Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

Authors : John A. Borghi, Ana E. Van Gulick

Neuroimaging methods such as magnetic resonance imaging (MRI) involve complex data collection and analysis protocols, which necessitate the establishment of good research data management (RDM). Despite efforts within the field to address issues related to rigor and reproducibility, information about the RDM-related practices and perceptions of neuroimaging researchers remains largely anecdotal.

To inform such efforts, we conducted an online survey of active MRI researchers that covered a range of RDM-related topics. Survey questions addressed the type(s) of data collected, tools used for data storage, organization, and analysis, and the degree to which practices are defined and standardized within a research group.

Our results demonstrate that neuroimaging data is acquired in multifarious forms, transformed and analyzed using a wide variety of software tools, and that RDM practices and perceptions vary considerably both within and between research groups, with trainees reporting less consistency than faculty.

Ratings of the maturity of RDM practices from ad-hoc to refined were relatively high during the data collection and analysis phases of a project and significantly lower during the data sharing phase.

Perceptions of emerging practices including open access publishing and preregistration were largely positive, but demonstrated little adoption into current practice.

URL : Data management and sharing in neuroimaging: Practices and perceptions of MRI researchers

DOI : https://doi.org/10.1371/journal.pone.0200562

Open and transparent research practices and public perceptions of the trustworthiness of agricultural biotechnology organizations

Authors : Asheley R. Landrum, Joseph Hilgard, Robert B. Lull, Heather Akin, Kathleen Hall Jamieson

Public trust in agricultural biotechnology organizations that produce so-called ‘genetically-modified organisms’ (GMOs) is affected by misinformed attacks on GM technology and worry that producers’ concern for profits overrides concern for the public good.

In an experiment, we found that reporting that the industry engages in open and transparent research practices increased the perceived trustworthiness of university and corporate organizations involved with GMOs.

Universities were considered more trustworthy than corporations overall, supporting prior findings in other technology domains.

The results suggest that commitment to, and communication of, open and transparent research practices should be part of the process of implementing agricultural biotechnologies.

URL : Open and transparent research practices and public perceptions of the trustworthiness of agricultural biotechnology organizations

DOI : https://doi.org/10.22323/2.17020204

Comparing scientific and technological impact of biomedical research

Author : Qing Ke

Traditionally, the number of citations that a scholarly paper receives from other papers is used as the proxy of its scientific impact. Yet citations can come from domains outside the scientific community, and one such example is through patented technologies—paper can be cited by patents, achieving technological impact.

While the scientific impact of papers has been extensively studied, the technological aspect remains largely unknown. Here we aim to fill this gap by presenting a comparative study on how 919 thousand biomedical papers are cited by U.S. patents and by other papers over time.

We observe a positive correlation between citations from patents and from papers, but there is little overlap between the two domains in either the most cited papers, or papers with the most delayed recognition.

We also find that the two types of citations exhibit distinct temporal variations, with patent citations lagging behind paper citations for a median of 6 years for the majority of papers. Our work contributes to the understanding of the technological, and societal in general, impact of papers.

URL : https://arxiv.org/abs/1804.04105

Authorial and institutional stratification in open access publishing: the case of global health research

Authors : Kyle Siler, Stefanie Haustein, Elise Smith, Vincent Larivière, Juan Pablo Alperin

Using a database of recent articles published in the field of Global Health research, we examine institutional sources of stratification in publishing access outcomes. Traditionally, the focus on inequality in scientific publishing has focused on prestige hierarchies in established print journals.

This project examines stratification in contemporary publishing with a particular focus on subscription vs. various Open Access (OA) publishing options.

Findings show that authors working at lower-ranked universities are more likely to publish in closed/paywalled outlets, and less likely to choose outlets that involve some sort of Article Processing Charge (APCs; gold or hybrid OA).

We also analyze institutional differences and stratification in the APC costs paid in various journals. Authors affiliated with higher-ranked institutions, as well as hospitals and non-profit organizations pay relatively higher APCs for gold and hybrid OA publications.

Results suggest that authors affiliated with high-ranked universities and well-funded institutions tend to have more resources to choose pay options with publishing. Our research suggests new professional hierarchies developing in contemporary publishing, where various OA publishing options are becoming increasingly prominent.

Just as there is stratification in institutional representation between different types of publishing access, there is also inequality within access types.

URL : Authorial and institutional stratification in open access publishing: the case of global health research

DOI : https://doi.org/10.7717/peerj.4269

Data sharing and reanalysis of randomized controlled trials in leading biomedical journals with a full data sharing policy: survey of studies published in The BMJ and PLOS Medicine

Authors : Florian Naudet, Charlotte Sakarovitch, Perrine Janiaud, Ioana Cristea, Daniele Fanelli, David Moher, John P A Ioannidis

Objectives

To explore the effectiveness of data sharing by randomized controlled trials (RCTs) in journals with a full data sharing policy and to describe potential difficulties encountered in the process of performing reanalyses of the primary outcomes.

Design

Survey of published RCTs.

Setting

PubMed/Medline.

