Archives des mots-clés : biomedical research

Researcher’s Perceptions on Publishing “Negative” Results and Open Access

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Authors : Lucía Echevarría, Alberto Malerba, Virginia Arechavala-Gomeza

Scientific advance is based on reproducibility, corroboration, and availability of research results. However, large numbers of experimental results that contradict previous work do not get published and many research results are not freely available as they are hidden behind paywalls.

As part of COST Action “DARTER”, a network of researchers in the field of RNA therapeutics, we have performed a small survey among our members and their colleagues to assess their opinion on the subject of publishing contradictory or ambiguous results and their attitude to open access (OA) publishing.

Our survey indicates that, although researchers highly value publication of “negative” results, they often do not publish their own, citing lack of time and the perception that those results may not be as highly cited. OA, on the other hand, seems to be widely accepted, but in many cases not actively sought by researchers due to higher costs associated with it.

URL : Researcher’s Perceptions on Publishing “Negative” Results and Open Access

DOI : https://doi.org/10.1089/nat.2020.0865

International authorship and collaboration across bioRxiv preprints

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Authors : Richard J Abdill, Elizabeth M Adamowicz, Ran Blekhman

Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors.

Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption.

We also describe a set of ‘contributor countries’ (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations.

Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.

URL :  International authorship and collaboration across bioRxiv preprints

DOI : https://doi.org/10.7554/eLife.58496

Evaluation of untrustworthy journals: Transition from formal criteria to a complex view

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Authors : Jiří Kratochvíl, Lukáš Plch, Martin Sebera, Eva Koriťáková

Not all the journals included in credible indexes meet the ethical rules of COPE, DOAJ, OASPA and WAMEand equally there may be trustworthy journals excluded from these indexes which means they cannot be used as definitive whitelists for trustworthy journals.

Equally the many methods suggested to determine trustworthiness are not reliable due to including questionable criteria. The question arises whether valid criteria for identifying an untrustworthy journal can be determined and whether other assessment procedures are necessary.

Since 2017, the Masaryk University Campus Library has been developing a suitable evaluation method for journals. A list of 19 criteria based on those originally suggested by Beall, COPE, DOAJ, OASPA and WAME were reduced to 10 objectively verifiable criteria following two workshops with librarians.

An evaluation of 259 biomedical journals using both the list of 19 and then 10 criteria revealed that 74 journals may have been incorrectly assessed as untrustworthy using the longer list.

The most common reason for failure to comply was in the provision of sufficient editorial information and declaration of article processing charges. However our investigation revealed that no criteria can reliably identify predatory journals.

Therefore, a complex evaluation is needed combining objectively verifiable criteria with analysis of a journal’s content and knowledge of the journal’s background.

URL : https://is.muni.cz/publication/1669782/en/Kratochvil-Plch-Sebera-Koritakova/Evaluation-of-untrustworthy-journals-Transition-from-formal-criteria-to-a-complex-view

Responsible, practical genomic data sharing that accelerates research

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Authors : James Brian Byrd, Anna C. Greene, Deepashree Venkatesh Prasad, Xiaoqian Jiang, Casey S. Greene

Data sharing anchors reproducible science, but expectations and best practices are often nebulous. Communities of funders, researchers and publishers continue to grapple with what should be required or encouraged.

To illuminate the rationales for sharing data, the technical challenges and the social and cultural challenges, we consider the stakeholders in the scientific enterprise. In biomedical research, participants are key among those stakeholders.

Ethical sharing requires considering both the value of research efforts and the privacy costs for participants. We discuss current best practices for various types of genomic data, as well as opportunities to promote ethical data sharing that accelerates science by aligning incentives.

URL : Responsible, practical genomic data sharing that accelerates research

DOI : https://doi.org/10.1038/s41576-020-0257-5

Transparency and open science principles in reporting guidelines in sleep research and chronobiology journals

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Authors : Manuel Spitschan, Marlene H. Schmidt, Christine Blume

Background

“Open science” is an umbrella term describing various aspects of transparent and open science practices. The adoption of practices at different levels of the scientific process (e.g., individual researchers, laboratories, institutions) has been rapidly changing the scientific research landscape in the past years, but their uptake differs from discipline to discipline.

Here, we asked to what extent journals in the field of sleep research and chronobiology encourage or even require following transparent and open science principles in their author guidelines.

Methods

We scored the author guidelines of a comprehensive set of 28 sleep and chronobiology journals, including the major outlets in the field, using the standardised Transparency and Openness (TOP) Factor.

This instrument rates the extent to which journals encourage or require following various aspects of open science, including data citation, data transparency, analysis code transparency, materials transparency, design and analysis guidelines, study pre-registration, analysis plan pre-registration, replication, registered reports, and the use of open science badges.

Results

Across the 28 journals, we find low values on the TOP Factor (median [25th, 75th percentile] 2.5 [1, 3], min. 0, max. 9, out of a total possible score of 28) in sleep research and chronobiology journals.

Conclusions

Our findings suggest an opportunity for sleep research and chronobiology journals to further support the recent developments in transparent and open science by implementing transparency and openness principles in their guidelines and making adherence to them mandatory.

URL : Transparency and open science principles in reporting guidelines in sleep research and chronobiology journals

DOI : https://doi.org/10.12688/wellcomeopenres.16111.1

Pandemic Publishing: Medical journals drastically speed up their publication process for Covid-19

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Author : Serge P.J.M. Horbach

In times of public crises, including the current Covid-19 pandemic, rapid dissemination of relevant scientific knowledge is of paramount importance. The duration of scholarly journals’ publication process is one of the main factors hindering quick delivery of new information.

While proper editorial assessment and peer review obviously require some time, turnaround times for medical journals can be up to several months, which is undesirable in the era of a crisis. Following initiatives of medical journals and scholarly publishers to accelerate their publication process, this study assesses whether medical journals have indeed managed to speed up their publication process for Covid-19 related articles.

It studies the duration of 14 medical journals’ publication process both during and prior to the current pandemic. Assessing a total of 669 articles, the study concludes that medical journals have indeed drastically accelerated the publication process for Covid-19 related articles since the outbreak of the pandemic. Compared to articles published in the same journals before the pandemic, turnaround times have decreased on average by 49%.

The largest decrease in number of days between submission and publication of articles was due to a decrease in the number of days required for peer review. For articles not related to Covid-19, no acceleration of the publication process is found.

While the acceleration of journals’ publication process is laudable from the perspective of quick information dissemination, it also raises concerns relating to the quality of the peer review process and the quality of the resulting publications.

URL : https://doi.org/10.1101/2020.04.18.045963

Striving for Modernity: Layout and Abstracts in the Biomedical Literature

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Authors : Carlo Galli, Maria Teresa Colangelo, Stefano Guizzardi

Most academic journals have a fairly consistent look: they are structured similarly, their text is divided into similar sections; for example, they have an abstract at the beginning of the manuscript, and their text is usually organized in two columns.

There may be different reasons for this similarity, ranging from the need to contain publication costs by using less page space to conforming to an internationally well-accepted format that may be perceived as the hallmark of academic articles.

We surveyed 35 medical journals founded before 1960 and looked for their change in format over time and how this was experienced by and explained to readers.

We then discussed what recent research has shown about the effects of layout on reading, looking for further explanations as to why this format was so successful.

URL : Striving for Modernity: Layout and Abstracts in the Biomedical Literature

DOI : https://doi.org/10.3390/publications8030038