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Advancing Evaluation: Moving Forward with DORA

“The declaration itself remains unchanged, but our aim is to spread the word much more effectively—about DORA and, especially, about the good practices it has already helped to establish in many institutions.” – Stephen Curry, Imperial College, London

Five years ago at the American Society of Cell Biology Annual Meeting in San Francisco, leading cell biologists, editors and publishers dissatisfied with the near exclusive reliance on journal impact factor as the primary means of measuring success in academia began creation of what would several months later become known as the San Francisco Declaration of Research Assessment, or DORA. The declaration calls attention to the inappropriate and flawed use of journal impact factors and the community need for assessment tools to measure research outcomes other than peer-reviewed publications.

The Current State

DORA states there is a “pressing need to improve the ways in which the output of scientific research is evaluated by funding agencies, academic institutions, and other parties.” The erroneous and inflated value of publishing in high-impact journals is seriously affecting the way that scientists judge each other, as well as adversely impacting the reproducibility of research. To make more fair and broaden the way scientists are evaluated, within DORA specific recommendations for publishers, funders, institutions, metrics organizations and, perhaps most importantly, researchers themselves, were built around the following tenets:

  • eliminate the use of journal-based metrics, such as Journal Impact Factors, in funding, appointment, and promotion considerations
  • assess research on its own merits rather than on the basis of the journal in which the research is published
  • capitalize on the opportunities provided by online publication (relaxing page, figure and reference limits, and exploring new indicators of significance and impact)

Anniversaries are often a time for retrospection, and as this year’s ASCB/EMBO meeting marks the fifth anniversary of the ASCB conference where DORA was born, those involved are taking the opportunity not only to look back at what has been achieved, but also to look forward at what more can be done. “DORA has been very useful in stimulating discussion and action on what truly robust processes of research and researcher evaluation should look like. It is focused on addressing the deleterious effects that the journal impact factor have had, particularly on research careers, but also on the pace and integrity of the scientific record,” says Stephen Curry of Imperial College London, one of the original signatories. Now, he says, is time for the initiative to “gain new ground, not just in Europe and North America, but all around the world.”

Grassroots Transitions

Those working now on revitalizing DORA see this upcoming anniversary year as an opportune window for an energetic transition from consensus-building to action. Says Bernd Pulverer, also an original signatory, “We’re seeing three stages, if you will, of DORA. The original declaration of the critical need to move away from journal impact factors was followed by a phase of community-building and signature gathering through the website. The stage has been set; all stakeholders, from scientists and policymakers to funders and publishers, need us to take action.”

Curry hopes that those stakeholders (especially researchers, funders, universities) who have been thinking about how to improve their research evaluation processes will be motivated to actually implement alternative or additional evaluation tools once they hear what is already taking place, often under the radar. “At my own institution, Imperial College, which is now a signatory, DORA was a valuable element in helping us to think through how to improve our hiring and promotion procedures.” The problem however, is that a critical mass of grassroots initiative and effort are needed to help propel the scientific community forward in this area. “To be sure,” says Pulverer, “change is not trivial to implement at either individual or institutional level, and one important function of the revitalized DORA project is to point to concrete examples of positive change and best practice.”

The barriers to shifting conversation to action are real: some countries offer direct financial incentives to authors for publishing in certain impact factor journals, in other places tenure and funding are often linked to those same publications. Early career researchers often feel compelled to restrict themselves to those journals (or have no input as to where their work is submitted), delaying publication. Sharing stories of change, both small and large, will help remove institutional and individual bias, integral considerations for DORA to be successful moving forward.

The Future State

To enable the revitalization, coming in 2018 are a new DORA website, extended outreach, and real-world examples of practices at institutions already thinking about and implementing innovative assessment mechanisms. There is no one size fits all solution to the research assessment quagmire, but those actively engaged with DORA believe that the scientific community is empowered to change the system in a grassroots manner. “Every one of us can act to change the system for the better—even without formal policy changes,” says Pulverer. “Research assessment invariably involves the research community, either directly as referees, as hiring principal investigators or in an institutional leadership function.”

The fact that misuse of journal impact factors transcends geography and subject area is illustrated by the wide variety of disciplines and countries represented both in the list of institutional and individual signatories of DORA. Plans for 2018 are shaping up. An influx of new funding has facilitated the hiring of a community manager to help promote DORA online and at conferences and meetings. Says Curry, “There are lots of exciting plans for 2018!” With discussions of appropriate recognition and credit for openly sharing data, datasets, microscopy images and analytical tools, the next five years hold promise for bringing the rhetorical concepts of DORA into practical implementation for the benefit of science and scientists of all career stages and in all geographies.

 

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For this post PLOS interviewed Stephen Curry, Assistant Provost (Equality, Diversity & Inclusion) and Professor of Structural Biology, Department of Life Sciences at Imperial College in London and Bernd Pulverer, Chief Editor, The EMBO Journal, and Head of Scientific Publications at EMBO in Heidelberg.

Unrestricted Text and Data Mining with allofPLOS

Content mining, machine learning, text and data mining (TDM) and data analytics all refer to the process of obtaining information through machine-read material. Faster than a human possibly could, machine-learning approaches can analyze data, metadata and text content; find structural similarities between research problems in unrelated fields; and synthesize content from thousands of articles to suggest directions for further research explorations. In consideration of the continually expanding volume of peer-reviewed literature, the value of TDM should not be underappreciated. Text and data mining is a useful tool for developing new scientific insights and new ways to understand the story told by the published literature.

