Biology subjects

Vassar, M.

Publications and source records attributed to Vassar, M..

10 recordsLinked to original sources

bioRxiv2022

The Main Themes and Experiences Shared with the Hashtag #BlackintheIvory: A Qualitative Analysis

BackgroundThe movement #BlackintheIvory gave Black academics an opportunity to connect through a social media platform allowing them to share common experiences in the pursuit of higher education. Through the analysis of Twitter posts, using the hashtag #BlackintheIvory, this study investigates the main themes identified among Black scholars in academia and their shared experiences with teaching, mentoring, collegiality, identity, service, and racism. MethodsUsing the Twitter API, we isolated all publicly available tweets, which can include text, images, and links to websites, posted with the hashtag #BlackintheIvory on the Twitter website (www.twitter.com) from the inception of the hashtag in June 2020 to the end of December 2020. To evaluate the tweets, we categorized the tweets inductively. Based on the content of the posts, we identified 6 themes: Teaching, Mentoring, Collegiality, Identity, Service, and Racism. ResultsOur search yielded a total of 12,538 original posts, including tweets between inception in June 2020 to December 2020 from profiles made public (excluding modified tweets and duplicate tweets). We selected and analyzed the top retweeted 2500 tweets, which is 20% (2500/12538) of the total number of downloaded tweets. The greatest percentage of posts were about Teaching (881; 35%), followed by Service (441; 18%) and Racism (414; 17%). The remaining tweets were categorized as Collegiality (388; 15%), Identity (210; 8%), and Mentoring (166; 7%) of the total number of tweets from June-December 2020. ConclusionThe experiences, perspectives, and narratives among the Black diaspora within #BlackintheIvory are not uniform. The commonality exists within the structural systemic racism which impacts Black academics within the ivory tower, this study is a resounding wake-up call for action. FundingThis study was not subject to any funding

scientific communication and education↗

bioRxiv2019

Transparent and Reproducible Research Practices in the Surgical Literature

Previous studies have established a baseline of minimal reproducibility in the social science and biomedical literature. Clinical research is especially deficient in factors of reproducibility. Surgical journals contain fewer clinical trials than non-surgical ones, suggesting that it should be easier to reproduce the outcomes of surgical literature. In this study, we evaluated a broad range of indicators related to transparency and reproducibility in a random sample of 300 articles published in surgery-related journals between 2014 and 2018. A minority of our sample made available their materials (2/186, 95% C.I. 0-2.2%), protocols (1/196, 0-1.3%), data (19/196, 6.3-13%), or analysis scripts (0/196, 0-1.9%). Only one study was adequately pre-registered. No studies were explicit replications of previous literature. Most studies (162/292 50-61%) declined to provide a funding statement, and few declared conflicts of interest (22/292, 4.8-11%). Most have not been cited by systematic reviews (183/216, 81-89%) or meta-analyses (188/216, 83-91%), and most were behind a paywall (187/292, 58-70%). The transparency of surgical literature could improve with adherence to baseline standards of reproducibility.

scientific communication and education↗

bioRxiv2019

Evaluation of Reproducible and Transparent Research Practices in Sports Medicine Research: A Cross-sectional study

BackgroundIn recent years, urgency has been placed on the \"reproducibility crisis\" facing biomedical research. Despite efforts toward improvement, certain elements needed to reproduce a study are often lacking from publications. The current state of reproducibility within the sports medicine research community remains unknown.\n\nPurposeOur study sought to evaluate the presence of eight indicators of reproducibility and transparency to determine the current state of research reporting in sports medicine research.\n\nStudy DesignCross-sectional review\n\nMethodsUsing the National Library of Medicine catalog, we identified 41 MEDLINE-indexed, English language sports medicine journals. From the 41 journals, we randomly sampled 300 publications that were recorded on PubMed as being published between January 1, 2014, and December 31, 2018. Two investigators extracted data in duplicate and blinded fashion.\n\nResultsOf the 300 publications sampled, 280 were accessible and were screened for empirical data. Studies that lack empirical data were excluded from our analysis. Of the remaining 195 with empirical data, 10 (5.13%) publications provided data availability statements, 1 (0.51%) provided a protocol, 0 (0.0%) provided an analysis script, and 9 (4.62%) were pre registered.\n\nConclusionReproducibility and transparency indicators are lacking in sports medicine publications. The majority of publications lack the necessary resources for reproducibility such as material, data, analysis scripts, or protocol availability. While the current state of reproducibility cannot be fixed overnight, we feel combined efforts of data sharing, open access, and verifying disclosure statements can help to improve overall reporting.

