Category: Science & Tech

Following the launch of PLOS Complex Systems earlier this year, we sat down with Editor-in-Chief Hocine Cherifi to learn more about his vision for the journal and developments in the field he’s keeping an eye on.

The journal has a broad, transdisciplinary scope, why is this important?

Complexity is a field that transcends traditional boundaries–it is not uncommon to see a researcher study economic, social, or natural complex systems at once. As such, the journal must be able to accommodate the broad range of interests many researchers in this space have. When we bring that all together, we can learn from each other. We want PLOS Complex Systems to be a space where researchers can connect and share approaches that they might not have discovered otherwise.

It is also a field that is growing rapidly, and this means more and more scientists are starting to use complex systems analysis tools. The journal must be accessible to people who consider themselves a biologist or sociologist, and encourage the diversity of perspectives and expertise that they bring to the community.

In this, I would like to highlight our commitment to constructive peer review. Building the journal’s editorial board was an intensive and intentional process, and I am very grateful for the time they have lent us so far, and will continue to invest in the journal. Their expertise is invaluable, and I am thrilled we can count on them to set the standard for the quality of research and discourse seen in PLOS Complex Systems_.

What developments are occurring in your field of expertise that excite you currently?

The thing that excites me most is the growth of dedicated coursework and degree programs for complex systems and networks. This is recognition of the importance of complexity science by academia as a whole and I am excited to see how students in these programs think, as well as the problems they want to address. My hope is that these programs will embrace the need for collaboration and subject expertise as well as inspire curious students.

How will Open Science play a key role in the journal achieving its vision and advancing the field?

Open Science is inclusive, transparent, and flexible, making it the optimal way to communicate complex networks research from across a range of disciplines to all its possible audiences. Open Science also increases visibility and reusability, not just of the research article, but the underlying methods and data of the research itself, which creates an opportunity for a wider community to further test and build from these components

This is particularly vital to ensuring that the datasets and methodologies that researchers create and leverage are properly vetted. With the prevalence of machine learning models, we must be conscientious of the data we use and the risk of perpetuating inequalities that may be hidden in these tools. 

Optimal windows exist for action and perception during the 0.8 seconds of a heartbeat, according to research from PLOS Biology. The sequence of contraction and relaxation is linked to changes in the motor system and its ability to respond to stimulation – findings that could have implications for treatments for depression and stroke that excite nerve cells. Learn more about the researchers’ findings in our Research Highlights summary below, or you can access the full article in PLOS Biology. 

Background

The ways in which we perceive and engage with the world are influenced by internal bodily processes such as heartbeats, respiration and digestion. Cardiac activity can influence auditory and visual perception, and touch and sensory perceptions have been shown to be impaired during the systolic phase of the cardiac cycle when blood vessels are briefly distended.

Esra Al of the Max Planck Institute for Human Cognitive and Brain Sciences, Germany, and colleagues, wanted to understand whether there were changes in cortical and corticospinal excitability — the ability to respond to stimuli — across the cardiac cycle. 37 healthy human volunteers aged between 18 and 40 years received a series of transcranial magnetic stimulation (TMS) pulses — non-invasive short magnetic pulses that stimulate nerve cells — above the right side of the brain.

Study Design and Findings

Motor and cortical responses as well as heartbeats were measured during the pulses and the authors found that higher excitability was recorded during the systolic phase. These simultaneous recordings of brain activity, heart activity, and muscle activity, suggest the timing of heartbeats and their neural processing are linked to changes in the excitability of the motor system.

TMS is used in treatments for depression and recovery after stroke. The research raises questions about whether these could be fine-tuned to improve results, as well as contributing to a greater understanding of brain-body interactions in health and in disease.

The authors add, “Intriguingly, this study uncovers a remarkable connection between the human heart and brain, revealing distinct time windows tailored for action and perception.”

For PLOS, increasing data-sharing rates—and especially increasing the amount of data shared in a repository—is a high priority. 

