Plos

Spreading the Word: PLOS Advances Research Through Media Partnerships

Last year, PLOS helped more than 2,300 articles receive media coverage in high-profile outlets including The New York Times, the BBC, National Geographic, Scientific American and The Washington Post. How do we do it? For starters, our press team sends out on average one press release per day, garnering the attention of the 1200 journalists on our press list, plus members of the media who haven’t heard of us yet.

But for us to make sure your research gets the recognition it deserves from other researchers, potential funders, and policy makers, our dedicated media team also leverages a robust network of partnerships to connect science and the media.

Science for non-scientists

Though all PLOS research is Open and accessible to everyone, many readers depend on journalists to distill complex scientific concepts for broader consumption. An important link in the transformation of Research Article to NY Times cover story are Science Media Centers (SMCs) which work with journalists to get the public access to the best scientific evidence and expertise.

Through SMCs, journalists can find “sources” or vetted experts in a given field to help add context to the research they’re reporting on. Some SMCs, such as SciLine, also offer fact sheets summarizing popular topics that have been reviewed and verified by experts.

We have been working with SMCs in the UK, US, Canada, Australia, New Zealand and Germany for over a year, for example by providing information that helps SMCs spread the word about PLOS work even further. In Europe, we also collaborate with the European Science Media Hub, part of the European Parliament, whose work helps facilitate the transfer of knowledge and training between the European Parliament, the scientific community, and the media.

Our partnership with these organizations is also helping us to shape best practice for communicating research, especially for new scholarly outputs like preprints.

Leveraging your network and your expertise

Perhaps the best place to seek promotion and recognition for your work is your own institution. Already, we work with top-tier institutions such as MIT, Harvard University, University of Cambridge, University of Oxford, the National Institutes of Health and more to help them promote the amazing research being done by their affiliated PLOS authors. We’re hoping to expand this program further, but even without formal partnership, we encourage all authors to contact their institution’s press office when their research is accepted for publication – your colleagues’ networks can be a huge asset to your career.

For authors who are keen to be hands-on in disseminating research, we also recommend contacting our partner Science Trends. This free platform allows authors to write their own “self-directed press release” in under 500 words which is then published on Science Trends and on social media to an audience of 500,000 followers. You can find more information on our website.

We’re dedicated to providing the best experience for our authors, pre and post-publication. We’ll continue innovating and promoting your work and we want you to feel empowered to do so as well. Check out our media toolkit for tips on publicizing your work, speaking to the media, and stepping up your social media game. Of course, our media relations team, Beth Baker and Charlotte Bhaskar, are always happy to help – contact them at onepress@plos.org.

 

The origins of avian flight, thermostat battles heating up, and other PLOS research making headlines in May!

New research from PLOS Computational Biology uses robots, reconstructed model dinosaur feathered forelimbs, and juvenile ostriches to simulate the first potential avian flight stroke in dinosaurs. This study shows that running on the ground naturally stimulates a flapping motion in feathered forelimbs, and suggests that this flap may be the origin of avian flight.

Author Zhao explains: “Our work shows that the motion of flapping feathered wings was developed passively and naturally as the dinosaur ran on the ground…although this flapping motion could not lift the dinosaur into the air at that time, the motion of flapping wings may have developed earlier than gliding.”

See videos of the robots and young ostriches strutting their stuff, and read more on CNN and Gizmodo.

http://blogs.plos.org/plos/files/2019/06/journal.pcbi_.1006846.s008.mp4

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A new study from PLOS ONE found that that in a test room set to temperatures ranging from 16.19 C/61.14 F -32.57 C/90.63 F, female study participants performed best on math and verbal tests at the higher end of the temperature range, while male participants performed most strongly on the same tests at lower temperatures. This is the first experimental research supporting anecdotal and survey responses indicating women tend to prefer warmer room temperatures than men, by showing that temperatures can affect both comfort and performance.

Authors Kajackaite and Chang summarize: “In a large laboratory experiment, over 500 individuals performed a set of cognitive tasks at randomly manipulated indoor temperatures. Consistent with their preferences for temperature, for both math and verbal tasks, women perform better at higher temperatures while men perform better at lower temperatures.”

Check out more of this hot topic as featured on the Guardian, the New York Times, Fox 5 News (with a video featuring author Tom Chang), and the Atlantic.

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Along a similar vein(!), new research from PLOS Medicine shows that the medical care received by heart failure patients in the UK may have important gaps around diagnoses, insufficient follow-up after hospitalisation, and improperly-prescribed dosages, among other issues; these problems significantly affected women and older people.  

Read more on the Daily Mail and the Telegraph.

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A 2016 mass die-off of puffins and other seabirds in the Bering Sea is reported in a new PLOS ONE study by Timothy Jones of the citizen science program COASST at University of Washington, Lauren Divine from the Aleut Community of St Paul Island Ecosystem Conservation Office, and colleagues. Up to 8,500 puffins and auklets may have died in this event, which appeared to be due to starvation; the authors suggest that climate shifts may have resulted in a lack of prey. Read more about this story on Vice, Discover Magazine, and Scientific American.

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Finally, in lighter news, a new study from PLOS ONE showed that wolves behave more prosocially towards their fellow pack mates than do pack dogs during a touchscreen-based task that allowed individual animals to provide food to others–though the study did not look at the behavior of pet dogs.

Author Rachel Dale notes: “This study shows that domestication did not necessarily make dogs more prosocial. Rather, it seems that tolerance and generosity towards group members help to produce high levels of cooperation, as seen in wolves.”

Check out further coverage on PBS News and Motherboard by Vice.

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Image captions and credits

  1. Seven-rigid-body system of Caudipteryx. The simplified rigid body system illustrates the mechanism of moving parts, main body, wings, legs, neck and head, and the tail of the Caudipteryx. The masses of all parts are represented by lumped mass points and the muscles at the joints are replaced with springs (As damping coefficient does not significantly affect the natural frequency, we simplified the joints which are composed of tendons, muscles, ligaments and soft tissues as purely elastic springs with no damping). Different effective masses of these seven primary modes of the simplified Caudipteryx show different possibilities to be excited. (Talori et al, 2019,  PLOS Computational Biology)
  2. Video: Observation on the juvenile ostrich. The forced vibrations of the wings of the young ostriches are easily found when they run on the ground. (Talori et al, 2019,  PLOS Computational Biology)
  3. Carcasses of tufted puffins, October 2016. (Aleut Community of St Paul Island Ecosystem Conservation Office)
  4. Touchscreen test (Dale et al., 2019, PLOS ONE)

 

Looking Good: Tips for creating your PLOS figures graphics

Enhance your research with tips and tools from the experts on the PLOS Production Team. This post is part of our new Format for Success series where we’ll share advice for generating figures and graphics that make submitting a breeze. Stay tuned for more. 

We know that preparing graphics files can be one of the most challenging parts of submitting your hard work to a publisher, when you would rather be observing in the field, experimenting in the lab, or conversing with the community. Like you, we want your research to shine and be noticed by your peers, adding to the scientific discourse and fostering collaboration in and across disciplines.

To help you create the best images possible and ensure a smooth article production experience, we’ve put together our top tips, distilled to a few major areas, for assessing your graphics files during submission:

  • Consider raster images vs vector imagesRaster images are made of pixels. A pixel is a single point or the smallest single element in a display device. Vector images are mathematical calculations from one point to another that form lines and shapes, which adjust to fit a monitor display and zoom.

Our journal article pages use raster graphics for in-article figure display, the lightbox figure viewer, and carousel thumbnails.  Raster graphics are easier to create, store, and transfer across platforms, but limit resolution to 600 dpi. Alternatively, vector graphics are only available in the article PDF accessed online, but will result in a more detailed image at high zoom.

  • Choose a resolution between 300 and 600 dpi – Effective resolutions below 300 dpi (dots/pixels per inch) often result in a blurry, jagged or pixelated image that is not optimal to publish, and resolutions above 600 dpi frequently must be resized or rescaled. We are required by the PLOS publishing platform, and community indexes like PubMed Central, to ensure content adheres to these resolutions.
  • Combine multi-panel images – Often, it’s useful to exhibit a Part A, Part B, and Part C, all within one figure image. To create a multi-paneled figure from individual images, we suggest using a presentation program like PowerPoint, Word or GIMP to arrange your panels, create labels, and scale or size your figures. Multi-paneled figures need to fit into a single page or be broken apart into separate figures in order to publish clearly and accurately.
  • Flatten image layers – Unflattened images can incorporate alpha channels, which include a transparent layer potentially containing “junk”, “artifacts”. Sometimes, an unflattened image can also render a figure into a complete black or white rectangle, obscuring all your content. We recommend that you flatten your graphics to combine all the layers into a single background layer, so we can ensure the quality of the output equals your intent.
  • Compress file size with LZW compression – Data compression helps to reduce file size and also decreases time required to download and upload content. With compressed files, we can help you reduce the size of your article PDF, improving a researcher’s ability to access your work and send it to colleagues.