Eligibility criteria

RCTs that had been submitted and published by The BMJ and PLOS Medicine subsequent to the adoption of data sharing policies by these journals.

Main outcome measure

The primary outcome was data availability, defined as the eventual receipt of complete data with clear labelling. Primary outcomes were reanalyzed to assess to what extent studies were reproduced. Difficulties encountered were described.

Results

37 RCTs (21 from The BMJ and 16 from PLOS Medicine) published between 2013 and 2016 met the eligibility criteria. 17/37 (46%, 95% confidence interval 30% to 62%) satisfied the definition of data availability and 14 of the 17 (82%, 59% to 94%) were fully reproduced on all their primary outcomes. Of the remaining RCTs, errors were identified in two but reached similar conclusions and one paper did not provide enough information in the Methods section to reproduce the analyses. Difficulties identified included problems in contacting corresponding authors and lack of resources on their behalf in preparing the datasets. In addition, there was a range of different data sharing practices across study groups.

Conclusions

Data availability was not optimal in two journals with a strong policy for data sharing. When investigators shared data, most reanalyses largely reproduced the original results. Data sharing practices need to become more widespread and streamlined to allow meaningful reanalyses and reuse of data.

 

A scoping review of comparisons between abstracts and full reports in primary biomedical research

Authors : Guowei Li, Luciana P. F. Abbade, Ikunna Nwosu, Yanling Jin, Alvin Leenus, Muhammad Maaz, Mei Wang, Meha Bhatt, Laura Zielinski, Nitika Sanger, Bianca Bantoto, Candice Luo, Ieta Shams, Hamnah Shahid, Yaping Chang, Guangwen Sun, Lawrence Mbuagbaw, Zainab Samaan, Mitchell A. H. Levine, Jonathan D. Adachi, Lehana Thabane

Background

Evidence shows that research abstracts are commonly inconsistent with their corresponding full reports, and may mislead readers.

In this scoping review, which is part of our series on the state of reporting of primary biomedical research, we summarized the evidence from systematic reviews and surveys, to investigate the current state of inconsistent abstract reporting, and to evaluate factors associated with improved reporting by comparing abstracts and their full reports.

Methods

We searched EMBASE, Web of Science, MEDLINE, and CINAHL from January 1st 1996 to September 30th 2016 to retrieve eligible systematic reviews and surveys. Our primary outcome was the level of inconsistency between abstracts and corresponding full reports, which was expressed as a percentage (with a lower percentage indicating better reporting) or categorized rating (such as major/minor difference, high/medium/low inconsistency), as reported by the authors.

We used medians and interquartile ranges to describe the level of inconsistency across studies. No quantitative syntheses were conducted. Data from the included systematic reviews or surveys was summarized qualitatively.

Results

Seventeen studies that addressed this topic were included. The level of inconsistency was reported to have a median of 39% (interquartile range: 14% – 54%), and to range from 4% to 78%. In some studies that separated major from minor inconsistency, the level of major inconsistency ranged from 5% to 45% (median: 19%, interquartile range: 7% – 31%), which included discrepancies in specifying the study design or sample size, designating a primary outcome measure, presenting main results, and drawing a conclusion.

A longer time interval between conference abstracts and the publication of full reports was found to be the only factor which was marginally or significantly associated with increased likelihood of reporting inconsistencies.

Conclusions

This scoping review revealed that abstracts are frequently inconsistent with full reports, and efforts are needed to improve the consistency of abstract reporting in the primary biomedical community.

URL : A scoping review of comparisons between abstracts and full reports in primary biomedical research

DOI : https://doi.org/10.1186/s12874-017-0459-5

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

Authors : Tim Ellison, Tim Koder, Laura Schmidt, Amy Williams, Christopher Winchester

Introduction

Journal publishers increasingly offer governmental and charitable research funders the option to pay for open access with a Creative Commons Attribution (CC BY) licence, which allows sharing and adaptation of published materials for commercial as well as non-commercial use.

The Open Access Scholarly Publishers Association recommends this licence as the least restrictive Creative Commons licence available. We set out to investigate whether pharmaceutical companies are offered the same options.

Methods

Using Journal Selector (Sylogent, Newtown, PA, USA), we identified journals with a 2015 impact factor of at least 15 on 24 May 2017, and excluded journals that only publish review articles from the analysis.

Between 29 June 2017 and 26 July 2017, we collected information about the journals’ 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-seven non-review journals listed in the Journal Selector database, from 14 publishers, had a 2015 impact factor of at least 15. All 37 journals offered some form of access with varying embargo periods of up to 12 months.

Of these journals, 23 (62%) offered immediate open access with a CC BY licence under certain circumstances (e.g. to specific research funders). Of these 23, only one journal confirmed that it offered a CC BY licence to commercial funders/pharmaceutical companies.

Conclusion

The open access policies of most medical journals with high impact factors restrict the dissemination of medical research funded by the pharmaceutical industry.

To give the scientific community freedom to read, reuse and adapt medical publications, publishers and academic journal editors would ideally allow pharmaceutical companies to fund unrestricted and immediate open access with a CC BY licence.

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

DOI : https://doi.org/10.1101/250613