Archives des mots-clés : biomedical research

Preprints in motion: tracking changes between posting and journal publication

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Authors : Jessica K Polka, Gautam Dey, Máté Pálfy, Federico Nanni, Liam Brierley, Nicholas Fraser, Jonathon Alexis Coates

Amidst the COVID-19 pandemic, preprints in the biomedical sciences are being posted and accessed at unprecedented rates, drawing widespread attention from the general public, press and policymakers for the first time.

This phenomenon has sharpened longstanding questions about the reliability of information shared prior to journal peer review. Does the information shared in preprints typically withstand the scrutiny of peer review, or are conclusions likely to change in the version of record?

We assessed preprints that had been posted and subsequently published in a journal between 1st January and 30th April 2020, representing the initial phase of the pandemic response. We utilised a combination of automatic and manual annotations to quantify how an article changed between the preprinted and published version.

We found that the total number of figure panels and tables changed little between preprint and published articles. Moreover, the conclusions of 6% of non-COVID-19-related and 15% of COVID-19-related abstracts undergo a discrete change by the time of publication, but the majority of these changes do not reverse the main message of the paper.

DOI : https://doi.org/10.1101/2021.02.20.432090

Publishing at any cost: a cross-sectional study of the amount that medical researchers spend on open access publishing each year

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Authors : Mallory K. Ellingson, Xiaoting Shi, Joshua J. Skydel, Kate Nyhan,Richard Lehman, Joseph S. Ross, Joshua D. Wallach

Objective

To estimate the financial costs paid by individual medical researchers from meeting the article processing charges (APCs) levied by open access journals in 2019.

Design

Cross-sectional analysis.

Data sources

Scopus was used to generate two random samples of researchers, the first with a senior author article indexed in the ‘Medicine’ subject area (general researchers) and the second with an article published in the ten highest-impact factor general clinical medicine journals (high-impact researchers) in 2019.

For each researcher, Scopus was used to identify all first and senior author original research or review articles published in 2019. Data were obtained from Scopus, institutional profiles, Journal Citation Reports, publisher databases, the Directory of Open Access Journals, and individual journal websites.

Main outcome measures

Median APCs paid by general and high-impact researchers for all first and senior author research and review articles published in 2019.

Results

There were 241 general and 246 high-impact researchers identified as eligible for our study. In 2019, the general and high-impact researchers published a total of 914 (median 2, IQR 1–5) and 1471 (4, 2–8) first or senior author research or review articles, respectively. 42% (384/914) of the articles from the general researchers and 29% (428/1471) of the articles from the high-impact medical researchers were published in fully open access journals.

The median total APCs paid by general researchers in 2019 was US$191 (US$0–US$2500) and the median total paid by high-impact researchers was US$2900 (US$0–US$5465); the maximum paid by a single researcher in total APCs was US$30115 and US$34676, respectively.

Conclusions

Medical researchers in 2019 were found to have paid between US$0 and US$34676 in total APCs. As journals with APCs become more common, it is important to continue to evaluate the potential cost to researchers, especially on individuals who may not have the funding or institutional resources to cover these costs.

URL : Publishing at any cost: a cross-sectional study of the amount that medical researchers spend on open access publishing each year

DOI : http://dx.doi.org/10.1136/bmjopen-2020-047107

An overview of biomedical platforms for managing research data

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Authors : Vivek Navale, Denis von Kaeppler, Matthew McAuliffe

Biomedical platforms provide the hardware and software to securely ingest, process, validate, curate, store, and share data. Many large-scale biomedical platforms use secure cloud computing technology for analyzing, integrating, and storing phenotypic, clinical, and genomic data. Several web-based platforms are available for researchers to access services and tools for biomedical research.

The use of bio-containers can facilitate the integration of bioinformatics software with various data analysis pipelines. Adoption of Common Data Models, Common Data Elements, and Ontologies can increase the likelihood of data reuse. Managing biomedical Big Data will require the development of strategies that can efficiently leverage public cloud computing resources.

The use of the research community developed standards for data collection can foster the development of machine learning methods for data processing and analysis. Increasingly platforms will need to support the integration of data from multiple disease area research.