Using PACE

To help you assess your figure images, PLOS also offers authors a free, web-based imaging review tool, PACE, that evaluates figures against our platform requirements and fixes the most-common image issues, detailing any changes made, or informs the user what outstanding issues may exist.  PACE compiles two, online review options in the form of typeset page mockups to give users an idea of how the uploaded image would appear in the final article. To use PACE, simply register with your email address: https://pacev2.apexcovantage.com.

Similar to undertaking a scientific protocol, PLOS’s production team follows specific rules to ensure that the accepted content is correctly transformed to XML and PDF in order to publish accurately in our journal sites and syndication targets. In short, graphic images must generally conform to the following:

  • File format – TIFF or EPS
  • Dimensions – Width: 789 – 2250 pixels (at 300 dpi). Height maximum: 2625 pixels (at 300 dpi).
  • Resolution – 300 – 600 dpi
  • File size – 10MB or under
  • Figure files naming – Fig1.tif, Fig2.eps, and so on. Match file name to caption label and citation.
  • Caption – Place within the manuscript as simple text, not within the figure file

We’ve posted additional graphics recommendations, as well as instructions for exporting graphics from specialized software, here: https://journals.plos.org/plosone/s/figures.

We hope these suggestions make figure preparation even easier so you can spend more time advancing your field and we can publish your work faster than ever.  We encourage you to email us at figures@plos.org with further questions.

PLOS welcomes the revised Plan S guidelines

As a fully Open Access publisher entirely ready to support cOAlition S-funded authors, we have always been in a position to give our support to this bold initiative, and entirely agree that the driving principles and overall objective of Plan S have not been lessened or changed. cOAlition S has clearly listened to constructive suggestions from the community, and there is now enhanced scope for continued community dialogue, alongside the forward momentum. There are a number of revisions which we recognize will make the transition easier for the community, and which clarify or acknowledge other important factors, such as:

  • Diversity of models underpinning OA – The clarification that neither Plan S nor OA insists on the APC/publication fee model is a key refinement. While this has been a dominant model of OA publishing (including ours) in the Global North, it is absolutely necessary for any OA policies, plans, or mandates to be clear that OA is the outcome for research, not a single or specific business model;
  • Commitment to research assessment based on intrinsic merit – PLOS is an active member of DORA and appreciates the emphasis on changing the reward and incentive system of research. The OA movement has always operated closely with movements to improve the culture of research, and so we welcome this acknowledgement;
  • Preprints and peer review – PLOS advocates the posting of preprints to accelerate sharing of knowledge and welcomes cOalition S’s  “strong encouragement” for the early sharing of research through preprints while acknowledging that preprint posting alone is not a route to Plan S compliance. The value of high quality peer review as a “significant addition of value to scholarly communication” as emphasized in the Plan S Rationale is recognized at PLOS and was a driver in our move to offer published peer review, giving authors and reviewers more choices about how they publish and claim credit for their work.

The timeline shift for Plan S implementation to 2021 will be helpful to gain even more community support for the initiative. But we (along with many other publishers) remind the community that PLOS is already 100% Plan S compliant, and our suite of seven journals is available immediately for your cOAlition S-funded work  in most scholarly disciplines relevant to Plan S.

PLOS was founded on the principle that scholarly knowledge is a public good. We welcome the bold move of funders aligned behind the fundamental principle that no scholarly publication should be locked behind a paywall.

Depositing and reporting of reagents: Accelerating open and reproducible science.

The following blog was written by Angela Abitua (ORCiD ID: 0000-0002-8059-4050) and Joanne Kamens (ORCiD ID: 0000-0002-7000-1477) from Addgene. PLOS is excited to support reagent repositories such as Addgene as yet another step to improve scientific reproducibility. Open access to research findings and the underlying methods, materials and data, and issues surrounding reproducibility, replication, and research waste will be discussed this June 2-5 at the 6th World Conference on Research Integrity in Hong Kong, where PLOS ONE’s Senior Editor, Renee Hoch, will present a talk on data availability and image integrity.

Without materials and data, there is no research. Barriers to scientific progress can result from something as basic as not having access to reliable, validated information for research materials. That barrier is raised further when scientists cannot obtain samples or data in a timely fashion. Data and material repositories are breaking down these barriers. As a publisher, PLOS is supporting better, more open science by recommending repositories and encouraging use of standardized, unique identifiers for materials.

Centralized depositing of materials advances science in so many ways. It saves authors the time and burden of shipping requested materials. Researchers who request from repositories save time by not having to recreate reagents or wait months or years to receive samples. Many scientists have been on the receiving end of a request that was filled by an incorrect or degraded sample, which further delays research. Repositories like the ones recommended by PLOS handle the logistics of material requests, letting the scientists focus on what’s important: doing research.

For example, repositories make it possible for researchers to get access to different cell lines (American Type Culture Collection, Coriell Institute), plant materials (Arabidopsis Biological Resource Center), organisms (Bloomington Drosophila Stock Center, Caenorhabditis Genetics Center, European Xenopus Resource Centre, Jackson Laboratory), plasmids (Addgene, DNASU, PlasmID) and many other biological materials. Moreover, many of these repositories provide web-based databases that are easy to search and provide openly available information about each material.

For reagent reporting, many repositories also support unique and persistent identification of reagents. Identifiers like Research Resource Identifiers (RRIDs) make it easy for authors to cite materials and improves reporting through standardized identification and a permanent link to information about each reagent. For example, each Drosophila strain at the Bloomington Fly stock Center is assigned a fly stock RRID. For mice, the Mutant Mouse Resource and Research Centers (MMRRC) provides a mouse RRID for mutant mouse strains. For plasmids, Addgene will automatically register a plasmid RRID upon deposit.

Depositing increases materials transparency and reproducibility

Addgene currently contains over 70,000 unique plasmids and has distributed over 1,000,000 plasmids worldwide since 2004. At Addgene, depositing plasmids is free and straightforward, with the added bonus that it provides quality control measures that contribute to improved reproducibility. Addgene performs full plasmid sequencing and each plasmid is assigned a unique RRID identifier, along with a plasmid webpage that provides sequence data, cloning information, and associated protocols. This ensures researchers have detailed information about each plasmid reagent. Moreover, each Addgene plasmid page provides an Articles Citing this Plasmid section which allows researchers to learn how the plasmid was used and validated by different labs.

Recognition and credit for depositing authors

Depositing materials at the time of publication also provides benefits to both authors and publishers. Depositing authors gain recognition and are cited whenever requestors use the published materials in their own research articles. In fact, data from Addgene supports that depositing published plasmids in Addgene’s repository increases their use and results in increased article citations. Deposition at the point of publication also ensures timely distribution of materials. Finally, the information linked to each deposited reagent serves as reliable open data for the materials reported in the publication, simplifying the manuscript-writing process. Overall, PLOS’s support of reagent repositories, follows the publisher’s steps in improving data availability and protocol sharing and is a welcome addition for improving materials access and scientific reproducibility.

New sharing practices will change science for the better

By encouraging authors to deposit materials at the time of publication, journals will help accelerate research through timely distribution and accurate identification of reagents. Biological repositories exist to serve the scientific community. Take Addgene’s involvement in the explosive advancement of CRISPR research. Since 2012, over 8,400 CRISPR plasmids have been deposited and Addgene has distributed over 144,000 CRISPR plasmids worldwide, enabling researchers to share, modify, and improve this game-changing molecular tool. It is a prime example of the positive impact that biological repositories are making on research.

Thanks to PLOS’s updated recommendations, the importance of depositing and sharing reagents is finally getting some much-needed recognition. If the positive outcomes of PLOS’s data availability and protocol sharing policies is any indication of what’s in store for open material sharing, the future of science looks bright: speedier, more transparent, and more reproducible research.

PLOS Journals Now OPEN for Published Peer Review

 

Starting today, ALL PLOS journals will offer authors the option to publish their peer review history alongside their accepted manuscript! We’ve been excited to make this announcement, and make major strides towards a more open publication process, since last fall when we signed ASAPbio’s open letter committing to transparent peer review options.

What will it look like?

Our philosophy going into this project has been to open up the peer review process in a way that gives authors and reviewers more choices about how they publish and claim credit for their work.

As before, our peer review process defaults to single-blind, although reviewers have the option to sign their names to their reviews if they wish. What we’ve added to our process is an option at acceptance for authors to decide whether to publish the full peer review history alongside their work. This package includes the editor’s full decision letter, complete with reviewer comments and authors’ responses for each revision of the manuscript. Peer review history will have its own DOI enabling reviewers to take credit and earn citations for their contributions. If the reviewers have chosen to sign their reviews, their name will also appear on the published reviews but they can also chose to remain anonymous.

All manuscripts submitted after May 22, 2019 will be eligible for this option if accepted at a PLOS Journal. Here’s a look at the variations of open our opt-in model provides:

 

A major step for PLOS, and scholarly communication

The peer review history reveals crucial perspectives and decisions that supply additional context for readers and researchers. Because of the potential benefits, we’re making this option available now on all seven PLOS journals.

