Registered Reports: One Year at PLOS ONE


A little over a year ago, PLOS ONE launched two new submission formats: Registered Report Protocols, peer-reviewed articles that describe planned research not yet initiated, and their follow-up Registered Reports, which report the results of the completed research and which receive an in-principle acceptance when their protocol is accepted for publication. It was part of a broader push for preregistration at PLOS.

When we added these options to the list of regular submission types we consider, the format wasn’t new: about 200 journals had already considered registered reports for publication, and the number has kept increasing since. The format had initially been relatively welcomed in the behavioral sciences and then made its way, sometimes with a few tweaks, to other disciplines. Preregistration in general has even been the norm in clinical trial research for years, albeit not necessarily with peer-review. And Registered Reports weren’t even entirely new at PLOS ONE: our partnerships with the Children’s Tumor Foundation and FluLab predate this launch.

But this launch had two distinctive features: we would publish the protocol (also called “stage-1 registered report”) of all the registered reports we would consider. We would do so regardless of the eventual results of the planned research, of course, but also regardless of whether the final report (also called “stage-2 registered report”) would be submitted or even completed. The Registered Report Protocol would be its own publication, and it would be so with the standard of any PLOS publication: with our expectations of data availability and rigorous ethics oversight, and with the possibility to make the full peer-review history available. It was, as far as we were aware, a distinctively transparent publishing format offering.

Other journals already published stage-1 Registered Reports, to be sure, but not at that scale and with the disciplinary breadth that PLOS ONE provides. This was this launch’s second distinctive feature: we were relying on an academic board of thousands of members to embrace this format with a different review process and criteria on as many study types and topics as the journal would normally consider.

For the 1st time since @RegReports were created in 2013, there is now at least one journal option for every research field across the full spectrum of physical, life and social sciences.

Chris Chambers, on PLOS ONE launching Registered Reports

The Registered Report format has been adapted and implemented in many ways across hundreds of journals (for instance at PLOS Biology). We made some choices with our own format: although deviations from the published protocol could invalidate the in-principle acceptance of the final report, we would consider such deviations, provided they are acknowledged and justified. We would also welcome exploratory, unregistered, or unplanned analyses in the final report, provided they are clearly identified as such. A Registered Report Protocol is an opportunity to receive early feedback on a study; it is the opportunity to claim ownership of a research project without having to wait for results to come in; it is also a tool against publication bias that drives us all not to publish null results. Above all, we envisioned Registered Report Protocols as a a mechanism for transparency in publishing and reporting rather than an unbreakable and inflexible vow. 

Our choice to distinguish clearly between the protocol and its final report, on the other hand, makes our format less adaptable to serial submissions and iterative registrations (which other journals publishing Registered Reports explicitly welcome). But authors wishing to do so with PLOS ONE can submit subsequent iterations of their registration (i.e., after the first follow-up to a published Registered Report Protocol) as regular research articles. But with that caveat, we wanted a format that is relatively flexible and that could be suited to as many study types and fields as we normally consider.

So what can we say a year later? We have received over 300 Registered Report Protocol submissions, about 60 of which are already published or accepted for publication (the first Registered Report Protocol was published in June of last year), by first authors from more than 20 countries. These submissions have acceptance and rejection rates comparable to our regular submissions. They cover many disciplinary areas: about 70% of the submissions are in medicine and health sciences, 15% in the behavioral and social sciences, and 8% in the life sciences. A call for papers in cognitive psychology, launched last fall in collaboration with the Center for Open Science, invited Registered Report Protocol submissions. Finally, we have already received a few follow-up Registered Report submissions. If and when we publish these stage-2 Registered Reports, they will be interlinked with their corresponding protocols so readers can easily navigate between them. 

The Registered Report Protocol submissions we received this past year are now published protocols for a systematic review on the effectiveness of public health interventions against COVID-19, a psychology survey study on trust in international relations, an animal study on neural plasticity, a study of biomedical sentence similarity measures, among others. They have been handled by a number of our Academic Editors and reviewers, many of whom were just discovering that Registered Reports were an option in their field. The journal’s editorial board members and reviewers have been instrumental in this successful rollout. As Andrew Miles, author of a published Registered Report Protocol, attested, “my research team and I benefited from careful reading by several excellent reviewers, as from an editor who pointed us to a data collection tool that we hadn’t previously been aware of.” 

Reproducibility of medical research findings has been found to be low, and Registered Reports give me the unique opportunity to describe in detail the statistical-methodological approach prior to having seen the data, and to get credit for it with respect to visibility in authorship. When we submitted our registered report to PLOS ONE we received very detailed reviewer comments, and we could improve our study design and analysis, as well as reporting. PLOS ONE publishes the [Registered Report Protocol] prior to the final study results, which has the advantage that the study can be brought to other people’s attention at a much earlier stage.