Application and Challenges

Researchers have leveraged text mining of abstracts and NCBI databases to advance precision medicine through discovery of disease-gene-variant relationships, employed text mining of journal articles for sleep disorder terminologies to determine publication trends, and used text mining to cluster and relationship-map BioMed Central journal content. A study posted on bioRxiv found that text mining full articles gave significantly better information that mining abstracts only, as expected. However, the authors of this study described challenges in the way content was presented and in the need to obtain copyright permissions. In addition to content availability and license status, support for early adopters and training for future practitioners are also cited as barriers to broad use of TDM for research purposes. The foundational value of CC BY licensing for TDM is that no additional permissions or documentation are required. Open Access facilitates TDM:

  • not on case-by-case basis, but for all people, in all places, and at all times
  • without lengthy legal agreements or restrictions
  • by providing unrestricted reuse, remix and mining rights
No Restrictions, No Conditions: allofPLOS

With more than 200,000 fully Open Access research articles available for content mining, PLOS can help advance the discussion and application of content mining through real-world experiences. Through our API we provide article text and meta-data in a single XML file format according to the Journal Article Tag Suite (JATS), the National Information Standards Organization (NISO) standard tag suite for archiving and exchanging journal article content.

The new allofPLOS project is a step forward in providing researchers easier opportunities for new discovery and illumination of non-obvious connections between data, research articles and fields of study. With allofPLOS, in addition to the content of every PLOS article (excluding Figures or Supplemental Data) provided in JATS XML format, the XML parsing tools are provided. By including tags, content and parsing tools together, we hope to simplify and streamline the process for those wanting to experiment with content mining and TDM tools.

With content mining, scientists, educators, policymakers and others can identify and map patterns and trends across millions of articles, extract the information they want, and gain new insights to advance research. TDM results can be shared as a new research article or as a database for others to use.

Setting the Stage for a Text and Data Mining Future

To support policies and public awareness that TDM for research purposes is compatible with current and future publishing industry practices, in 2015 PLOS participated in construction of The Hague Declaration on Knowledge Discovery in the Digital Age, a set of five core principles and a roadmap for action to enable researchers to carry out TDM of digital content on the web without legal repercussions. Unrestricted access to the scientific literature together with standards that promote machine readability of the facts, data and ideas contained within ensures that journal content is available for maximum discovery and reusability.

“We are producing so much information, not just as published literature but as even data from sensors, from monitoring activities, monitoring the planet, and monitoring species, and living things and nonliving things it is simply not humanely possible to attract full value from this, let alone value that we don’t even know that exists inside it,” says Puneet Kishor, former Science and Data Policy Manager, Creative Commons, in a video on The Hague Declaration website. “Using computers and machines is the only way programmatically to figure out what’s hidden inside,” he says.

Next Steps

Visit the PLOS Text and Data Mining page to download the PLOS research article corpus and XML parsing tools, and stay tuned to this space for upcoming stories of how researchers are using these tools. Download one of the HowOpenIsIt?®  Open Access Spectrum guides to see where various permissions for machine readability fall on the Open Access continuum.

Anytime You’re in Listening Mode: PLOScast Two-year Anniversary

In today’s fast-paced world with its onslaught of environmental, societal and political challenges, science-related podcasts can provide an interesting, educational and even entertaining escape. Podcasts bring an interactive, personal approach and sense of intimacy to topics that might be dry when presented in written form. Plus, you can listen during your commute to the lab, library or office, while you’re exercising, cooking, or anytime you’re in headphone mode.

The growth in science podcasts provides evidence of their potential to deliver important stories to a broad audience. Podcasts are not just about stories, though. Ciencia Puerto Rico (CienciaPR) has increased the amount of culturally relevant scientific news content in Puerto Rico through essays, articles and articles distributed as podcasts, and the University of California considered podcasts as a mechanism to enhance and accelerate research. Podcasts were integral to an early proposal for an online bioinformatics curriculum and are an appropriate component to transform science communication through incorporation of rich media.

At PLOS, we’re celebrating the two-year anniversary of our own podcast, PLOScast. According to PLOScast founding host and PLOS staff researcher Elizabeth Seiver, PLOScast was established to give the organization a modern forum for thought leadership in the publishing space, but it quickly moved beyond this boundary. PLOScast engages listeners through interviews with innovators and thought leaders on the changing experiences of scientists in a digital world, the future of academia and its ongoing challenges, and scholarly publishing developments in an increasingly diverse landscape. These are serious issues, and PLOScast approaches them with integrity, diligence and humor. The show explores all things Open (access, peer review and science), including research tools; ideas for improving science communication; and exemplary, practical habits of successful scientists in all disciplines.

“PLOScast enables us to discuss issues that are important to scientists, with some of the thought leaders in their fields. It also increases the visibility of the work that the greater scientific community contributes, every day.”—Elizabeth Seiver

When PLOScast launched at the end of 2015, development involved getting the logistics and day-to-day operations straightened out. None of the team members had experience with podcasting, so they needed to learn the basics, including what kind of equipment was needed, how to edit a sound file, and how to best promote each episode. Over time, the script itself has evolved to better engage the audience and optimize the listener experience. “I try to keep the listener in mind more now,” says Seiver. “I think at the beginning I was more focused on having the conversation itself, but now I try to have a running voice in the back of my mind thinking about the listener, asking ‘will other people understand this reference? Is this what other people want to know about this topic?’”

Scientists and those interested in academics are certainly listening—PLOScast has over 16,000 plays in the past two years. With its reputation growing, plans are to diversify beyond the traditional one-on-one interview format and to expand its voice to provide early career researchers (ECRs) an opportunity to participate. The manager of PLOS’ ECR Community, Sara Kassabian, recently joined the PLOScast hosting team (yes, two people make a team), contributing an interview with preprint maven Jessica Polka for her inaugural episode. In “How ECRs like Jessica Polka are reinventing science publishing,” Polka goes beyond the topic of preprints to discuss opportunities for ECRs in #scicomm and the role of twitter in creating positive change in #science.