URL : An overview of biomedical platforms for managing research data

DOI : https://doi.org/10.1007/s42488-020-00040-0

Evaluation of Data Sharing After Implementation of the International Committee of Medical Journal Editors Data Sharing Statement Requirement

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Authors : Valentin Danchev, Yan Min, John Borghi, Mike Baiocchi, John P. A. Ioann

Importance

The benefits of responsible sharing of individual-participant data (IPD) from clinical studies are well recognized, but stakeholders often disagree on how to align those benefits with privacy risks, costs, and incentives for clinical trialists and sponsors.

The International Committee of Medical Journal Editors (ICMJE) required a data sharing statement (DSS) from submissions reporting clinical trials effective July 1, 2018. The required DSSs provide a window into current data sharing rates, practices, and norms among trialists and sponsors.

Objective

To evaluate the implementation of the ICMJE DSS requirement in 3 leading medical journals: JAMA, Lancet, and New England Journal of Medicine (NEJM).

Design, Setting, and Participants

This is a cross-sectional study of clinical trial reports published as articles in JAMA, Lancet, and NEJM between July 1, 2018, and April 4, 2020. Articles not eligible for DSS, including observational studies and letters or correspondence, were excluded.

A MEDLINE/PubMed search identified 487 eligible clinical trials in JAMA (112 trials), Lancet (147 trials), and NEJM (228 trials). Two reviewers evaluated each of the 487 articles independently.

Exposure

Publication of clinical trial reports in an ICMJE medical journal requiring a DSS.

Main Outcomes and Measures

The primary outcomes of the study were declared data availability and actual data availability in repositories. Other captured outcomes were data type, access, and conditions and reasons for data availability or unavailability. Associations with funding sources were examined.

Results

A total of 334 of 487 articles (68.6%; 95% CI, 64%-73%) declared data sharing, with nonindustry NIH-funded trials exhibiting the highest rates of declared data sharing (89%; 95% CI, 80%-98%) and industry-funded trials the lowest (61%; 95% CI, 54%-68%).

However, only 2 IPD sets (0.6%; 95% CI, 0.0%-1.5%) were actually deidentified and publicly available as of April 10, 2020. The remaining were supposedly accessible via request to authors (143 of 334 articles [42.8%]), repository (89 of 334 articles [26.6%]), and company (78 of 334 articles [23.4%]).

Among the 89 articles declaring that IPD would be stored in repositories, only 17 (19.1%) deposited data, mostly because of embargo and regulatory approval. Embargo was set in 47.3% of data-sharing articles (158 of 334), and in half of them the period exceeded 1 year or was unspecified.

Conclusions and Relevance

Most trials published in JAMA, Lancet, and NEJM after the implementation of the ICMJE policy declared their intent to make clinical data available. However, a wide gap between declared and actual data sharing exists.

To improve transparency and data reuse, journals should promote the use of unique pointers to data set location and standardized choices for embargo periods and access requirements.

URL : Evaluation of Data Sharing After Implementation of the International Committee of Medical Journal Editors Data Sharing Statement Requirement

DOI :10.1001/jamanetworkopen.2020.33972

Methodological quality of COVID-19 clinical research

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Authors : Richard G. Jung, Pietro Di Santo, Cole Clifford, Graeme Prosperi-Porta, Stephanie Skanes, Annie Hung, Simon Parlow, Sarah Visintini, F. Daniel Ramirez, Trevor Simard & Benjamin Hibbert

The COVID-19 pandemic began in early 2020 with major health consequences. While a need to disseminate information to the medical community and general public was paramount, concerns have been raised regarding the scientific rigor in published reports.

We performed a systematic review to evaluate the methodological quality of currently available COVID-19 studies compared to historical controls. A total of 9895 titles and abstracts were screened and 686 COVID-19 articles were included in the final analysis.

Comparative analysis of COVID-19 to historical articles reveals a shorter time to acceptance (13.0[IQR, 5.0–25.0] days vs. 110.0[IQR, 71.0–156.0] days in COVID-19 and control articles, respectively; p < 0.0001).

Furthermore, methodological quality scores are lower in COVID-19 articles across all study designs. COVID-19 clinical studies have a shorter time to publication and have lower methodological quality scores than control studies in the same journal. These studies should be revisited with the emergence of stronger evidence.