Ulrike Held, PLOS ONE Author
Is reporting quality in medical publications associated with biostatisticians as co-authors? A registered report protocol

Registered Reports are now just one of an increasing menu of publication formats. Recently, PLOS ONE launched new protocol types: Study Protocols and Lab Protocols. The Study Protocol format closely resembles that of Registered Report Protocols, but doesn’t come with an in-principle acceptance of the final report. Under the leadership of our new Editor-in-Chief Emily Chenette, PLOS ONE will continue to work with our communities to improve scientific communication, using the principles of openness, transparency, rigor, and reproducibility as guides.

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A new Editor-in-Chief for PLOS ONE


Dear PLOS ONE community,

What a joy it is to write this letter – to have the opportunity to reflect on the strengths of PLOS ONE and consider how we can best meet your needs in the years ahead. I’m writing to you to share what you can expect from me as Editor-in-Chief of PLOS ONE, and to call for your feedback and your perspective on what we’ve gotten right, and where we can improve.

I am a molecular biologist by training. I received my PhD in Genetics and Molecular Biology from the University of North Carolina at Chapel Hill in 2004, and studied gene expression signatures in lung cancer cells while a postdoc at Duke University. As a brand-new postdoc I had the experience that I am sure will be familiar to many of you of writing grants to secure funding for my research – and I realised, during this process, that what I really loved about scientific research was not the process of making the discoveries myself, but reading papers and considering how pieces of research fit together to advance discoveries. So, in 2007, I left the lab to begin working in science publishing. I joined PLOS ONE in 2018 after positions at the FEBS Journal and Nature Cell Biology. I feel very lucky to have had the opportunity to work closely with our former Editor-in-Chief Joerg Heber, who brought such meaningful and important changes to the journal to support scientific communication and our academic community.

I am excited to continue this work to serve the PLOS ONE community. From our board of nearly 10,000 Academic Editors to the authors, reviewers and readers who support the journal, we are embedded in a community of scientists and researchers who want to transform scholarly communication. I am committed to listening to our community to understand how we can best meet your needs and working with you to change science communication for the better – and always with the principles of openness, transparency, rigor and reproducibility in mind.

PLOS ONE has always supported these principles: we strongly believe that open science is trusted science. Under Joerg’s leadership, our commitment became increasingly tangible as we worked closely with our community to develop policies and practices that support Open Science throughout the lifecycle of a research project (Figure 1). In 2018, we developed links with bioRxiv to support authors who wished to post a preprint of their manuscript at the time of submission to PLOS ONE. Although our publication times are fairly speedy, this step helps ensure that all research is publicly available as soon as possible and helps authors receive credit for and feedback on their work. Importantly, preprints also offer a way to begin addressing some of the current limitations with the peer-review process, including issues around transparency, recognition and trust.

In 2019, we released Peer Review History to allow authors to opt in to making the reviewers’ reports and decision letters part of the publication record. Reviewers can also opt in to signing their reviews to receive credit for their work and bring additional recognition to this essential job. We’ve also recently launched Study Protocols, which complement our existing Registered Report framework in supporting authors to receive early feedback on their study design. Lab Protocols, another new article type, were developed in partnership with protocols.io, and represent a sleek and efficient way to peer-review and share research methods while allowing those who developed a specific technique to receive credit for their important contributions.

Figure 1: Recent steps along the path towards Open Science

I am proud of what the journal has accomplished in recent years towards the goal of transforming scholarly communication. From supporting preprints and other Open Science initiatives to enabling authors to publish (and receive credit for) the continuum of research, we are leading a transformation in research communication. But there is more to do. 

What matters to me most is that you feel that your work has a home in PLOS ONE. Addressing this means building deeper links with our communities – listening to and learning from you, and understanding how we can support you in publishing your research, whether as protocols, preprints or papers. The steps that we take towards greater transparency, openness and trust in research will be with our community as partners. 

I will also continue to create opportunities for reviewers and editors to receive credit for their work, and investigate new avenues for author feedback. For example, we’ve recently developed links with the Peer Community In communities, have explored hosting preprint journal clubs and have developed a pilot project to integrate comments on preprints into the “traditional” review process. We will keep experimenting, keep tweaking and keep refining as we assess ways to make the review process more meaningful and impactful for all involved. 

Finally, I will ensure that we deliver on our commitment to supporting research into areas around inequities and inequalities, while seeking to identify and minimise potential sources of bias in our manuscript-handling practices. Some of this work has already begun, and I look forward to sharing our progress with you. 

I want you to know how important your feedback is to me and to the journal, and I welcome all comments and suggestions on what we’re doing right and where we can improve. You can find me on Twitter at @emilychenette, or reach me via email at echenette@plos.org.

Thank you so much for your support of PLOS ONE and Open Science. I look forward to working with you all to continue PLOS’ mission of transforming research communication.

Emily

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Building a home for the Physical Sciences at PLOS ONE

Historically, PLOS ONE is best known in the life sciences and biomedical fields. However, as a multidisciplinary journal, we have always welcomed research from all subject areas, including the natural and medical sciences, engineering, mathematics, and social sciences and related humanities.  

