Plos

Aperta Source Code is Now Available

We’re happy to announce that the source code for the Aperta submission system can now be found on GitHub. Aperta has been developed using reliable and modern technologies and the shared code provides an opportunity for both the research communication and open source communities to build on and enhance it.

Moving forward, you will continue to see our commitment to the principles of openness and transparency in our publishing strategies, innovations, policies and partnerships.  In short, we want to help foster an environment conducive to responsible Open Science and be part of the collective effort to propel it into new and exciting territory.

Aperta is a Linux and Mac supported platform for managing the submission and review of research outputs. More information about the system and its capabilities can be found on the APERTA-wiki. Questions about Aperta can be logged in the issue tracker.

PLOS ONE and Children’s Tumor Foundation partnership announce second cycle of DDIRR Awards

The Children’s Tumor Foundation (CTF), the largest non-governmental funder of neurofibromatosis (NF) research, and PLOS ONE, a leading peer-reviewed scientific journal, are pleased to announce the successful completion of the first funding cycle of the Drug Discovery Initiative Registered Report (DDIRR) 2017 Awards, a funder-publisher partnership integrating the Registered Reports model into the grant application process.

Registered Reports pre-determine the research questions, methodology and design of a study to be carried out, and are designed to enhance the rigor, reproducibility and transparency of the science produced. CTF and PLOS ONE partnered together to review the 2017 DDIRR applications and granted three awards: Dr. Andrea McClatchey of Massachusetts General Hospital, Dr. Lei Xu of Massachusetts General Hospital, and Dr. Aaron Schindeler from the University of Sydney. The researchers also obtained an in-principle acceptance (IPA) to publication in the journal PLOS ONE. Provided the study is conducted according to plan, acceptance in principle is honored regardless of study outcome – thereby eliminating publication bias and maximizing the transparency of the funded work.

The reports are being placed on the Open Science Framework registered report portal (https://osf.io/rr/), where authors will have the opportunity to make public or embargo their reports until publication of results. The awards have a duration of 12 months and will conclude in May 2019. As soon as results are added to the registered report, PLOS ONE will review compliance with the proposed protocol and publish their results, even if they are negative. By securing publication before they start their research, applicants can eliminate the bias of a result-based approach. The process was designed to maintain independence of funding and publishing decisions, while at the same time optimizing processes, thereby avoiding duplication and preventing research waste.

This new award constitutes an evolution of the Drug Discovery Initiative (DDI) Awards that CTF had introduced in 2006 as a funding program for promising ideas that could lead to larger studies or move drugs into the clinic. Feedback on the new DDIRR program from both applicants and reviewers has been unanimously positive, and the Foundation together with PLOS ONE editors have also announced a new cycle for DDIRR in 2018-2019. The Foundation will invite applicants to submit their proposals starting on September 24, 2018, with the anticipated assignment of new awards in the first quarter of 2019.

“The overall outcome of this first round of DDIRR has been very positive. Reviewers have focused their attention to protocols and study designs, allowing researchers to have their statistics ready for publication,” said Salvatore La Rosa, Ph.D., Vice President of Research and Development for the Children’s Tumor Foundation. “As this particular grant program focuses on hypothesis-testing research, the quality and rigor of the applications are critical to soundly move proof-of-concept experiments from the lab into the clinic. This new program increases our ability to do that.”

“We are delighted to continue our collaboration with CTF on the Registered Reports model for the DDI Awards. We hope this can serve as a model for other funders. The Registered Reports provide researchers with peer reviewed study designs and an in-principle acceptance of the completed study at PLOS ONE. The deposited reports at the Open Science Framework portal ensure full transparency of the research project – a win for everyone involved,” adds Joerg Heber, Editor-in-Chief of PLOS ONE.

Source: First Funding Cycle of the Drug Discovery Initiative Registered Report (DDIRR) Awards Announced.

PLOS Responds to Ebola Outbreak with New Channel & Expedited Peer Review

Early sharing and expedited peer review of relevant research

In response to the ongoing Ebola outbreak in the Democratic Republic of Congo, we are creating a PLOS Channel for Ebola Research.  The Channel will make it easy for researchers to keep up with developments and important research related to the outbreak. We will work with authors and our editorial boards to provide rapid review and facilitate the responsible dissemination of preprints. We believe these responses are urgently needed during serious and rapidly developing threats to public health.

All relevant articles published across PLOS will be included in the Ebola Channel, alongside major contributions curated from the broader literature. You can also send any questions or content recommendations to ebola@plos.org or tweet us @PLOSChannels using the hashtag #PLOSEbola.

How do I make my Ebola research available quickly?

We’ve created a taskforce to identify editors and reviewers, and to manage an expedited review process across all our journals and platforms.  For authors, we recommend the following:

  • If you want to share a single observation (no more than 1 figure or table with commentary) submit to PLOS Currents: Outbreaks
  • Submit any other research to one of the 7 PLOS journals; all Ebola-related submissions will be prioritized. (Note that fee waiver assistance is available as needed)
  • Share your data and manuscript ahead of submission: large datasets should be deposited in a relevant repository, and manuscripts submitted to a preprint server. Include the DOIs or accession numbers for datasets and preprint in your submission.

In addition to expediting research publications, PLOS believes all data on the Ebola outbreak should be shared as rapidly and openly as possible. We endorse the Wellcome Trust’s statement demanding availability of data and research on Ebola. Editorial consideration of research submissions to PLOS journals will not be prejudiced by the early sharing of data or preprints.

Lessons learned: delivering rapid responses to emergency outbreaks

PLOS saw surges in submissions in previous outbreaks, notably the Ebola outbreak of 2014 and the Zika outbreak of 2015/2016. In each emergency, we provided resources to serve the community. In addition, concerns about data sharing during the 2014 Ebola outbreak led PLOS and other journal editors to issue a joint statement encouraging early data sharing. A recent report in PLOS Medicine showed that, while increased use of preprints in the 2016 Zika outbreak accelerated the dissemination of research results, the proportion of published articles on Zika that were preceded by preprints remained low.

Our shared responsibility in public health emergencies

We believe research, healthcare, and publishing communities have a responsibility to work together to respond rapidly to public health emergencies. PLOS is committed to disseminating new research findings as efficiently and effectively as possible. We appreciate the opportunity to facilitate access to your work.

 

PLOS Announces Prize to Celebrate the First Year of Channels

One year ago, PLOS launched its Channels program, providing central hubs for specific research communities. Channels are resources for scientists, making it easy to keep up to date with developments in a particular area of study and offering a way for exceptional research to be recognized and highlighted. All Channel content is curated by our expert Channel Editors, who are active leaders in their fields of research.

Our first Channel, launched a year ago, was the Veterans Disability & Rehabilitation Research Channel, soon followed by Channels for Tuberculosis, Cholera, Disease Forecasting & Surveillance, Responding to Climate Change and the Open Source Toolkit. To celebrate the first year of these Channels, we are awarding a prize of $500 to the authors of the best PLOS research featured in our first three Channels (Veterans Disability & Rehabilitation Research, Tuberculosis and Open Source Toolkit), with the winners chosen via a public vote. The polls will soon be available on Twitter and we’ll share more information about the competition on the PLOS Channels and Collections blog in the next few days.