Other journals that have experimented with published peer review models have shown that the quality of feedback provided is at least as good as other models – we think it has the potential to be even better through increased accountability and transparency. We’re building off the foundations and lessons learned by these examples and are confident our model can offer authors more choices to make their research and the publishing process open, and showcase the rigorous review of their work.

Through the scale of our publishing output across all seven PLOS journals, we see this as an opportunity to make a significant change in the scholarly communication landscape and lay the foundation for a more open view of the manuscript handling process from start to finish.

Open beyond Open Access

While the benefits of transparency are numerous, we see published peer review as a crucial first step towards solving two fundamental problems: reviewer credit and public understanding of the peer review process. So far, Open Access has made it possible for research to reach a global community of readers but we have not yet demonstrated the work that goes on behind the scenes to validate scientific claims.

Publishing peer review history is a means of enriching the scientific record by giving context to evaluation and publication decisions. We hope this is also an important step toward elevating peer reviews to scholarly outputs in their own right that reviewers can take credit for.

In conjunction with the work it describes, peer review history can also be a source of material for educating students and the general public about peer review. Our content is also machine readable, paving the way for deeper analysis and discussion by the community.

Looking ahead

We’ve developed this option in consultation with our editors who are dedicated to improving our journals, and we also committed to reporting back our findings. As we learn more about how published peer review shapes author and reviewer choices, and reader experience, we’ll continue to update you on what we find.

 

PLOS Receives Meritorious Achievement Award from the Council of Science Editors

We are honored, and humbled, to receive the 2019 CSE Award for Meritorious Achievement. The honor is bestowed upon individuals or institutions that highlight the goals of CSE, particularly those that improve scientific communication through the pursuit of high standards in all activities connected with editing.

Kerry Kroffe, PLOS’ Director of Editorial Services, accepted the award on our behalf earlier this month at CSE’s annual meeting in Columbus, Ohio.

Photo courtesy of Matt Reese Productions

 

 

 

 

 

 

 

 

 

 

 

Past winners include Annette Flanagin, EQUATOR Network, Ana Marušić, MD, PhD, Amy Brand and ORCID.

We’re heading to NetSci 2019!

Note: PLOS is excited to sponsor the Open NetSci Hackathon and support NetSci 2019.

We can’t wait to see you at NetSci 2019! We’re gearing up for the hackathon (May 25-26) and conference (May 27-31), and want to help you make the most of your NetSci experience. Get ready to meet PLOS staff, tell us the latest research you’re reading, and submit your manuscript to our PLOS ONE Science of Stories call for papers.

Open NetSci Hackathon

Join us for NetSci’s inaugural hackathon. This year’s theme is open code and data, and our CC BY content is made for this! The hackathon will also feature keynote speaker Cassidy Sugimoto and experts on site to help with projects.  

Anyone registered for the NetSci 2019 School and Satellites can join, free of charge, and groups and individual participants are welcome. Learn how to sign up and get involved here.

Chat with us and #shareyourcode
  • Throughout the hackathon and the conference we want you to tweet about any papers, code bases or open code projects using the hashtag #shareyourcode and tagging @PLOSChannels. We’ll feature select works in the PLOS Complexity Channel, curated by Channel Editors including NetSci’s very own Laurent Hébert-Dufresne.
  • At the NetSci conference, PLOS ONE editor Deanne Dunbar will be attending NetSci and will be taking part in the “Chat with the Editors” panel.
  • If you’re a PLOS ONE Academic Editor, we’ll be holding a meet up May 30– email us to attend!
Submit to our call

There’s still time to submit your research to the PLOS ONE Science of Stories call for papers! The call and upcoming Collection include research with diverse perspectives from the humanities and the sciences to:

  • Explore the nature of narrative and narrative thinking in texts and other media.
  • Propose methods to extract stories from datasets and vice versa.
  • Analyze how narratives are transformed and how they cooperate or compete with each other as they move through time and space.
  • Communicate data-rich narratives to the public.

Guest Editors handling submissions are Peter Dodds, Mirta Galesic , Matthew Jockers and Mohit Iyyer. To learn more about our Editors’ perspectives and the call check out their recent blog post. The call is open until June 14.

We look forward to seeing you at NetSci 2019 and wish everyone a great conference!

Mini Frogs and other PLOS Research Making Headlines in March and April!

Mini Frogs and other PLOS Research Making Headlines in March and April!

Five tiny new frog species found in Madagascar–meet the Mini frogs

Three of these five new species, all of which range from 7.7-15 mm in length, belong to an entirely new genus: Mini. These Madagascan frogs’ miniscule scale enriches the picture of convergent evolution towards tininess in frog species (in addition to being extremely cute).

Lead author Mark Scherz says: ‘When frogs evolve small body size, they start to look remarkably similar, so it is easy to underestimate how diverse they really are. Our new genus name, , says it all: adults of the two smallest species Mini mum and Mini scule, are 8–11 mm, and even the largest member of the genus, Mini ature, at 15 mm, could sit on your thumbnail with room to spare.’

Check out some of the media coverage this article’s received from outlets including National GeographicIFLScience and Smithsonian.com, too!

 

(Don’t!) Feel the Burn–SPF moisturizer tends to be applied less effectively than traditional sunscreen

A new PLOS ONE study showed that users applying an SPF30 moisturizer applied it less effectively compared to traditional SPF30 sunscreen users, and missed significant areas around the eyelid. Even more concerningly, a post-study questionnaire revealed that participants were unaware of their incomplete coverage. As we move into summer here in the Northern Hemisphere, don’t forget your eyes need sun protection (and sunglasses are always an option, too!)

Co-author Austin McCormick adds: “Moisturiser is not as well applied as sunscreen; therefore, if planning prolonged sun exposure we advise sunscreen be used. If using moisturiser we advise one with SPF: any SPF is better than none, but it should not be considered the equal of sunscreen.”

For additional summer reading about this PLOS article, head to BBC News, NPR, and Today.com, among others!

 

Climate Change May Contribute to Hay Fever Increase

If you suffer from hay fever, climate change might be contributing to your allergies. A recent study in PLOS ONE showed that areas in the USA where the onset of spring was earlier than normal–or significantly later than normal–corresponded to an increased prevalence in hay fever sufferers. Lead author Amir Sapkota and colleagues used NASA satellite data along with CDC National Health Interview data to compile this first quantitative dataset pointing to a link between spring timing and allergies. The authors speculate that early spring means a longer season for tree pollen, whereas a late spring may mean a high pollen concentration across many different species–in either case, bad news for allergy sufferers.

Sapkota adds: “We need to better prepare, and increase community resilience to minimize the disease burden associated with climate change.”

See more coverage on this paper from outlets including CBS and Ecowatch.com.

 

 

Articles Cited

  1. Scherz MD, Hutter CR, Rakotoarison A, Riemann JC, Rödel M-O, Ndriantsoa SH, et al. (2019) Morphological and ecological convergence at the lower size limit for vertebrates highlighted by five new miniaturised microhylid frog species from three different Madagascan genera. PLoS ONE 14(3): e0213314. https://doi.org/10.1371/journal.pone.0213314
  2. Lourenco EAJ, Shaw L, Pratt H, Duffy GL, Czanner G, Zheng Y, et al. (2019) Application of SPF moisturisers is inferior to sunscreens in coverage of facial and eyelid regions. PLoS ONE 14(4): e0212548. https://doi.org/10.1371/journal.pone.0212548
  3. Sapkota A, Murtugudde R, Curriero FC, Upperman CR, Ziska L, Jiang C (2019) Associations between alteration in plant phenology and hay fever prevalence among US adults: Implication for changing climate. PLoS ONE 14(3): e0212010. https://doi.org/10.1371/journal.pone.0212010

Image captions and credit

  1. An adult male Mini mum, one of the world’s smallest frogs, rests on a fingernail with room to spare. Credit: Dr Andolalao Rakotoarison. CC-BY.
  2. B&W photo; UV photo non sunscreen showing deep dermal pigmentation, a sign of uv damage; UV photo after sunscreen application; UV photo after moisturiser with SPF application (dark areas on images taken with a UV-sensitive camera show SPF protection/coverage). Credit: Austin McCormick et al, 2019. CC-BY.
  3. Sacramento River Bend Outstanding Natural Area. Credit: Eric Coulter, BLM. Public Domain.

 

 

 

It’s Our Preprint Anniversary!

Can you believe it’s been one whole year since we launched our preprint-posting partnership with bioRxiv? This calls for a celebration!

Just last May, we began offering authors the choice of having PLOS post their manuscript to the preprint server, bioRxiv, when they submitted to a PLOS journal*. Our opt-in service has made it easier for authors to post their work early and has encouraged many authors to try preprinting their research for the first time. As of today, we’ve posted more than 2,500 preprints!

Many of our authors have now seen their work go from preprint to published and it’s amazing to see the transformation their work has taken – just take a look at the examples below.

