Étiquette : biomedical research

Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

Authors : Clarissa F. D. Carneiro, Victor G. S. Queiroz, Thiago C. Moulin, Carlos A. M. Carvalho, Clarissa B. Haas, Danielle Rayêe, David E. Henshall, Evandro A. De-Souza, Felippe Espinelli, Flávia Z. Boos, Gerson D. Guercio, Igor R. Costa, Karina L. Hajdu, Martin Modrák, Pedro B. Tan, Steven J. Burgess, Sylvia F. S. Guerra, Vanessa T. Bortoluzzi, Olavo B. Amara

Preprint usage is growing rapidly in the life sciences; however, questions remain on the relative quality of preprints when compared to published articles. An objective dimension of quality that is readily measurable is completeness of reporting, as transparency can improve the reader’s ability to independently interpret data and reproduce findings.

In this observational study, we compared random samples of articles published in bioRxiv and in PubMed-indexed journals in 2016 using a quality of reporting questionnaire. We found that peer-reviewed articles had, on average, higher quality of reporting than preprints, although this difference was small.

We found larger differences favoring PubMed in subjective ratings of how clearly titles and abstracts presented the main findings and how easy it was to locate relevant reporting information.

Interestingly, an exploratory analysis showed that preprints with figures and legends embedded within text had reporting scores similar to PubMed articles.

These differences cannot be directly attributed to peer review or editorial processes, as manuscripts might already differ before submission due to greater uptake of preprints by particular research communities.

Nevertheless, our results show that quality of reporting in preprints in the life sciences is within a similar range as that of peer-reviewed articles, albeit slightly lower on average, supporting the idea that preprints should be considered valid scientific contributions.

An ongoing second phase of the project is comparing preprints to their own published versions in order to more directly assess the effects of peer review.

URL : Comparing quality of reporting between preprints and peer-reviewed articles in the biomedical literature

DOI : https://doi.org/10.1101/581892

Open access policies of leading medical journals: a cross-sectional study

Authors : Tim S Ellison, Laura Schmidt, Amy Williams, Christopher C Winchester

Objectives

Academical and not-for-profit research funders are increasingly requiring that the research they fund must be published open access, with some insisting on publishing with a Creative Commons Attribution (CC BY) licence to allow the broadest possible use.

We aimed to clarify the open access variants provided by leading medical journals and record the availability of the CC BY licence for commercially funded research.

Methods

We identified medical journals with a 2015 impact factor of ≥15.0 on 24 May 2017, then excluded from the analysis journals that only publish review articles. Between 29 June 2017 and 26 July 2017, we collected information about each journal’s open access policies from their websites and/or by email contact.

We contacted the journals by email again between 6 December 2017 and 2 January 2018 to confirm our findings.

Results

Thirty-five medical journals publishing original research from 13 publishers were included in the analysis. All 35 journals offered some form of open access allowing articles to be free-to-read, either immediately on publication or after a delay of up to 12 months.

Of these journals, 21 (60%) provided immediate open access with a CC BY licence under certain circumstances (eg, to specific research funders). Of these 21, 20 only offered a CC BY licence to authors funded by non-commercial organisations and one offered this option to any funder who required it.

Conclusions

Most leading medical journals do not offer to authors reporting commercially funded research an open access licence that allows unrestricted sharing and adaptation of the published material.

The journals’ policies are therefore not aligned with open access declarations and guidelines. Commercial research funders lag behind academical funders in the development of mandatory open access policies, and it is time for them to work with publishers to advance the dissemination of the research they fund.

URL : Open access policies of leading medical journals: a cross-sectional study

DOI : http://dx.doi.org/10.1136/bmjopen-2018-028655

Ten years of AoB PLANTS the open access journal for plant scientists: inception and progress since 2009

Author : Michael B Jackson

AoB PLANTS is a not-for-profit, open access, plant science journal and one of three peer-reviewed journals owned and managed by the Annals of Botany Company. This article explains events and thinking that led to the starting of AoB PLANTS and how the unique features of the Journal came to be formalized prior to its launch in September 2009.

The article also describes how the Journal’s management developed over the first 10 years and summarizes the Journal’s achievements in a decade where open access journals have proliferated despite subscription journals continuing to dominate the publishing of peer-reviewed botanical science.

URL : Ten years of AoB PLANTS the open access journal for plant scientists: inception and progress since 2009

DOI : https://doi.org/10.1093/aobpla/plz025

Over-optimization of academic publishing metrics: observing Goodhart’s Law in action

Authors : Michael Fire, Carlos Guestrin

Background

The academic publishing world is changing significantly, with ever-growing numbers of publications each year and shifting publishing patterns. However, the metrics used to measure academic success, such as the number of publications, citation number, and impact factor, have not changed for decades.

Moreover, recent studies indicate that these metrics have become targets and follow Goodhart’s Law, according to which, “when a measure becomes a target, it ceases to be a good measure.”

Results

In this study, we analyzed >120 million papers to examine how the academic publishing world has evolved over the last century, with a deeper look into the specific field of biology. Our study shows that the validity of citation-based measures is being compromised and their usefulness is lessening.