scientific communication and education↗

bioRxiv2019

Evaluation of Reproducibility in Urology Publications

Take Home MessageMany components of transparency and reproducibility are lacking in urology publications, making study replication, at best, difficult.\n\nIntroductionReproducibility is essential for the integrity of scientific research. Reproducibility is measured by the ability of investigators to replicate the outcomes of an original publication by using the same materials and procedures.\n\nMethodsWe sampled 300 publications in the field of urology for assessment of multiple indicators of reproducibility, including material availability, raw data availability, analysis script availability, pre-registration information, links to protocols, and whether the publication was freely available to the public. Publications were also assessed for statements about conflicts of interest and funding sources.\n\nResultsOf the 300 sample publications, 171 contained empirical data and could be analyzed for reproducibility. Of the analyzed articles, 0.58% (1/171) provided links to protocols, and none of the studies provided analysis scripts. Additionally, 95.91% (164/171) did not provide accessible raw data, 97.53% (158/162) did not provide accessible materials, and 95.32% (163/171) did not state they were pre-registered.\n\nConclusionCurrent urology research does not consistently provide the components needed to reproduce original studies. Collaborative efforts from investigators and journal editors are needed to improve research quality, while minimizing waste and patient risk.

scientific communication and education↗

bioRxiv2019

Reproducible and Transparent Research Practices in Published Neurology Research

BackgroundThe objective of this study was to evaluate the nature and extent of reproducible and transparent research practices in neurology research.\n\nMethodsThe NLM catalog was used to identify MEDLINE-indexed neurology journals. A PubMed search of these journals was conducted to retrieve publications over a 5-year period from 2014 to 2018. A random sample of publications was extracted. Two authors conducted data extraction in a blinded, duplicate fashion using a pilot-tested Google form. This form prompted data extractors to determine whether publications provided access to items such as study materials, raw data, analysis scripts, and protocols. In addition, we determined if the publication was included in a replication study or systematic review, was preregistered, had a conflict of interest declaration, specified funding sources, and was open access.\n\nResultsOur search identified 223,932 publications meeting the inclusion criteria, from which 300 were randomly sampled. Only 290 articles were accessible, yielding 202 publications with empirical data for analysis. Our results indicate that 8.99% provided access to materials, 9.41% provided access to raw data, 0.50% provided access to the analysis scripts, 0.99% linked the protocol, and 3.47% were preregistered. A third of sampled publications lacked funding or conflict of interest statements. No publications from our sample were included in replication studies, but a fifth were cited in a systematic review or meta-analysis.\n\nConclusionsCurrent research in the field of neurology does not consistently provide information needed for reproducibility. The implications of poor research reporting can both affect patient care and increase research waste. Collaborative intervention by authors, peer reviewers, journals, and funding sources is needed to mitigate this problem.

scientific communication and education↗

bioRxiv2019

An evaluation of Nephrology Literature for Transparency and Reproducibility Indicators: Cross-sectional Review

BackgroundReproducibility is critical to diagnostic accuracy and treatment implementation. Concurrent with clinical reproducibility, research reproducibility establishes whether the use of identical study materials and methodologies in replication efforts permit researchers to arrive at similar results and conclusions. In this study, we address this gap by evaluating nephrology literature for common indicators of transparent and reproducible research.\n\nMethodsWe searched the National Library of Medicine catalog to identify 36 MEDLINE-indexed, English language nephrology journals. We randomly sampled 300 publications published between January 1, 2014, and December 31, 2018. In a duplicated and blinded fashion, two investigators screened and extracted data from the 300 publications.\n\nResultsOur search yielded 28,835 publications, of which we randomly sampled 300 publications. Of the 300 publications, 152 (50.67%) were publicly available whereas 143 (47.67%) were restricted through paywall and 5 (1.67%) were inaccessible. Of the remaining 295 publications, 123 were excluded because they lack empirical data necessary for reproducibility. Of the 172 publications with empirical data, 43 (25%) reported data availability statements, 4 (2.33%) analysis scripts, 4 (2.33%) links to a protocol, and 10 (5.81%) were pre-registered.\n\nConclusionOur study found that reproducible and transparent research practices are infrequently employed by the nephrology research community. Greater efforts should be made by both funders and journals, two entities that have the greatest ability to influence change. In doing so, an open science culture may eventually become the norm rather than the exception.

bioinformatics↗

bioRxiv2019

Analysis of Practices to Promote Reproducibility and Transparency in Anaesthesiology Research: Are Important Aspects Hidden Behind the Drapes?

IntroductionReliable, high-quality research is essential to the field of anaesthesiology. Reproducibility and transparency has been investigated in the biomedical domain and in the social sciences, with both lacking to provide necessary information to reproduce the study findings. In this study, we investigated 14 indicators of reproducibility in anaesthesiology research.\n\nMethodsWe used the National Library of Medicine (NLM) catalogue to search for all anaesthesiology journals that are MEDLINE indexed and provided English texts. PubMed was searched with the list of journals to identify all publications from January 1, 2014 to December 31, 2018. We randomly sampled 300 publications that fit the inclusion criteria for our analysis. Data extraction was then conducted in a blinded, duplicate fashion using a pilot-tested Google form.\n\nResultsThe PubMed search of these journals identified 171,441 publications, with 28,310 being within the time frame. From the 300 publications sampled, 296 full-text publications were accessible. Most of the studies did not include materials or protocol availability statements. The majority of publications did not provide a data analysis script statement (121/122, 99% [98% to 100%]) or a preregistration statement (94/122, 77% [72% to 81%]).\n\nConclusionAnaesthesiology research needs to drastically improve indicators of reproducibility and transparency. By making research publically available and improving accessibility to detailed study components, primary research can be reproduced in subsequent studies and help contribute to the development of new practice guidelines.