Interested in getting your paper featured in a Channel? Authors are encouraged to suggest their papers for inclusion in a relevant Channel – simply contact us at channels@plos.org (email) or @PLOSChannels (Twitter) to let us know about your work, and Channel Editors will consider it for the next update. PLOS authors can also suggest a target Channel when submitting their manuscript, via the cover letter or the submission form.

PLOS believes that bringing communities together means research is shared more freely, and discoveries can be accelerated. If you’d like to discuss working with PLOS on a Channel for your community, email channels@plos.org – we’d love to hear your ideas.

Power to the Preprint

Preprints are here!!! Starting today authors submitting their manuscript to most PLOS journals* can also choose to post their article on bioRxiv, Cold Spring Harbor Laboratory’s preprint server for the life sciences. This is an important development for both PLOS, for bioRxiv, for the authors we serve, and for the life sciences. For PLOS, it enables us to achieve a long-standing aspect of our vision to make research more quickly available to enable discovery and reuse.  For bioRxiv, this development will augment the server’s already rapidly climbing manuscript submission rate. And authors will gain the opportunity of sharing their work before peer review on a trusted platform.

“Collaborating with bioRxiv is part of a much bigger strategy for PLOS moving forward, one in which we’ll renew our roots of being a catalytic open publisher” said Alison Mudditt, CEO of PLOS. “To accelerate innovation, we’ll often act in partnership with others in the community, which will move us closer to our vision of how scientific communication should work.”

“We warmly welcome the further integration of PLOS journals with bioRxiv,” said John Inglis, co-founder of bioRxiv. “The server’s goal is the acceleration of research and providing unrestricted access to manuscripts before they enter an often lengthy process of peer review is one of several ways bioRxiv is delivering on its promise.”

So what are preprints exactly?

A preprint is an openly available scientific manuscript that an author uploads to a public server like bioRxiv prior to peer review. The preprint contains data and methodologies and is typically the same manuscript that is submitted to a journal.

Why are preprints important?

Well, for starters, early sharing of ideas can lead to new discoveries and collaboration, and early feedback can help improve your manuscript. We are committed to putting your science first. By allowing a submission to be posted on bioRxiv, authors accelerate the dissemination of their work and invite commentary by a broader community, which PLOS editors may evaluate as part of peer review.

How will it work? This graphic is a visual representation:

In short, PLOS will perform initial manuscript screening compatible with bioRxiv standards, covering appropriate scope and article type, plagiarism detection, and other basic ethical and technical criteria. Articles will then post to the bioRxiv server and be freely accessible online. Authors must choose to opt-in to this preprint process when they submit papers to PLOS.

When sharing this post on Facebook or Twitter please use the hashtag #powertothepreprint to help increase visibility and awareness for preprints. Publish with PLOS and post your preprint on bioRxiv and let’s keep science open, and accessible, together.

*PLOS Medicine continues to permit authors to post preprints of their research, but given particular issues related to research in human health, will not initially be offering transfer of submitted manuscripts to bioRxiv.  PLOS Biology also continues to encourage authors to post preprints and will enable this automated preprint posting service to submitting authors in a few months.

Joint Publisher Statement

PLOS, together with the Science, Nature, Proceedings of the National Academy of Sciences and Cell families of journals issued a joint statement that addresses a recently proposed rule from the Environmental Protection Agency (EPA).

PLOS has always been a strong proponent of sharing data to improve the transparency of scientific research, but we recognize that some datasets cannot be made publicly available for ethical reasons. The EPA proposed rule is presented as informed by the journals’ policies. However, insisting on public availability of data would allow the EPA to exclude relevant data simply because it cannot be made publicly available. We believe this could prevent the use of relevant scientific evidence in the regulatory process.

You can read the joint statement here.

Citation

J. Berg, P. Campbell, V. Kiermer, N. Raikhel, D. Sweet, Science. 10.1126/science.aau0116 (2018).

Making a home for the Physical Sciences and Engineering in PLOS ONE

Calling all physicists, chemists, earth scientists, computer scientists and engineers: help PLOS ONE make science more open, more reproducible and more transparent.

PLOS ONE is known for its multi- and interdisciplinary approach. The journal is open for papers in all areas of science. From particle physics to pulmonology, we particularly welcome papers that break down barriers between disciplines. Historically speaking, however, most of our initiatives and publications have focused on biomedical topics. Given that all of PLOS’ founders came from biomedical fields, this focus arose organically.

But PLOS ONE’s approach to consider all rigorous research irrespective of impact and PLOS’ commitment to driving innovations in Open Science and Open Access in a non-profit framework have always attracted a diverse group of researchers and disciplines. Indeed, communities in physics, chemistry, earth sciences, computer sciences and engineering have adopted PLOS ONE as an outlet of choice in the past. We have published influential papers on complex networks, 3D printing, polymer chemistry, climate change and machine learning, to name but a few topics.

To build on these strengths, PLOS ONE has created a  Physical Sciences and Engineering team as part of a wider effort to better serve our communities through subject-specific in-house editorial groups. The team is led by me, Division Editor Leonie Mueck (Physics, Computer Science, Engineering). I am proud to present the team working beside me:   

  • Associate Editor Victoria Black (Earth Sciences)
  • Associate Editor Helen Howard (Chemistry and Materials Science)

You can meet us at many 2018 conferences, including the ACS National Meeting, MACRO2018, Goldschmidt2018, the 2018 MRS Fall Meeting, the 2018 AGU Fall Meeting, and NetSci 2018.

Physical Sciences and Engineering is a vast remit and we are building an experienced editorial board in the different research fields, an editorial family which you are invited to join as an Academic Editor. PLOS ONE is a journal that is run by the community for the community, and we invite researchers in the field to join us in our efforts.

Together with some of these communities, we have already started working on various editorial projects:

There are more projects in Physical Sciences and Engineering in the pipeline, and we are committed to sharing our progress with you as we move forward. We want to hear from you, the researchers in these communities. Share your thoughts and help us shape physical sciences and engineering at PLOS ONE! Your perspectives will help shape future projects, topics for calls for papers and how to support you with Open Science initiatives. Please fill out this form if you want to share your ideas with us.

One Small Step for Preprints, One Giant Step Forward for Open Scientific Communications

Thanks to our recent partnership with bioRxiv, PLOS authors will have the choice of posting their submitted manuscript on the bioRxiv preprint server on May 1st. Preprints enable authors to accelerate the dissemination of their work and invite commentary by a broader community, which PLOS editors will evaluate as part of peer review.

Posting your work before formal peer review has other significant advantages:

  • You can stake an intellectual claim to methods, results and ideas contained within that paper, while obtaining citations.
  • Your work can be discovered. Many journals, including PLOS Genetics, use preprint servers to identify and solicit manuscripts.
  • Early posting can lead to collaborations by fostering connections with researchers in different disciplines.

Still not convinced of the value of the preprint and its role in accelerating scientific communication? There are a lot of resources on this topic. Here’s a sampling:

PLOS is committed to putting your science first. Please send any questions, concerns or delights that you have regarding preprints to preprints@plos.org following our launch on May 1st. Publish with PLOS and post your preprint on bioRxiv and let’s keep science open and accessible, together.

Reproducibility and Recognition: One year later

This blog is authored by PLOS staff with contributions by Lenny Teytelman, protocols.io CEO.

