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Over the first few months of 2021, F1000Research has been reflecting on some of our top research from 2020. From articles with the most views and downloads to the most successful blog posts from F1000Research-published authors, take a look at our top 10 articles from 2020.

The past year in research at F1000Research has been a busy one. With extra pressure applied to the global scientific community by the COVID-19 pandemic, it is no surprise that submissions to F1000Research platforms increased by 65% in 2020 compared to 2019, with a 49% increase in articles published. Comparing early 2020 to early 2021, there has been a further increase in submissions over the first 2 months by over 100% and a subsequent rise in articles published of over 90%.

As we reflect on the past year of research challenges and opportunities, we have highlighted a handful of the most successful articles published with F1000Research. Starting with the best performing by views, downloads and social media appreciation, we also feature articles hand-picked by the Editors, as well as those featured on the blog.

Top in 2020: most views and downloads

Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China – Robert L. Kruse, Johns Hopkins Hospital (MD, USA)

Published in February 2020, this Opinion Article offered an early perspective for the treatment of COVID-19, considering drug repurposing, neutralizing monoclonal antibody therapy, and an oligonucleotide strategy targeting the viral RNA genome.

“Excellent article. Very thoughtful and thorough while understandable to a clinician.”

Comment from Sandra Wainwright, Yale New Haven Health (CT, USA)

It is no surprise that COVID-19 is the topic of focus for the best performing article for views and downloads over the past year, achieving 56,486 views and 11,782 downloads at the time of writing this blog post.

This “authoritative review” – as described by Reviewer, Yi-Wei Tang from the Danaher Diagnostic Platform (Shanghai, China) – begins by explaining that a vaccine would be the priority focus for outbreak control, but goes on to present arguments for exploring different treatments for COVID-19 at a time where no therapy had yet been proven effective.

As Tang explained in the Reviewer Report, “After briefly covered several treatment strategies, the author focused on options to block virus from entering cells. Figure 1 is terrific.”

As a stark reminder of the rapid response to COVID-19, this Opinion Article highlights the speed at which real progress has been made since February 2020. Just 1 year later in March 2021, there are now several therapeutic options and effective vaccination programmes continue to be rolled out around the world.

Top on Twitter

Effective image visualization for publications – a workflow using open access tools and concepts – Christopher Schmied, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (Berlin, Germany) and Helena Jambor, Technische Universität Dresden (Germany)

This Software Tool Article begins by explaining how 25% of figures in biomedical publications contain research images, but that a lack of experience may lead to compromised legibility or even accessibility if these images have been prepared inappropriately.

Great treasure found here. Thanks for it!

Comment from Nicolas Goudin, Necker Bioimage Analysis (Paris, France)

As a suggested solution to this issue, Schmied and Jambor proposed a ‘workflow for effective and ethical image presentation’, presented as a cheat sheet and aimed at novice users of open source image processing and presentation software.

However, the utility and lasting impact of an open and inherently useful resource such as this is not limited for use by novice users, as Guillaume Jacquemet from the University of Turku (Finland) explained in the Reviewers Reports:

“The article is of very high quality and will be very useful for students and seasoned microscopists alike. I will certainly make it a mandatory read for my lab members.”

Have you struggled to make image figures for papers or talks? @helenajambor and me created a workflow https://t.co/jGYltPQnEI with cheat sheets for easy and scientifically accurate image visualizations @FijiSc @bioimageanalysis #opensource Thank you @NEUBIAS_COST @F1000Research pic.twitter.com/9Payh5Xnq7

— Christopher Schmied (@ChriSchmied) November 30, 2020

Find out more from the authors – read the full blog post >>

Editor’s choice

1 – Recognizing the value of software: a software citation guide – Daniel S. Katz (University of Illinois at Urbana-Champaign; IL, USA) et al.

As indicated by the title, the authors suggest that software can often be overlooked, despite being fundamental to research.

“A very well written overview about how to make research software more important to research and researchers.”

Comment from Oliver Bertuch, Forschungszentrum Jülich GmbH (Germany)

The team goes on to explain how software could be better recognised if cited the same way as other research articles and books, for example, proposing a set of community-driven guidelines.

The Method Article provides general guidance for citing software, but also leaves room and even encourages specific communities to take these steps further to better tailor the approach to their own audiences and disciplines.

Find out more from the authors – read the full blog post >>

2 – Epidemiology of mental health problems in COVID-19: a review – Md. Mahbub Hossain (Nature Study Society of Bangladesh) et al.

This Review, published in June 2020, examines the reported psychological impact the COVID-19 pandemic was already having on the global population, citing an increased ‘burden’ of mental health problems including anxiety, depression and suicidal behaviour.

“Thank you for giving me the opportunity to review this article reporting the epidemiology of mental health problems in COVID-19.”

Reviewer Report from Reindolf Anokye, Edith Cowan University (Joondalup, Australia)

The authors claim that the evidence reviewed suggested that ‘a psychiatric epidemic is cooccurring with the COVID-19 pandemic’, calling for more attention from the global health community and strategic interventions to help manage the psychosocial challenges as well as the promotion of mental health during the pandemic.

Reviewer, Reindolf Anokye, thanked the authors for their invitation to review their contribution, and reported:

“This is an important, well-written article that will contribute to the literature in public health. The authors have done a great job putting this together…”

3 – An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action – Hartwig Anzt  (Karlsruhe Institute of Technology, Germany and University of Tennessee, USA) et al.

We revisit the importance of software in research with the next Editor’s Choice article, as the authors begin with an assertion for the central role of software in research.

“These sections are accompanied with a story using a fictional character, Kim, which helps to relate these aspects to typical career stages of a research software engineer.”