Research data is a vital part of the scientific record, essential to both understanding and reproducing published research. And data repositories are the most effective and impactful way to share research data. Not only is deposited data safer and more discoverable, articles with data in a repository have a 25% higher citation rate on average.

With support from the Wellcome Trust, we’ve been experimenting with two solutions designed to increase awareness about data repositories and promote data repository use among both authors and readers. One solution didn’t achieve its expected outcome in the context we tested it (a “negative” result) while the other shows promise as a tool for increasing engagement with deposited data. The mixed outcomes are an example of why it’s so important to share all research results regardless of their outcome – whether “positive” or “negative” results. We hope that our experiences, what we’ve learned, and above all the data and results, can help the scholarly communications community to develop new and better solutions to meet the challenges we all face, and advance Open Science.

Read on for a quick summary of the studies we conducted. Or get the full details from our new preprint on Figshare, and explore the data for yourself.

PLOS data repository experiments, 2021-2023

Experiment 1: Using iconography to highlight data shared in a repository

Question

Does highlighting data in a repository linked to published research articles with an eye-catching graphic in the form of an Accessible Data icon increase access to the associated dataset?

Hypothesis

We hypothesized that:

1. the Accessible Data icon would be associated with a statistically significant increase in engagement with datasets, and 
2. the icon would motivate authors to deposit their data in a repository in order to have the icon applied to their article

Implementation

An Accessible Data icon automatically appeared on any article published after 2014 that included a link in its Data Availability Statement to one of three popular data repositories (Dryad, Figshare, and OSF) beginning on March 29 2022. Readers can see and click on the icon from any eligible PLOS journal article and be directed straight to the data in the repository.

Data

Usage data relating to the number of Accessible Data icon link clicks, and internal data from Figshare, one of three selected repositories. A survey of 4,898 researchers, and follow-up interviews with 12 researchers.

Results

In the first 12 months of the experiment (April 2022-March 2023) we recorded more than 20,000 reader clicks on the icon across all PLOS properties. Through analysis of 543 Figshare datasets linked to PLOS articles, we observed that in the 12 months prior to the launch of the icon, the average number of views received per month was 2.5, rising to 3.0 in the 12 months following the launch (a statistically significant relative increase of 20%).

Survey respondents who were aware of the Accessible Data feature and who had used a repository were asked to what extent the feature influenced their decision to use a repository: 51% answered that they were influenced either somewhat or strongly by the existence of the feature. 

Respondents were also asked about the impact of the Accessible Data feature on their future likelihood of submitting to a repository: 40% were more or much more likely to use a repository.

Experiment 2: Integrating Dryad into the Editorial Manager submission system for PLOS Pathogens to ease repository use

Question

If authors have the option to submit their data to a repository as part of journal submission, will repository use increase?

Hypothesis

We predicted an absolute increase of 10 percentage points in the use of data repositories by PLOS Pathogens authors, from the 2020 baseline of 25% to 35%.

Implementation

A new option appeared on the Attached Files screen in the PLOS Pathogens Editorial Manager submission system on October 5 2021, allowing authors to upload research data to Dryad. Authors were redirected into the Dryad system via a popup window where they entered the required information and files and received a Dryad DOI, which they could then include in the Data Availability Statement later in the submission process. 

Details and instructions were added to the journal submission guidelines, Editorial Manager submission system, and PLOS website, and the offering was promoted through established channels including email, social media, and advertising.

Data

Usage data from the Editorial Manager submission system and Dryad. Survey data from 654 researchers who submitted to PLOS Pathogens. 

Results

About 2% of submitting PLOS Pathogens authors (44 submitting author groups) used the integrated repository feature. PLOS Pathogens’ repository use for the first half of 2023 was 33%, however this appears to be part of an ongoing organic increase that began prior to the experiment.

Among the 574 survey respondents who did not share or plan to share data using the Dryad integration, the biggest reasons included lack of awareness (35%), uncertainty in how to use the integration (26%), and that data had already been uploaded to another repository (21%).