The top 10 most popular episodes by number of plays cover issues ranging from altmetrics and their history (episode 14) to big data in the social sciences (episode 23) and how to work with public information officers to increase the visibility of your science (episode 8). The top 10 (including number of plays as of October 31, 2017) in order are:

  1. Episode 8: How to Communicate Science: An interview featuring Matt Shipman (969 plays)
  2. Episode 2: The Postdoc Crisis featuring Liz Silva (856)
  3. Episode 9: The History of Scientific Publishing: An interview featuring Aileen Fyfe (769)
  4. Episode 3: Managing Scientific Data featuring Tracy Teal (738)
  5. Episode 1 Part 1: Open Peer Review and Scientific Communities (706)
  6. Episode 17 Part 1: The Science of Science featuring Eamon Duede (694)
  7. Episode 23: Big Data in the Social Sciences: An interview featuring Ian Mulvany (668)
  8. Episode 14: Understanding Altmetrics with Stacy Konkiel (636)
  9. Episode 22: Building Taxonomies: An interview featuring Bob Kasenchak (598)
  10. Episode 20: Science Communication and Critique: An interview featuring Hilda Bastian (598)

Interestingly, PLOScast launched with a broad ranging discussion on collaboration and publications with Cameron Neylon, formerly PLOS’ Advocacy Director. Part of this conversation covered bioRxiv, prior to that preprint server’s current phase of rapid growth. The second year began with an interview with James Fraser from UCSF on preprints and their ability to help authors stake a claim on ideas, methods or results. The interview with Polka marks the beginning of year three for PLOScast; as with the rest of the scientific community, preprints are an increasingly central part of PLOS’ conversation on how to move science communication forward.

To mark this achievement milestone for PLOScast, we have a new icon that’s fun and quirky yet at its core remains PLOS. We leave listeners around the globe with the top five favorites of the PLOScast crew:

New PLOScasts are posted monthly; you can find PLOScast on iTunes, SoundCloud, Google Play or sign up for an RSS feed on the PLOScast main page so you don’t miss an episode.

PLOS Channels Provide Opportunity for Discovery, Exploration and Contextual Insights

Last month, the new PLOS Cholera Channel joined existing Veterans Disability & Rehabilitation Research, Tuberculosis and Open Source Toolkit Channels in providing distinct and cohesive scholarly homes for research communities. These innovative forums increase the visibility of curated, quality research and reliable news and commentary, bridging a gap in relevance that contributes to public misunderstanding of research.

The Channels Program launched with Veterans Disability & Rehabilitation Research (VDRR), and as Veterans Day in the US approaches it’s an opportunity to take a moment to relay the channels origin story, highlight the latest content and re-introduce the editors behind this program.

“It is imperative that scientists and consumers explore novel and innovative strategies to share research findings. Towards this end, as an editor of the PLOS Channel for Veterans Disability and Rehabilitation Research, I look forward to highlighting research aimed at helping Veterans with disability and/or chronic illness increase function and participation in daily life.”—Lisa Brenner, VDRR Channel Editor

For those intimately involved with the generation, use or reuse of research, channels provide a central information source for the latest developments, whether published in PLOS journals or elsewhere.

Beyond Traditional Journal and Editorial Boundaries

As global forums for research, news and discussion, all PLOS Channels deliver a similar contemporary layout for easy navigation and reading, developed with feedback from multiple audiences in mind: basic and clinical scientists, policymakers, science journalists, educators, students and patients. The Featured Research section pulls from PLOS and other Open Access article sources. A Related Content section contains news, occasional events and journal commentary that speak directly and with integrity to the channel topic. Although not peer reviewed, web articles and commentary in the Related Content section are selected by channel editors for the reliability of the source, relevance to the topic and when possible, to provide broad perspective on global issues from local journalists. PLOS hopes the mix of quality peer-reviewed research and exploratory journalistic content will help bridge current knowledge and communication gaps between scientists and the lay public.

Channel editors, selected either from existing PLOS Editorial Board members or recruited together with the channel focus, are an integral component of any given channel. Their expertise and ability to bring in supplementary material through commentary, blogs, news and more helps research communities and the public stay up to date with the latest advances, research trends and societal impact of work in the field of focus. To highlight their foundational work and dedication to this innovative effort in science communication, these editors are profiled at the bottom of the respective channel.

Stories of Channel Origins

Channels originate either from community demand or engaged editors or partners. VDRR provides a new home for the community formerly served by the Journal of Rehabilitation Research & Development (JRRD), no longer published by the US Department of Veterans Affairs. VDRR offers international researchers and practitioners a dedicated online space to share and read state-of-the-art research, information and resources to assist Veterans with chronic illness and disabilities worldwide. Meet the four editors on the Channels and Collections blog.

Editors of the Tuberculosis Channel exemplify the academic strength, community knowledge and dedication to science and medicine this position provides for each channel. The channel was proposed by Dr. Soumya Swaminathan during her tenure as Secretary, Department of Health Research, Ministry of Health & Family Welfare, Government of India, and Director General of the Indian Council of Medical Research. In October, Swaminathan was appointed Deputy Director-General of the World Health Organization in Geneva, the second-highest position at the health agency. Meet both TB Channel editors.

Born as the PLOS Open Source Toolkit: Hardware Collection, the Open Source Toolkit Channel builds on the success of the Collection and now includes peer-reviewed and web articles addressing software and its application. The dedication of this community to all aspects of open source in advancing science and medicine was a determining factor in transitioning this PLOS Collection to a PLOS Channel. Meet the two editors.

The recently launched Cholera Channel was proposed by Dr. Andrew Azman, Deputy Editor of PLOS Neglected Tropical Diseases; he is joined as a channel editor by international experts in global health and infectious disease. Those engaged in the fight against cholera include academics, healthcare workers, policymakers, patients and civil society—all sharing a vision that collective action can stop cholera transmission and end cholera deaths through strengthened international collaboration and improved coordination. Meet the four editors on the Speaking of Medicine blog.

Supporting this community, until now with no specialist journal or centralized publication venue for their work, is key to PLOS Channels’ mission to serve as resources for research communities. Current Editor’s Picks

Each Channel showcases an Editor’s Pick, updated regularly, to bring the latest research front and center to readers. On the VDRR Channel, the latest Editor’s Pick covers a study for early screening of Parkinson’s disease using voicing tasks and text-dependent speech options, published in PLOS ONE.