For many scientists, there is a common frustration with methods sections of research papers that lack sufficient details, which are necessary to follow up on the work. The mission of protocols.io is to encourage precision and to facilitate the sharing of these details.  We’re excited that our partnership with them over the past year is providing yet another catalyst for transforming research communication. Our combined aim is simple: improve the rigor of published research papers by encouraging authors to report precise protocols accompanying their manuscripts on protocols.io.

“In addition to helping the PLOS papers and the scientists reading them, this partnership also had a dramatic impact on the adoption of protocols.io. The new author guidelines at PLOS helped protocols.io to also connect in a similar way to 200 other journals,” says protocols.io CEO Lenny Teytelman. “As a result, the number of scientists creating new protocols every month has more than tripled on protocols.io over the past year.”

Figure Legend: Number of scientists creating new protocols each month on protocols.io

“Partnering with organizations like protocols.io and bioRxiv is a way for PLOS to achieve its Open Science mission in the spirit of collaboration,” says PLOS Executive Editor Veronique Kiermer. “Leveraging the effective platform that protocols.io has developed enables us to take a leap forward in promoting reproducibility.”

Out of the hundreds of protocols accompanying PLOS articles published over the past year, we want to highlight a few great and diverse examples of what scientists have chosen to share via their Materials & Methods sections:

Looking ahead to the rest of 2018: protocols.io continues to broaden its scope to include “all research” instead of simply biomedical and the life sciences. And thanks to our continued partnership authors will soon see an improvement to the platform interface for clinical trials, neuroscience and other fields; a better experience for reporting reagents and equipment; and easier to use templates.

Publish with PLOS and your protocols with protocols.io and let’s keep science open, transparent and reproducible together.

 

PLOS Update

 

When I was appointed PLOS’ CEO last year, I committed myself to transparency with the communities we serve. That’s why, while this is a difficult blog to write, it’s important for me to share that I am making the hard decision to eliminate 18 positions at PLOS. Much of this is related to a strategic decision to shift from developing a proprietary platform for submissions to creating innovation partnerships with a wider community (Most readers are already aware of this from my previous blog.) It’s also driven by the need to be fiscally responsible and remain a sustainable nonprofit organization that continues to lead transformations in scientific communications.

I’d like to reiterate what we’ve communicated internally. Our people and their passion are the most important part of what makes PLOS so special. The people whose roles have been eliminated are all excellent at what they do, and their leaving is a result of operational decisions, not performance.

Moving forward, we’ll be a leaner organization. This doesn’t mean we won’t continue to fully support our researchers and scientists. We’ve been careful in where we’ve streamlined operations and those who engage with us should not see any disruption.

This is a pivotal moment in the life of PLOS and Open Access (OA) as it was envisioned by our founders 17 years ago. While OA has seen strong adoption, much has evolved in the landscape. Changing how and when we share, access and evaluate all research outputs is more critical to science than ever. It will take many of us working together, in various forms of partnership, to accelerate and advance a culture and ecosystem of open innovation.

Over the past two decades, I’ve been part of multiple transformations in publishing. This is what’s most exciting and daunting about our industry. Disruption takes stamina and a willingness to embrace the unknown while acting responsibly in the moment. This is our goal and commitment as we explore ways to drive innovation in our industry forward.

You’ll continue to hear from me throughout the year as I share our wins and our challenges toward that vision. It’s my hope that through transparency and open dialogue, we can maintain the trust our community has placed in us.

Thank you for reading.

Alison Mudditt

Display without Delay: Search, Browse & Cite PLOS Articles with Quick Abstracts from Google Scholar

Working off your mobile device? No problem. We just made it easier to use your phone to find and scan PLOS articles.

If you’re someone who’s out in the field more than in the lab, you may have been challenged finding research on the fly. That’s now in the past. To expedite discovery and access to PLOS research articles, we’ve worked with Google Scholar to include PLOS abstracts in their new Quick Abstracts feature. Researchers around the world can now view complete abstracts and explore citations quickly and efficiently from any mobile device. For scientists, educators, policy makers and journalists, this means more efficient and timely access to the academic literature.

How It Works

Google Scholar Quick Abstracts allows researchers to tap on any search result to browse the full abstract text of a PLOS article directly on their cell phone, then either return to the search results or swipe right and left to read additional abstracts. From a link at the bottom of the abstract text, readers are taken directly to the complete article. Quick Abstracts even serves up preprint abstracts from bioRxiv, further extending discoverability of work by authors who opt to post their preprints at time of submission to PLOS journals.

Quick Abstracts includes all the expected features of Google Scholar, including saving to “My Library” through the star button, and display of citing and related articles. Additionally, an entire discovery network is available through use of search strings on the Google Scholar homepage. For example, entering “site:journals.plos.org” in the search bar retrieves abstracts of the entire database of PLOS research articles.

Innovation for All

Research, discovery and knowledge on the go shouldn’t be restricted to technology-driven economies. While the majority of cell phone users in the United States and Europe benefit from 3G, and even 4G, technologies and fast data delivery speeds on their mobile devices, this is not the case globally. Quick Abstracts integrates mobile network optimization that enables abstract display without delay, especially important for communities in the global south browsing and reading journals such as PLOS Neglected Tropical Diseases, PLOS Pathogens, PLOS Medicine and related research in additional PLOS journals.

Open. Fast. Global.

The adoption of Quick Abstracts is a logical extension of our ongoing relationship with Google Scholar—one based on making research more open and available throughout the global scholarly research community. Our CC BY licensing, Open Access ethos and mobile-ready delivery of journal content enables innovators like Google Scholar to bring their latest technologies to PLOS, for the benefit of our authors and the wider scientific community. Like our partnership with protocols.io for laboratory methods citations and collaboration with bioRxiv for preprints with our journal submissions, this is just one more example of how we’re working with external collaborators to transform research communication.

No more waiting to get back to your desk, lab or laptop to explore a potential new project, prepare for journal club or add to your reference list—head to scholar.google.com from your cell phone for abstract display without delay.

 

PLOS Extends a Profound Thank You

To all our Reviewers, Guest Editors and Editorial Board members, thank you! 2018 marks the fourth year that we formally and publicly acknowledge our community of reviewers and editors for sustaining public access to rigorous peer-reviewed research, enhancing our journals’ abilities to communicate the work of researchers and communities, and inspiring the work of our staff.

A Passion to Go Beyond

Our contributor community selflessly guides papers through the editorial process and provides feedback to authors. Many also actively stand up for Open Access, open data and Open Science as they attend conferences, debate with colleagues or share research via social media, email or even, yes, conversation! Our reviewers and editors devote time and energy to PLOS Collections, Special Issues, PLOS Channels, Editorials, Perspectives, blog posts, interviews, career advice, educational material and more to enrich the primary literature, provide context and engage the public. These endeavours help make PLOS a unique place to publish and for that we are greatly appreciative.

Those who volunteer their services to PLOS, and the greater scientific community, are more than just dedicated scientists: they share an entrepreneurial spirit as we advance scholarly communication with requirements for ORCID iDs for corresponding authors, implementation of CRediT for author contributions, community engagement for improved evaluation, integration of preprint Editors and experimentation with software development. Throughout all of these innovations, some successful (108,000 ORCID entries in our system uniquely identify authors to ensure complete and accurate recognition of work, regardless of changes to name or institution) and others less so, PLOS continues to be, in the words of our CEO, an organization “willing to take risks in order to best serve scientific communities.” We have tremendous appreciation for Reviewers, Guest Editors and Editorial Board Members who are confident to travel the road with us toward a world of readily discoverable, freely available, thoroughly reliable and fully reusable research outcomes.