 

Posted

  Published

  Aug 21, 2018 If a fish can pass the mark test, what are the implications for consciousness and self-awareness testing in animals?

  Feb 7, 2019 in PLOS Biology

  June 4, 2018 Precise prediction of antibiotic resistance in Escherichia coli from full genome sequences

  Dec 14, 2018 in PLOS Computational Biology July 2, 2018 Genetically modified pigs are protected from classical swine fever virus

  Dec 13, 2018 in PLOS Pathogens

 

Why we preprint

Whether you’re an author, an editor, or just an avid science reader, preprints offer a lot of advantages for how we share and consume information: they allow research to be shared openly and broadly, spark feedback and collaborations that may not have happened otherwise, enable authors to claim results and demonstrate their work for timely opportunities such as grant proposals and promotions. But if you really want to know how preprints advance science, just ask our authors:


“As statisticians, we provide analysis and data visualization methods for scientists in the field. Sharing code through GitHub and preprints through bioRxiv provides researchers with the latest methodologies as early as possible. The other benefit is that the scientific community can provide researchers with useful feedback prior to publication. This means that we can tailor new methods to scientists’ needs. These interactions were very enriching, and I recommend Open Science to everybody.”

Stijn Hawinkel, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium

A unified framework for unconstrained and constrained ordination of microbiome read count data

 

 

“Publishing a preprint is a great way to get feedback as early as possible from the community. We actually improved the final version of our paper not only based on the great reviews we received from the formal peer review process, but also based on the feedback we learned through Twitter, and other channels.”

Charlotte Herzeel, ExaScience Life Lab, IMEC, Leuven, Belgium

elPrep 4: A multithreaded framework for sequence analysis

 

 

I posted a preprint to bioRxiv when I submitted to PLOS Genetics because I wanted to share our story with scientific community. At submission, I believed we had a complete story that would interest researchers working on various aspects of adhesion biology. I knew that the story would likely develop further after peer review, but I wanted to share the core results with the community.”

Adam Kwiatkowski, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila

 

What’s next

Champagne! But our work on preprints isn’t over yet. We’re experimenting with new ways to raise awareness and interaction with preprint manuscripts through events like live preprint journal clubs, hosted by PREreview, and expanding our preprint offerings to include programs like Preprint Editors on PLOS ONE and PLOS Genetics.We’re also going through ALL of our data on preprints that we’ve collected over the past year to share back to you. Please join us in celebrating this month and stay tuned for more insights into our preprint program soon.

 

*Facilitated posting to bioRxiv has been available on PLOS ONE, PLOS Computational Biology, PLOS Genetics, PLOS NTDs, and PLOS Pathogens since May 2018 and on PLOS Biology since July 2018

We Couldn’t Do It without YOU

Every year, we get to work with new authors, reviewers, and editors who are ushering in the next wave of scientific advancement. We love publishing your work, reading your reviews, and learning from your expertise and we just want to say THANK YOU for supporting PLOS.

Wow, did we really do all of that?

We did! This has been a banner year for PLOS journals. In 2018 we saw more research articles published in PLOS Biology than ever before, began publishing Topic Pages in PLOS Genetics and Benchmarking articles in PLOS Computational Biology, partnered with bioRxiv to post over 1,300 preprints, and committed to moving forward with published and signed peer review. That’s on top of all of the special issues, Calls for Papers, and collections we’ve published in topics ranging from Climate Change and Health to Gender and NTDs.

We’d also like to extend a warm welcome to more than 3,000 new members of the PLOS ONE Editorial Board who have joined us this year to provide more expertise for submission areas that need it most – we’re glad you’re here!

For everything we do at PLOS, we are supported by the dedication of our research communities.

Together, we’re stronger

We are a community of more than 8,000 editors, 65,000 reviewers, and 150,000 authors. When we work together, we can make change happen in scholarly communication. Last year PLOS Pathogens editors hosted six writing workshops to help Early Career Researchers improve their skills and equip them with the tools they need to become authors. We also hosted interactive events like live-streamed preprint journal clubs to bring authors and experts from the community together for real-time feedback on their work.

We’re listening to your feedback from our surveys, event meetups, and Section Calls and want to continue evolving our services in ways that matter to you.

We’re working on new ways for reviewers to get credit for their work through ORCiD as well as signed and published peer reviews. We’re also going to continue the process improvements we’ve started on PLOS ONE to bring a faster, clearer process to our authors along with a number of exciting new options on other journals – stay tuned!

Cite it, share it, celebrate it

For everyone who has contributed to our success this year: our dedicated Editorial Board, incredible Guest Editors, and inspiring reviewers – these articles are for you!

We’re sure we will have many more opportunities to thank you this year but please join us in celebrating your achievements this week by sharing your PLOS contributions with #PLOSCommunity.

Celebrate Open Data Day with Us!

 

Around the world tomorrow groups from all sectors will be celebrating Open Data Day – an annual event that highlights the benefits of open data and encourages the adoption of open data policies in government, business and civil society. As publishers, data availability is crucial for the validation and foundation of new research and key to our mission to help researchers advance the scientific record. In the spirit of Open Data Day, we’ve decided to defer to researchers and data enthusiasts to answer the questions: why is data important and how can we make it better?

We got our answers from Sudhakaran Prabakaran, one of a number of dedicated volunteers at Cambridge University known as the Data Champions who are helping advise members of the research community on managing their data. Read his thoughts below.

Who are the Data Champions? What kinds of data questions do you help researchers navigate?

I think it’s a fantastic forum. [We have] a lot of discussions and people exchange ideas and not necessarily just in the sciences but also in every other field. [Data management] can be kind of confusing, even simple things like can I put my [datasets] in Dropbox? Can I share them in Google Drive? You’re talking about even labeling stuff in desktop computers. There is no clarity because this landscape is fast-moving and people are not trained to catch up with that kind of speed at which things change.

What are you working on right now? How does open data play a role in it?

Our lab thrives on open data. We train machine learning algorithms that looks at specific regions of the human genome and trying to identify the most important mutations and then identify drugs to target them. Most of the datasets I work with people have already published and analyzed those datasets and they’ve extracted what they want. I’m kind of looking at things that they don’t want – I’m looking at non-coding regions, just kind of digging deeper into the datasets.

Why do you think open data is important? What do you think the future open data landscape looks like?

I don’t think open data is enough…it’s the analysis also. For example, we train a lot of machine learning algorithms and in the process we fail many, many times and we know the pitfalls we know what to avoid. But if you share that process with other people that will enable them to overcome it, to get there. It is very difficult and that process can be shared with people.

I think future young people are going to be brought up in an environment where they can just click something and get access to the code and get access to the data themselves. And then the issues of reproducibility would be mitigated if you can share what you’ve done and the data set is there for other people to work with.

What advice would you give to authors and researchers to encourage them to share their data?

I think we have encountered these scenarios even as a data champion in my own department. I think if you if you have incentives, as in [getting] your DOI and authorships for the dataset even before publication then it’s easy to share. It’s your data, [someone] can probably do a different kind of analysis and publish it but they have to cite this data and you will be benefited by that.

And it’s in the best interest of the authors to share it ahead of time because of reproducibility.

 

What can you do to encourage good data management?

You can practice the open data lifestyle by sharing your research data in an open repository and making it available when you submit your manuscript. If you’re reviewing a submission, knowing how to evaluate the associated datasets can be tricky which is why we’ve worked with the Data Champions to cover everything you need to know in this Reviewer’s Quick Guide to Assessing Datasets. If the manuscript you’re reviewing doesn’t have an associated dataset, request it!

About the Data Champions Program

The Data Champions Programme is a network of volunteers who advise members of the research community on proper handling of research data. In this, they promote good research data management (RDM) and support Findable, Accessible, Interoperable, and Re-usable (FAIR) research principles. It is run by the Research Data Management Facility at the University of Cambridge.

 

‘How do we define success?’ – Rethinking failure and success in science

Independent of the context, failure is a word that hardly ever leaves us indifferent. Fear of failure is human nature, and it is common that we prefer not to talk about failures if we can avoid it.  When we think about this in a professional context, failure can have clear and immediate ramifications for reputation and career progression and – as with any other professional – researchers are not immune to this fear of failure

Part of this approach to failure in research is due to the fact that the research system has traditionally rewarded those who are the first to report a finding over those who are second, and those who report a positive result over those reporting a negative one. However, research generally involves a trial-and-error approach and a plethora of negative findings, or protocols that require troubleshooting before they are fine-tuned. Thus ‘failed’ experiments are common; more so than is often recognized or reported. Much effort and many hours of meticulous research endeavour go unrecognized by the current research assessment frameworks, resulting in a considerable squandering of potentially important research outcomes.

The ‘Failures: Key to success in science’ event at the Cambridge Festival of Ideas 2018 aimed to reflect on these considerations in a conversation involving our five panelists and the audience around the notions of failure and success in science.

Our five panellists kicked off the conversation by giving their perspective on what a successful research career should look like.

