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. 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.

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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:

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.


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.

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 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


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;
  • [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;
  • 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;
  • 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;
  • 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;
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, 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.


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;


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 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 homepage ( 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

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; to learn more about the Day of Action visit

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.


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