An Impressive Community Workload

Continuing our quest for transparency in the publishing process, we include the number of newly submitted and published research articles brought to the public in 2017 in each of the seven journals’ thank you articles. We released this information for the first time last year and will continue to do so as it provides additional insight and appreciation for the workload of our reviewers and editors. That workload in 2017 supported publication of more than 23,000 research articles.

Our global network of more than 74,000 reviewers and 7,200 editors ensures that Research Articles, Perspectives, Editorials and more achieve the highest quality possible. The more than 15 million article views per month (on average) this past year hints at the enthusiasm that PLOS reviewers and editors share, for science and scientists. Enthusiasm is not enough, however. This geographically diverse contributor community also shares a commitment to responsible and fair examination of the science, ethics, reporting guidelines, data availability and journal publication criteria associated with each submission.

Efforts to Ease Process and Enrich Training

We’ve listened to our reviewer and editor communities who want more training, especially Early Career Researchers. In response we developed the PLOS Reviewer Center, to provide detailed, journal-agnostic peer review guidance from experienced researchers, staff editors, Editorial Board members, and other reviewers. The Reviewer Center is still under development, so we encourage you to take a look around and let us know what you find useful or missing via the feedback form.

Through the PLOS Reviewer Center anyone can:

  • Learn the basics of peer review and get helpful tips for handling reviewer tasks, from accepting a review invitation to completing a review
  • Access video, templates, checklists and other customized tools for reviewers
  • View recent articles and commentary about trends and studies on peer reviewers, the peer review process, and other related topics

In addition to the Reviewer Center, we’ve made more comprehensive our guidelines for Reviewers and Editors, provided editors more journal transfer options to accelerate publication of peer-reviewed manuscripts, made reviews public to increase transparency of the review process and experimented with signing reviews. A detailed overview of the Editorial and Peer Review Process is available on all journal sites.

For the Record

A published and citable journal article thank you provides reviewers and editors recognition and an academic citation for their inspired service to colleagues, institutions, funders and the public. Each reviewer’s and editor’s name is listed in the Supporting Information of each journal’s published article; links to these articles are below.

We’re in the midst of expanding the size and scope of the PLOS ONE Editorial Board to achieve stronger subject area coverage across all relevant disciplines. If you’d like to learn more, please email us at edboardmgmt@plos.org.

Once again, thank you!

PLOS Collaborates on Recommendations to Improve Transparency for Author Contributions

In a new report, a group convened by the US National Academy of Sciences and including a dozen journal editors reflects on authorship guidelines and recommends new ways to make author contributions more transparent.

What does it mean to be author number seven on a twenty-five–author article?

Establishing transparency for each author’s role in a research study is one of the recommendations in a report published today in the Proceedings of the National Academy of Sciences (PNAS) by a group led by Marcia McNutt, President of the National Academy of Sciences. The recommendations issued by this group, which included one of us, were adapted based on community feedback and peer review from an original draft presented as a preprint. PLOS supports the recommendations for increased transparency and has already put some of them in practice.

A more systematic description of author contributions is a prerequisite to providing due credit for roles that are instrumental to the research enterprise, especially those roles that are too often ignored or devalued. For example, collecting, curating and sharing a dataset or developing a new methodological approach that can be reused by others are key contributions that may not always land a ‘first author position’ but have applications beyond a single article and deserve recognition.

Transparency also brings more accountability to a system where questionable and even detrimental practices (such as guest, ghost or conscripted authorship) have been documented. While transparency requirements cannot entirely eliminate abuse, transparent description of individual author contributions can deter inaccurate representations and can expose institutionalized authorship practices that should be questioned.

Paradoxically, a concern often heard about emphasizing contributions is that they risk diluting individual author responsibility for the overall integrity of a study. The recommendations address this concern by stipulating authorship standards that require each author to be “personally accountable for [their] own contributions and to ensure that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and the resolution documented in the literature.” Thus, having one’s contributions precisely described does not absolve any author of responsibility for the accuracy and rigor of the entire study.

The paper also recommends mechanisms by which publishers can bring a minimum level of standardization to the description of author contributions. In particular, the group advocates for the implementation of ORCID identifiers and the CRediT taxonomy as emerging standards in the industry. While many journals already require specification of author contributions, a more fully integrated system of persistent identifiers (like ORCID iDs for authors and DOIs for articles) connected via a standardized vocabulary of relationships (like the CRediT taxonomy for contributions) will make the information both human- and machine-readable and allow it to be surfaced more easily.

PLOS journals have adopted both ORCID and CRediT since 2016; the roles and ORCID iDs provided by authors are now visible with one click on the author name in the by-line. ORCID information is passed on to CrossRef, which updates ORCID records with authors’ permissions.

In our experience, the CRediT taxonomy has worked well, but the definition of some individual terms could be improved. In particular, those related to data may benefit from some refinement to distinguish generation of data from its subsequent curation. As others examine the possibility of using the taxonomy, we encourage a collaborative approach with CASRAI’s CRediT Committee, the taxonomy steward, to match the needs of different communities.

Not all roles in the CRediT taxonomy immediately qualify a participant for authorship; that qualification is determined by journal policy. To determine who should be an author, PLOS currently follows the recommendation established by the International Committee of Medical Journal Editors (ICMJE) for medical journals which posits that authorship should be associated with a substantive intellectual contribution as well as participation in drafting or revising the manuscript. While PLOS Medicine checks that all four ICMJE criteria are met by all authors, the experience at other PLOS journals indicates that in fields outside medicine, not all authors state they have participated in the drafting or revising of the manuscript. The proposed adaptation of authorship criteria in the current PNAS report, which includes writing as a qualification for authorship but does not require it, aims not to exclude important contributors from authorship. Conversely, the inclusion of writing without other intellectual contribution to a study as a role worthy of authorship may not find acceptance in all disciplines. The intent is not to impose a monolithic approach to authorship, but to accommodate a broad range of community standards transparently. When contributors do not meet authorship criteria, CRediT can also serve to document their precise contributions as acknowledged colleagues, supported by other means of credit like citations of protocols and datasets.

On a new website, the report’s authors commit to reflect upon and improve current authorship guidelines and practices at the journals they represent, and they encourage other journals to do the same. Such introspection and subsequent discussion are timely, as research studies are increasingly large-scale and multi-disciplinary affairs. As more work goes into providing due credit for scholarly contributions like methods development, data collection and data sharing, transparency in authorship roles should advance in tandem.

Competing Interests Disclosure: Veronique Kiermer is an author of the recommendations discussed and Chair of the ORCID Board. Larry Peiperl serves on the ICMJE.

 

Image Credit: Wikipedia

Rare Disease Day Spotlight on PLOS Authors: Open Data Repositories in Practice

Science increasingly involves collaborative research groups, program partnerships and shared learnings to encourage transparency, reproducibility and a responsible transition to a more open way of doing science. Open Science policies and best practices are currently under discussion, definition and development across the wide spectrum of activities that make up the research cycle, from open notebooks, open data and transparent peer review to the interoperability of meta-data and digital identifiers. In particular for open research practices, adoption of emergent and recent policies (i.e. PLOS Data Policy) could be strengthened if accompanied by examples of successful implementation. Examples can serve as a powerful motivator for improved understanding and behavioral change for those confronted with the uncertainties of a more open landscape for the practice and communication of science.

