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Adoption of Transparency and Openness Promotion (TOP) Guidelines across Journals

Authors : Inga Patarčić, Jadranka Stojanovski

Journal policies continuously evolve to enable knowledge sharing and support reproducible science. However, that change happens within a certain framework. Eight modular standards with three levels of increasing stringency make Transparency and Openness Promotion (TOP) guidelines which can be used to evaluate to what extent and with which stringency journals promote open science.

Guidelines define standards for data citation, transparency of data, material, code and design and analysis, replication, plan and study pre-registration, and two effective interventions: “Registered reports” and “Open science badges”, and levels of adoption summed up across standards define journal’s TOP Factor. In this paper, we analysed the status of adoption of TOP guidelines across two thousand journals reported in the TOP Factor metrics.

We show that the majority of the journals’ policies align with at least one of the TOP’s standards, most likely “Data citation” (70%) followed by “Data transparency” (19%). Two-thirds of adoptions of TOP standard are of the stringency Level 1 (less stringent), whereas only 9% is of the stringency Level 3.

Adoption of TOP standards differs across science disciplines and multidisciplinary journals (N = 1505) and journals from social sciences (N = 1077) show the greatest number of adoptions. Improvement of the measures that journals take to implement open science practices could be done: (1) discipline-specific, (2) journals that have not yet adopted TOP guidelines could do so, (3) the stringency of adoptions could be increased.

URL : Adoption of Transparency and Openness Promotion (TOP) Guidelines across Journals

DOI : https://doi.org/10.3390/publications10040046

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Open science and conflict of interest policies of medical and health sciences journals before and during the COVID-19 pandemic: A repeat cross-sectional study

Authors : Antoni D. Gardener, Ellen J. Hick, Chloe Jacklin, Gifford Tan, Aidan G. Cashin, Hopin Lee, David Nunan, Elaine C. Toomey, Georgia C. Richards

Objectives

To audit the transparent and open science standards of health and medical sciences journal policies and explore the impact of the COVID-19 pandemic.

Design

Repeat cross-sectional study.

Setting

19 journals listed in Google Scholar’s Top Publications for health and medical sciences.

Participants

Blood, Cell, Circulation, European Heart Journal, Gastroenterology, Journal of Clinical Oncology, Journal of the American College of Cardiology, Nature Genetics, Nature Medicine, Nature Neuroscience, Neuron, PLoS ONE, Proceedings of the National Academy of Sciences, Science Translational Medicine, The British Medical Journal, The Journal of the American Medical Association, The Lancet, The Lancet Oncology, and The New England Journal of Medicine.

Main outcome measures

We used the Transparency and Openness Promotion (TOP) guideline and the International Committee of Medical Journal Editors (ICMJE) requirements for disclosing conflicts
of interest (COIs) to evaluate journals standards.

Results

TOP scores slightly improved during the COVID-19 pandemic, from a median of 5 (IQR: 2–12.5) out of a possible 24 points in February 2020 to 7 (IQR: 4–12) in May 2021, but overall, scores were very low at both time points. Journal policies scored highest for their adherence to data transparency and scored lowest for preregistration of study protocols and analysis plans and the submission of replication studies. Most journals fulfilled all ICMJE provisions for reporting COIs before (84%; n = 16) and during (95%; n = 18) the COVID-19 pandemic.

Conclusions

The COVID-19 pandemic has highlighted the importance of practising open science. However, requirements for open science practices in audited policies were overall low, which may impede progress in health and medical research. As key stakeholders in disseminating research, journals should promote a research culture of greater transparency and more robust open science practices.

URL : Open science and conflict of interest policies of medical and health sciences journals before and during the COVID-19 pandemic: A repeat cross-sectional study

DOI : https://doi.org/10.1177/20542704221132139

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Knowledge Production: Analysing Gender- and Country-Dependent Factors in Research Topics through Term Communities

Authors : Parminder Bakshi-Hamm, Andreas Hamm

Scholarly publications are among the most tangible forms of knowledge production. Therefore, it is important to analyse them, amongst other features, for gender or country differences and the incumbent inequalities.

While there are many quantitative studies of publication activities and success in terms of publication numbers and citation counts, a more content-related understanding of differences in the choice of research topics is rare.

The present paper suggests an innovative method of using term communities in co-occurrence networks for detecting and evaluating the gender- and country-specific distribution of topics in research publications. The method is demonstrated with a pilot study based on approximately a quarter million of publication abstracts in seven diverse research areas.

In this example, the method validly reconstructs all obvious topic preferences, for instance, country-dependent language-related preferences. It also produces new insight into country-specific research focuses. It emerges that in all seven subject areas studied, topic preferences are significantly different depending on whether all authors are women, all authors are men, or there are female and male co-authors, with a tendency of male authors towards theoretical core topics, of female authors towards peripheral applied topics, and of mixed-author teams towards modern interdisciplinary topics.

URL : Knowledge Production: Analysing Gender- and Country-Dependent Factors in Research Topics through Term Communities

DOI : https://doi.org/10.3390/publications10040045

Publié le

Academic Tracker: Software for tracking and reporting publications associated with authors and grants

Authors : P. Travis Thompson, Christian D. Powell, Hunter N. B. Moseley

In recent years, United States federal funding agencies, including the National Institutes of Health (NIH) and the National Science Foundation (NSF), have implemented public access policies to make research supported by funding from these federal agencies freely available to the public.

