An open science peer review oath

Common Interests Without Common Expertise: Reflections on Early-career Experiences in Cross-Disciplinary Research

Cross-disciplinary research enables us to tackle complex problems that require expertise from different fields. Such collaborations involve researchers who have different perspectives, communication styles, and knowledge bases, and can produce results far greater than the sum of their parts. However, in an era of increasing scientific specialization, there exist many barriers for students and early-career researchers (ECRs) interested in training and undertaking interdisciplinary research endeavors. This perspective examines the challenges that students and ECRs perceive and experience in cross-disciplinary work and proposes pathways to create more inclusive and welcoming research environments. This work emerges from a National Science Foundation (NSF)-funded workshop held during the Society for Integrative and Comparative Biology (SICB) Annual Meeting in January 2023 in Austin, TX. The workshop brought together seasoned interdisciplinary scientists with undergraduate and graduate students to identify and discuss perceived challenges through small group discussions and experience sharing. Through summarizing a range of student concerns about embarking on careers as interdisciplinary scientists and identifying ways to dismantle institutional and lab management-level barriers, we aim to promote an inclusive and collaborative problem-solving environment for scientists of all experience levels.

A method to improve the reproducibility of findings from epigenome- and transcriptome-wide association studies

Reproducibility is a cornerstone of scientific progress. In epigenome- and transcriptome-wide association studies (E/TWAS) failure to reproduce may be the result of false discoveries. Whereas multiple methods exist to control false discoveries due to sampling error, minimizing false discoveries due to outliers and other data artefacts remains challenging. We propose a robust E/TWAS approach that outperforms alternative methods to improve reproducibility such as split-half replication. Furthermore, robust E/TWAS results in only a minor loss of power if there are no outliers and can in the presence of outliers, likely a more realistic scenario, even be more powerful than regular E/TWAS.

Systematic Review on Characteristics and Reporting Quality of Animal Studies in Liver Regeneration Triggered by Portal Vein Occlusion and Associating Liver Partition and Portal Vein Ligation for Staged Hepatectomy: Adherence to the ARRIVE Guidelines

BACKGROUND

Portal vein occlusion and associating liver partition and portal vein ligation for staged hepatectomy techniques are in the spotlight of oncological liver surgery. Research involving animal models is indispensable to study the mechanisms of liver regeneration. Inaccurate reporting acts as a significant barrier during the correct interpretation of preclinical findings. Hence, we performed a systematic review to evaluate the status quo of the reporting standards and to assess the potential factors influencing reporting in animal studies, which are focusing on portal vein occlusion and/or associating liver partition and portal vein ligation for staged hepatectomy techniques.

MATERIALS AND METHODS

A systematic review was performed in the PubMed and Ovid MEDLINE databases. Baseline study characteristics were recorded, and quality assessment was performed using the Animals in Research: Reporting in vivo Experiments (ARRIVE) checklist.

RESULTS

A total of 107 research articles were included for the comprehensive assessment. In the subgroup analysis, newer reports and studies from the post-ARRIVE era, and reports from Europe were all associated with significantly higher ARRIVE scores (P < 0.05). Univariable regression analysis confirmed these factors as predictors of higher reporting quality. However, in the multivariable analysis, only publishing in the post-ARRIVE era has been found as single independent predictor of higher reporting standards (P = 0.028 post-ARRIVE total score 75th percentile; P = 0.000 post-ARRIVE total score median).

CONCLUSIONS

Although an improving trend has been observed in reporting quality over the past years, this effect was clearly insufficient. Our results emphasize the need for further measures to improve the methodical quality at all levels of planning, execution, and reporting of preclinical studies in liver regeneration research.

Reviewer selection biases editorial decisions on manuscripts

Many journals, including the Journal of Neurochemistry, enable authors to list peer reviewers as 'preferred' or 'opposed' suggestions to the editor. At the Journal of Neurochemistry, the handling editor (HE) may follow recommendations or select non-author-suggested reviewers (non-ASRs). We investigated whether selection of author-suggested reviewers (ASRs) influenced decisions on a paper, and whether differences might be related to a reviewer's, editor's or manuscript's geographical location. In this retrospective analysis, we compared original research articles submitted to the Journal of Neurochemistry from 2013 through 2016 that were either reviewed exclusively by non-ASRs, by at least one ASR, by at least one reviewer marked by the author as 'opposed' or none. Manuscript outcome, reviewer rating of manuscript quality, rating of the reviewers' performance by the editor (R-score), time to review, and the country of the editor, reviewers and manuscript author were analyzed using non-parametric rank-based comparisons, chi-square (χ2 ) analysis, multivariate linear regression, one-way analysis of variance, and inter-rater reliability determination. Original research articles that had been reviewed by at least one ASR stood a higher chance of being accepted (525/1006 = 52%) than papers that had been reviewed by non-ASRs only (579/1800 = 32%). An article was 2.4 times more likely to be accepted than rejected by an ASR compared to a non-ASR (Pearson's χ2 (1) = 181.3, p < 0.05). At decision, the editor did not simply follow the reviewers' recommendation but had a balancing role: Rates of recommendation from reviewers for rejection were 11.2% (139/1241) with ASRs versus 29.0% (1379/4755) with non-ASRs (this is a ratio of 0.39 where 1 means no difference between rejection rates for both groups), whereas the proportion of final decisions to reject was 24.7% (248/1006) versus 45.7% (822/1800) (a ratio of 0.54, considerably closer to 1). Recommendations by non-ASRs were more favorable for manuscripts from USA/Canada and Europe than for Asia/Pacific or Other countries. ASRs judged North American manuscripts most favorably, and judged papers generally more positively (mean: 2.54 on a 1-5 scale) than did non-ASRs (mean: 3.16) reviewers, whereas time for review (13.28 vs. 13.20 days) did not differ significantly between these groups. We also found that editors preferably assigned reviewers from their own geographical region, but there was no tendency for reviewers to judge papers from their own region more favorably. Our findings strongly confirm a bias toward lower rejection rates when ASRs assess a paper, which led to the decision to abandon the option to recommend reviewers at the Journal of Neurochemistry. Open Data: Materials are available on https://osf.io/jshg7/.

When will 'open science' become simply 'science'?

Open science describes the practice of carrying out scientific research in a completely transparent manner, and making the results of that research available to everyone. Isn’t that just ‘science’?