Perhaps it’s a question of making clear to the broad stakeholder community, at all stages and across multiple disciplines, the practical benefit of these polices moving us all toward a more Open Science. It’s not just a theoretical pursuit of Open Science for the sake of being open. The current energy behind Open Science in the European Union, as well as in the United States, stems also from a frustration over wasted resources, time and talent. Practicing Open Science well does enhance reproducibility through improved clarity of methods and reagents, and accelerated reuse of data and code by others.

A Celebration of Open Data

A major benefit of open data is that data can be reused, not only for validation work but also for pushing science forward. Teams of scientists with diverse expertise collaborated to explore preexisting data sets to advance breast cancer research, in the US National Cancer Institute’s Up For A Challenge (U4C) Contest. Finalists in the US National Institutes of Health, Howard Hughes Medical Institute and Wellcome Trust Open Science Prize competition (which included projects by PLOS authors and their related publications) “demonstrated the huge potential for data to be reused to develop new applications and uncover new knowledge,” wrote Robert Kiley, Head of Open Research, and David Carr, Programme Manager, Wellcome Trust, in Figshare’s State of Open Data Report 2017. The report provided insight into how researchers approach publishing their data. In response to surveys asking where they published their data, researchers most commonly did so as an appendix to an article (slightly over 30%) or in a data repository (slightly under 30%), with 20% having published data in a data journal (see the summary infographic).

Open Data Day (March 3, 2018) is an opportunity to showcase the benefits of open data and open data systems, and, according to the grassroots collective’s website, “to encourage the adoption of open data policies in government, business and civil society around the world.” This year, the focus is on four key areas where open data can help solve universal problems: opening research data, tracking public money flows, informing open mapping projects and providing open data for equal development. In Copenhagen, Open Data Day will include announcement of the Danish Open Data Award and in London activities are planned related to Open Science and reproducible research. Participants in The Philippines will benefit from a roundtable discussion on open research as it applies locally and globally. There are no shortage of ideas and data sources for Open Data Day.

Publisher Actions

PLOS took a leadership position in open data in 2014 with our strengthened Data Policy, and since 2015 our journals maintain a list of recommended repositories to help authors share their data. When we assess repositories for inclusion in our list we are guided by criteria that meet the FAIR principles on open data. We consider this our responsibility as a publisher. The FAIR guiding principles state that beyond making data open as an important component in the data ecosystem, data also need to be Findable, Accessible, Interoperable and Reusable. For inclusion on PLOS’ list of recommended repositories, several criteria were developed, some of which are listed below. For a more complete description of repository criteria, visit the EveryONE blog on Open Data Day!

  1. Datasets should be available at no cost. All PLOS articles are available to readers free of charge and we believe cost should not be a barrier to access either the scientific literature or accompanying datasets. Repositories are not considered for our recommended list if they charge readers access or subscription fees.
  2. Repository with stated licensing policies should offer CC 0 or CC BY licenses (or equivalents), for maximum reproducibility and reuse.
  3. To ensure that datasets will be permanently accessible at the specified location, repositories must issue a stable identifier at publication, such as a digital object identifier (DOI) or an equally robust accession number.
  4. FAIRsharing.org works with a community of journals, funders and databases in support of standards, polices and educational material to enable funders, librarians, journals, researchers and developers to thrive in the open data world. The repository chosen by PLOS authors should have an entry created in the FAIRsharing database, to allow it to be linked to the PLOS entry.

In addition to considering the PLOS Data Policy and providing a Data Availability Statement for their individual data and datasets, selecting the appropriate data repository is an important part of a researcher’s overall experimental and data plan. To assist authors in choosing the best repository, in addition to the current list of recommended repositories, the complete list of repository criteria will soon be available on PLOS journal websites.

Researcher Participation

What is the practical importance of open data? As one specific example we can look to a coincidence of timing: February 28 is Rare Disease Day. Rare diseases constitute a group of more than 6,000 different diseases and affect more than 300 million people worldwide. To put this number in perspective, 1 in 20 people live with a rare disease in their life, according to EURORDIS, an alliance of over 700 patient organizations from nearly 70 countries in Europe. In light of Rare Disease Day’s close temporal alignment with Open Data Day, we highlight a selection of articles on rare diseases published at PLOS that utilize a variety of repository options to best make their associated data available. These are examples of authors doing the right thing to advance rare disease research, collective knowledge, and future therapeutic interventions.

  • Sorenson et al. (2017) used the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) repository to store their genomic and transcriptomic data relating to fibrolamellar hepatocellular carcinoma (a rare variant of liver cancer).
  • Guilhem et al. (2017) used the Data Archiving and Networking Services (DANS) EASY repository to deposit data files from their research on hereditary hemorrhagic telangiectasia (a disease leading to abnormal blood vessel formation). The EASY repository is one of PLOS’ recommended repositories.
  • Andersen et al. (2017) carried out a bibliometric analysis on multiple myeloma research (a cancer of white blood cells). Few, if any, dedicated repositories exist exclusively for bibliometric work, so data underlying work like this can be deposited to a discipline-independent repository—in this case Figshare. While subject-specific repositories are preferred, in cases where they are not available authors may use a cross-disciplinary repository.
  • Hytönen et al. (2016) published genome data relating to their work on three rare bone diseases in the European Nucleotide Archive (ENA) hosted by EMBL-EBI.
  • Piersanti et al. (2015) also used the GEO repository to store their microarray data on gene expression changes in brain cells following infection with viral vectors. This work contributes to the development of gene therapy that could be used in the treatment of several rare diseases affecting the brain.

The theme for Rare Disease Day this year is a carry-over from last year—research. If scientists working in these disease areas make their data open and available for reuse and re-examination, they can extend the impact of their efforts and may open a window to unrealized diagnoses, therapies and perhaps even cures.

In the pursuit of Open Science, practical and even incremental change has the power and potential to bolster momentum and encourage a spirit of collaboration that ultimately brings about large-scale cultural shift. We have seen evidence of this most recently with the preprint movement in biomedical and life sciences. Making open data the norm, whenever possible, and following FAIR sharing principles are additional practices that, like preprints, have the capacity to transform the work and culture of science.

Join the PLOS Communications LinkedIn Group to stay up to date on author interviews, research and organisation highlights.

PLOS and Cold Spring Harbor Laboratory Enter Agreement to Enable Preprint Posting on bioRxiv

Editor’s Note: This press release also appears on the Cold Spring Harbor Laboratory Newsstand.

Public Library of Science (PLOS) and Cold Spring Harbor Laboratory (CSHL) announce an agreement that enables the automatic posting of research articles submitted to PLOS journals on bioRxiv, CSHL’s preprint server for the life sciences. This collaboration between bioRxiv and PLOS empowers authors to share their work on a trusted platform before peer review, accelerating the pace of biomedical research.

PLOS is committed to enhancing the integrity of preprints and confidence in them as research outputs. PLOS will perform initial manuscript screening compatible with bioRxiv standards, covering scope, plagiarism, and previous publication, as well as other basic ethical and technical criteria. Articles will then post automatically to the bioRxiv server without the need for additional actions by the author. By allowing their submission to be posted on bioRxiv, authors accelerate the dissemination of their work and invite commentary by a broader community, which the PLOS editors will evaluate as part of peer review. Authors may choose to opt-out of this process when they submit papers to PLOS.

