Archives des mots-clés : biomedical research

Analytical code sharing practices in biomedical research

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Authors : Nitesh Kumar Sharma, Ram Ayyala, Dhrithi Deshpande et al.

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared.

We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10−9).

Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10−07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research.

By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

URL : Analytical code sharing practices in biomedical research

DOI : https://doi.org/10.1101/2023.07.31.551384

Open(ing) Access: Top Health Publication Availability to Researchers in Low- and Middle-Income Countries

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Authors : John L. Kilgallon, Saumya Khanna, Tanujit Dey, Timothy R. Smith, Kavitha Ranganathan

Introduction

Improving access to information for health professionals and researchers in low- and middle-income countries (LMICs) is under-prioritized. This study examines publication policies that affect authors and readers from LMICs.

Methods

We used the SHERPA RoMEO database and publicly available publishing protocols to evaluate open access (OA) policies, article processing charges (APCs), subscription costs, and availability of health literature relevant to authors and readers in LMICs.

Categorical variables were summarized using frequencies with percentages. Continuous variables were reported with median and interquartile range (IQR).

Hypothesis testing procedures were performed using Wilcoxon rank sum tests, Wilcoxon rank sum exact tests, and Kruskal-Wallis test.

Results

A total of 55 journals were included; 6 (11%) were Gold OA (access to readers and large charge for authors), 2 (3.6%) were subscription (charge for readers and small/no charge for authors), 4 (7.3%) were delayed OA (reader access with no charge after embargo), and 43 (78%) were hybrid (author’s choice).

There was no significant difference between median APC for life sciences, medical, and surgical journals ($4,850 [$3,500–$8,900] vs. $4,592 [$3,500–$5,000] vs. $3,550 [$3,200–$3,860]; p = 0.054). The median US individual subscription costs (USD/Year) were significantly different for life sciences, medical, and surgical journals ($259 [$209–$282] vs. $365 [$212–$744] vs. $455 [$365–$573]; p = 0.038), and similar for international readers.

A total of seventeen journals (42%) had a subscription price that was higher for international readers than for US readers.

Conclusions

Most journals offer hybrid access services. Authors may be forced to choose between high cost with greater reach through OA and low cost with less reach publishing under the subscription model under current policies.

International readers face higher costs. Such hindrances may be mitigated by a greater awareness and liberal utilization of OA policies.

URL : Open(ing) Access: Top Health Publication Availability to Researchers in Low- and Middle-Income Countries

DOI : https://doi.org/10.5334/aogh.3904

Biomedical supervisors’ role modeling of open science practices

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Authors : Tamarinde L Haven, Susan Abunijela, Nicole Hildebrand

Supervision is one important way to socialize Ph.D. candidates into open and responsible research. We hypothesized that one should be more likely to identify open science practices (here publishing open access and sharing data) in empirical publications that were part of a Ph.D. thesis when the Ph.D. candidates’ supervisors engaged in these practices compared to those whose supervisors did not or less often did.

Departing from thesis repositories at four Dutch University Medical centers, we included 211 pairs of supervisors and Ph.D. candidates, resulting in a sample of 2062 publications. We determined open access status using UnpaywallR and Open Data using Oddpub, where we also manually screened publications with potential open data statements. Eighty-three percent of our sample was published openly, and 9% had open data statements.

Having a supervisor who published open access more often than the national average was associated with an odds of 1.99 to publish open access. However, this effect became nonsignificant when correcting for institutions. Having a supervisor who shared data was associated with 2.22 (CI:1.19–4.12) times the odds to share data compared to having a supervisor that did not.

This odds ratio increased to 4.6 (CI:1.86–11.35) after removing false positives. The prevalence of open data in our sample was comparable to international studies; open access rates were higher. Whilst Ph.D. candidates spearhead initiatives to promote open science, this study adds value by investigating the role of supervisors in promoting open science.

URL : Biomedical supervisors’ role modeling of open science practices

DOI : https://doi.org/10.7554/eLife.83484

Attitudes Toward Providing Open Access for Use of Biospecimens and Health Records: A Cross-Sectional Study from Jordan

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Authors : Kamal M Al-Shami, Wesam S Ahmed, Karem H Alzoubi

Purpose

Biospecimen repositories and big data generated from clinical research are critically important in advancing patient-centered healthcare. However, ethical considerations arising from reusing clinical samples and health records for subsequent research pose a hurdle for big-data health research. This study aims to assess the public’s opinions in Jordan toward providing blanket consent for using biospecimens and health records in research.

Participants and Methods

A cross-sectional study utilizing a self-reported questionnaire was carried out in different cities in Jordan, targeting adult participants. Outcome variables included awareness of clinical research, participation in clinical research, and opinions toward providing open access to clinical samples and records for research purposes.

Descriptive analysis was utilized for reporting the outcome as frequency (percentages) out of the total responses. Univariate and multivariate logistic regression were used to investigate the association between independent variables and the outcome of interest.

Results

A total of 1033 eligible participants completed the questionnaire. Although the majority (90%) were aware of clinical research, only 24% have ever participated in this type of research. About half (51%) agreed on providing blanket consent for the use of clinical samples, while a lower percentage (43%) agreed on providing open access to their health records.

Privacy concerns and lack of trust in the researcher were cited as major barriers to providing blanket consent. Participation in clinical research and having health insurance were predictors for providing open access to clinical samples and records.