Enforcement is primarily through annual and final reports submitted to these funding agencies, where all peer-reviewed publications must be registered through the appropriate mechanism as required by the specific federal funding agency. Unreported and/or incorrectly reported papers can result in delayed acceptance of annual and final reports and even funding delays for current and new research grants.

So, it’s important to make sure every peer-reviewed publication is reported properly and in a timely manner. For large collaborative research efforts, the tracking and proper registration of peer-reviewed publications along with generation of accurate annual and final reports can create a large administrative burden. With large collaborative teams, it is easy for these administrative tasks to be overlooked, forgotten, or lost in the shuffle. In order to help with this reporting burden, we have developed the Academic Tracker software package, implemented in the Python 3 programming language and supporting Linux, Windows, and Mac operating systems.

Academic Tracker helps with publication tracking and reporting by comprehensively searching major peer-reviewed publication tracking web portals, including PubMed, Crossref, ORCID, and Google Scholar, given a list of authors. Academic Tracker provides highly customizable reporting templates so information about the resulting publications is easily transformed into appropriate formats for tracking and reporting purposes.

The source code and extensive documentation is hosted on GitHub (https://moseleybioinformaticslab.github.io/academic_tracker/) and is also available on the Python Package Index (https://pypi.org/project/academic_tracker) for easy installation.

Publié le

A quantitative and qualitative open citation analysis of retracted articles in the humanities

Authors : Ivan Heibi, Silvio Peroni

In this article, we show and discuss the results of a quantitative and qualitative analysis of open citations to retracted publications in the humanities domain. Our study was conducted by selecting retracted papers in the humanities domain and marking their main characteristics (e.g., retraction reason).

Then, we gathered the citing entities and annotated their basic metadata (e.g., title, venue, etc.) and the characteristics of their in-text citations (e.g., intent, sentiment, etc.). Using these data, we performed a quantitative and qualitative study of retractions in the humanities, presenting descriptive statistics and a topic modeling analysis of the citing entities’ abstracts and the in-text citation contexts.

As part of our main findings, we noticed that there was no drop in the overall number of citations after the year of retraction, with few entities which have either mentioned the retraction or expressed a negative sentiment toward the cited publication.

In addition, on several occasions, we noticed a higher concern/awareness when it was about citing a retracted publication, by the citing entities belonging to the health sciences domain, if compared to the humanities and the social science domains. Philosophy, arts, and history are the humanities areas that showed the higher concerns toward the retraction.

URL : A quantitative and qualitative open citation analysis of retracted articles in the humanities

DOI : https://doi.org/10.1162/qss_a_00222

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Science in motion: A qualitative analysis of journalists’ use and perception of preprints

Authors : Alice Fleerackers, Laura L. Moorhead, Lauren A. Maggio, Kaylee Fagan, Juan Pablo Alperin

This qualitative study explores how and why journalists use preprints—unreviewed research papers—in their reporting. Through thematic analysis of interviews conducted with 19 health and science journalists in the second year of the COVID-19 pandemic, it applies a theoretical framework that conceptualizes COVID-19 preprint research as a form of post-normal science, characterized by high scientific uncertainty and societal relevance, urgent need for political decision-making, and value-related policy considerations.

Findings suggest that journalists approach the decision to cover preprints as a careful calculation, in which the potential public benefits and the ease of access preprints provided were weighed against risks of spreading misinformation.

Journalists described viewing unreviewed studies with extra skepticism and relied on diverse strategies to find, vet, and report on them. Some of these strategies represent standard science journalism, while others, such as labeling unreviewed studies as preprints, mark a departure from the norm. However, journalists also reported barriers to covering preprints, as many felt they lacked the expertise or the time required to fully understand or vet the research.

The findings suggest that coverage of preprints is likely to continue post-pandemic, with important implications for scientists, journalists, and the publics who read their work.

URL : Science in motion: A qualitative analysis of journalists’ use and perception of preprints

DOI : https://doi.org/10.1371/journal.pone.0277769

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Indicators of research quality, quantity, openness and responsibility in institutional review, promotion and tenure policies across seven countries

Authors : Nancy Pontika, Thomas Klebel, Antonia Correia, Hannah Metzler, Petr Knoth, Tony Ross-Hellauer

The need to reform research assessment processes related to career advancement at research institutions has become increasingly recognised in recent years, especially to better foster open and responsible research practices. Current assessment criteria are believed to focus too heavily on inappropriate criteria related to productivity and quantity as opposed to quality, collaborative open research practices, and the socio-economic impact of research.

Evidence of the extent of these issues is urgently needed to inform actions for reform, however. We analyse current practices as revealed by documentation on institutional review, promotion and tenure processes in seven countries (Austria, Brazil, Germany, India, Portugal, United Kingdom and United States of America).

Through systematic coding and analysis of 143 RPT policy documents from 107 institutions for the prevalence of 17 criteria (including those related to qualitative or quantitative assessment of research, service to the institution or profession, and open and responsible research practices), we compare assessment practices across a range of international institutions to significantly broaden this evidence-base.

Although prevalence of indicators varies considerably between countries, overall we find that currently open and responsible research practices are minimally rewarded and problematic practices of quantification continue to dominate.

URL : Indicators of research quality, quantity, openness and responsibility in institutional review, promotion and tenure policies across seven countries

DOI : https://doi.org/10.1162/qss_a_00224