Reviewer Report from Radovan Bast, UiT The Arctic University of Norway (Tromsø, Norway)

This Opinion Article calls for actions towards creating a sustainable software environment in Germany, proposing strategies and measures with the goal to ensure that ‘software is recognised as a first-class citizen in research’.

Uniquely, the authors employ a fictional character – Kim, a post-graduate PhD student in researchonomy – to tell the story of her career as they explore key challenges with funding, infrastructure and legal issues surrounding the sustainability of software in research.

Both Reviewers for this paper reported enjoying following the story of Kim, as context was provided for how a software engineer may encounter different issues at different stages of their career.

As Radovan Bast summarised:

“The article is thoroughly researched, well-written, and offers an excellent overview of the challenges when building an environment for sustainable research software. Most of the discussed challenges and recommendations carry beyond Germany and are relevant and transferable to other countries.”

4 – Data extraction methods for systematic review (semi)automation: a living review protocol – Lena Schmidt (University of Bristol, UK) et al.

This Study Protocol proposes a methodology for a Living Systematic Review, based on the constant surveillance of published methods and tools for data extraction for (semi)automating the systematic review process, as indicated in the title.

According to the authors, evidence-based medicine researchers struggle to keep up with the sheer volume of primary research articles published, and therefore a strategy for better managing or automating the data extraction process is required for facilitating faster routes to publication.

By conducting a Living Systematic Review of the methods and tools available for data extraction, the team hopes to increase transparency in the reporting and assessment of automation technologies, as well as reduce research duplication and waste.

Best on the blog

1 – COVID-19 and blood groups – there is an elephant in the room, but who cares? Do we need additional rules for preprints? – Joern Bullerdiek, University of Rostock and University of Bremen (Germany)

“To help avoid such problems in the future, I recommended establishing some additional rules for preprints.”

Blog quote from Joern Bullerdiek

This Opinion Article explores the current relationship between preprint publications, the media and the subsequent communicated message to the public following misguided attention to a publication on the association of ABO blood groups and COVID-19.

Bullerdiek proposes three key rules, recommending more time for peer or community comment, full disclosure of these comments and that no press releases are to be shared by the authors during that time.

On the blog, Bullerdiek explains his motivations for writing the Opinion Article further, discussing whether stricter rules are necessary to prevent misinformed and unnecessary public anxiety.

Find out more from the author – read the full blog post >>

2 – ‘The long tail of Covid-19’ – The detection of a prolonged inflammatory response after a SARS-CoV-2 infection in asymptomatic and mildly affected patients – Ivan Doykov (University College London Institute of Child Health, UK) et al.

As the pandemic has been referred to a few times now in the context of the top research published by F1000Research over the past year, this article offers a look to the future as we begin to explore the after-effects of contracting the virus.

“This provides important findings and a very useful methodology for future follow-up studies in Long COVID-19 cohorts.”

Reviewer Report from Paul Skipp, University of Southampton (UK)

By employing targeted proteomics methodologies, the team at the UCL Institute of Child Health have been identifying and investigating potential biomarkers for Long Covid – the ‘next chapter’ of the pandemic.

On the blog, Wendy Heywood (also from the UCL Institute of Child Health) outlines the project and explains how the team has adapted the research to apply to larger cohort and the rapid pace at which COVID-19 research is evolving.

Find out more from the authors – read the full blog post >>

3 – It’s the network, stupid: a population’s sexual network connectivity determines its STI prevalence – Chris R. Kenyon (Institute of Tropical Medicine, Antwerp, Belgium and University of Cape Town, South Africa) and Wim Delva (Ghent University, Belgium and University of Stellenbosch, South Africa)

Stepping away from COVID-19 for a moment, this Opinion Article explores possible reasoning behind the difference in the prevalence of sexually transmitted infections – including HIV and bacterial vaginosis – in different populations.

Kenyon and Delva argue by way of critical analysis that it is in fact the sexual network associated with an individual that would increase the risk of contracting an STI, with the most ‘connected’ networks reporting higher prevalence of STIs, HIV and bacterial vaginosis.

As Reviewer, Ann Jolly (University of Ottawa, Canada), explained:

“I think this article is thought provoking and even if one is not entirely convinced by it, it adds much deeper and more critical thought to assumptions of mathematical modellers and epidemiologists about the immediate causes of HIV than I have ever seen. I am glad it is published.”

On the blog, to commemorate Sexual Health Awareness Week 2020, Alanna Orpen (F1000Research) explores the idea of ‘knowing your sexual connectivity network’ as a risk factor, sexual intercourse diaries and networks associated with sexual risk taking.

Find out more – read the full blog post >>

4 – The worldwide clinical trial research response to the COVID-19 pandemic – the first 100 days – Perrine Janiaud (Stanford University, CA, USA and University of Basel, Switzerland) et al.

“Just imagine what would be possible if we translated this to other medical fields. What if we could have similar trials implemented at the same speed to explore variations of hospital care?”

Blog quote from Lars Hemkens, University of Basel (Switzerland)

Returning to COVID-19, for the final time, this Research Article explored the first 100 days (up to 9 April 2020) of clinical trial research from around the world to identify missed opportunities for collaboration and associated research waste.

The authors conclude that early coordination and direction could have helped to guide the rapid initiation of clinical trial research, if only to prevent a waste of research efforts and resources in order to meet an ‘ambitious research agenda’.

On the blog, Perrine Janiaud and Lars Hemkens (University of Basel) discuss the benefits of international collaboration, open research and the application of research synergy to other healthcare challenges.

Find out more from the authors – read the full blog post >>