URL : Methodological quality of COVID-19 clinical research

DOI : https://doi.org/10.1038/s41467-021-21220-5

COVID‐19 and the generation of novel scientific knowledge: Evidence‐based decisions and data sharing

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Authors : Lucie Perillat, Brian S. Baigrie

Rationale, aims and objectives

The COVID‐19 pandemic has impacted every facet of society, including medical research. This paper is the second part of a series of articles that explore the intricate relationship between the different challenges that have hindered biomedical research and the generation of novel scientific knowledge during the COVID‐19 pandemic.

In the first part of this series, we demonstrated that, in the context of COVID‐19, the scientific community has been faced with numerous challenges with respect to (1) finding and prioritizing relevant research questions and (2) choosing study designs that are appropriate for a time of emergency.

Methods

During the early stages of the pandemic, research conducted on hydroxychloroquine (HCQ) sparked several heated debates with respect to the scientific methods used and the quality of knowledge generated.

Research on HCQ is used as a case study in both papers. The authors explored biomedical databases, peer‐reviewed journals, pre‐print servers and media articles to identify relevant literature on HCQ and COVID‐19, and examined philosophical perspectives on medical research in the context of this pandemic and previous global health challenges.

Results

This second paper demonstrates that a lack of research prioritization and methodological rigour resulted in the generation of fleeting and inconsistent evidence that complicated the development of public health guidelines.

The reporting of scientific findings to the scientific community and general public highlighted the difficulty of finding a balance between accuracy and speed.

Conclusions

The COVID‐19 pandemic presented challenges in terms of (3) evaluating evidence for the purpose of making evidence‐based decisions and (4) sharing scientific findings with the rest of the scientific community.

This second paper demonstrates that the four challenges outlined in the first and second papers have often compounded each other and have contributed to slowing down the creation of novel scientific knowledge during the COVID‐19 pandemic.

DOI : https://doi.org/10.1111/jep.13548

‘Nepotistic journals’: a survey of biomedical journals

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Authors : Alexandre Scanff, Florian Naudet, Ioana Cristea, David Moher, Dorothy V M Bishop, Clara Locher

Context

Convergent analyses in different disciplines support the use of the Percentage of Papers by the Most Prolific author (PPMP) as a red flag to identify journals that can be suspected of questionable editorial practices. We examined whether this index, complemented by the Gini index, could be useful for identifying cases of potential editorial bias, using a large sample of biomedical journals.

Methods

We extracted metadata for all biomedical journals referenced in the National Library of Medicine, with any attributed Broad Subject Terms, and at least 50 authored (i.e. by at least one author) articles between 2015 and 2019, identifying the most prolific author (i.e. the person who signed the most papers in each particular journal).

We calculated the PPMP and the 2015-2019 Gini index for the distribution of articles across authors. When the relevant information was reported, we also computed the median publication lag (time between submission and acceptance) for articles authored by any of the most prolific authors and that for articles not authored by prolific authors.

For outlier journals, defined as a PPMP or Gini index above the 95th percentile of their respective distributions, a random sample of 100 journals was selected and described in relation to status on the editorial board for the most prolific author.

Results

5 468 journals that published 4 986 335 papers between 2015 and 2019 were analysed. The PPMP 95th percentile was 10.6% (median 2.9%). The Gini index 95th percentile was 0.355 (median 0.183). Correlation between the two indices was 0.35 (95CI 0.33 to 0.37). Information on publication lag was available for 2 743 journals.

We found that 277 journals (10.2%) had a median time lag to publication for articles by the most prolific author(s) that was shorter than 3 weeks, versus 51 (1.9%) journals with articles not authored by prolific author(s).

Among the random sample of outlier journals, 98 provided information about their editorial board. Among these 98, the most prolific author was part of the editorial board in 60 cases (61%), among whom 25 (26% of the 98) were editors-in-chief.

Discussion

In most journals publications are distributed across a large number of authors. Our results reveal a subset of journals where a few authors, often members of the editorial board, were responsible for a disproportionate number of publications.

The papers by these authors were more likely to be accepted for publication within 3 weeks of their submission. To enhance trust in their practices, journals need to be transparent about their editorial and peer review practices.

URL : ‘Nepotistic journals’: a survey of biomedical journals

DOI : https://doi.org/10.1101/2021.02.03.429520