Editors of the Tuberculosis Channel focus on research that demonstrates an in vitro diagnostic test commonly used to accurately detect Mycobacterium tuberculosis complex and rifampin resistance in high-incidence TB settings performs comparably in low TB-incidence settings. Editors of the Open Source Toolkit Channel chose to feature a PLOS Biology Community Page describing a tool for ethomics, the high-throughput approach to behavioral studies. “Ethoscopes: An open platform for high-throughput ethomics” originated as a preprint on bioRxiv and describes open source software and hardware solutions for monitoring animal behavior.

Currently the Cholera Channel highlights “Identification of burden hotspots and risk factors for cholera in India: An observational study” describing disease hotspots and risk factors for transmission. Using district-level data from the Integrated Disease Surveillance Program, the authors offer their open research results to policymakers for development of a cholera prevention and control roadmap.

From epidemiological studies using existing census data to translational research and innovations for behavioral studies of experimental model organisms, these diverse choices highlight channel editors’ broad perspective in curating content of interest for their scholarly communities.

A Focus on Cholera: PLOS’ Newest Channel

While universal access to safe water and appropriate sanitation is the key to cholera prevention, global progress towards these goals has been slow. The disease remains a global public health threat, with ongoing risk factors that include poor sanitation, lack of enough clean drinking water and poverty. The Cholera Channel features articles on applied and basic research related to the global fight against this disease and spans a range of topics with application to cholera prevention and control, including computational studies exploring the dynamics and spread of cholera; epidemiologic studies and translational science. Also covered is applied field research on the efficacy, effectiveness and impact of cholera control programs such as water and sanitation interventions and oral cholera vaccines.

PLOS aspires to put researchers back at the center of science communication, working in the best interests of all stakeholders—for the benefit of science and the public. Innovations such as the Channels Program, with collaboration from like-minded organizations, push the boundaries of scientific publishing beyond traditional journal, publisher and editorial constraints. Additional channels are currently in planning; bookmark https://channels.plos.org/ or your Channel of interest and check back every two weeks for the latest research, news and developments.

Open Access Week 2017 – Open in Order to…

As a proud co-founder of Open Access Week, we hope you will join us in celebrating progress and promoting awareness to help make Open Access – the founding principle of PLOS – the new norm in scholarship and research globally. This year’s theme is “Open in Order to…” and invites the community to focus on what openness enables.

Since PLOS’ beginning, we’ve been open in order to accelerate progress in science and medicine through publishing, advocacy and innovation to benefit the research community and beyond. PLOS is open in order to ensure that: research outcomes are discoverable, accessible and available for discussion; science communication is constructive, transparent and verifiable; and publishing advances reproducibility, transparency and accountability.

Join PLOS in an Open Access Week Event (and find other events near you):
  • Wed 10/25 5:30–8:00 pm PDT Open House & Poetry Slam at PLOS – Please join us at the PLOS office for refreshments, office tours to see how we work and an Open Mic Poetry Slam with guests invited to share poems, songs, or free verse on the OA Week theme: “Open in order to….” We’ll have fun prizes for all who choose to share!
  • Wed 10/25–Fri 10/27 FORCE 2017 | Changing the CultureAlison Mudditt, PLOS Chief Executive Officer and Emma Ganley, PLOS Biology Chief Editor will be in Berlin at this conference that brings together a diverse group of people interested in changing the way in which scholarly and scientific information is communicated and shared
Explore PLOS Journals – which have now published more than 200,000 research articles: Follow PLOS Channels: Be Open in Order to: Get involved:
  • Learn about FASTR – As Open Access takes center stage with the Fair Access to Science and Technology Research Act in Congress, PLOS reaffirms its commitment to and support of Open Access
  • Join the conversation with PLOS Science Wednesdays 1:00 pm EDT – the Ask Me Anything (AMA) series with PLOS authors on redditscience
Publish with PLOS and share your work with the world Stay in touch with PLOS

Have a great Open Access Week!
 

Cross-Journal Initiative Helps Manuscripts Take Flight

All properly executed science deserves to be published as quickly as possible. One common frustration of scientists related to publication speed is the review-rejection cycle that in action resembles a cross between cycling on a hamster wheel and jumping through a hoola-hoop. To offer authors a way out of this cycle of delay, PLOS launched a journal transfer initiative earlier this year that provides authors an alternative to starting from scratch for papers not initially accepted by a subset of PLOS journals.

How It Works

Manuscripts submitted to PLOS Computational Biology, PLOS Genetics, PLOS Neglected Tropical Diseases or PLOS Pathogens undergo the usual rigorous peer review. The paper’s editors assess the reviews and if they decide the work does not meet the journal’s criteria for perceived novelty or impact but is sound, well-designed and well-executed, they will offer acceptance and publication in the multidisciplinary journal, PLOS ONE. Publication can take place in as little as three weeks after the offer is accepted by the authors.

Papers which merit publication will go through the peer review and revision process only once, saving authors, reviewers and academic editors time, speeding the way to publication for quality research.

Why It Works

The benefit to authors is that instead of rejecting the paper outright, editors now may use the decision letter to offer either immediate publication or publication after minor revisions. Importantly, to move the paper along faster for authors – rather than moving the goal posts – the same academic editor will consider the revision. This also ensures consistency of the feedback to authors and expedites the work for editors. Provided the authors agree to the offer, the manuscript will be published in PLOS ONE with both the original date of submission to PLOS Computational Biology, PLOS Genetics, PLOS Neglected Tropical Diseases or PLOS Pathogens and the name of that journal’s academic editor listed in the article’s metadata. As for all articles published by PLOS, this metadata appears together with citation, copyright, data availability, funding and competing interest information.

Open In Order To Succeed

PLOS has piloted this initiative over the past six months and we’re pleased to report that with substantial support from journal editorial boards and uptake from authors, we will continue this initiative that relieves authors, reviewers and editors of some of the repetition involved in publishing while bringing quality work to the public, faster. There are now notifications of the program on the relevant journal Editorial and Peer Review Process pages. Alongside existing manuscript transfer routes between PLOS journals, this newest initiative offers an effective means for scientists to rapidly communicate ideas, results and discoveries to each other and to the broader public.