Our next steps

As a result of these experiments and our findings, we’ve made the decision to discontinue the PLOS Pathogens integration with Dryad. PLOS will continue its publisher membership of Dryad and our authors are still encouraged to use it to share data in their own workflows. We look forward to exploring other ways to increase use of repositories. Because of the promising results from the Accessible Data icon, we decided to extend the service to include an additional six repositories, for nine total. We look forward to seeing—and sharing—the outcomes from this next phase of work.

We’ve spent the past few months getting our systems ready and building a strong community of editors for each journal who will represent the full diversity of the research communities we aim to serve. With our teams in place, we’re excited to begin accepting submissions to each journal and bring the expert knowledge of researchers in these spaces to a broad audience of stakeholders.

For authors who have been eagerly preparing their manuscripts, you can now submit your work to PLOS Complex Systems or to PLOS Mental Health! More information about the journals including research sections, publication criteria, submission guidelines, and our inaugural Editorial Board members are now available on the journal websites linked below.

About the journals

PLOS Mental Health is an inclusive journal led by Editors-in-Chief Charlene Sunkel and Rochelle Burgess, working alongside staff Executive Editor Karli Montague-Cardoso and in collaboration with a diverse Editorial Board. The journal is seeking research that addresses challenges and gaps in the field of mental health research, treatment, and care in ways that put the lived experience of individuals and communities first. 

PLOS Complex Systems will bring together leading research of broad significance that facilitates understanding of complex systems in all disciplines, led by Editor-in-Chief Hocine Cherifi in collaboration with our Editorial Board of researchers actively working in the field.   

Both journals are intended to bring a broad range of research disciplines and expert perspectives together through broad scopes that facilitate information-sharing and cross-talk among stakeholders. They’re also built on PLOS’ foundation of Open Science principles and will work with research communities to define the practices that improve research integrity, transparency, equity, and visibility in the field. 

Making OA publication more accessible

Both journals are supported by PLOS’ institutional partnership models.PLOS Mental Health will use our Global Equity model which provides regionally equitable opportunities for institutions to cover the cost of Open Access publication on behalf of their authors. PLOS Complex Systems will be supported by our Flat Fee model, which streamlines the process for institutions to reduce or eliminate author fees. 

Find out if your publication fee is already covered

Authors can check our Institutional Partners page to see if their institution is already a PLOS partner–we’ll be adding details about the new journals this week. Authors whose institution or funder is based in a Research4Life country are automatically eligible for similar publishing benefits and can view our fees page for eligibility criteria and additional publication fee support options. 

Keep in touch!

You can help us increase the reach of rigorous mental health and complex systems research and join the discussion by following the journals on X (formerly known as Twitter) @PLOSMentalHlth and @PLOSComplexSys. We want to hear from you!

For more information about the journals (or to be the first to know when first articles publish) sign up to receive news and updates for PLOS Complex Systems and PLOS Mental Health.

Open Access Week is a special commemoration for us as one of the original co-founders of the event, along with SPARC and Students for Free Culture. It shows how far we’ve come, but also what we still have to accomplish. This year’s theme is “Community over Commercialization,” and we’re giving you a sneak peek into how PLOS prioritizes that ethos in our day-to-day thinking.

PLOS started with an open letter. A call to the research community to build a better future through transparency and inclusion, standing in direct opposition to the profit-motivated practices at large commercial journal publishers. That spirit still drives the organization today.

Community Publishing

We are a mission-driven organization that aims to transform scholarly research communication. Most of our readers know PLOS best as a nonprofit, Open Access publisher. The research communities we serve are at the heart of each of our journals. We only launch new journals and open research initiatives after consulting with representatives of the relevant research communities. It’s not our goal to simply add more options to the list researchers have to choose from today, but to consider journals as vehicles for change and identify the role PLOS can play in providing a venue for researchers to share their work more openly. Journal attributes, such as the level of editorial selectivity, scope, editorial policies, leadership/Editorial Board membership and our business models are shaped by community consultation, centering on their unmet needs, and aim to shift research behaviors from closed to open.