‘How do we define success?’ asked Cathy Sorbara (Co-chair of CamAWiSE, Cambridge for Women in Science and Engineering), maintaining that science does not have a defined endpoint, that collaboration should be a key part of the research process, and that scientists need to think about how they communicate their work, particularly to those unfamiliar with research. Tapoka Mkandawire (PhD candidate, Sanger Institute) felt that a key aspect of success is to work on something that you feel passionate about and are keen to share. The audience was interested in the forms that communication of research could take and the panellists noted that communication about research should not be restricted to publications, putting forward ideas around visual formats such as videos. Tapoka noted that her research group has developed a comic book to more easily describe their work to children.

A common theme was that the binary classification of success vs failure is somewhat unfair. Should a result be tagged as failure only because it’s negative and not been published? Fiona Hutton (Head of STM Open Access Publishing at Cambridge University Press) advocated the development of a more collaborative open pathway for research, with more openness at all steps of the process, such as that demonstrated with open lab notebooks, to capture the incremental steps that make up the research process. The sharing of negative and null results should be encouraged as well, as a move away from frameworks that rely on impact factors to assess the quality of research; Fiona mentioned DORA as a good initiative in this space, which is gaining support from institutions and funders.

Arthur Smith (Deputy Manager of Scholarly Communication (Open Access), University of Cambridge) and Stephen Eglen (Reader in Computational Neuroscience, University of Cambridge) tackled the challenges with the current research system and acknowledged that this places Principal Investigators (PIs) as the ‘survivors’ of the system, with only a few reaching the top of a steep pyramidal career structure. Stephen stressed that the driving force for getting into research should be a genuine interest in science and not the goal to eventually become a PI. Arthur noted that there are many other career paths available after a PhD and that the skills gained can be used in many other areas, such as the private sector. The training of PhD students should include aspects that go beyond publishing, and should balance this with the development of communication and other skills.

To round up the discussion we asked panellists to provide recommendations for steps that can help shift perceptions about success and failure in science. Here is what they told us:

  • More support for early career researchers, so that they can have an informed, broader view of their career, and of the options after a PhD.
  • Further recognition for the wide range of different roles that scientists play beyond the publication of research findings – for example, peer review activities, mentorship, etc.
  • Provision of credit for recording and reporting troubleshooting, for any work that may not follow the shape of a conventional publication but which would help others engaged in related research.
  • More training for those in a research path, to help them develop a variety of transferable skills, and to recognize the value of those skills.
  • Increased diversity – higher diversity can only be beneficial in driving change towards how success is defined.

Achieving these aims and helping to sway current views about failures in research represents a formidable task, but – much like science itself – change progresses one step at a time and we hope that the engaging conversation at the Festival of Ideas provided one such step to shift how we define “success” in research. As we pursue initiatives towards such change, let’s remind ourselves of Arthur Smith’s definition of success: ‘Success is what makes you happy’.

 

From Preprint to Publication

Live preprint journal clubs provide early feedback for PLOS ONE authors

We love it when preprints go on to be accepted as formal journal publications and we are especially excited to announce that EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma, a featured preprint in our Open Access week event, is now published in PLOS ONE!

In October, we celebrated OA Week’s theme of “Designing Equitable Foundations for Open Knowledge” by teaming up with PREreview to host virtual preprint journal clubs where researchers from around the world could share their expert opinions on preprints AND get credit for their reviews. Thanks to this event, the authors of this preprint received crowd-sourced feedback on their work even as their submission underwent formal peer review by PLOS ONE.

Lead author Borong Shao took advantage of the unique opportunity to participate in the discussion and we asked her to tell us what she thought of preprints and the virtual journal club experience. Read her thoughts below:

Can you tell us a little bit about your research? What made you decide to post the work as a preprint?

We were working on the topic of molecular signature identification using multiple Omics data. The reason why we posted our work was to let our new results reach the research community. Based on our experience, preprint works are also read and discussed by researchers, as well as the formally accepted ones.

How does your field or research community feel about preprints in general?

In my opinion, preprints are welcomed if the work has a great idea to share. This can assist or even inspire other researchers in their work without waiting for the article to be formally accepted.

Tell us about your experience discussing your preprint at a live journal club—How did you feel about the opportunity?

I was a bit nervous because I had no such experience before. I wondered whether the audience would have positive or negative opinions about my work, although I think my work has its value. I was excited too, because our work is read by researchers all over the world. Some of them are from a relevant but not the same discipline. I was curious to know their opinions on our manuscript.

Did you use any of the feedback from the virtual journal club? Did you find this kind of feedback useful in general?

Both my professor and me found the suggestions from the virtual journal club very helpful. They gave us useful advice from the viewpoints of both readers and researchers. Much of the feedback can be implemented in a short time to improve the quality of our work. Some other feedback can be learned and used in our future research. There were a few mistakes that we might not have found out, if not learned from PREreview feedback.

 

Preprints aren’t just helpful to authors– early comments from your community can also help editors at the journal conduct their evaluation of the work. PLOS ONE Academic Editor Aamir Ahmad had the opportunity to handle Dr. Shao’s submission and felt that the early feedback process was “a great initiative… the feedback was excellent in general and the authors did a good job of incorporating the changes.”

PLOS wholeheartedly supports preprints and the myriad benefits they offer researchers.  We’re making it easier for authors to share their work as a preprint, immediately upon submission, through our posting service in partnership with bioRxiv and we were happy to find another partner in PREreview who have pioneered live preprint journal clubs for early discussions like these to take place.

You can find more information on preprints here and live-streamed journal clubs here. Please also join us in congratulating Dr. Shao and her co-authors on their recent publication!

 

PLOS Provides Feedback on the Implementation of Plan S

We welcome Plan S as a ‘decisive step towards the realisation of full open access’1, in particular the push it provides towards realization of a research process based on the principles of open science. This is fully aligned with our mission to bring scientists together to share work as rapidly and widely as possible, to advance science faster and to benefit society as a whole. Our publications have operated in line with the core principles outlined in Plan S since the launch of our first journal, PLOS Biology, in 2003. We recognize that wide adoption of support for Plan S may bring additional competition within the open access publishing space. We welcome this evolution as a positive change in research culture, resulting in greater availability of information, growing inclusion in the scientific process and increasing the speed of discovery and innovation.  Below is our response to the call for public feedback.

Feedback Questions

  1. Is there anything unclear or are there any issues that have not been addressed by the guidance document?

While welcoming Plan S, its principles and stated intentions, there are some points where we believe additional clarification would be beneficial.

A. Changing research assessment

We are glad to see emphasis on changing research assessment and commitment to the principles of DORA as part of Plan S. We believe this is critical to enabling change in publication behaviours, allowing the value of research outputs to be assessed on their merits rather than through an aggregated metric based on publication venue. However, we note that although the original publication of Plan S states that members of cOalition S ‘commit to fundamentally revise the incentive and reward system of science, using the San Francisco Declaration on Research Assessment (DORA) as a starting point’1, the implementation guidance states only that ‘cOAlition S members intend to sign DORA and implement those requirements in their policies.’ We ask cOalition S to provide clarity regarding the steps that will be taken to drive the ‘fundamental change’ indicated in the original publication.

B. Transformative agreements

While recognizing the need for a route for subscription journals to transition away from publication behind paywalls, we believe that without stringent guidelines and compliance checks, ‘transformative deals’ may have significant unintended consequences, reducing choice and narrowing the market. As identified by Adam Tickell in his 2015 review2 the need for ‘OA policy to offer greater choice to research producers’ remains, and we believe this should be a primary consideration for cOalition S in considering the future shape of the research and innovation market, particularly as it relates to the assessment and communication of research findings.

‘Transformative agreements’ offer advantage to the largest players and to publishers with substantial subscriptions business, as smaller publishers have to ‘wait in line’ to enter negotiations while those, including but not limited to PLOS, without legacy subscription businesses cannot participate. We acknowledge that the intention of cOalition S members is that ‘transformative agreements’ should not decrease the amount of money available in the system to fund publishing in other compliant venues, however, we believe this is the likely outcome as limited institutional and library publication budgets become tied into large ‘read and publish’/’publish and read’ (RAP/PAR) deals. This perpetuates the dominance of the ‘big deal’ in the market, which in its rebranded ‘publish and read’ form, has the potential to become the status quo rather than a step towards transformation, much as hybrid journals have become the status quo in relation to open access. Moreover, the transition of subscription ‘big deals’ into ‘RAP/PAR’ deals risks locking the high cost of subscriptions into an open access future, if deals so far are anything to judge by. We would like to see a ‘clear and time-specified commitment to a full Open Access transition’ as outlined in the implementation guidelines, be a central requirement for all journals covered by a ‘transformative agreement’ in order to be considered compliant with Plan S. We also ask for greater clarity on the allowed start and end dates for these agreements.

C. Deposition in open repositories

While we understand that this is a recommendation rather than a mandatory criterion for compliance with Plan S, we believe that the proposal that there be ‘direct deposition of publications by the publisher into Plan S compliant author designated or centralised Open Access repositories’ has the potential to add cost and complexity to compliance.