Open Access has changed the way readers and researchers around the world discover, use and reuse the scientific literature. Open data provides opportunities for new analysis, new discovery and even previously unrecognized new directions in research. Together with open source software, open source hardware and preprint servers, forward movement along the path toward a more Open Science has the potential to expand the venues, styles, and frequency of sharing work. Let your manuscript take flight! PLOS authors who take this opportunity for rapid publication in PLOS ONE can play an active role in accelerating the discovery and dissemination of their work. With International Open Access Week right around the corner, what better motto to adopt than Open In Order To Succeed—for it is success that we seek for reviewers, editors and most importantly, all authors.

Lasker Award for Public Service Honors Planned Parenthood Federation of America

“It is the commitment and impact [of the organization] that is the key concern.” —Alfred Sommer, Chair of the Jury, 2017 Lasker~Bloomberg Public Service Award

The mission of the Albert and Mary Lasker Foundation is to improve health by “accelerating support for medical research through recognition of research excellence, education and advocacy.” Each year, Lasker Awards are given to scientists that embody this mission. Organizations are also eligible for awards through the Lasker~Bloomberg Public Service Award that alternates years with the Lasker~Koshland Special Achievement Award in Medical Science.

 

Dr. Alfred Sommer; Johns Hopkins Bloomberg School of Public Health

This year’s recipient of the Public Service Award is Planned Parenthood Federation of America (PPFA), “for providing essential health services and reproductive care to millions of women for more than a century.” PPFA began in Brooklyn, New York, where in 1916 Margaret Sanger opened the first birth control clinic in the US; in 1942 the organization changed its name from The American Birth Control League to Planned Parenthood. To place the 2017 Lasker~Bloomberg Public Service Award in context, PLOS interviewed Chair of the Jury Alfred Sommer, University Distinguished Service Professor and Dean Emeritus, Johns Hopkins Bloomberg School of Public Health.

With this award, PPFA joins other collaborative efforts including Médecins Sans Frontières, Bill & Melinda Gates and the NIH Clinical Center as Lasker Public Service Awardees. Since recent previous awardees in this category were individuals, PLOS asked Sommer what does this say about how science and medicine work today, or about the efforts needed to impact human health. “The intent of the Public Service Award has always been recognition of contributions to expanding investments in biomedical/health research and advancing the public’s health,” he responds. “In recent years there has been slightly greater attention paid to the latter, and therefore to the individuals and institutions that have made a real difference.”

Sommer was circumspect and honest when asked to reflect on the timing of the committee’s decision process, in relation to political discourse in the US at that time over the proposal to replace the Affordable Care Act with a plan that would defund approximately 40% of Planned Parenthood’s annual budget. “The discussion is always free-wheeling, and every member is free to raise whatever perspectives they like,” he says. “I am not at liberty to discuss the actual vote, but I can say there was broad agreement with this year’s choice (as there usually is every year, once the discussion and votes are taken).” He continues that the Lasker Awards are “meant to recognize extraordinary achievements, and bring these achievements to the attention of the public. It was no different in this case.”

The origin story of Planned Parenthood is fascinating. While family planning may be the founding service, it’s likely the public doesn’t realize the breadth of services offered by the organization, from sex education programs that reach 1.5 million people annually to over 4 million tests and treatments to both men and women (in 2015 alone) for sexually transmitted infections. “The purpose of all Lasker Awards is to better inform the public about the individual, work, and organization that is being honored,” says Sommer. In recognizing PPFA, he continues, “we would hope that the public will have a better understanding of all the contributions to health made by PPFA.”

While publications and publicity are not a requirement for receipt of the Public Service Award, placing this type of information into the public domain helps to inform policy and to improve health outcomes. Among the PLOS journals, two articles have corresponding or contributing authors affiliated with PPFA. In the recent PLOS ONE article, “Parents’ views on sex education in schools: How much do Democrats and Republicans agree?” researchers from Planned Parenthood found that comprehensive sex education is supported by a vast majority of parents, both Democrats and Republicans.

In the PLOS Medicine article, “Comparison of Outcomes before and after Ohio’s Law Mandating Use of the FDA-Approved Protocol for Medication Abortion: A Retrospective Cohort Study” researchers followed outcomes of a law that took effect in 2011 requiring abortion providers to follow specific US Food and Drug Administration guidelines, created in 2000, when giving patients a combination of two drugs to induce abortion. Their findings, covered by The Guardian and Los Angeles Times, indicate that women experienced a higher rate of complications and were nearly three times more likely to require additional medical intervention after the law was implemented.

Some say that receiving a Lasker Award hints at prediction of a Nobel Prize. To put this attention to awards and prizes in context, it’s worth understanding the compelling origins and motivations of the Lasker Foundation directly from “The Lasker Legacy” video. After watching you might want to make your voice heard through suggested resources on the PLOS Stand Up for Science webpage. Work from individual scientists receiving this year’s Lasker Awards is described in a previous post.

 

Image Credit:

Centers for Disease Control and Prevention/Doug Jordan; Public Health Image Library

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Alfred Sommer is University Distinguished Service Professor and Gilman Scholar, Johns Hopkins University; Dean Emeritus and Professor of Epidemiology and International Health, Johns Hopkins Bloomberg School of Public Health; Professor of Ophthalmology, Johns Hopkins School of Medicine. He served as Dean of the Johns Hopkins Bloomberg School of Public Health from 1990-2005. Sommer is a member of both the National Academy of Science and the National Academy of Medicine, and chaired the Board (on which he still serves) of the Lasker Foundation from 2008-2014. His research interests include outcomes assessment, child survival, epidemiology of visual disorders, glaucoma, vitamin A deficiency, blindness prevention strategies, cost-benefit analysis, the growing interface between medicine and public health, and clinical guidelines. He is most widely known for and received the 1997 Lasker Clinical Medical Research Award for his work on Vitamin A therapy for preventing infections and blindness. Sommer served as Chair of the Jury for the 2017 Lasker~Bloomberg Public Service Award.