scientific communication and education↗

bioRxiv2019

Evaluation of Reproducible and Transparent Research Practices in Pulmonology

RationaleStudy reproducibility is valuable for validating or refuting results. Provision of reproducibility indicators, such as materials, protocols, and raw data in a study to improve its potential for reproduction. Efforts to reproduce noteworthy studies in the biomedical sciences have resulted in an overwhelming majority of them being found to be unreplicable, causing concern for the integrity of research in other fields, including medical specialities.\n\nObjectiveHere, we analyzed the reproducibility of studies in the field of pulmonology.\n\nMethods300 pulmonology articles were randomly selected from an initial PubMed search for data extraction. Two authors scoured these articles for reproducibility indicators including materials, protocols, raw data, analysis scripts, inclusion in systematic reviews, and citations by replication studies as well as other factors of research transparency including open accessibility, funding source and competing interest disclosures, and study preregistration.\n\nMain ResultsFew publications included statements regarding materials (11%), protocols (1%), data (21%), and analysis script (0%) availability. Less than 10% indicated preregistration. More than half of the publications analyzed failed to provide a funding statement. Conversely, 66% of the publications were open access and 70% included a conflict of interest statement.\n\nConclusionOverall, our study indicates pulmonology research is currently lacking in efforts to increase replicability. Future studies should focus on providing sufficient information regarding materials, protocols, raw data, and analysis scripts, among other indicators, for the sake of clinical decisions that depend on replicable or refutable results from the primary literature.

scientific communication and education↗

bioRxiv2018

Evaluation of the NCCN guidelines using the RIGHT Statement and AGREE II instrument: a cross-sectional review.

IntroductionRobust, clearly reported clinical practice guidelines (CPGs) are essential for evidence-based clinical practice. The Reporting Items for practice Guidelines in HealThcare (RIGHT) statement and Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument were published to improve the methodological and reporting quality in healthcare CPGs.\n\nMethodsWe applied the RIGHT statement checklist and AGREE II instrument to 48 National Comprehensive Cancer Network (NCCN) guidelines. Our primary objective was to assess the adherence to RIGHT and AGREE II items. Since neither RIGHT nor AGREE-II can judge the clinical usefulness of a guideline, our study is designed to only focus on the methodological and reporting quality of each guideline.\n\nResultsThe NCCN guidelines demonstrated notable strengths and weaknesses. For example, RIGHT statement items 19 (conflicts of interest), 7b (description of subgroups), and 13a (clear, precise recommendations) were fully reported in all guidelines. However, the guidelines inconsistently incorporated patient values and preferences and cost, nor did they consistently describe the method for assessing the quality and certainty of evidence. Regarding the AGREE II instrument, the NCCN guidelines scored highly on the domains 4 (clear, precise recommendations) and 6 (handling of conflicts of interest), but lowest on domain 2 (inclusion of all relevant stakeholders).\n\nConclusionsIn this investigation we found that NCCN CPGs demonstrate key strengths and weaknesses with respect to the reporting of key items essential to CPGs. We recommend the continued use of NCCN guidelines and adherence to the RIGHT and AGREE II items. Doing so serves to improve the evidence delivered to healthcare providers, thus potentially improving patient care.

epidemiology↗

bioRxiv2018

Authorship inflation and author gender in pulmonology research.

IntroductionHonorary authorship and equal gender representation are two pressing matters in scientific research. Honorary authorship is the inclusion of authors who do not meet the criteria established by the International Committee of Medical Journal Editors (ICMJE) authorship guidelines. The inclusion of honorary authors in the medical literature has led to an increase of the number of authors on studies and a decrease in single author studies in various fields.\n\nMethodsOur primary objective was to assess authorship trends in two major pulmonology journals (selected on the basis of Google Scholar rankings): Thorax and American Journal of Respiratory and Critical Care Medicine. We reviewed all articles published in both journals in the years 1994, 2004, and 2014 using Web of Science and extracted data such as number of authors and gender of the first and last authors.\n\nResultsThe total number of authors steadily increased from 1994 to 2014. The median number of authors grew from about four in 1994 to nearly seven in 2014, which is approximately a 75% increase. When we compiled all the data, we found the percentage of female authors from both journals had increased from 17% to 29.9% during the study period.\n\nDiscussionWe found an increase in the average number of authors on pulmonology publications between 1994 and 2014 as well as an increase in the number of females with a lead or main author position. This may be due to a variety of factors, such as increased team science. However, our data in conjunction with data from other areas of medicine, indicate that honorary authorship may be contributing to the trends we identified.

scientific communication and education↗