Currently, we and many other publishers syndicate our published articles to PMC/Europe PMC. The process of direct deposition to each repository is not without cost, requiring both staff and technical resources to set up and to run. These costs will increase should it become necessary to deposit to a range of ‘author designated’ repositories. This is especially the case given the importance of equitable treatment of publications from researchers in different disciplines and/or geographical regions, particularly as cOalition S grows.

We encourage cOalition S to reconsider this recommendation and propose deposition in a small number of recognized repositories or dispatch services, to facilitate compliance.

D. Publication costs and APC caps

In the published guidance, cOalition S calls for ‘full transparency and monitoring of Open Access publication costs and fees’ and indicates the potential for ‘standardisation of fees and/or APC caps’. We understand that the cOalition has revised this position and intends to call for transparency but not to introduce set caps. We welcome this change of approach which we would like to see reflected in the next iteration of the written guidance. We believe that requiring transparency will allow funders, or others paying the costs of publication, to assess the value of their payments while minimizing the opportunity to give rise to unintended consequences.

In considering potential unintended consequences, there is a useful parallel with the introduction of tuition fees at universities in England. Since tuition fees were introduced in 1998, they have been capped by the UK government. According to a House of Commons Library briefing paper3, each time that the cap has been raised, almost all English HEIs have increased their fees to the maximum allowed level. When it was announced that the cap would increase to £9,000 from 2012, Lord Willetts, then Minister for Universities and Science, said that the maximum fee would be charged only in ‘exceptional circumstances’4 and it was anticipated that this would ‘create a market in fees’5. This market did not emerge and in fact, nearly all HEIs set their fees at the maximum allowed rate. We believe that there is significant potential for an analogous situation to emerge in relation to APCs. Rather than creating a market where publishers set APCs at the lowest level that covers their costs sustainably, it is more likely that caps would encourage APCs to be set at the maximum allowed level even if this is substantially higher than the publisher’s costs.

Additionally, the cost associated with the publication of an individual article is highly variable dependent on publication venue. The level of editorial activity, including building relationships with, and providing support to, authors, referees and academic editors is a significant contributor to cost but generates substantial value for the research community. The level of selectivity of the journal or platform is also an influencing factor, as more selective publications incur additional costs through assessing articles that do not go on to be published in that venue. While we recognize and support the need to change the measure of selectivity from one focused on journal impact factors, we believe that the ability to differentiate levels of selectivity based on appropriate and meaningful criteria should continue, where selective  journals and platforms can demonstrate their value through community engagement and cost transparency. We believe that this will support a thriving research and innovation ecosystem more effectively than moving to a ‘one size fits all’ approach.

  1. Published simultaneously as follows: a) M. Schiltz, available from https://www.scienceeurope.org/wp-content/uploads/2018/09/cOAlitionS.pdf; b) Schiltz M (2018) Science without publication paywalls: cOAlition S for the realisation of full and immediate Open Access. PLoS Biol. 16(9): e3000031. https://doi.org/10.1371/journal.pbio.3000031; c) Schiltz M (2018) Science Without Publication Paywalls: cOAlition S for the Realisation of Full and Immediate Open Access. PLoS Med 15(9): e1002663. https://doi.org/10.1371/journal.pmed.1002663; d) Schiltz M (2018) Science Without Publication Paywalls: cOAlition S for the Realisation of Full and Immediate Open Access. Front. Neurosci. 12:656. doi: 10.3389/fnins.2018.00656
  2. Open access to research publications Independent Advice, Professor Adam Tickell Provost and Vice-Principal, University of Birmingham Chair of the Universities UK Open Access Coordination Group, https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/499455/ind-16-3-open-access-report.pdf
  3. House of Commons Library, Briefing Paper, Number 8151, 19 February 2018 Higher education tuition fees in England, https://dera.ioe.ac.uk/31330/1/CBP-8151%20_Redacted.pdf
  4. As above p.6
  5. As above p.10, Section 3.2

 

  1. Are there other mechanisms or requirements funders should consider to foster full and immediate Open Access of research outputs?

We believe that diversity and equality of opportunity, including for new entrants to the market, should be retained and encouraged to ensure to a thriving and diverse research and innovation ecosystem. Referring to part (B) of our answer to Question 1, we encourage cOalition S to consider this opportunity to move from ‘big deal’-style arrangements as rapidly as possible to avoid further consolidation around the largest players in the market.

Focusing on regulation of existing business models, both transformative agreements and APCs, may have the unintended consequence of creating barriers to the diversification in the market. We applaud the the support indicated in the implementation guidance for ‘a diversity of models and non-APC based outlets’ and encourage cOalition S to ensure equal emphasis on the development of new business models, alongside consideration of established approaches. We believe this is vital in order to maintain choice for researchers.

Boosting Open Science Hardware in an academic context: opportunities and challenges

Written by: Jenny Molloy (University of Cambridge), Juan Pedro Maestre (University of Texas, Austin)

Experimental science is typically dependent on hardware: equipment, sensors and machines. Open Science Hardware means sharing designs for this equipment that anyone can reuse, replicate, build upon or sell so long as they attribute the developers on whose shoulders they stand. Hardware can also be expanded to encompass other non-digital input to research such as chemicals, cell lines and materials and a growing number of open science initiatives are actively sharing these with few or no restrictions on use.

A growing number of academics are developing and using open hardware for research and education in addition to sharing their papers, data and software through broader open research practices. This brought a large cohort to the Gathering for Open Science Hardware (GOSH) in Shenzhen China during October 2018, an four day event which convened over 110 of the most active users and developers of open science hardware from 34 countries and multiple backgrounds including academia, industry, community organising, NGOs, education, art and more. PLOS kindly supported an unconference session during GOSH 2018 where students and researchers shared the following opportunities and challenges to boosting open science hardware in an academic context and planned a course of action to forward the goal of the Global Open Science Hardware Roadmap to make open science hardware ubiquitous by 2025.

Opportunities for open science hardware in academia

Open science hardware has some important intrinsic benefits. Firstly, it can reduce the cost of research, democratising opportunity and enabling limited budgets to stretch further. Joshua Pearce of Michigan Tech University has calculated a return on investment of hundreds to thousands of percent for funders of open hardware through a drastic reduction in lab costs. Secondly, it reduces duplication of effort by building on the work of others and thirdly, it provides opportunities to customise hardware to suit your optimal experimental design, rather than designing your experiment to fit the limitations of available hardware. Moreover, sharing more details of experimental designs facilitates replicability in science. This is needed more than ever given current lack of trust towards science in some societal contexts and fears within several scientific communities of a “reproducibility crisis”.

Gaining additional credit, citations and collaborations are all significant potential opportunities for academics developing open science hardware and are necessary to incentivise those activities. However, cultural change is required within existing systems of academic publication and reward to realise the opportunities. Change is coming, for example the recently established Journal of Open Hardware and HardwareX encourage formal publication of research advances and designs that well documented and appropriately licensed, while the PLOS Open Source Toolkit channel highlights and rewards open hardware publications. We know that open approaches can reap rewards but there is room for further evidence in the hardware context. Open access publications and shared datasets can confer a citation advantage and many projects developing open research tools projects report high numbers of collaborations and significant funding that may not have been possible without their culture of sharing. The Structural Genomics Consortium is involved in publishing over two papers per week, partially a result of hundreds of collaborations through making data and tools freely available. Research funders can be responsive to openness as a strategy to maximise impact: UK-based research centre OpenPlant was awarded £12m to make open technologies for plant synthetic biology and two open source projects on diagnostics for infectious diseases were awarded >£1m from the UK’s Global Challenges Research Fund.

Educational use of open science hardware also reaps both tangible and intangible benefits for universities. It represents an opportunity to increase the quality of teaching and learning by providing access to instruments that would otherwise be too expensive in the numbers required for effective teaching. It also contributes to building critical thinking skills and breaking open the “black box” of laboratory equipment. There are many academics in the GOSH Community involving their students directly in developing open science hardware, such as air quality sensors at the University of Texas Austin or biological instrumentation through the Biomaker Challenge in Cambridge. Still others such as the Centro de Tecnologia Acadêmica at UFRGS in Brazil are using open hardware tools extensively in student lab practicals and research projects.

Challenges to address if open science hardware is to become ubiquitous

There are several barriers to wider adoption of open science hardware in academia. One stumbling block is institutional buy-in and support: in these times of limited funding, many universities have become conservative about approaches to intellectual property and patenting of inventions. Encouraging an open approach to maximising societal and scientific impacts through technology and knowledge transfer requires a compelling narrative. This includes reassurance that openness is contextual. In some cases the traditional route of IP protection and restrictive licensing may be optimal to achieve intended outcomes, in others it is not and  open approaches should be considered a strategic option. It is also important to emphasise that open does not equal non-commercial. Indeed there are many examples of entrepreneurial academics and companies spinning off to sell open hardware back into academia but also to industry, non-profits, educational institutions and directly to the public.

