Public Library of Science

In this Formal Comment, representatives from PLOS, Nature and JAMA call for action on adopting a principle-based approach for a responsible authorship culture.

Researchers who serve on grant review and hiring committees have to make decisions about the intrinsic value of research in short periods of time, and research impact metrics such Journal Impact Factor (JIF) exert undue influence on these decisions. Initiatives such as the Coalition for Advancing Research Assessment (CoARA) and the Declaration on Research Assessment (DORA) emphasize responsible use of quantitative metrics and avoidance of journal-based impact metrics for research assessment. Further, our previous qualitative research suggested that assessing credibility, or trustworthiness, of research is important to researchers not only when they seek to inform their own research but also in the context of research assessment committees. To confirm our findings from previous interviews in quantitative terms, we surveyed 485 biology researchers who have served on committees for grant review or hiring and promotion decisions, to understand how they assess the credibility of research outputs in these contexts. We found that concepts like credibility, trustworthiness, quality, and impact lack consistent definitions and interpretations by researchers, which had already been observed in our interviews. We also found that, in our sample, assessment of credibility is very important to the majority (90%, 95% CI [87–92%]) of researchers serving in these committees but fewer than half of participants are satisfied with their ability to assess credibility. This gap between importance of an assessment and satisfaction in the ability to conduct it was reflected in multiple aspects of credibility we tested, and it was greatest for researchers seeking to assess the integrity of research (such as identifying signs of fabrication, falsification, or plagiarism), and the suitability and completeness of research methods. Non-traditional research outputs associated with open science practices—research data, code, protocols, and preprints—are particularly hard for researchers to assess, despite the potential of Open Science practices to signal trustworthiness. A substantial proportion of participants (57% [52%, 61%] of participants) report using journal reputation and JIF to assess credibility of research articles and outputs, despite journal reputation and JIF being proxies for credibility that rely on characteristics of research outputs that are extrinsic, rather than intrinsic, to the output itself. While our results only describe the practices and perspectives of our sample, they may suggest opportunities to develop better guidance and better signals to support the evaluation of research credibility and trustworthiness—and ultimately support research assessment reform, away from the use of proxies for impact and towards assessing the intrinsic characteristics and values researchers see as important.

Large open health datasets present unique opportunities for studies that when well-designed, conducted, and reported, can offer valuable contributions to health and medicine. However, recent years have seen a concerning proliferation of analyses lacking robust or novel findings. In this Editorial, we provide guidance to authors for conducting and reporting high-quality secondary analyses using these datasets.

ABSTRACT Despite its fundamental concern with knowledge acquisition and dissemination, Library and Information Science (LIS) lacks a clearly articulated epistemological foundation. This paper addresses two related questions: what kind of epistemological foundation best serves LIS, and how libraries – as a central site of LIS theory and practice – should be conceived for epistemic evaluation. In response to the first, I challenge the claim that social epistemology (SE) is unsuited to LIS because of its epistemologically prescriptive nature. Drawing on the distinction between evaluative and prescriptive normativity, I show that SE can offer evaluative standards to inform LIS without being prescriptive about adherence to those standards. In response to the second, I argue that libraries can be conceived as social epistemic systems and examine two contextual factors that explain how they function as such: their role as epistemic environments and the social practices that partially constitute them. Analysis of these practices reveals that ethical and political considerations are embedded in libraries’ epistemic functioning. These arguments reveal the limits of purist conceptions of epistemic performance and motivate an integrated approach to SE as a foundation for LIS – one that remains veritistic while also drawing on empirical insights and attending to ethico-political concerns.

Francis Jenkinson (1853–1923) was University Librarian at Cambridge, but is also remembered as an entomologist who assembled an outstanding collection of Diptera. His flies are housed at the University Museum of Zoology in Cambridge, alongside some notebooks and correspondence, though his diaries and the majority of letters are held at the University Library. Jenkinson was part of the circle of dipterists at the forefront of taxonomical work in the early twentieth century, but his collecting network also included his family, friends and domestic staff, most notably his housekeeper Annie Allard (1871–1956). Jenkinson’s collecting sites were similarly diverse, from his gardens and house in Cambridge, to Logie in the Scottish Highlands, and the windows of the University Library. Taken together, Jenkinson’s insects and papers give us a nuanced picture of his collecting practices, one that recovers the contributions of a wider range of actors whose voices have sometimes been silenced by time and changing interests in the scientific record. They also reveal how collecting flies was intrinsically governed by time, from the life cycle of the insects, to knowledge of the best times to collect, or the demanding schedule of pinning captures before the natural process of decay made them unpliable. By exploring the connections between ‘fly-time’ and institutional, domestic and social time, we see how ‘fly-time’ profoundly influenced human time and led to a range of strategies in an attempt to gain order and control through the archive.

Background:POCUS is increasingly in utility and application across a variety of specialities. Although several professional societies, including the European Society of Intensive Care Medicine (ESICM) have recommended focussed Neurological ultrasound be a core competency, recommendations on how best to achieve this competency are lacking.Aim:The purpose of this systematic review was to assess what best-practice and evidence-based recommendations are available to achieve competency in Neurological Point-of-care ultrasound (NeuroPOCUS).Methods:We undertook a structured systematic review of publications and studies on the training of NeuroPOCUS for intensive care.Results:Our search strategy yielded a total of 4965 publications, reduced to 3551 following de-duplication. Despite this, only 28 publications were relevant following review of title and abstract and only 12 of these on full-text review. We identified three prospective studies, four consensus statements and five publications as posters and published abstracts. Structured analysis of these revealed minimal evidence-based teaching recommendations, and significant variability in teaching method.Conclusion:Compared to other modalities of POCUS (e.g. Cardiac and Lung), NeuroPOCUS lags behind with regards to utilisation and training in the general intensive care setting. Further work is needed to establish how this technique can be effectively taught and assessed for clinical application.

Abstract BackgroundColorectal cancer (CRC) progression from adenoma to adenocarcinoma is associated with global reduction in 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). DNA hypomethylation continues upon liver metastasis. Here we examine 5hmC changes upon progression to liver metastasis.Results5hmC is increased in metastatic liver tissue relative to the primary colon tumour and expression of TET2 and TET3 is negatively correlated with risk for metastasis in patients with CRC. Genes associated with increased 5-hydroxymethylcytosine show KEGG enrichment for adherens junctions, cytoskeleton and cell migration around a core cadherin (CDH2) network. Overall, the 5-hydroxymethylcyosine profile in the liver metastasis is similar to normal colon appearing to recover at many loci where it was originally present in normal colon and then spreading to adjacent sites. The underlying sequences at the recover and spread regions are enriched for SALL4, ZNF770, ZNF121 and PAX5 transcription factor binding sites. Finally, we show in a zebrafish migration assay using SW480 CRISPR-engineered TET knockout and rescue cells that reduced TET expression leads to a reduced migration frequency.ConclusionTogether these results suggest a biphasic trajectory for 5-hydroxymethyation dynamics that has bearing on potential therapeutic interventions aimed at manipulating 5-hydroxymethylcytosine levels.

Detailed method descriptions are essential for reproducibility, research evaluation, and effective data reuse. We summarize the key recommendations for life sciences researchers and research institutions described in the European Commission PRO-MaP report.