Conclusion

The lack of public trust in Jordan toward data privacy is evident from this study. Therefore, a governance framework is needed to raise and maintain the public’s trust in big-data research that warrants the future reuse of clinical samples and records. As such, the current study provides valuable insights that will inform the design of effective consent protocols required in data-intensive health research.

URL : Attitudes Toward Providing Open Access for Use of Biospecimens and Health Records: A Cross-Sectional Study from Jordan

DOI : https://doi.org/10.2147/PPA.S402769

Hybrid Gold Open Access Citation Advantage in Clinical Medicine: Analysis of Hybrid Journals in the Web of Science

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Authors : Chompunuch Saravudecha, Duangruthai Na Thungfai, Chananthida Phasom, Sodsri Gunta-in, Aorrakanya Metha, Peangkobfah Punyaphet, Tippawan Sookruay, Wannachai Sakuludomkan, Nut Koonrungsesomboon

Biomedical fields have seen a remarkable increase in hybrid Gold open access articles. However, it is uncertain whether the hybrid Gold open access option contributes to a citation advantage, an increase in the citations of articles made immediately available as open access regardless of the article’s quality or whether it involves a trending topic of discussion.

This study aimed to compare the citation counts of hybrid Gold open access articles to subscription articles published in hybrid journals. The study aimed to ascertain if hybrid Gold open access publications yield an advantage in terms of citations.

This cross-sectional study included the list of hybrid journals under 59 categories in the ‘Clinical Medicine’ group from Clarivate’s Journal Citation Reports (JCR) during 2018–2021. The number of citable items with ‘Gold Open Access’ and ‘Subscription and Free to Read’ in each journal, as well as the number of citations of those citable items, were extracted from JCR.

A hybrid Gold open access citation advantage was computed by dividing the number of citations per citable item with hybrid Gold open access by the number of citations per citable item with a subscription.

A total of 498, 636, 1009, and 1328 hybrid journals in the 2018 JCR, 2019 JCR, 2020 JCR, and 2021 JCR, respectively, were included in this study. The citation advantage of hybrid Gold open access articles over subscription articles in 2018 was 1.45 (95% confidence interval (CI), 1.24–1.65); in 2019, it was 1.31 (95% CI, 1.20–1.41); in 2020, it was 1.30 (95% CI, 1.20–1.39); and in 2021, it was 1.31 (95% CI, 1.20–1.42).

In the ‘Clinical Medicine’ discipline, the articles published in the hybrid journal as hybrid Gold open access had a greater number of citations when compared to those published as a subscription, self-archived, or otherwise openly accessible option.

URL : Hybrid Gold Open Access Citation Advantage in Clinical Medicine: Analysis of Hybrid Journals in the Web of Science

DOI : https://doi.org/10.3390/publications11020021

PreprintMatch: A tool for preprint to publication detection shows global inequities in scientific publication

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Authors : Peter Eckmann, Anita Bandrowski

Preprints, versions of scientific manuscripts that precede peer review, are growing in popularity. They offer an opportunity to democratize and accelerate research, as they have no publication costs or a lengthy peer review process. Preprints are often later published in peer-reviewed venues, but these publications and the original preprints are frequently not linked in any way.

To this end, we developed a tool, PreprintMatch, to find matches between preprints and their corresponding published papers, if they exist. This tool outperforms existing techniques to match preprints and papers, both on matching performance and speed. PreprintMatch was applied to search for matches between preprints (from bioRxiv and medRxiv), and PubMed.

The preliminary nature of preprints offers a unique perspective into scientific projects at a relatively early stage, and with better matching between preprint and paper, we explored questions related to research inequity.

We found that preprints from low income countries are published as peer-reviewed papers at a lower rate than high income countries (39.6% and 61.1%, respectively), and our data is consistent with previous work that cite a lack of resources, lack of stability, and policy choices to explain this discrepancy.

Preprints from low income countries were also found to be published quicker (178 vs 203 days) and with less title, abstract, and author similarity to the published version compared to high income countries. Low income countries add more authors from the preprint to the published version than high income countries (0.42 authors vs 0.32, respectively), a practice that is significantly more frequent in China compared to similar countries.

Finally, we find that some publishers publish work with authors from lower income countries more frequently than others.

URL : PreprintMatch: A tool for preprint to publication detection shows global inequities in scientific publication

DOI : https://doi.org/10.1371/journal.pone.0281659

Investigation of potential gender bias in the peer review system at Reproduction

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Authors : Marie Biolková, Tom Moore, Karen Schindler, Karl Swann, Andy Vail, Lindsay Flook, Helen Dick, Greg Fitzharris, Christopher A. Price, Norah Spears

This study examined whether publication outcome was affected by the gender of author, handling associate editor (AE), or reviewer, and whether there was gender bias in reviewer selection, in the journal Reproduction.

Analyses were carried out on 4289 original research manuscripts submitted to the journal between 2007 and 2019. Both female and male AEs appointed more male reviewers than female reviewers, but female AEs were significantly more likely to appoint female reviewers than male AEs were (p < 0.001).

When examining the gender of either first or last author manuscripts, those with female authors that were reviewed by female reviewers received better scores than those with male authors that were reviewed by female reviewers (p < 0.05): where the reviewer was male, no such effect was observed.

Acceptance rates of manuscripts were similar for both female and male authors, whether first or last, regardless of AE gender. Overall, there was no significant correlation between gender of first or last author, or of AE, on the likelihood of acceptance of a research paper.

These data suggest no bias against female authors during the peer review process in this reproductive biology journal.

URL : Investigation of potential gender bias in the peer review system at Reproduction

DOI : https://doi.org/10.1002/leap.1537