Funding for ongoing support and scaling of open science hardware efforts is a perennial and important topic of discussion at GOSH. In the case of open science hardware, private investors may not consider open designs as maximizing profit opportunities but they can still be profitable and generate significant social and scientific returns. A major task for the GOSH academic working group formed at the unconference session is therefore to compile justification for a diverse range of funders including private philanthropists, social impact investors and venture funds to support open science hardware and further the goal of making it ubiquitous and widely used by 2025.

The final topic of discussion during our session was creating awareness among the scientific community both online and offline at major scientific conferences. Offering community-level incentives, support and guidelines to document and share open science hardware is feasible and there is much low-hanging fruit. However, we have seen in other areas of open research that to obtain ubiquity these community efforts need to be backed by formal incentives and rewards. In other words, the value of open approaches has to be recognised in decisions around funding, promotions and hiring decisions.

Furthering open science hardware through community action

Four priority actions emerged which correspond closely to recommendations in the Global Open Science Hardware Roadmap: i) leverage the GOSH Community and network to produce guidance and case studies for universities, funders and other stakeholders; ii) put open science hardware on the agenda at large disciplinary conference; iii) raise awareness through mainstream academic channels; and iv) take the initiative within our own institutions to experiment with ideas and build local communities.

We invite anyone who are interested in open science hardware to join this work to ensure that more researchers, students and those outside of academia have access to vital enabling technologies for science. You can sign the GOSH manifesto, join the GOSH Forum to share your projects and contact organizers@openhardware.science for more information.

NOTE: The PLOS Open Source Toolkit collects papers from across publishers that describe software and hardware with research applications. The site is curated and managed by five active researchers, including the author of this blog post, Jenny Molloy. Meet all the editors here and here.  We’re on a mission to make exciting, cost-effective, and high-utility tools accessible to all researchers to eliminate barriers to scientific innovation and increase reproducibility. We post new content monthly. Subscribe for notifications. Currently featured: an open source K-mer based machine for subtyping HIV-1 genomes.

Acknowledgements

Many thanks to PLOS for their kind support enabling people in need of financial support to attend GOSH and to the participants in the unconference session: Juan Pedro Maestre (University of Texas, Austin), Pierre Padilla (UPCH), Andre Chagas (University of Sussex), Jenny Molloy (University of Cambridge), Moritz Riede (University of Oxford), Benjamin Pfaffhausen (Freie Universität Berlin), Marina de Freitas (CTA-UFRGS), Minerva Castellanos Morales (Scintia), Tobias Wenzel (EMBL), Anne-Pia Marty (University of Geneva), Alex Kutschera (Technical University of Munich), Eduardo Padilha (University of São Paulo).

Images

GOSH 2018: https://www.flickr.com/photos/goshcommunity/44847829654/in/dateposted/

Other GOSH images and credits can be found here.

Illustrations from the GOSH Roadmap can be found here.

All Gathering for Open Science Hardware photos and roadmap images are in the public domain under a CCZero waiver and available on Flickr https://www.flickr.com/photos/goshcommunity/

FluoPi: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0187163

(one frame, other options in the figures)

Image credit: Nuñez et al (2017), licensed under CC-BY 4.0.

Caption: Bacteria and cell-free protein expression systems generating fluorescent proteins and imaged using the FluoPi.

OpenFlexure Scope: Openflexurescope.jpg

Image credit: Dr Richard Bowman, University of Bath

Caption: Open source, 3D-printed microscope stage imaging onion cells on a Raspberry Pi camera. The stepper motors enable focusing and moving of the sample stage.

Public Lab: https://publiclab.org/system/images/photos/000/020/856/large/IMG_20170622_113106_860_2.jpg

Image Credit: Public Lab, licensed under CC-BY-SA 3.0

Caption: Members of Public Lab balloon mapping oil spills and water pollution with open source kits.

DropBot: https://www.microfluidic-chipshop.com/wp-content/uploads/2018/02/DropBot-DB3-120-998×1024.jpg

Image Credit: Sci-Bots Inc.

Caption: Open hardware digital microfluidics system made by Sci-Bots.

 

PLOS Board Appointments

 

After a careful search and much consideration, we are excited to share with our community five new appointments we’ve made to the PLOS Board. This is a pivotal time for PLOS, and as you’ll see, each member will bring us a different perspective, which will enable us to expand the ways in which we serve our scientific communities.

Our new Board Chair is Alastair Adam, currently CEO of innovative digital textbook publisher, FlatWorld, who brings to the role not only a strong understanding of publishing – including scientific journals – but also his business savvy and strategic skills. Alastair joined the Board effective November 1 and assumed the Chair role on January 1, 2019, replacing our longtime Board Chair, Gary Ward (more on Gary a little later).

We also added Dr. Simine Vazire, who is currently a Professor in the Department of Psychology at UC Davis where her research focuses on one of the oldest and most fundamental questions in psychology: how do we know ourselves? In 2017, she was awarded a Leamer-Rosenthal Prize for Open Social Science in recognition of her efforts to advance reproducibility, openness and credibility in the social sciences. She held a previous role as a senior editor of Collabra: Psychology and Editor-in-Chief of Social Psychological and Personality Science. Her scientific and editorial expertise bring a well-rounded and diverse perspective to our Board, and will help to ensure that working scientists retain a strong voice on our Board.

Dr. Victoria Coleman joined the Board in May 2018. She is currently the Chief Technology Officer at the Wikimedia Foundation where she sets the organization’s technical roadmap for the evolution, development, and delivery of core platforms and architecture.  Victoria brings valuable technology experience to the Board at a time when PLOS, like many mid-size publishers, faces important and difficult choices about its technology infrastructure. Victoria serves in several advisory roles including the Board of the Santa Clara University Department of Computer Engineering and as Senior Advisor to the Director of the University of California Berkeley’s Center for Information Technology Research in the Interest of Society.

We also wanted to ensure that we maintain deep experience in PLOS’ core biomedical science fields, and we are very lucky to have Professor Keith Yamamoto of UCSF agree to join us (effective February 1, 2019). Keith is both a highly regarded scientist running his own research lab and has extraordinary experience in the policy arena focusing much of his career on science practice, education, communication, and advocacy including strong and early support for OA. He currently serves as UCSF’s first vice chancellor for Science Policy and Strategy.

Last but by no means least, Suresh Bhat joined us on November 1, 2018 as incoming Chair of the Finance Committee. Suresh brings to PLOS not only deep financial knowledge but also experience at a top research university and a passion for education. Suresh has headed finance programs for a number of financial institutions. He is currently CFO and Treasurer at the Hewlett Foundation, prior to that, he was CFO at the Haas School of Business at UC Berkeley (and is a Haas and Cal alum).

I would be remiss if I did not take the opportunity here to express my heartfelt thanks to both Gary Ward, our now former Board Chair, and Mike Eisen, one of the co-founders of PLOS, both of whom left the Board in 2018.  In his seven years as Board Chair, Gary has led the Board with passion, wisdom and integrity, and has been both counsel and friend to many of us in the organization. Mike is of course irreplaceable in every way. His vision, zeal and dedication are a big reason that PLOS not only exists but has had such a deep impact on scientific communication. I have no doubt that Mike will continue to be one of PLOS’ greatest advocates (and yes, let us know when we get it wrong – as good friends do!).

While goodbyes are never easy, we are excited to embark on this new chapter for PLOS with the fresh wisdom of so many exceptional, dedicated individuals. Please join us in welcoming our new Board members!

PLOS Authors Say “Yes” to Preprints

We’ve surpassed 1,300 preprint posts to bioRxiv!

This is an incredible milestone for us and for all of our authors who chose to opt-in to our preprint service since we announced our partnership with Cold Spring Harbor Laboratory’s bioRxiv six months ago. We wanted to bring an easy preprint-posting option directly to the submission process for our authors and are thoroughly excited with the results we’ve seen so far.

The road to preprints

As we began this journey, about 4% of our authors reported that they had posted their submission to a preprint server. While this base remains consistent, our preprint-posting service has built upon it to offer authors more choices. In the past six months we’ve seen an additional 14% opt-in to have PLOS post a preprint on their behalf, indicating that 18% of our authors want to use preprints to share their research.

Of course, the opt-in rate varies by discipline. On PLOS Computational Biology 46% of our authors choose to make a preprint of their manuscript available, with half of those posting before submission and the other half requesting PLOS post to bioRxiv on their behalf. In biology in general, the adoption is high. PLOS Biology, which joined the service later, is already showing a promising trend towards preprints by 39% of our authors (23% of which elect to have PLOS post on their behalf).

Every opt-in we get is screened by editorial staff before posting to ensure the article fits bioRxiv’s scope and that no sensitive information is accidentally shared. We have also taken a conservative approach and avoided posting research that could have an impact on human health before the claims have been peer reviewed, which is why we do not yet offer to post preprints for PLOS Medicine authors. We’re working in partnership with bioRxiv to refine the posting criteria as we learn more about the needs for early sharing in different communities.

