push the boundaries of what is possible in scientific publishing.”

Beyond Slogans: After the March for Science Has Passed

Sheryl P. Denker — Mon, 15 May 2017 07:00:36 +0000

0000-0001-7318-5892

“Science and democracy are logical allies, they both flourish with an open network of ideas, evidence and an uncompromising examination of results.” – Cindy Schaffer, former microbiologist with the Environmental Protection Agency

Clever slogans, such as “May the Facts Be with You” or “There Is No Planet B” flourished at the Earth Day March for Science as scientists and supporters of science around the globe chanting “Less Invasions More Equations” and “All Six American Nobel Prize Winners Last Year Were Immigrants” took to the streets demanding attention to the tangible impact of science on humans “Do You Have Polio? Thank A Scientist” and the environment “Ice Has No Agenda, It Just Melts.”

It is powerful for scientists and science-based organizations to show how important scientific facts are to everyday life, irrespective of political alignment, but what happens to this momentum after the collective advocacy effort has passed? What difference does it make, many have asked, and what role should each of us play, considering daily professional and personal commitments and demands on our attention and time. These are the issues faced by every social movement in search of long-lasting tangible impact.

Science Not Silence

The official slogan of March for Science, “Science Not Silence,” is a phrase that has potential to propel advocacy beyond the day of the march. “Because the results of scientific research benefit our everyday lives, we have taken for granted that science would be a vital, respected part of discussions about societal issues that impact health, the environment, technology and other science-based issues,” says Erika Shugart, Executive Director at the American Society for Cell Biology (ASCB).

“This is no longer the case. If science is not represented and advocated for, then it will be ignored or, even worse, replaced by discredited information,” she continues. “We can no longer be silent and assume science will be at the table, we must stand up for science.”

“My interpretation [of “Science Not Silence”] is that we need to use science and evidence-based scientific results to inform government policy and that we, as scientists, need to speak up about our research rather than staying silent,” says Elizabeth Blaber, Visiting Research Scientist at NASA Ames Research Center in Mountain View. “More often than not, scientists get caught up in their research, writing grants and publishing papers; we forget that our results can really make a difference to the general population. We can use our results to help inform policymakers about important decisions that they need to make about climate policy, research funding, health care policies and the next step for NASA’s human exploration endeavors,” she says.

Blaber cites the unique insight scientists working as government contractors have into government science and the bureaucracy of government agencies. “Science not silence means education to us, educating policymakers on the importance of each scientific study that is being conducted in and outside of government agencies and how these studies collectively make all of our lives better in an unimaginable number of ways.”

Beyond the March

How we harness the excitement and momentum of the march and translate that into action is not a single solution for each scientist or scientific discipline. “When you ask ‘what next?’ that’s when I run into difficulty,” says Dan Schaffer, former National Oceanic and Atmospheric Administration Weather Research Software Engineer. “We can march every week all day long but in the end, there are far more important and difficult decisions we have to make if we are to do something significant about the issue of climate change, for example.” For some scientists, this means bringing scientific evidence into daily habits (and convincing others to do the same). “Here in Prius driving, solar panel powered Boulder, Colorado, folks like to talk about what we’re doing about climate change.” Yet some of these same climate scientists “fly as far as Australia for climate change conferences,” he says. “One round trip from Denver to London is equivalent to driving one of those Prius 9,000 miles. That trip to Sydney? 16,000 miles.”

Individual behavioral changes can, collectively, make an impact. March for Science provides easy opportunities on their Week of Action page. For example, by clicking on ‘Science Connects Saturday’ (available everyday) you can send an email to your representatives just by filling in a few form fields. The relevant representative is determined automatically by your zip code entry. ‘Science Discovers Monday’ leads to suggestions for game night fun, science-style.

For some, follow up from the March for Science means being more open and emphatic, publicly, about what is evidence-based science and what is not. “As a former microbiologist at the Environmental Protection Agency, it disheartens me to hear that we have to prove that science matters,” says Cindy Schaffer. “The more active we, as scientists, can be in promoting real science,” she continues, “the better chance we will have for the false news to remain false in the general public’s mind.”

The message “Science Is Nonpartisan” took to the streets as a demonstration of “This Is What Democracy Looks Like.” These slogans call out for participation of the public in open, honest and constructive discussion. Says ASCB’s Shugart, “It is up to scientific societies and other organizations to help harness this energy to be a force for good in our communities.” Several organizations make it easy to participate, as we choose, in the democratization of science. Visit the PLOS Stand Up for Science page to learn how; email communications@plos.org if your professional association or society is taking action and wants to be listed on Stand Up for Science.

Image Credit: Bob Hemstock

Progress and Challenges for Neglected Tropical Diseases: An Anniversary Assessment

Sheryl P. Denker — Mon, 24 Apr 2017 05:02:46 +0000

0000-0001-7318-5892

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 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, all who have been involved with the journal either as frequent contributors or editors. These leading scientists from the WHO Regional Director’s Office of Africa (drawing on expertise gained in Tanzania); the 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 how providing access to publication – as a reader, author and editor – can help build capacity for 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.” Molyneux is a long-term editorial advisor for PLOS NTDs.

In the 10th Anniversary Collection, Editorial Board members and other experts 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.

With support from the Bill and Melinda Gates Foundation 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

Sheryl P. Denker — Tue, 18 Apr 2017 22:11:39 +0000

0000-0001-7318-5892

“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

PLOS — Tue, 04 Apr 2017 22:11:43 +0000

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

Sheryl P. Denker — Mon, 03 Apr 2017 00:00:29 +0000

0000-0001-7318-5892

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 NIH Cuts Should Worry Us, by PLOS Co-Founder Harold Varmus

PLOS — Wed, 22 Mar 2017 17:34:55 +0000

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, Lewis Thomas University Professor & Senior Advisor to the Dean & Provost at Weill Cornell Medicine, is co-recipient of the 1989 Nobel Prize in Physiology or Medicine and former director of the National Institutes of Health (1993-1999) and the National Cancer Institute (2010-2015). Varmus co-founded the Public Library of Science (PLOS) in 2000 with Patrick O. Brown and Michael B. Eisen.