Biology subjects

Ioannidis, J. P.

Publications and source records attributed to Ioannidis, J. P..

7 recordsLinked to original sources

bioRxiv2020

A systematic examination of preprint platforms for use in the medical and biomedical sciences setting

ABSTRACTObjectives The objective of this review is to identify all preprint platforms with biomedical and medical scope and to compare and contrast the key characteristics and policies of these platforms. We also aim to provide a searchable database to enable relevant stakeholders to compare between platforms.Study Design and Setting Preprint platforms that were launched up to 25th June 2019 and have a biomedical and medical scope according to MEDLINE’s journal selection criteria were identified using existing lists, web-based searches and the expertise of both academic and non-academic publication scientists. A data extraction form was developed, pilot-tested and used to collect data from each preprint platform’s webpage(s). Data collected were in relation to scope and ownership; content-specific characteristics and information relating to submission, journal transfer options, and external discoverability; screening, moderation, and permanence of content; usage metrics and metadata. Where possible, all online data were verified by the platform owner or representative by correspondence.Results A total of 44 preprint platforms were identified as having biomedical and medical scope, 17 (39%) were hosted by the Open Science Framework preprint infrastructure, six (14%) were provided by F1000 Research Ltd (the Open Research Central infrastructure) and 21 (48%) were other independent preprint platforms. Preprint platforms were either owned by non-profit academic groups, scientific societies or funding organisations (n=28; 64%), owned/partly owned by for-profit publishers or companies (n=14; 32%) or owned by individuals/small communities (n=2; 5%). Twenty-four (55%) preprint platforms accepted content from all scientific fields although some of these had restrictions relating to funding source, geographical region or an affiliated journal’s remit. Thirty-three (75%) preprint platforms provided details about article screening (basic checks) and 14 (32%) of these actively involved researchers with context expertise in the screening process. The three most common screening checks related to the scope of the article, plagiarism and legal/ethical/societal issues and compliance. Almost all preprint platforms allow submission to any peer-reviewed journal following publication, have a preservation plan for read-access, and most have a policy regarding reasons for retraction and the sustainability of the service. Forty-one (93%) platforms currently have usage metrics, with the most common metric being the number of downloads presented on the abstract page.Conclusion A large number of preprint platforms exist for use in biomedical and medical sciences, all of which offer researchers an opportunity to rapidly disseminate their research findings onto an open-access public server, subject to scope and eligibility. However, the process by which content is screened before online posting and withdrawn or removed after posting varies between platforms, which may be associated with platform operation, ownership, governance and financing.In concurrence with an increase in the number of preprint servers and platforms supporting biomedical and medical sciences research since 2013, there has been substantial growth in the number of preprints posted in this research area.The significant benefits of accelerated dissemination of research that preprints offer has attracted the support of many major funders.The raised profile of preprints has led to their wider acceptance in institutional and individual level assessment.This is the first full examination of the characteristics and policies of 44 preprint platforms with biomedical and medical scope. We use a robust methodological approach to extract relevant information from web-based material with input from preprint platform owners.Despite concerns regarding the permanence and quality of preprints, most preprint platforms have long-term preservation strategies and many have screening checks (for example, a basic check for the relevance of content) in place. For some platforms, these checks are performed by researchers with content expertise.We provide a searchable database as a valuable resource for researchers, funders and policymakers in the biomedical and medical science field to determine which preprint platforms are relevant to their research scope and which have the functionality and policies that they value most.Competing Interest StatementJessica Polka is Executive Director of ASAPbio.View Full Text

scientific communication and education↗

bioRxiv2019

Academic criteria for promotion and tenure in faculties of biomedical sciences: a cross-sectional analysis of 146 universities