Fundamentals of Cell Growth Regulation, HPV Vaccine Development and Planned Parenthood Reap 2017 Lasker Awards

Each year, the Albert and Mary Lasker Foundation recognizes research excellence with a set of three awards given for major advances in the “understanding, diagnosis, treatment, cure or prevention of human disease.” This year’s awards were given for Basic Medical Research, Clinical Medical Research and Public Service.

The Albert Lasker Basic Medical Research Award was given to Michael N. Hall for discovery of and investigations into “nutrient-activated TOR proteins and their central role in the metabolic control of cell growth.” TOR (Target of Rapamycin) is a highly conserved protein and a central regulator through its role as a nutrient sensor, coupling nutrient availability to protein synthesis and cell growth. A critical signaling protein, TOR forms multiprotein associations that function as distinct clusters, either as TORC1 (TOR Complex 1) or TORC2 (TOR Complex 2), depending upon those additional proteins. In their 2007 PLOS ONE article, Hall and colleagues identified novel TOR interacting proteins specific for each complex, investigating the role of phosphorylation and complex function for each. More recently, work from the Hall group published in PLOS Genetics demonstrated a role for TORC1 in bone formation and, in yeast cells, characterized the signaling state of the TORC1 complex with the use of antibody tools.

The Lasker~DeBakey Clinical Medical Research Award was jointly awarded to John Schiller and Douglas Lowy for their collaborative efforts, innovations and ”technological advances that enabled development of human papillomavirus (HPV) vaccines for prevention of cervical cancer and other tumors caused by human papillomaviruses.” Papillomavirus infection on the skin and mucous membranes of humans and animals can cause benign warts (papillomas) or malignancies, especially anogenital carcinomas, and in genetically predisposed or immunocompromised individuals can cause skin cancer. Development of safe and effective vaccines has potential to reduce the incidence of cervical cancer and other malignancies resulting from HPV.

Schiller and Lowry collaborated on three articles published with PLOS. In the early days of PLOS Pathogens, they demonstrated that carrageenan, a sulfated polysaccharide extracted from red algae, was an extremely potent infection inhibitor for sexually transmitted genital HPVs. Their most recent joint publication (also in PLOS Pathogens) investigates papillomavirus in various mouse models, to gain insights into immune system influences on infection progression in humans. These articles, together with results of a clinical trial of bivalent HPV vaccination have received nearly 83,000 views. For further reading in PLOS journals, view Schiller’s  and Lowy’s publication lists.

The Lasker~Bloomberg Public Service Award alternates years with the Lasker~Koshland Special Achievement Award in Medical Science. For more on this year’s Public Service Award, given to Planned Parenthood Federation of America, check back next week for our interview with Chair of the Jury Alfred Sommer.

In publishing their work Open Access, these outstanding scientists and citizens advance medicine, public health and basic research for the benefit of all. PLOS celebrates their work and dedication.

 

Image Credit: Albert and Mary Lasker Foundation

To Sign or Not to Sign: A Slice of Transparency in Peer Review

Scientists depend on the proper evaluation of research that creates the foundation for future work, and the public expects curated scientific content to be trustworthy. All forms of peer review, whether for ethical, technical and sound science criteria or for additional novelty, significance and perceived impact help ensure rigor in scientific research.

There is, however, community and public skepticism regarding the quality, trustworthiness and authenticity of the review process, from the initial stage of evaluation before reviewer assignment to the final editorial decision. Making peer review more transparent, at any stage, has the potential to revitalize the process and restore trust in the system.

Efforts to increase transparency in peer review should address challenges that include:

Reshaping Peer Review

Change is already happening as the scientific community develops variations on themes of open and transparent, and as publishers provide more peer review offerings that range from community participation to open but anonymous, to fully open and signed reviews. While not yet functioning at scale, experiments incorporating more transparent ways to discuss and assess papers over the entire lifecycle of the research are inching their way into practice. This way, the publication of an article isn’t the single defining event in its life; it is just one chapter of its story. Many of the arguments in favor of increased transparency in peer review also hold true in the discussion of benefits of preprint submissions. According to researchers working with neuroimaging, as stated in their PLOS Biology Community Page, “preprints allow the wider community to give feedback to the authors about the manuscript and potentially improve it, which is beneficial for both the authors as well as the journal the paper will be submitted to. For example, the present paper received useful comments from three individuals in addition to the appointed peer reviewers.”

A Question of Signing

At PLOS, we’ve looked at one slice of transparency in peer review—signed reviews made available exclusively to the authors. In a research project that used a survey mechanism to collect experiences and opinions, our Publishing Operations team underwent an assessment of reviews from 2013-2016 in three of the PLOS journals (PLOS ONE, PLOS Medicine and PLOS Computational Biology).

“Our reviewer community is particularly engaged, and that’s what makes working at PLOS on this issue so exciting. Together we will be able to create solutions, both incremental and substantial, that bring constructive feedback to authors and transparency to the review process.” Helen Atkins, PLOS Director of Publishing Operations

Some of what we learned is that reviewers who were not in the habit of signing reviews simply had never been asked, or were not sure of the benefits. But it’s not as easy as just educating in these areas. These scientists also indicated that not signing allows them to be more honest and safe from retribution. We also discovered that signing can improve reviewer accountability and constructiveness, and help authors learn of a reviewer’s area of expertise. Authors who favored receiving signed reviews valued having this additional information as it provides potential for more open communication, moving research forward. The full results of this project, presented by Elizabeth Seiver, PLOS Researcher and Helen Atkins are part of the Editorial and Peer-Review Process Innovations Session on Tuesday, September 12 during the International Congress on Peer Review and Scientific Publication.

Simple but Substantive Practices

In the PLOS ONE article “Peer Review Quality and Transparency of the Peer-Review Process in Open Access and Subscription Journals,” the focus is a general aspect of transparency in peer review—how academic journals (and/or publishers) present their peer-review process to the public. According to the authors of this study, a transparent peer review system “conveys to readers and potential contributors how the peer review is implemented and how articles are selected for publication.” The researchers found that “author’s ratings of peer-review transparency predicted their assessment of the quality of peer-review at that journal.”  Even small changes in practices and on publisher websites can help in this area. In addition, guidelines from the Committee on Publication Ethics, “Principles of Transparency and Best Practice in Scholarly Publishing,” stating that all journal content apart from editorial material should be subject to peer review from outside experts must be met.