Here are just a few ways that we think about our journals and our Open Science mission.

Although the theme of “Community over Commercialization” is evident everywhere at PLOS, it is perhaps best expressed through our publishing program, which is also the truest expression of our Open Science mission.  PLOS partners with like-minded organizations and scholars, and our unique editorial approach is closely aligned with the UNESCO recommendation for Open Science which emphasizes transparency, collaboration, and inclusion; and the United Nations Sustainable Development Goals, which have a global community perspective.

When PLOS decided to launch new journals, we knew had to build them from a new blueprint in order to fulfill our aims and mission namely by:

• including the broadest range of researchers’ voices globally
• ensuring that these new Open Science platforms would be shaped at every level by the communities they aimed to serve
• striving to amplify the perspectives of all researchers and stakeholders in global issues including from Lower middle-income countries
• leveraging the diversity of the editorial boards, which shape content, policies, and practices that are reflective of the research communities working in these fields

Community funding

As Open Access has grown, we saw a need to try something new: supporting its cost in a regionally equitable way with our focus on community, not profits, which brings us to our business models, which underpin our approach. At issue: Article Processing Charges (APCs) helped demonstrate that Open publishing could be viable and allowed Open Access to become a meaningful force in scholarly communication.

But APCs don’t work for everyone. Not all disciplines or regions have the same level of funding, and publishing costs can deplete author grants and reduce the amount available for research, while for publishers, administering individual publication fees carries significant overhead which leads to higher costs overall.

We firmly believe that all researchers should have the opportunity to both read and publish under an Open Access license, and that solutions for sustainable Open Access publishing need to involve all stakeholders. That’s why PLOS is leading the charge in developing non-APC alternative funding models. All these business models address specific challenges in Open Access publishing and were created with input from the community.

A future of Openness through community

Although PLOS is primarily a publisher, we advocate for Open Research practices because we believe that Open Science is better science—more rigorous, more trustworthy, more equitable, more reproducible, more creative, faster, and more impactful for society. PLOS’ has a built-in philosophy of sharing what we learn (e.g. OS research) and openly seeking input and collaboration in how we innovate is a defining principle of how we work.

PLOS’ mission is to lead a transformation in scholarly publishing from a closed to an Open model. We believe we can best accomplish that by empowering our community to engage in Open Science practices on a large scale, as part of their regular scientific communications while collaborating with other actors in scholarly communication such as institutions, funders, and policymakers to move towards a better Open Science ecosystem.

Since 2015 Charla Lambert, Diversity Equity & Inclusion Officer for CSHL, and Stephen Matheson, Associate Editorial Director at PLOS have collaborated to coach researchers to improve the clarity and effectiveness of their professional writing through their annual Scientific Writing Retreat. We caught up with them just before their 8th annual retreat, taking place this November at the Banbury Conference Center in Long Island.

The Scientific Writing Retreat has been a long term partnership (8 years now!). What changes have you observed in scientific writing norms and best practices in the time you’ve been running the retreat? Has your advice to writers changed at all? Any predictions on where science writing may be headed in the future?

Stephen Matheson (SM): Preprinting has gone from a semi-controversial practice that was resisted by some publishers, to a practice that is still misunderstood and opposed by some subcommunities in science but is overall uncontroversial and broadly embraced. We used to discuss preprints as a separate topic in our session on publishing—we stopped doing that a couple years ago.

I think our advice to writers is… well, timeless. Two of our fundamental principles are that good scientific writing is just good writing; and that one must know oneself as a writer before trying to adopt particular practices or habits. Those things haven’t changed at all, though I think it will soon get harder to find oneself (as a writer) than it was before Bard and ChatGPT. GPTs will change scientific writing, and all writing, and we’ll start addressing that this year using materials developed by Charla in her teaching at CSHL.