ObjectivesTo determine the presence of a set of pre-specified traditional and progressive criteria used to assess scientists for promotion and tenure in faculties of biomedical sciences among universities worldwide. DesignCross-sectional study. SettingNot applicable. Participants170 randomly selected universities from the Leiden Ranking of world universities list were considered. Main outcome measuresTwo independent reviewers searched for all guidelines applied when assessing scientists for promotion and tenure for institutions with biomedical faculties. Where faculty-level guidelines were not available, institution-level guidelines were sought. Available documents were reviewed and the presence of 5 traditional (e.g., number of publications) and 7 progressive (e.g., data sharing) criteria was noted in guidelines for assessing assistant professors, associate professors, professors, and the granting of tenure. ResultsA total of 146 institutions had faculties of biomedical sciences with 92 having eligible guidelines available to review. Traditional criteria were more commonly reported than progressive criteria (t(82)= 15.1, p= .001). Traditional criteria mentioned peer-reviewed publications, authorship order, journal impact, grant funding, and national or international reputation in 95%, 37%, 28%, 67%, and 48% of the guidelines, respectively. Conversely, among progressive criteria only citations (any mention in 26%) and accommodations for extenuating circumstances (37%) were relatively commonly mentioned; while there was rare mention of alternative metrics for sharing research (2%) and data sharing (1%), and 3 criteria (publishing in open access mediums, registering research, and adhering to reporting guidelines) were not found in any institution reviewed. We observed notable differences across continents on whether guidelines are accessible or not (Australia 100%, North America 97%, Europe 50%, Asia 58%, South America 17%), and more subtle differences on the use of specific criteria. ConclusionsThis study demonstrates that the current evaluation of scientists emphasizes traditional criteria as opposed to progressive criteria. This may reinforce research practices that are known to be problematic while insufficiently supporting the conduct of better-quality research and open science. Institutions should consider incentivizing progressive criteria. RegistrationOpen Science Framework (https://osf.io/26ucp/) What is already known on this topicO_LIAcademics tailor their research practices based on the evaluation criteria applied within their academic institution. C_LIO_LIEnsuring that biomedical researchers are incentivized by adhering to best practice guidelines for research is essential given the clinical implications of this work. C_LIO_LIWhile changes to the criteria used to assess professors and confer tenure have been recommended, a systematic assessment of promotion and tenure criteria being applied worldwide has not been conducted. C_LI What this study addsO_LIAcross countries, university guidelines focus on rewarding traditional research criteria (peer-reviewed publications, authorship order, journal impact, grant funding, and national or international reputation). C_LIO_LIThe minimum requirements for promotion and tenure criteria are predominantly objective in nature, although several of them are inadequate measures to assess the impact of researchers. C_LIO_LIDeveloping and evaluating more appropriate, progressive indicators of research may facilitate changes in the evaluation practices for rewarding researchers. C_LI

scientific communication and education↗

bioRxiv2019

Sample size evolution in neuroimaging research: an evaluation of highly-cited studies (1990-2012) and of latest practices (2017-2018) in high-impact journals

We evaluated 1038 of the most cited structural and functional (fMRI) magnetic resonance brain imaging papers (1161 studies) published during 1990-2012 and 273 papers (302 studies) published in top neuroimaging journals in 2017 and 2018. 96% of highly cited experimental fMRI studies had a single group of participants and these studies had median sample size of 12, highly cited clinical fMRI studies (with patient participants) had median sample size of 14.5, and clinical structural MRI studies had median sample size of 50. The sample size of highly cited experimental fMRI studies increased at a rate of 0.74 participant/year and this rate of increase was commensurate with the median sample sizes of neuroimaging studies published in top neuroimaging journals in 2017 (23 participants) and 2018 (24 participants). Only 4 of 131 papers in 2017 and 5 of 142 papers in 2018 had pre-study power calculations, most for single t-tests and correlations. Only 14% of highly cited papers reported the number of excluded participants whereas about 45% of papers in 2017 and 2018 reported excluded participants. Targeted interventions from publishers and funders could facilitate increase in sample sizes and adherence to better standards.

neuroscience↗

bioRxiv2019

Excess significance bias in repetitive transcranial magnetic stimulation literature for neuropsychiatric disorders

IntroductionRepetitive transcranial magnetic stimulation (rTMS) has been widely tested and promoted for use in multiple neuropsychiatric conditions, but as for many other medical devices, some gaps may exist in the literature and the evidence base for rTMS clinical efficacy remains under debate. We aimed to empirically test for an excess number of statistically significant results in the literature on rTMS therapeutic efficacy across a wide range of meta-analyses and to characterize the power of studies included in these meta-analyses.\n\nMethodsBased on power calculations, we computed the expected number of \"positive\" datasets for a medium effect-size (standardized mean difference, SMD=0.30) and compared it with the number of observed \"positive\" datasets. Sensitivity analyses considered small (SMD=0.20), modest (SMD=0.50), and large (SMD=0.80) effect sizes.\n\nResults14 meta-analyses with 228 datasets (110 for neurological disorders and 118 for psychiatric disorders) were assessed. For SMD=0.3, the number of observed \"positive\" studies (n=94) was larger than expected (n=35). We found evidence for an excess of significant findings overall (p<0.0001) and in 8/14 meta-analyses. Evidence for an excess of significant findings was also observed for SMD=0.5 for neurological disorders. 0 (0 %), 0 (0 %), 3 (1 %), and 53 (23 %) of the 228 datasets had power >0.80, respectively for SMDs of 0.30, 0.20, 0.50, and 0.80.\n\nConclusionMost studies in the rTMS literature are underpowered. This results in fragmentation and waste of research efforts. The somewhat high frequency of \"positive\" results seems spurious and may reflect bias.\n\nTrial Registration: PROSPERO 2017 CRD42017056694

scientific communication and education↗

bioRxiv2019

Hypothesis, analysis and synthesis: it's all Greek to me!

