A survey of biomedical journals to detect editorial bias and nepotistic behavior

Efficacy and safety of irreversible electroporation in unresectable perihilar cholangiocarcinoma: a systematic review and meta-analysis

OBJECTIVES

The prognosis of patients with perihilar-cholangiocarcinoma (PHC) is poor, with the majority presenting with unresectable disease at diagnosis. Palliative chemotherapy (CHT) is the standard treatment for unresectable PHC. Irreversible electroporation (IRE) has been introduced as a novel ablation technique, working predominantly nonthermal. This review aims to analyse the efficacy and safety of IRE in treating unresectable PHC.

METHODS

This systematic review and meta-analysis was performed according to a specific protocol designed a priori, and reported according to the PRISMA. PubMed/MEDLINE, Scopus, and Cochrane CENTRAL were searched up to December 2023. Primary Outcome of interest of our meta-analysis was the mean Overall Survival (OS). Secondary outcomes were progression-free survival (PFS) and adverse event rate (AE).

RESULTS

The mean OS was estimated at 25.49 months (CI, 21.47-38.72, I2 81.37%), PFS 17.86 (CI, 13.00-22.72, I2 11.42%), with an AE incidence of 12% (CI, 7%-31%, I2 83.57%). High heterogeneity was found among studies, with no single study fully responsible for it, suggesting high variability among facilities/populations.

CONCLUSION

IRE is effective and relatively safe for unresectable PHC. However, the lack of prospective studies and randomized trials comparing chemotherapy or locoregional treatment with IRE prevents drawing sufficiently robust conclusions.

ADVANCES IN KNOWLEDGE

IRE appears a safe and effective technique for treating unresectable perihilar cholangiocarcinoma.

Recommendations for accelerating open preprint peer review to improve the culture of science

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.

Quantitative research assessment: using metrics against gamed metrics

Quantitative bibliometric indicators are widely used and widely misused for research assessments. Some metrics have acquired major importance in shaping and rewarding the careers of millions of scientists. Given their perceived prestige, they may be widely gamed in the current "publish or perish" or "get cited or perish" environment. This review examines several gaming practices, including authorship-based, citation-based, editorial-based, and journal-based gaming as well as gaming with outright fabrication. Different patterns are discussed, including massive authorship of papers without meriting credit (gift authorship), team work with over-attribution of authorship to too many people (salami slicing of credit), massive self-citations, citation farms, H-index gaming, journalistic (editorial) nepotism, journal impact factor gaming, paper mills and spurious content papers, and spurious massive publications for studies with demanding designs. For all of those gaming practices, quantitative metrics and analyses may be able to help in their detection and in placing them into perspective. A portfolio of quantitative metrics may also include indicators of best research practices (e.g., data sharing, code sharing, protocol registration, and replications) and poor research practices (e.g., signs of image manipulation). Rigorous, reproducible, transparent quantitative metrics that also inform about gaming may strengthen the legacy and practices of quantitative appraisals of scientific work.

Supporting open science at PLOS Biology

Open science is key to PLOS Biology's mission, both in its daily operations and in the role we aspire to have in the scholarly ecosystem. Here, we reflect on open science at the journal and discuss how and why we shall continue to hold it central to everything we do.

Inaccuracy in the Scientific Record and Open Postpublication Critique

There is growing evidence that the published psychological literature is marred by multiple errors and inaccuracies and often fails to reflect the changing nature of the knowledge base. At least four types of error are common-citation error, methodological error, statistical error, and interpretation error. In the face of the apparent inevitability of these inaccuracies, core scientific values such as openness and transparency require that correction mechanisms are readily available. In this article, I reviewed standard mechanisms in psychology journals and found them to have limitations. The effects of more widely enabling open postpublication critique in the same journal in addition to conventional peer review are considered. This mechanism is well established in medicine and the life sciences but rare in psychology and may assist psychological science to correct itself.

Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields

Many factors influence selection of a target journal for publishing scientific papers, including "fit" within the journal's scope, acceptance rate, readership, open access options, submission and publication costs, journal quality, and timeliness of publication. Timeliness of publication can be a critical factor affecting career development, but many journals are not transparent about turnaround times. Here we evaluated 49 journals publishing papers in zoological medicine and related fields between 2017 and 2022, and aggregated and examined distributions of turnaround time of journals that publicly provided the requisite data, in order to aid authors in selecting target journals that best meet their needs. Of 49 journals evaluated, 39 provided necessary dates for reconstructing turnaround times. Of these, median times to acceptance ranged from 37 to 338 days, and median times to publication ranged from 41 to 403.5 days. The percentage of papers published in greater than 1 year ("slow") ranged from 0 to 57.1%, while the percentage of papers published in under 6 months ("timely") ranged from 0.8 to 99.8%. Acceptance rates and times to first decision were available for only 22% and 20%, respectively, of journals evaluated. Results may prove useful for authors deciding where to submit their works, depending on how they prioritize the many factors involved.

Prolific non-research authors in high impact scientific journals: meta-research study

Journalistic papers published in high impact scientific journals can be very influential, especially in hot fields. This meta-research analysis aimed to evaluate the publication profiles, impact, and disclosures of conflicts of interest of non-research authors who had published > 200 Scopus-indexed papers in Nature, Science, PNAS, Cell, BMJ, Lancet, JAMA or New England Journal of Medicine. 154 prolific authors were identified, 148 of whom had published 67,825 papers in their main affiliated journal in a non-researcher capacity. Nature, Science, and BMJ have the lion's share of such authors. Scopus characterized 35% of the journalistic publications as full articles and another 11% as short surveys. 264 papers had received more than 100 citations. 40/41 most-cited papers in 2020-2022 were on hot COVID-19 topics. Of 25 massively prolific authors with > 700 publications in one of these journals, many were highly-cited (median citations 2273), almost all had published little or nothing in the Scopus-indexed literature other than in their main affiliated journal, and their influential writing covered diverse hot topics over the years. Of the 25, only 3 had a PhD degree in any subject matter, and 7 had a Master's degree in journalism. Only the BMJ offered conflicts of interest disclosures for prolific science writers in its website, but even then only 2 of the 25 massively prolific authors disclosed potential conflicts with some specificity. The practice of assigning so much power to non-researchers in shaping scientific discourse should be further debated and disclosures of potential conflicts of interest should be emphasized.

Accelerated Peer Review and Paper Processing Models in Academic Publishing

Some journals and publishers offer a free or paid rapid peer review service. In the latter case, such a service is offered at a premium, i.e., for an additional fee, and authors receive, in return, a privileged service, namely faster peer review. In the cut-throat world of survival in academia, the difference of a few weeks or months in terms of speed of peer review and publication may bring untold benefits to authors that manage to benefit from accelerated peer review. We examine the deontological aspects behind this two-tier peer review system, including some positive, but mainly negative, aspects. Some paid accelerated peer review services thrive. We examine the paid accelerated peer review services by Taylor & Francis, Future Medicine Ltd., Elsevier, and two stand-alone journals that are OASPA members. This suggests that there is a demand, and thus market, for faster peer review. However, this privilege risks creating a two-tiered system that may divide academics between those who can pay versus those who cannot. We recommend that those papers that have benefited from accelerated peer review clearly indicate this in the published papers, as either a disclaimer or within the acknowledgements, for maximum transparency of the peer review and publication process.

Would Moving Forward Mean Going Back? Comment on Maselli et al. Direct Access to Physical Therapy: Should Italy Move Forward? Int. J. Environ. Res. Public Health 2022, 19, 555

In a recent communication, Maselli and colleagues [...].

Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives

Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.

Are highly ranked dental journals at risk of editorial bias? An examination of information on the reporting of peer-review practices

The objective of the present study was to assess how clearly and transparently reported are the editorial policies of highly ranked dental journals regarding the handling of submitted manuscripts. A total of 92 dental journals classified by impact factor had their websites scrutinized between 22 July and 06 September 2021 for all information on their policies regarding the handling of submitted manuscripts by editors. The information included items that could indicate potential risk of editorial bias. A total of 49 (53.3%) of the selected journals allowed the submission of all types of manuscripts, while 26 (28.3%) journals did not allow some types of manuscripts to be submitted (some manuscripts are only commissioned). The criteria for the acceptance of submitted manuscripts were clearly reported in eight (8.7%) journals, and only one reported the criteria in a hierarchical fashion. Sixteen (17.4%) journals reported a policy for handling the submitted manuscript when an editor was the author of the manuscript. Nine (9.8%) journals reported the possibility of a rebuttal letter by authors after manuscript rejection, but for most (62%) journals this information was not reported.The reporting of editorial policies regarding the peer-review process in highly ranked dental journals should be improved.