Charla Lambert (CL): I think the rise of generative AI this year will be the biggest change, though its effects on scientific writing norms are TBD and playing out in real time. It will certainly affect people’s writing, editing, and creation processes in ways that we don’t yet foresee. It has the potential to be really beneficial for people who struggle with writing, people whose primary language isn’t English, people who don’t have access to or funds for professional editing services or training, etc.  But I agree with Stephen that it also has the potential to mask people’s individual style in writing and, as a scientific community we’d then lose out on a lot of distinct and engaging voices.

I’m curious how bringing together expertise from different organizations and different areas of scientific communications has helped shape the training that you’ve created. What are some of the benefits and/or challenges of collaboration? Has your work together impacted how you think about scientific writing and science communications broadly?

SM: There is no single good/best way to write. That’s one principle we emphasize from the beginning, so we are effectively obligated to provide students with diverse writing coaches who come from different areas of science and who have different (sometimes strikingly different) habits and practices in writing. We all enjoy our collaboration very much, which is good because the retreat would be ineffective without that diversity. 

There is no single good/best way to write.

The only challenge created by our collaboration is the fact that our course only happens once a year and is planned by a team that is dispersed among as many as four different institutions in three states. Charla and the CSHL courses team do the vast bulk of the preparation.

How has our collaboration changed how I think about scientific writing? 

1. Teaching and coaching in the retreat has led me to more strongly emphasize the (potential) importance of dramatic flair (e.g. “twists”, pause for effect) and similar tactics that seem at first to be inappropriate in scientific writing. It is all too common for the pursuit of precision and completeness to overshadow and doom the more important pursuit of clarity. 

2. We urge students to reflect on their strengths and especially on their weaknesses (“Identify your kryptonite”) and then work with both. This is great advice in any part of life and I actively include it in mine.

CL: Stephen’s correct that we place an intentional emphasis on diversity when assembling the slate of coaches in a given year—diversity in backgrounds, experiences, positions, writing styles, and approaches to coaching writers. One of the amazing things that happens each year is a recognition among the “students” that there really are core principles they keep hearing from all the different coaches. Everything we suggest tends to stem from the audience for a given piece, the goals in writing to that audience, and clarity in the writing to achieve those goals. We don’t prescribe an abstract set of do’s and don’ts—there’s an explicit recognition that everyone’s writing process is different and what works well for one person won’t necessarily work for another—but everyone leaves the retreat with some tools for examining clarity in their own writing.

And yes, the big challenge to collaboratively running this retreat is getting to do it only once a year! There have been many jokes over the years about starting a consulting company, a train-the-trainer model, or even a podcast about writing (I’m still not sure who’d listen to that, haha). The curriculum and experience are definitely ongoing needs in science. I love running the retreat with Stephen and the great coaches and co-instructors we work with, but we all have limited bandwidth.

Do you find that trainees benefit from working together as part of the course? Are there benefits or challenges to workshopping with researchers from different disciplines and institutions?

SM: Small groups are a HUGE part of the retreat and are consistently rated very favorably by students. 

CL: Absolutely. Peer feedback groups are essential, and we spend time talking about how to give and receive feedback constructively so the time in small groups is effective. We intentionally create the groups so that, as much as possible, people are working on similar things (manuscripts, grants, fellowships, job applications, etc.) and are from very different subdisciplines. There’s a power to hearing from peers what you do well when writing, and there’s a power to hearing from peers in different subdisciplines what might be confusing in your writing. The small groups help develop empathy for and a sharp focus on the audience.

Peer feedback groups are essential, and we spend time talking about how to give and receive feedback constructively so the time in small groups is effective.