The linguistic foundations of science and technology have relied on a range of terms many of which are borrowed from ancient languages, a known but little researched fact from a statistical perspective. Precise definitions and novel concepts are often crafted with those -- frequently used -- terms, yet their etymology from Greek or Latin might not always be fully appreciated. Herein, we demonstrate that frequently used terms span almost the entire PubMed(R) database, while a handful of terms of Greek origin retrieve 80% of all entries. We argue that the etymology of those critical terms needs to be fully grasped to ensure correct use, in conjunction with other concepts. We further propose a number of terms for genomics, using prepositions that can accurately define subtle sub-disciplines of this ever-expanding field. Finally, we invite commentary by both the science community and the humanities, for possible adoption of suggested terms, not least to avoid inaccurate usage or inappropriate notions that may compromise clarity of meaning.

scientific communication and education↗

bioRxiv2017

Systematic Identification of Correlates of HIV-1 Infection: An X-Wide Association Study in Zambia

BackgroundHIV-1 remains the leading cause of death among adults in Sub-Saharan Africa, and over 1 million people are infected annually. Better identification of at-risk groups could benefit prevention and treatment programmes. We systematically identified factors related to HIV-1 infection in two nationally representative cohorts of women that participated in Zambias Demographic and Health Surveys (DHS).\n\nMethodsWe conducted a comprehensive analysis to identify and replicate the association of 1,415 social, economic, environmental, and behavioral indicators with HIV-1 status. We used the 2007 and 2013-2014 DHS surveys conducted among 5,715 and 15,433 Zambian women, respectively (727 indicators in 2007; 688 in 2013-2014; 688 in both). We used false discovery rate criteria to identify indicators that are strongly associated with HIV-1 in univariate and multivariate models in the entire population, as well as in subgroups stratified by wealth, residence, age, and history of HIV-1 testing.\n\nFindingsIn the univariate analysis we identified 102 and 182 variables that are associated with HIV-1 in the 2007 and 2013-2014 surveys, respectively, among which 79 were associated in both. Variables that were associated with HIV-1 status in all full-sample models (unadjusted and adjusted) as well as in at least 17 out of 18 subgroups include being formerly in a union (adjusted OR 2007 2.8, p<10-16; 2013-2014 2.8, p<10-29), widowhood (adjusted OR 2007 3.7, p<10-12; 2013-2014 4.2, p<10-30), history of genital ulcers in the last 12 months (adjusted 2007 OR 2.4, p<10-5; 2013-2014 2.2, p<10-6), and having a woman for the head of the household (2007 OR 1.7, p<10-7; 2013-2014 OR 2.1, p<10-26), while owning a bicycle (adjusted 2007 OR 0.6, p<10-6; 2013-2014 0.6, p<10-8) and currently breastfeeding (adjusted 2007 OR 0.5, p<10-9; 2013-2014 0.4, p<10-26) were associated with decreased risk. Using the identified variables, area under the curve for HIV-1 positivity ranged from 0.76 to 0.82.\n\nInterpretationOur X-wide association study in Zambian women identifies multiple under-recognized factors correlated with HIV-1 infection in 2007 and 2013-2014, including widowhood, breastfeeding, and being the head of the household. These variables could be used to improve HIV-1 testing and identification programs.

epidemiology↗

bioRxiv2016

When null hypothesis significance testing is unsuitable for research: a reassessment

Null hypothesis significance testing (NHST) has several shortcomings that are likely contributing factors behind the widely debated replication crisis of psychology, cognitive neuroscience and biomedical science in general. We review these shortcomings and suggest that, after about 60 years of negative experience, NHST should no longer be the default, dominant statistical practice of all biomedical and psychological research. Different inferential methods (NHST, likelihood estimation, Bayesian methods, false-discovery rate control) may be most suitable for different types of research questions. Whenever researchers use NHST they should justify its use, and publish pre-study power calculations and effect sizes, including negative findings. Studies should optimally be pre-registered and raw data published. The current statistics lite educational approach for students that has sustained the widespread, spurious use of NHST should be phased out. Instead, we should encourage either more in-depth statistical training of more researchers and/or more widespread involvement of professional statisticians in all research.

neuroscience↗