PLOS and CSHL also plan to work collaboratively towards solutions for preprint licensing that enable broad dissemination and reuse; the addition of badges to papers which signal that additional services for authors have been performed by PLOS and potentially other organizations; submission and screening standards in the biomedical sciences; and the implementation of new forms of manuscript assessment to augment or improve current methods of peer review.

“The opportunity to partner with a like-minded organization such as CSHL to realize a longstanding PLOS goal is a strategy for us moving forward,” said Alison Mudditt, Chief Executive Officer, PLOS. “A key part of our mission has always been to act as a catalyst, not only demonstrating the viability of new models through our own operations but also supporting them elsewhere. In the case of preprints, we can magnify our impact by partnering and helping shape how that future develops for all posted content on bioRxiv.”

The bioRxiv preprint server was initiated by CSHL in November 2013 and received major support in May 2017 from the Chan Zuckerberg Initiative. It currently hosts over 20,000 manuscripts from bioscientists in 104 countries and has a rapidly rising rate of submission.

“Helping researchers communicate at the speed of science has been the principal goal of bioRxiv since its launch,” said John Inglis, co-founder of bioRxiv at CSHL, “and over one hundred thousand authors have taken advantage of that opportunity. We are delighted to have reached an agreement with PLOS to offer that benefit to tens of thousands more authors who are ready to share their work and open it up to the community response and feedback that bioRxiv makes possible.”

“This collaboration highlights PLOS’ commitment to the growing preprint movement in the biological sciences and bioRxiv’s support for scientists’ desire to share their research freely and widely,” said Louise Page, Chief Innovation Officer, PLOS. “The screened submissions to bioRxiv from PLOS illustrate how publishers can drive preprints and create new outputs in response to researcher-led initiatives that increase transparency and promote early dissemination of science.”

Retrospection and Direction: A Q&A with Peter Walter

“In our panel it is the stated and adhered to policy that we will not consider where a paper is published. Rather, in our evaluations we assess its real impact in a field. Change of this sort and defiance of the status quo is badly needed in all committees and panels that make decisions that impact the future of our next-generation scientists, even if it entails a bit more work.”-from “On Publishing and the Sneetches: A Wake-up Call?

These are words written by Dyche Mullins and Peter Walter, in 2016. Walter is one of this year’s Breakthrough Prize in Life Sciences recipients and a leader in the scientific community not only for his scientific investigations but also for his continuous dedication to mentoring and teaching younger scientists, and for taking a progressive but circumspect stand on issues that impact the quality of scientific life. As a follow-up to last month’s Breakthrough Prize overview, PLOS interviewed Walter on some of the broader issues surrounding his work and publishing in general. Walter has strong opinions related to impact factors and Open Access; he remains open minded regarding preprints. His valuable and modest insights are below, with minimal editing.

 

Image courtesy of UCSF

PLOS: Which of your PLOS articles were most impactful for your work related to the prize, and why?

Walter: The Brickner and Walter paper [“Gene Recruitment of the Activated INO1 Locus to the Nuclear Membrane”] stands out, in my view, as this story organically grew out of our ongoing work on the unfolded protein response, yet opened an entirely new field: that the physical location of a genetic locus inside the nucleus can be dynamic and affect gene regulation. This paper also served to seed Jason Brickner’s independent career: Shortly after this publication, he was recruited to Northwestern University. Since then, his lab has vastly expanded upon this topic and he is now internationally recognized as one of the very leaders of cell biological mechanisms that control transcriptional memory.

PLOS: Do you have a personal favorite among your PLOS publications? Perhaps one that was either controversial or that sparked scientific debate/conversation at time of publication?

Walter: The Pincus et al. paper [“BiP Binding to the ER-Stress Sensor Ire1 Tunes the Homeostatic Behavior of the Unfolded Protein Response”] is one of my all-time favorites: It demonstrates the power of computational modeling for generating new hypotheses and then experimentally testing them. In this case, modeling suggested experiments that we would not have thought of otherwise, and the results showed beyond reasonable doubt that BiP dissociation from the ER-resident stress sensor Ire1 is not the regulatory switch that activates the UPR. The work inspired rethinking, and it is now clear that in both, yeast and metazoans, unfolded proteins per se are agonists that bind directly to the stress sensors Ire1 (and PERK). Despite the seminal insights provided in this publication, the field remains attached to the notion that BiP dissociation is causal for Ire1 activation—providing an important insight into the surprisingly inflexible thinking of established scientists (including myself, at times…).

PLOS: In your experience speaking with the public or non-scientists in general, what concept(s) about the unfolded protein response pathway do they typically find most interesting or resonates strongly?

Walter: Trained as a chemist, I personally cherish the many unorthodox molecular mechanisms by which the unfolded protein response regulates ER [endoplasmic reticulum] homeostasis. However, beauty at a molecular scale is mostly appreciated by aficionados and only rarely resonates with the public and non-scientists. We are now in a most fortunate era where our work tangibly links to a broad spectrum of diseases, including cancer and neurodegeneration, where our knowledge has become foundational to the exploration of new treatment strategies. As such, our work provides a wonderful platform on which to demonstrate the power and value to society of curiosity-driven research in which we seek understanding of how healthy cells work in disease-agnostic approaches and then use that knowledge to learn what goes wrong in disease and how to fix it.

PLOS: Our readers span the range of career stages. What is your opinion of the value or challenge to publishing in Open Access journals?

Walter: The challenge for the next generation of researchers is to break out of the stranglehold that the for-profit publishing industry has put on our community. The misguided emphasis on abstruse metrics, e.g., impact factor, in addition to the poorly transparent review procedures by our “vanity journals” and their hand-me-down cousins distort our most fundamental values. My colleagues and I have clearly laid out our views on this topic [in addition to the ASCB Newsletter referenced in the opening quote see the commentary co-authored with Martin Raff and Alexander Johnson, entitled “Painful Publishing”].

Just as with scientific models, old patterns are hard to break. We need our young scientists to recapture control. The myth that one can only get a job/grant/promotion with [high impact factor journal] papers has been debunked internationally (e.g., Jason Brickner and Liang Ge in China). The challenge ahead is to spread the word and make sure that no young scientist who made an important discovery will ever be held back by the name of the journal where ground breaking findings were published.

“Open-access and publishing (to “make public”) are synonymous in my view, and scientist-run non-profit open-access journals that manage to deliver consistently customer-friendly, transparent, and constructive reviews and timely feedback are destined to lead the movement.”

PLOS: Finally, have you or collaborator ever posted a preprint? If not, would you consider doing so, and why/why not?

Walter: To date, we have posted two preprints—I consider them experiments with the new forum. For now, I remain agnostic to the process. Science is moving fast enough for my taste (if not too fast sometimes), and I remain unsure whether an invitation to put un-reviewed stories out there will be that beneficial overall. Many things will need to be worked out: Does a preprint establish priority for a discovery? How will “better-first-and-sloppy-than-second-and-who-cares” science be regarded by the community? How will we deal with predatory scientists who appropriate ideas and results from our students or postdocs and then race to scoop them? Also, personally, I read most papers only once, and it is the first impression that sticks. The concept of looking at evolving versions rather than a final, best-as-can-be product is rather vulnerable in my opinion. We’ll see; I remain open-minded.