Learning from Early Career Researchers

Many ECRs do not get appropriate training on how to prepare or review manuscripts. Improved transparency in peer review would not only satisfy mid-to senior-level scientists, but in providing some form of open dialogue or open accountability it enables these scientists to lead by example and provide mentorship to the next generation of reviewers.

Young and upcoming scientists have plenty of ideas when it comes to improving transparency in peer review. At PLOS, we received over 150 essays on how to revamp peer review from Early Career Researchers applying for our ECR Travel Award Program. These creative young scientists described what they consider to be characteristics of the optimal peer review process and how they might build this process either from scratch or using aspects of existing practice.

Their ideas, edited for brevity, include:

  • Invite reviewers to publish reviews of the article (should they wish to reveal their identity) as an accompanying commentary, for no additional fee. If reviewers know they could gain an additional publication for their efforts, this would motivate them to review more articles and respond in a constructive and timely fashion. Victoria Leong; orcid.org/0000-0003-0666-9445
  • [Provide] incentives for reviewing that encourages kind, open but fair responses; we would also be affecting a positive change in the culture of science; which will advance the science itself. Rebecca Gelding; orcid.org/0000-0003-4883-8075
  • Reviews should be open, archived and after publication, reviewers should be revealed. This aims to ensure two aspects of quality control: reviewers take more seriously their job since it will be public with their name tag on it; and reviewing records can be used when considering career development. Juan Rocha; orcid.org/0000-0003-2322-5459
  • Review record should also be one of the criteria judging and advancing a researcher’s professional development. Knowing that a reviewer’s identify would be revealed later and shared among peers, a reviewer would have more incentive to avoid giving low-quality comments. Xiao-Peng Song; orcid.org/0000-0002-5514-0321
  • A transparent, open review process may promote accountability among reviewers. A peer reviewer whose dated comments are published as supplementary material with the article has a greater incentive to conduct a thorough and timely review of the manuscript. These same published comments could also be accessed by other researchers who are struggling to address similar issues in their own studies. Sericea Stallings-Smith; orcid.org/0000-0002-4876-9965
Slices of the Transparency Pie

Solutions that will help peer review achieve its scholarly ideal are not untenable; the challenge lies in that they must satisfy a diverse researcher and stakeholder community. While some improvements are easier to implement than others, even small slices that expedite and enrich the process of assessment in fundamentally new ways contribute to advancing science and discovery for the broader scientific community.

Publishers have an opportunity to improve both speed and efficiencies: to improve review forms that may be cumbersome or insufficient to provide thoughtful and constructive feedback to authors and to provide training for reviewers and editors that mitigate potential bias. Additional possibilities include direct or facilitated mentoring of early career researchers to improve their understanding of the principles of peer review and how it is practiced within the scientific community. Imagine the impact of a global editorial and reviewer contributor community, appropriately trained, recognized and incentivized.

For more insights on peer review listen to the following PLOScast episodes and read the following posts on The PLOS Blogs Network. PLOScasts PLOS BLOGS

 

Image Credit:

Etsy; FuzzyButtFarm

Tensions in Scientific Culture Contribute to Reproducibility Challenges

“Once a system is running a certain way it’s hard to change course.”—Richard Harris, award-winning science correspondent for National Public Radio

Scientists, publishers, journalists and the public talk of the problem of reproducibility in experimental science. There are committees, symposia, peer-reviewed articles, blogs and opinion pieces documenting the issue and exploring remedies to the challenge of reproducibility. NPR science correspondent Richard Harris takes this societal challenge one step further in his book with a title that in no uncertain terms calls attention to the root cause of the reproducibility challenge—Rigor Mortis: How Sloppy Science Creates Worthless Cures, Crushes Hope and Wastes Billions.

PLOS interviewed Harris about the lack of rigor in experimental research that he describes in his book, and from a discussion that covered materials standards, publishing fewer papers with greater confidence, text and data mining and the cultural shift required to improve the rigor in science, one unifying theme emerged—tension. Tension between evaluation and culture, hands-on training and coursework, between making work public and ensuring its reliability, and between responsible reporting and satisfying the needs of a news organization.

These lines of tension contribute to the current structural rigidity in the culture of science that, according to Harris, make scientific rigor a difficult challenge to address. As he delved into biomedical sciences in 2014 after nearly a decade reporting on climate change and the environment, Harris took a broad look at the state of the research enterprise and asked, what are the consequences of limited funds on the structural influences supporting the current state of academic biomedical research?

Evaluation and Culture

The biggest obstacles influencing rigor, according to Harris, are the “underlying cultural issues” that confront science. He cites the financial crunch, career pressures and the hyper competitiveness of science, particularly in biomedical sciences, as examples. These are, he thinks, also the hardest problems to solve. “Even if you poured huge amounts of new money into biomedical research this problem would not go away quickly. It’s changing a mindset.” Fundamentally the “incentives are misaligned,” says Harris, to reward numbers of papers and how many of them are published in high profile journals, rather than “careful work where one is highly confident in results.”

Hands-on Training and Coursework

On the point of experimental responsibility, Harris’ book follows a path of practical recommendations to improve scientific rigor, including:

  • Improve experimental design and provide methods training
  • Validate cell lines, antibodies, gene constructs
  • Apply appropriate statistical analysis
  • Disclose experimental and analytical methods

During his research for the book, Harris was quite surprised to find out how little formal training there is in experimental methodology, particularly in biomedical research. He did note, however, that NIH is now funding attempts to develop curriculum, following an unsuccessful search to find the best training courses in the country to replicate. There is “huge room for improvement” in this area, he says, but how to integrate this into a training program? Changing a system that’s already in place to accommodate that is difficult, especially without reward and recognition for faculty teaching those courses. “Should it start more robustly at the end of the undergrad career?” One potential solution discussed during the interview is for post-docs to teach these courses to incoming graduate students, as part of a summer or first-quarter orientation program.

