Étiquette : biomedical research

Publication in a medical student journal predicts short- and long-term academic success: a matched-cohort study

Authors : Ibrahim S. Al-Busaidi, Cameron I. Wells, Tim J. Wilkinson

Background

Medical student journals play a critical role in promoting academic research and publishing amongst medical students, but their impact on students’ future academic achievements has not been examined.

We aimed to evaluate the short- and long-term effects of publication in the New Zealand Medical Student Journal (NZMSJ) through examining rates of post-graduation publication, completion of higher academic degrees, and pursuing an academic career.

Methods

Student-authored original research publications in the NZMSJ during the period 2004–2011 were retrospectively identified. Gender-, university- and graduation year-matched controls were identified from publicly available databases in a 2:1 ratio (two controls for each student authors).

Date of graduation, current clinical scope of practice, completion of higher academic degrees, and attainment of an academic position for both groups were obtained from Google searches, New Zealand graduate databases, online lists of registered doctors in New Zealand and Australia, and author affiliation information from published articles.

Pre- and post-graduation PubMed®-indexed publications were identified using standardised search criteria.

Results

Fifty publications authored by 49 unique students were identified. The median follow-up period after graduation was 7.0 years (range 2–12 years). Compared with controls, student–authors were significantly more likely to publish in PubMed®-indexed journals (OR 3.09, p = 0.001), obtain a PhD (OR 9.21, p = 0.004) or any higher degree (OR 2.63, p = 0.007), and attain academic positions (OR 2.90, p = 0.047) following graduation.

Conclusion

Publication in a medical student journal is associated with future academic achievement and contributes to develop a clinical academic workforce. Future work should aim to explore motivators and barriers associated with these findings.

URL : Publication in a medical student journal predicts short- and long-term academic success: a matched-cohort study

Alternative location : https://bmcmededuc.biomedcentral.com/articles/10.1186/s12909-019-1704-x

 

Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

Authors : Charles Vesteghem, Rasmus Froberg Brøndum, Mads Sønderkær, Mia Sommer, Alexander Schmitz, Julie Støve Bødker, Karen Dybkær, Tarec Christoffer El-Galaly, Martin Bøgsted

Compelling research has recently shown that cancer is so heterogeneous that single research centres cannot produce enough data to fit prognostic and predictive models of sufficient accuracy. Data sharing in precision oncology is therefore of utmost importance.

The Findable, Accessible, Interoperable and Reusable (FAIR) Data Principles have been developed to define good practices in data sharing. Motivated by the ambition of applying the FAIR Data Principles to our own clinical precision oncology implementations and research, we have performed a systematic literature review of potentially relevant initiatives.

For clinical data, we suggest using the Genomic Data Commons model as a reference as it provides a field-tested and well-documented solution. Regarding classification of diagnosis, morphology and topography and drugs, we chose to follow the World Health Organization standards, i.e. ICD10, ICD-O-3 and Anatomical Therapeutic Chemical classifications, respectively.

For the bioinformatics pipeline, the Genome Analysis ToolKit Best Practices using Docker containers offer a coherent solution and have therefore been selected. Regarding the naming of variants, we follow the Human Genome Variation Society’s standard.

For the IT infrastructure, we have built a centralized solution to participate in data sharing through federated solutions such as the Beacon Networks.

URL : Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives

DOI : https://doi.org/10.1093/bib/bbz044

The effect of bioRxiv preprints on citations and altmetrics

Authors : Nicholas Fraser, Fakhri Momeni, Philipp Mayr, Isabella Peters

A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences.

We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals.

We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship.

bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.

URL : https://www.biorxiv.org/content/10.1101/673665v1

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