 

Editor’s Note: Some of the issues Walter raises above are covered in the PLOS Computational Biology article “Ten simple rules to consider regarding preprint submission.” Major funders including Wellcome Trust and NIH, and publishers such as PLOS, PeerJ and eLIFE are actively working on external policies and internal practices to facilitate authors’ use of preprints; PLOS Biology has formalized a policy whereby complimentary studies (those submitted within six months of publication or preprint posting and already addressing the same question) will be considered for publication. Newly minted scientists are encouraged to use preprints as a way of, as Walter recommends, recapturing control. The cartoon above on use ideas for preprints from the group PREreview is available for download on figshare.

 

****************
Peter Walter is Professor, Department of Biochemistry and Biophysics at the University of California, San Francisco (UCSF) and Investigator, Howard Hughes Medical Institute. He served as President of the American Society of Cell Biology in 2016 and as Department Chair in Biochemistry and Biophysics at UCSF from 2001 until 2008. He is an elected member of the German Academy of Natural Scientists Leopoldina, the US National Academy of Sciences, the National Academy of Inventors, the American Association for Arts and Science, and the European Molecular Biology Organization. He is recipient of multiple awards including the Breakthrough Prize in Life Sciences (2018), Vilcek Prize in Biomedical Science (2015) and Lasker Basic Medical Research Award (2014). He is co-author of the widely-used textbooks Molecular Biology of the Cell and Essential Cell Biology and alumnus of the Djerassi Artist-in-Residence program.

 

Image Credit: Peter Walter lab; University of California, San Francisco

The Editor’s Note was updated on 1/30/3018 to indicate the policy at PLOS Biology is formalized and to provide the link to the Criteria for Publication on the journal’s information page.

Transformational Work Over a Career: Breakthrough Prize in Life Sciences for PLOS Authors

How do you measure lifetime achievement? It’s not by assessing individual works but by consideration and evaluation of consistent contributions to a discipline over time. Contributions may be independently substantial, but in science, a researcher’s impact is more often made through gradual insights that accrue meaning as a discipline advances. Over the course of a career, creative thinkers and leaders in science can significantly influence a field, and humanity more broadly.

A recently established award provides one measure of lifetime achievement for life sciences—the Breakthrough Prize. Established in 2013, the Breakthrough Prize in Life Sciences honors “transformative advances toward understanding living systems and extending human life.” The prize encourages celebration and recognition of “outstanding minds.” Those scientists who “think big, take risks and have made a significant impact on our lives” each receive $3 million for their work that provides fundamental and far-reaching understanding of biological mechanisms.

The Breakthrough Prize in Life Sciences is designed to bring public attention, financial reward and a bit of glamor to outstanding scientists who over the course of their careers have changed the way scientists think about basic principles. Through a central component of the award, the impact of honored scientists’ work is extended to a broader general audience. Recipients are invited to present public talks – with recorded lectures made available to the public – “allowing everyone to keep abreast of the latest developments in life sciences, guided by contemporary masters of the field,” according to the Breakthrough Prize website. Breakthrough Prizes are also awarded in fundamental physics and mathematics.

This year, five scientists received life sciences prizes; collectively these creative thinkers have published 30 papers in PLOS journals (13 in PLOS Biology, 16 in PLOS ONE and one in PLOS Genetics), providing their work to the global community free of access and reuse restrictions. The 2018 Breakthrough Prizes in Life Sciences were awarded to:

    • Joanne Chory, for pioneering work elucidating mechanisms by which plants “optimize their growth, development, and cellular structure to transform sunlight into chemical energy.” Chory has published work with PLOS on how the circadian clock coordinates plant growth through synchronized gene expression, on growth patterning in the model plant system Arabidopsis and a novel approach to identify required gene regulatory elements, and on diurnal and clock-regulated transcription factors and their target cis-regulatory elements in additional plant models. The Chory team first published with PLOS in 2004.
DOI: 10.1371/journal.pbio.0060225
    • Kim Nasmyth, for elucidating the “sophisticated mechanism that mediates the perilous separation of duplicated chromosomes during cell division and thereby prevents genetic diseases such as cancer.” Nasmyth’s work in PLOS Biology covers the influence of excess heterochromatin (highly packed DNA) segments and cohesin protein accumulation on sister chromatid separation, and that the protein shugoshin protects centromeres until chromosomes are ready to separate. He and colleagues from the Research Institute of Molecular Pathology, in Vienna, Austria, first published with PLOS in 2005.
DOI: 10.1371/journal.pbio.0030086
    • Don Cleveland, for characterizing molecular mechanisms involved in the pathogenesis of inherited Amyotrophic Lateral Sclerosis (ALS), “including the role of glia in neurodegeneration, and for establishing antisense oligonucleotide therapy in animal models of ALS and Huntington disease.” Cleveland’s work using post-mortem human tissue samples and transgenic mice showed that mRNA oxidation is an early event associated with motor neuron deterioration in ALS, and possibly other neurological diseases. His work on the enzyme superoxide dismutase, responsible for breaking down toxic, charged oxygen molecules known as superoxide radicals, included assessing the therapeutic effect of human fetal spinal neural stem cells grafted into the lumbar spine of transgenic rats presymptomatic for ALS. Cleveland and his many colleagues first published with PLOS (twice) in 2008.
DOI: 10.1371/journal.pone.0042614

Two scientists, Kazutoshi Mori of Kyoto University, Japan, and Peter Walter of the University of California, San Francisco, received Breakthrough Prizes for their independent work on “elucidating the unfolded protein response, a cellular quality-control system that detects disease-causing unfolded proteins and directs cells to take corrective measures.” The unfolded protein response (UPR) is a phylogenetically conserved endoplasmic reticulum-to-nucleus signaling pathway that senses unfolded proteins early on in the biosynthetic process, and then transmits that information to the cell nucleus. This information stimulates a genetic transcription program designed to re-establish cellular homeostasis by increasing the intracellular machinery and processes that help proteins fold.

    • Various cellular insults, writes Mori in his team’s PLOS Biology article, “including exposure to pharmacological agents that perturb protein folding, genetic mutation of ER chaperones or chaperone substrates, viral infection, metabolic demands, and even normal differentiation and function of professional secretory cells” impact the UPR in similar and unique ways. His earlier work published with PLOS examined the differential influence of low-level, severe and chronic stress on UPR activation. More recently, Mori has extended his investigations to the development of a high-throughput screening assay that incorporates a molecular biosensor to identify small molecule activators of the endoplasmic reticulum stress response in malignant glioma cells.
DOI: 10.1371/journal.pbio.0040374
    • Since 2004, Walter has published 12 papers with PLOS covering the role of endoplasmic reticulum expansion in the UPR in yeast; a teasing out of the relationship between cell proliferation, cell death and protein folding in human embryonic kidney cell lines; and the importance of targeting a key transcription factor to the cell membrane, to provide the appropriate cellular response to protein folding status in bacteria. Walter’s first two papers published in PLOS Biology, presented as a series together with a Synopsis, described amplitude adjustment signals for the UPR in yeast. Prior to this work, the UPR was thought to largely be a binary, on or off, function.
DOI: 10.1371/journal.pone.0003528

Perhaps more than other prize recipients, Joanne Chory was surprised by her inclusion as an awardee, explaining to the San Diego Union-Tribune, “this prize has been more associated with biomedical things.” The award may be a nod to the relevance of Chory’s current work to climate change. Those interested in the connection between mechanisms of sunlight and clock-regulated plant development to global warming may find of interest the Ecological Impacts of Climate Change Collection and newly launched Responding to Climate Change Channel.