Making Work Public and Ensuring Reliability

Steps can be taken to improve the situation. For example, researchers with grants from the National Institutes of Health are required to authenticate the cell lines used in their work. “There’s no simple solution to be imposed from top down, it needs to also work bottom up,” says Harris when considering what key additional recommendations the community might consider. “Young scientists are more open to sharing and that leads to transparency, that helps solve some of the issues.” It’s not a silver bullet but it improves things if people can put their data out there, he says. Increased sharing and transparency addresses a number of these issues, and “to the extent that the culture of the young scientist is open to that, that’s great. Although it’s hard for them to change the culture, but over time this can help.”

A “more nimble publication system might encourage scientists to publish confirmatory or negative results,” Harris states. When asked specifically about the role of preprints and alternative forms of science communication, he acknowledges that experiments in openness and transparency are interesting although it’s unclear how successful they will be. Will that additional literature be less reliable, he wonders? “It’s the job of the entire community, not simply the scientist who makes a claim, to figure out what’s right and what’s wrong,” he says, when discussing the viable options of prepublication sharing of work and use of blogs and commenting as forums for peer review. However, as a science journalist, he ponders: “Do we want more literature out there or do we want more strict checks and less literature? Personally, I would like to see less literature, have people spend more time thinking about what they’re doing and being sure they’re right.”

Responsible Reporting and News Flow

Science journalists can help the issue of scientific rigor, acknowledges Harris. “They should step back from doing the story of the day. It takes more time to think about things from a broader perspective, but that’s more important than ever.” Science journalists must find a balance between that and satisfying the needs of their news organizations. Even an award-winning science correspondent like Harris admits that he needs to think differently about how he does his job on a day to day basis. “Look at what’s published and fits into the broader trend and context of similar results, and what it means elsewhere,” he recommneds. These are results that should be the focus of science journalists.

Easing the Tug of War

The good news is that many institutions now evaluate candidates for jobs and promotions based on a set limit of publications, chosen by the author to best represent their contributions to science. Additional efforts to broaden evaluation within the constraints of the existing scientific culture include recognition and credit for reagent validation, peer review activities and training others on experimental responsibility. Dedicating more time to thinking and less time to drafting and revising manuscripts may not the working philosophy of many labs or the culture of science, but it’s an issue getting attention and was expressed as a concern by leaders of the organization Rescuing Biomedical Research.

Everyone has a stake in the current structure of the scientific enterprise, says Harris, from journals caring about impact factors [PLOS de-emphasizes journal impact factors] to deans making sure scientists draw in funding and overhead for their institutions.

“The biomedical research enterprise is driven by economics; economic systems are much harder to change and that should be something the overall enterprise should be thinking about—how to rethink that.”

Harris believes clinical medicine in the 1990s experienced similar cultural stresses, but ClinicalTrials.gov, a web-based resource from the National Library of Medicine that provides public access to information about clinical studies and the availability of experimental drugs, got people “past some of these issues without making them rethink their place in the scientific universe.” Hopefully academic biomedical research can do the same.

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Richard Harris, science correspondent for National Public Radio (NPR) received the 2010 Kavli Science Journalism Award from the American Association for the Advancement of Science (AAAS) for his reporting on BP’s Deepwater Horizon oil spill in the Gulf of Mexico. He also received the award in 1988 and 1995. He currently covers biomedical sciences with a focus on investigative stories and in 2014 completed an eight-part series examining the stresses on biomedical research in the US caused by fluctuating funding levels.

 

Tug of War Image Credit: falco; pixabay.com

 

A Publishing Milestone to Celebrate: 200,000 PLOS Research Articles and Counting

In 2003, PLOS published its first research article and this month we’re proud to announce that we have now published more than 200,000 research articles across our seven Open Access journals. It has been an amazing journey to reach this milestone.

“In only 14 years of existence, PLOS has helped catalyze the rapid growth of the Open Access literature. The 200,000th article is a remarkable milestone for PLOS and for the scientific community that has supported the Open Access movement.”-Veronique Kiermer, PLOS Executive Editor

We’d like to take this opportunity to thank those who have helped rapidly create this large corpus of diverse, Open Access research:

PLOS was incorporated in 2001 as an Open Access advocacy organization and became a publisher to prove the value of Open Access, beginning with PLOS Biology in 2003 and PLOS Medicine in 2004 as open alternatives to prestigious subscription journals. In 2005, PLOS launched PLOS Genetics, PLOS Pathogens, and PLOS Computational Biology as proof of concept to show that research communities built around and across specific areas and disciplines could thrive with an Open Access model. In late December 2006, PLOS ONE spearheaded the innovative editorial approach focused on evaluation of research independent of perceived impact; this editorial approach has now been adopted by journals from nearly every scientific publisher. Since its founding, PLOS ONE has published more than 175,000 research articles based on three compelling features: advancing quality science for everyone, moving publication forward in all scientific disciplines, and favoring speed to publication over subjective assessment of significance.

In 2007, with the support of the Bill & Melinda Gates Foundation, PLOS launched a fourth community journal, PLOS Neglected Tropical Diseases (NTDs). Together with the journal’s leadership and global community, we now proudly celebrate the 10th Anniversary of PLOS NTDs and the more than 4,500 research articles that contribute to advances in the field.

Open Access continues to gain momentum but there is further work to be done. At PLOS, we are constantly looking for ways to use emerging technology and new ideas to open up scientific communication—to make it faster, more efficient, more connected and more useful. We look forward to the next 200,000 articles and continued involvement with the scientific community.

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

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 supports today’s 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.

Today, July 12, 2017, is 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) will see a message of explanation and letter of support for net neutrality in the form of a pop up window. This message will appear only today, once per site, per device. Visitors to these web pages can 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 is purposefully not placing this notice on any journal content or information pages, so that access to our content is 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/.

Immediate and Lasting Impact: Top Ten New Species of 2017

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 that 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.

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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

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 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 Masters in 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

“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

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.

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