In particular, the number of publications has ceased to be a good metric as a result of longer author lists, shorter papers, and surging publication numbers. Citation-based metrics, such citation number and h-index, are likewise affected by the flood of papers, self-citations, and lengthy reference lists.

Measures such as a journal’s impact factor have also ceased to be good metrics due to the soaring numbers of papers that are published in top journals, particularly from the same pool of authors.

Moreover, by analyzing properties of >2,600 research fields, we observed that citation-based metrics are not beneficial for comparing researchers in different fields, or even in the same department.

Conclusions

Academic publishing has changed considerably; now we need to reconsider how we measure success.

URL : Over-optimization of academic publishing metrics: observing Goodhart’s Law in action

DOI : https://doi.org/10.1093/gigascience/giz053

Scientific misconduct and accountability in teams

Authors : Katrin Hussinger, Maikel Pellens

Increasing complexity and multidisciplinarity make collaboration essential for modern science. This, however, raises the question of how to assign accountability for scientific misconduct among larger teams of authors. Biomedical societies and science associations have put forward various sets of guidelines. Some state that all authors are jointly accountable for the integrity of the work.

Others stipulate that authors are only accountable for their own contribution. Alternatively, there are guarantor type models that assign accountability to a single author. We contribute to this debate by analyzing the outcomes of 80 scientific misconduct investigations of biomedical scholars conducted by the U.S. Office of Research Integrity (ORI).

We show that the position of authors on the byline of 184 publications involved in misconduct cases correlates with responsibility for the misconduct. Based on a series of binary regression models, we show that first authors are 38% more likely to be responsible for scientific misconduct than authors listed in the middle of the byline (p<0.01). Corresponding authors are 14% more likely (p<0.05).

These findings suggest that a guarantor-like model where first authors are ex-ante accountable for misconduct is highly likely to not miss catching the author responsible, while not afflicting too many bystanders.

URL : Scientific misconduct and accountability in teams

DOI : https://doi.org/10.1371/journal.pone.0215962

Governance of a global genetic resource commons for non-commercial research: A case-study of the DNA barcode commons

Authors : Janis Geary, Tania Bubela

Life sciences research that uses genetic resources is increasingly collaborative and global, yet collective action remains a significant barrier to the creation and management of shared research resources. These resources include sequence data and associated metadata, and biological samples, and can be understood as a type of knowledge commons.

Collective action by stakeholders to create and use knowledge commons for research has potential benefits for all involved, including minimizing costs and sharing risks, but there are gaps in our understanding of how institutional arrangements may promote such collective action in the context of global genetic resources.

We address this research gap by examining the attributes of an exemplar global knowledge commons: The DNA barcode commons. DNA barcodes are short, standardized gene regions that can be used to inexpensively identify unknown specimens, and proponents have led international efforts to make DNA barcodes a standard species identification tool.

Our research examined if and how attributes of the DNA barcode commons, including governance of DNA barcode resources and management of infrastructure, facilitate global participation in DNA barcoding efforts. Our data sources included key informant interviews, organizational documents, scientific outputs of the DNA barcoding community, and DNA barcode record submissions.

Our research suggested that the goal of creating a globally inclusive DNA barcode commons is partially impeded by the assumption that scientific norms and expectations held by researchers in high income countries are universal. We found scientific norms are informed by a complex history of resource misappropriation and mistrust between stakeholders.

DNA barcode organizations can mitigate the challenges caused by its global membership through creating more inclusive governance structures, developing norms for the community are specific to the context of DNA barcoding, and through increasing awareness and knowledge of pertinent legal frameworks.

URL : Governance of a global genetic resource commons for non-commercial research: A case-study of the DNA barcode commons

Alternative location : https://www.thecommonsjournal.org/articles/10.18352/ijc.859/

Crowdsourcing in medical research: concepts and applications

Authors : Joseph D. Tucker, Suzanne Day, Weiming Tang, Barry Bayus

Crowdsourcing shifts medical research from a closed environment to an open collaboration between the public and researchers. We define crowdsourcing as an approach to problem solving which involves an organization having a large group attempt to solve a problem or part of a problem, then sharing solutions.

Crowdsourcing allows large groups of individuals to participate in medical research through innovation challenges, hackathons, and related activities. The purpose of this literature review is to examine the definition, concepts, and applications of crowdsourcing in medicine.

This multi-disciplinary review defines crowdsourcing for medicine, identifies conceptual antecedents (collective intelligence and open source models), and explores implications of the approach. Several critiques of crowdsourcing are also examined.

Although several crowdsourcing definitions exist, there are two essential elements: (1) having a large group of individuals, including those with skills and those without skills, propose potential solutions; (2) sharing solutions through implementation or open access materials.

The public can be a central force in contributing to formative, pre-clinical, and clinical research. A growing evidence base suggests that crowdsourcing in medicine can result in high-quality outcomes, broad community engagement, and more open science.

URL : Crowdsourcing in medical research: concepts and applications

DOI : https://doi.org/10.7717/peerj.6762