International lifetime achievement awards are given in many fields, including economics, music and physical sciences, among others. With support of founding sponsors Mark Zuckerberg, Priscilla Chan, Sergey Brin, Anne Wojcicki and Yuri Milner, life sciences has another prize of its own, with a musical perk. This year’s awardees were honored at a gala hosted by Morgan Freeman with a performance of “See You Again” by Wiz Khalifa and Nana Ou-Yang.

 

Hero image credit: breakthroughprize.org

Unique Opportunity for Communication of Cell Motility Research: ASCB Celldance Videos

Cell biology research relies heavily on all types of microscopy to capture – for visualization and analysis –  cell structures, cell movements and cell-cell interactions. For the eighth consecutive year, the American Society for Cell Biology (ASCB) has supported interested cell biology labs in the creation of video projects describing their work for interpretive and educational value.

Posters advertising past Celldance videos, courtesy of ASCB

The Celldance video program provides participating labs financial support to develop video stories of their cell motility research, in addition to post-production assistance for sound and editing services. PLOS supports this ASCB Public Information Committee program that helps showcase the value of basic research, aids in communicating complex scientific concepts to the public and provides scientists a unique opportunity to fine-tune their communication skills.

This year, two labs working in collaboration and a third lab developed Celldance videos for presentation at the joint ASCB|EMBO 2017 Annual Meeting. Dyche Mullins’ lab at the University of California, San Francisco, in collaboration with the Lillian Fritz-Laylin lab at the University of Massachusetts, Amherst, created a video honoring foundational research on actomyosin and muscle movement by Albert Szent-Gyorgyi and describing how the molecules that constitute the cell’s skeleton, or cytoskeleton, influence the way a cell moves through both wide open and narrow matrices. The Guillaume Duménil lab at the Institut Pasteur created a video that emphasizes the value of cohesive basic and clinical research programs and describes the group’s studies on infection caused by the Gram-negative bacterium Neisseria meningitidis, responsible for meningitis and sepsis.

One of the reasons the Mullins lab submitted work to the ASCB Celldance contest was to be able to convey the fundamental importance of molecular and cellular motion to a general audience. Mullins appreciates that fundamental problems in cell biology are often challenging to explain to non-specialists. Article types such as PLOS Research Matters, for both PLOS Pathogens and PLOS Biology, can help in this regard, by enhancing public understanding of science and the benefits of basic research to public health, society, life, and the environment. In addition, “A short film can explain concepts that are extremely difficult to convey in a brief elevator conversation or even a long lecture,” says Mullins.

Paring down several initial ideas the group wanted to convey was key to creating a coherent narrative. The team decided to begin with the importance of molecular and cellular motion, then to introduce the idea that “this is a universal feature of life, even microscopic life living in ponds,” says Mullins. Once the images were in place, the team experimented with audio voice-overs but eventually settled on captions to guide the viewer through the story. “It’s like an old-fashioned silent movie,” he says.

We Know Life by Motion; Mullins/Fritz-Laylin

Sometimes even scientists need help understanding what they see under the microscope. Fascinating 3D lattice light sheet movies of crawling cells from the Fritz-Laylin lab were also motivation for wanting to participate in Celldance. “There is so much information in these movies that we had a hard time understanding what we were seeing,” says Mullins. By enlisting the help of visualization experts, the research teams could “suddenly see a wealth of new details. We were no longer seeing cells as ghostly apparitions, barely discernible at the business end of a microscope, but as real, three-dimensional beasts. We wanted to share this experience with a wider audience.”

 

Neisseria Meningitidis: At Home in Human Capillaries; Duménil

 

 

 

 

 

Says Duménil of his Celldance experience, “From a scientific point of view, I find it useful to see an infection as a story that starts with the encounter of the pathogen and its host, the story develops with the different stages of the infection, cellular barriers are crossed, cells invaded, organs infected and the outcome can be happy or sad.” For Duménil, the opportunity was not only about explaining science to the public in an accessible format. It was also, he says, “an opportunity to show the people who do the actual research and our lab environment at the Institut Pasteur.” For more on the work of the Duménil lab and video, see the upcoming partner Celldance blog on Speaking of Medicine.

Neisseria Meningitidis: At Home in Human Capillaries; Duménil

An Open Letter to the Community from PLOS CEO, Alison Mudditt

As the new PLOS CEO, I’ve spent my first months assessing the organization and planning for a thriving future. We are in the midst of shaping our next innovative steps in pursuit of maximal openness and transparency in research communication, and assessing what changes we need to make as an organization. Some of these changes will likely go unnoticed outside of PLOS. Others may cause speculation. For clarity and transparency’s sake, I’ve chosen to write an open letter to the communities PLOS serves, so we can encourage open dialogue and so that you can share in our continuing evolution.

Since the very beginning PLOS has been a publisher, advocacy organization and innovator. Our roots in innovation run deep; from mobilizing scientists’ desire for free and Open Access to the literature and building PLOS ONE to the journal it is today, to pioneering Article-Level Metrics as an alternative to journal impact factors and launching our forward-thinking data policy to positively influence credit, recognition and reproducibility.

One of our top priorities this coming year is to improve the author experience since our authors are at the center of everything we do. Among their top concerns are ‘time to first decision’ and ‘time to publication’. We share their concerns and are committed to reducing this time as much as possible across all our journals. We are embarking on an ambitious plan to reinvigorate PLOS ONE’s editorial board, increase the efficiency of reviewer assignment, and develop and deploy new analytical capabilities to ensure no manuscript is unnecessarily stalled.

Part of this initiative will involve changes around the workflow system – Aperta™ – we set out to develop several years ago with the goal to streamline manuscript submission and handling. At the time we began, there was very little available that would create the end-to-end workflow we envisioned as the key to opening research on multiple fronts. But the development process has proved more challenging than expected and as a result, we’ve made the difficult decision to halt development of Aperta. This will enable us to more sharply focus on internal processes that can have more immediate benefit for the communities we serve and the authors who choose to publish with us. The progress made with Aperta will not be wasted effort: we are currently exploring how to best leverage its unique strengths and capabilities to support core PLOS priorities like preprints and innovation in peer review. This will be part of our planning for 2018.

Innovation is not unlike science itself; there are hurdles to success, determination is integral to advance in one’s work, and knowing when to set aside any particular project to move forward is key. What I, and hopefully others, appreciate is that PLOS continues to be an organization willing to take risks in order to best serve scientific communities across the full spectrum of topics and interests.

Moreover, it’s our goal to optimize the openness and integrity of the publication process by ensuring that research outcomes are discoverable, freely available and reusable and that science communication is constructive, transparent and verifiable. You will be hearing more from me on our core initiatives in early 2018.

PLOS is steadfast in our commitment to our mission and communities and I look forward to sharing our milestones with the scientific and publishing community in 2018 and beyond.

Sincerely,

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.

 

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

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.

Sider