One anecdote I’ll share: One year, the work in small groups spun out into a full-class discussion on journal clubs and the climate in science. As coaches, we give both positive and constructive feedback, and we ask the students to give positive feedback in small groups before getting mired in more critical comments of someone else’s writing. This often takes a lot of practice because the students are typically used to seeing science function only on critical or “negative” feedback. At the end of the retreat, one of the students expressed surprise that they benefited from hearing positive feedback instead of just critical comments from their peers. Another student asked why journal clubs don’t typically prescribe both positive and constructive feedback—the class agreed that journal clubs often devolve into negative commentary, sometimes even ad hominem attacks. Finally, a third student who was an early-career faculty member realized they could run their journal clubs differently, and vowed to do so in the future. It was a really satisfying integration of all the different professional hats I wear!

Thank you both!

Written by Marcel LaFlamme

For almost a year, Open Science Indicators have offered the ability to measure three Open Science practices: data sharing, code sharing, and preprint posting. Now, PLOS and DataSeer are adding a fourth indicator for protocol sharing. As we expand the tool’s capabilities, we invite your feedback on the approach we’ve taken in this preliminary data release.

What is a protocol?

The word protocol means different things in different fields, so first we want to clearly signal what types of research output are in scope for this indicator. In line with the community-developed definition used in the PRO-MaP recommendations, we are defining protocol as “detailed and/or step-by-step instructions for carrying out a research procedure.” Clinical study protocols, review protocols, registered report protocols, and other protocols describing a study that will take place in the future generally do not meet this definition, although we’re currently scoping work on a fifth indicator that is likely to include these outputs.

How we got here

In 2022, PLOS conducted a study of researcher practices and priorities around sharing detailed methods information including protocols. The study found that, while methods sections of research articles are regarded as adequate for evaluating study findings, they are not widely perceived as adequate for reproducing results or reusing a method in a different context. To ensure that methods information is usable for a range of research tasks, study participants reported publicly sharing protocols through channels including peer-reviewed publications, supplementary information, dedicated repositories, and other websites.

With these results in mind, we drafted a set of requirements built on our OSI measurement framework and consulted on them with stakeholders including tool providers, meta-researchers, and other methods experts. We then worked with DataSeer to operationalize the requirements. Our current approach detects links to or citations of outputs from an allowlist of publications and repositories known to focus on protocols. In keeping with our approach to measuring data and code sharing, we also detect relevant metadata from supplementary information where available. Please consult our methods documentation for more detail.

What the data say

From 2019 through mid-2023, the rate of protocol sharing for research articles published in PLOS journals hovered around 8%. In contrast to trends in other Open Science practices over the same period, adoption of protocol sharing by PLOS authors did not appear to change appreciably – according to these preliminary results. We assume that not all articles generate protocols, but the rate of protocol generation was not calculated for this release.

Among a comparator set of about 18,000 Open Access research articles from PubMed Central, the rate of protocol sharing did appear to increase from 10% in 2019 to 15% in the first half of 2023. Additional qualitative research may help to explain why these trendlines diverge, whether because of limitations in our data sources or actual differences in author behavior.

Preliminary analysis of the locations of protocols associated with PLOS articles indicates that a clear majority (84%) appear as peer-reviewed publications, with Nature Protocols and the Springer Protocols collection as the most cited sources. Sharing in dedicated repositories like protocols.io and Protocol Exchange became less common over the reporting period, falling from 11% in 2019 to 2% in the first half of 2023, while sharing via supplementary information became more common. The use of repositories is often viewed as a best practice for protocol sharing because these protocols can be updated as they evolve over time.

What’s next

Our roadmap for further developing the protocols indicator includes adding detection of protocols on lab websites and other online locations. We plan to look more deeply at citations of published protocols, so that we can understand the extent to which authors are pointing to procedures actually used in their study as opposed to referencing protocols for some other reason. We also want to be able to assess how often researchers share their own protocols versus protocols created by others.

Just as importantly, we’d like to hear from you: are there publications or repositories missing from our allowlist? How should we address the limitations of an allowlist-based approach? And are there other ways of communicating detailed methods information that we should consider? We’d be grateful for your input by November 15; you can comment below or write to mlaflamme [at] plos.org to share your perspective.