Overall, the openness to new research outputs we’ve seen among our community of authors is inspiring and we hope to see preprint adoption grow even more over the coming year.  

 

Author choice

We like preprints because they put your research first. We’re making it easier for you to choose preprints as a way to rapidly disseminate your research results, establish priority, accumulate citations for your work, and receive input from your community that may help shape the future of your research.

That said, preprints aren’t for everyone or for every paper which is why authors choose when and how their work becomes available. We’re also listening to our community’s feedback to make our service as inclusive as possible.

Many of our authors still prefer to wait for peer review before making their results public. However, about a fifth of the authors who responded to a survey about why they had opted out said they are unfamiliar with preprints. We’re hoping to change that by offering everything you need to know at plos.org/preprints. More information about preprints is available on bioRxiv along with their posting guidelines. ASAPbio also offers very useful guidance for preprints, including preprint policy at other journals which may help clarify any concerns you have about submitting a manuscript after you’ve posted a preprint.

Where we go from here

We’ll continue learning from our community and sharing more information that helps you make the right decision for your paper. We’re also encouraging other preprint options to authors in areas that don’t fall under bioRxiv’s scope. Both PLOS Genetics and PLOS ONE have dedicated Preprint Editors to solicit submissions from various preprint servers and we’re looking at more opportunities.

If you’re thinking of posting a preprint for the first time, take advantage of this checklist to get started and review all the benefits preprints could have for your work.

 

Attention Earth Sciences: PLOS ONE wants YOUR Preprint

Dedicated team of Editorial Board Members are now actively seeking manuscripts in the Earth Sciences from preprint servers EarthArXiv and ESSoar.

Preprint servers offer a myriad of benefits to authors who are excited to share their work with the community as soon as possible, so we’ve offered our authors the ease of automatically posting their life science submissions on bioRxiv. But PLOS ONE is a community of many different voices and we want to help promote preprints in all disciplines. This includes providing authors with more reasons to post a preprint – on top of the advantages that posting a preprint already offer such as faster dissemination and allowing for input from the whole community. We’re therefore delighted to announce the introduction of a new program to invite submissions of posted preprint manuscripts specifically in the Earth and Space sciences. Our aim is to support authors posting their papers with a fast and efficient peer review process and journal publication of their work.

Introducing PLOS ONE Preprint Editors

Going forward, we’ve tasked a small group of PLOS ONE Editorial Board members with reviewing and inviting preprint submissions from EarthArXiv and ESSOAr that they feel would be a good fit for the journal. This group will be led by Section Editors Guy Schumann (Bristol University, UK) and Juan Añel (University of Vigo, Spain) along with dedicated Preprint Editors, Xialoe Sun (Stockholm University, Sweden) and Julien Bouchez (Institut de Physique du Globe de Paris, France).

As part of this program, submissions invited through preprint servers will receive special attention from the staff editors which may include extra promotion on social media. Climate change papers may also be recommended to the “Responding to Climate Change” Channel, of which Juan Añel is also an editor.

“As a preprint editor one can have a substantial positive impact and contribute a potentially very high added-value to the scientific community of a particular research field.”

  • Guy Schumann, Section Editor PLOS ONE

We are truly excited to place this program in the hands of these individuals who’ve proven their dedication to their communities and eagerness to advance scholarly outputs for scientific communication in the Earth and Space sciences.

Why we choose preprints

Recruiting research from preprint servers is nothing new in academic publishing, other journals like PLOS Genetics and eLife already do so. Preprints represent huge opportunities for improvement on slow publication times. When it comes to critical issues like climate change and others, getting results out sooner can have a dramatic impact on our ability to advance science and foster early collaboration and debate on new research results.

“For me, a main advantage of preprints is that they can help to advance science faster, with public exposure of what is going on, what is cutting-edge”

  • Juan Añel, Section Editor PLOS ONE

I’ve never posted a preprint before, should I?

Yes! The benefits are endless. Preprints are an easy way to generate exposure for your research before you even decide where to submit (ESSOAr also accepts uploads of conference posters and other materials). When you post a preprint, you have immediate and unlimited reach allowing you stake the first claim on your methods and results, and even get early feedback from your community. Sounds great, right? Preprints are also beneficial for early career researchers who need discoverable, citable content that speaks to their academic contributions and can help advance their careers.

“Particularly for young scientists, who are the major driving force for science today and need a… good publication record to look for their next job, preprints would be a very [good] choice for them to publicize their findings in a timely way and “decorate” their CV”.

  • Xiaole Sun, Preprint Editor PLOS ONE

We encourage you to join us in our support of preprints, not just in the earth sciences but across all disciplines. Preprints are already one of the fastest growing research outputs, and we can all do our part to making it an even more successful outlet for new communities that are just beginning to explore its potential.

 

Towards minimal reporting standards for life scientists

A group of journal editors and experts in reproducibility and transparent reporting are putting together a  framework for minimal reporting standards in the life sciences. Part of this group, PLOS Executive Editor Veronique Kiermer shares a joint announcement.

Transparency in reporting benefits scientific communication on many levels. While specific needs and expectations vary across fields, the effective use of research findings relies on the availability of core information about research materials, data, and analysis. These are the underlying principles that led to the design of the TOP guidelines, which outline a framework that over 1,000 journals and publishers have elected to follow.

In September 2017, the second major TOP guidelines workshop hosted by the Center for Open Science led to a position paper suggesting a standardized approach for reporting, provisionally entitled the TOP Statement.

Based on discussions at that meeting and at the 2017 Peer Review Congress, in December 2017 we convened a working group of journal editors and experts to support this overall effort by developing a minimal set of reporting standards for research in the life sciences. This framework could both inform the TOP statement and serve in other contexts where better reporting can improve reproducibility.

In this “minimal standards” working group, we aim to draw from the collective experience of journals implementing a range of different approaches designed to enhance reporting and reproducibility (e.g. STAR Methods), existing life science checklists (e.g. the Nature Research reporting summary), and results of recent meta-research studying the efficacy of such interventions (e.g. Macleod et al. 2017; Han et al. 2017); to devise a set of minimal expectations that journals could agree to ask their authors to meet.

An advantage of aligning on minimal standards is consistency in policies and expectations across journals, which is beneficial for authors as they prepare papers for publication and for reviewers as they assess them. We also hope that other major stakeholders engaged in the research cycle, including institutional review bodies and funders, will see the value of agreeing on this type of reporting standard as a minimal expectation, as broad-based endorsement from an early stage in the research life cycle would provide important support for overall adoption and implementation.

The working group will provide three key deliverables:

  •       A “minimal standards” framework setting out minimal expectations across four core areas of materials (including data and code), design, analysis and reporting (MDAR)
  •       A “minimal standards” checklist intended to operationalize the framework by serving as an implementation tool to aid authors in complying with journal policies, and editors and reviewers in assessing reporting and compliance with policies
  •       An “elaboration” document or user guide providing context for the “minimal standards” framework and checklist

While all three outputs are intended to provide tools to help journals, researchers and other stakeholders with adoption of the minimal standards framework, we do not intend to be prescriptive about the precise mechanism of implementation and we anticipate that in many cases they will be used as a yardstick within the context of an existing reporting system. Nevertheless, we hope these tools will provide a consolidated view to help raise reporting standards across the life sciences.

We anticipate completing draft versions of these tools by spring 2019.  We also hope to work with a wider group of journals, as well as funders, institutions, and researchers to gather feedback and seek consensus towards defining and applying these minimal standards.  As part of this feedback stage, we will conduct a “community pilot” involving interested journals to test application of the tools we provide within the context of their procedures and community. Editors or publishers who are interested in participating are encouraged to contact Veronique Kiermer and Sowmya Swaminathan for more information.

In the current working group, we have focused our efforts on life science papers because of extensive previous activity in this field in devising reporting standards for research and publication.  However, once the life science guidelines are in place we hope that we and others will be able to extend this effort to other areas of science and devise similar tools for other fields.  Ultimately, we believe that a shared understanding of expectations and clear information about experimental and analytical procedures have the potential to benefit many different areas of research as we all work towards greater transparency and the support that it provides for the progress of science.

We are posting this notification across multiple venues to maximize communication and outreach, to give as many people as possible an opportunity to influence our thinking.  We welcome comments and suggestions within the context of any of these posts or in other venues.  If you have additional questions about our work, would like to be informed of progress, or would like to volunteer to provide input, please contact Veronique Kiermer and Sowmya Swaminathan.

On behalf of the “minimal standards” working group:

Karen Chambers (Wiley)

Andy Collings (eLife)

Chris Graf (Wiley)

Veronique Kiermer (Public Library of Science; vkiermer@plos.org)

David Mellor (Center for Open Science)

Malcolm Macleod (University of Edinburgh)

Sowmya Swaminathan (Nature Research/Springer Nature; s.swaminathan@us.nature.com)

Deborah Sweet (Cell Press/Elsevier)

Valda Vinson (Science/AAAS)

 

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