Two years ago we formed a set of dedicated editorial teams in different subject areas across the PLOS ONE scope, with the aim of facilitating stronger interactions with our authors and our editorial board, as well as improving how we handle individual manuscripts. In this blog post, I’d like to outline how the team that I’m part of, Physical Sciences and Engineering, has been working to engage with researchers across physical sciences communities and to advance the PLOS mission by helping scientists and engineers to publish exciting research that is open, transparent and reproducible. 

Crossing disciplinary boundaries

In the last year alone we have published exciting papers in core physical sciences fields from climate change and natural language processing to fluid dynamics and statistics. What makes a multidisciplinary journal special, though, is the opportunity to provide a home for research which does not naturally sit in one traditional discipline or which forms previously unexplored connections between subject areas. 

Two recent papers we have published in recent months nicely highlight this interdisciplinary focus. 

First, a study authored by Braun and colleagues brought together chemists and archaeologists interested in the prospect of using isotopic ratios to provenance iron objects. The authors carried out a series of smelting experiments on Levantine iron ore samples, then used mass spectrometry to show that the ratio of osmium isotopes was preserved from ore to metal. This observation is notable because it means the Os isotopic ratio can be used to identify the source of iron in objects found in the Levant region, since ore from different sites has a characteristic isotopic ratio, and therefore as a promising tool for understanding the economic, social and geo-political aspects of iron production in the ancient world.

An iron bar is smelt on an anvil. https://doi.org/10.1371/journal.pone.0229623

A study authored by Lawley and colleagues from the mathematics and biology departments at Duke University used a mathematical model of oxygen uptake in insects to gain insight into the role of spiracles, small openings in the tracheal wall. It was previously known that spiracles alternate between closed, open and ‘fluttering’ states, the latter when they open and close rapidly, but the benefits of fluttering remain unclear. By defining a diffusion differential equation model, the authors found that a rapid fluttering state allows for comparable oxygen uptake to the open state but with much less water loss. This result suggests that insects can achieve both high oxygen intake and low water loss by keeping the spiracles closed most of the time and fluttering while open.  

Open spiracles on a Cluentius Sphinx Moth caterpillar. Image from Wikimedia Commons

We have also recently launched a call for papers programme in order to build dedicated collections of research on different themes from across the physical sciences and engineering. Collections we have published so far have covered topics as diverse as Machine Learning in Healthcare, Open Biomaterials Research, Open Quantum Computing and Simulation, Science of Stories and Mathematical Modelling of Infectious Disease Dynamics, providing an opportunity for readers and prospective authors to see the broad range of interdisciplinary research we publish at PLOS ONE. Right now we have an open call on Cities as Complex Systems, encompassing complex systems and networks research applied to questions in urban science.

Getting to know you

Our team has enjoyed meeting researchers from across the globe at conferences, workshops and other events. In 2019 we attended meetings on ubiquitous computing and wearables, quantitative biology, geology and geochemistry, robotics, complex networks and materials science, learning about what matters to researchers when it comes to sharing their science with other researchers and the broader public. One highlight for us was NetSci 2019, where our Associate Editor Deanne Dunbar participated in a spirited ‘Meet the Editor’ panel discussion on the current challenges and future directions of publishing in the (relatively) nascent subject of network science. Our Associate Editor Hanna Landenmark also had the chance to connect with early career researchers at the organic bioelectronics meeting Orbitaly2019, where she ran a workshop on authorship and reviewing. 

Conversations we have had at meetings have also led to us significantly expanding our editorial board, with more than 800 scientists from physical sciences fields becoming PLOS ONE Academic Editors since 2018! This depth and breadth of expertise means we ensure that our editorial and review process is fast and thorough, led by experts in the scientific community.

Supporting reproducible research

Reproducibility is a key pillar of open science and the PLOS ONE mission. For all research we emphasise the importance of reproducibility by making it one of our core publication criteria, and via our open data policy. Within individual subject areas in the physical sciences, however, we often hear demand from researchers for additional guidance or editorial policies so that reported research can better meet community standards. Working with our academic editors we have recently developed new policies to support the reproducibility of studies reporting data from NMR spectroscopy and crystallography experiments, with plans to develop specific author guidelines in other areas in 2020. 

Electron density map of nucleotide binding at the active site of T. thermophilus methylenetetrahydrofolate dehydrogenase. https://doi.org/10.1371/journal.pone.0232959

Get in touch!

We have a number of other exciting projects planned for 2020 at PLOS ONE and we are always keen to hear from you! We regularly highlight new physical sciences and engineering papers every fortnight on the PLOS ONE homepage, on this blog and via our Twitter account @PLOSONE. You can also get in touch with us via the form below to share your ideas on how to make publishing physical sciences research easier and accessible to all!

Featured image: Jill Hemman, CC-BY 2.0, Flickr

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Maintaining high research integrity standards at PLOS ONE

Since 2006, PLOS ONE has published >200,000 articles, providing an inclusive home for primary research spanning all scientific disciplines and representing researchers from around the globe. As reflected in the journal’s publication criteria and policies,