Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

Wallach, John R.; Boyack, Kevin W.; Ioannidis, John P. A.

doi:10.1371/journal.pbio.2006930

Cited by 215 publications

(275 citation statements)

References 35 publications

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“…For example, re-estimating heterozygosity levels directly from reads of each species allowed to show a strong effect of hybrid origin, but not of cellular mechanism of asexuality ( Figure 2). Another advantage of using the same methods for each species is that it diminishes the "researcher degrees of freedom" [100][101][102]. For example, the analysis of polyploid genomes requires choosing methods to call heterozygosity and ploidy.…”

Section: Resultsmentioning

confidence: 99%

Genomic features of parthenogenetic animals

Jaroň

Bast²,

Nowell

et al. 2018

Preprint

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Evolution under asexuality is predicted to impact genomes in numerous ways, but empirical evidence remains unclear. Case studies of individual asexual animals have reported peculiar genomic features which were suggested to be caused by asexuality, including high heterozygosity, a high abundance of horizontally acquired genes, a low transposable element load, or the presence of palindromes. We systematically characterized these genomic features in published genomes of 26 asexual animals representing at least 18 independent transitions to asexuality. Surprisingly, not a single feature is systematically replicated across a majority of these transitions, suggesting that no genomic feature is characteristic of asexuality and that previously reported patterns were lineage specific rather than caused by asexuality. We found that only asexuals of hybrid origin were characterized by high heterozygosity levels. Asexuals that were not of hybrid origin appeared to be largely homozygous, independently of the cellular mechanism underlying asexuality. Overall, despite the importance of recombination rate variation for the evolution of sexual animal genomes, the genome-wide absence of recombination does not appear to have had the dramatic effects which are expected from classical theoretical models. The reasons for this are probably a combination of lineage-specific patterns, impact of the origin of asexuality, and a survivorship bias of asexual lineages. Box 1: Transitions to asexualityMeiotic sex and recombination evolved once in the common ancestor of eukaryotes [41].Asexual animals therefore derive from a sexual ancestor, but how transitions from sexual to asexual reproduction occur can vary and have different expected consequences for the genome [13]. Hybrid origin:Hybridization between sexual species can generate hybrid females that reproduce asexually [13,42]. Asexuality caused by hybridization can generate a highly heterozygous genome, depending on the divergence between the parental sexual species prior to hybridization. Hybridization can also result in a burst of transposable element activity [12]. Intraspecific origins: Endosymbiont infection. Infection with intracellular endosymbionts (such asWolbachia, Cardinium or Rickettsia) can cause asexuality, a pattern that is frequent in species with haplodiploid sex determination [43]. This type of transition often (but not always) results in fully homozygous lineages because induction of asexuality frequently occurs via gamete duplication (see Box 2). Spontaneous mutations/Contagious asexuality. Spontaneous mutations can alsounderlie transitions from sexual to asexual reproduction. In addition, asexual females of some species produce males that mate with females of sexual lineages, and thereby generate new asexual strains (contagious asexuality). In both cases, the genomes of incipient asexual lineages are expected to be very similar to those of their sexual relatives and subsequent changes should be largely driven by the cellular mechanism underlying asexuality (Box 2). an...

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Section: Resultsmentioning

confidence: 99%

Genomic features of parthenogenetic animals

Jaroň

Bast²,

Nowell

et al. 2018

Preprint

View full text Add to dashboard Cite

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“…Publications without empirical data (e.g., editorials, reviews, news, simulations, or commentaries without reanalysis) were only analyzed for statements including conflict of interest, open access, and funding because protocols, data sets, and reproducibility were not relevant. Case studies and case series were listed as empirical studies; however, questions pertaining to the availability of materials, data, protocol, and registration were excluded due to previous study recommendations 14 . Data extraction criteria for each included and excluded study design are described in Table 1.…”

Section: Assessment Of Reproducibility and Transparency Characteristicsmentioning

confidence: 99%

Can Orthopaedics become the Gold Standard for Reproducibility? A Roadmap to Success

Fladie

Evans

Checketts

et al. 2019

Preprint

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Background:Scientific research is replete with poor accessibility to data, materials, and protocol, which limits the reproducibility of a study. Transparency with regard to materials, protocols, and raw data sets enhances reproducibility by providing the critical information necessary to verify, replicate, and resynthesize research findings. The extent to which transparency and reproducibility exist in the field of orthopaedics is unclear. In our study, we aimed to evaluate transparency and reproducibility-related characteristics of randomly sampled publications in orthopaedic journals. Methods:We used the National Library of Medicine catalog to identify English language and MEDLINE-indexed orthopaedic journals. From the 74 journals meeting our inclusion criteria, we randomly sampled 300 publications using a refined PubMed search that were published between January 1, 2014, and December 31, 2018. Two investigators were trained for data extraction and analysis. Both investigators were blinded and independently extracted data from the 300 studies. Results:Our initial search yielded 68,102 publications, from which we drew a random sample of 300 publications.Of these 300 publications, 286 were screened for empirical data and 14 were inaccessible. For analysis purposes, we excluded publications without empirical data. Of the 182 with empirical data, 13 studies (7.1%) included a data availability statement, 9 (4.9%) reported materials were available, none (0.0%) provided analysis scripts, 2 (1.1%) provided access to the protocol used, 5 (2.7%) were preregistered, and only 2 (1.1%) provided a statement about being a replicated study. Conclusions:Components necessary for reproducibility are lacking in orthopaedic surgery journals. The vast majority of publications did not provide data or material availability statements, protocols, or analysis scripts, and had no preregistration statements. Intervention is needed to improve reproducibility in the field of orthopaedics. The current state of reproducibility in orthopaedic surgery could be improved by combined efforts from funding agencies, authors, peer reviewers, and journals alike. Level of Evidence: N/A

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“…Systematic reviews and meta-analyses generally do not contain the necessary data measuring materials thus excluding them from evaluating for material availability. Case reports and case series contain empirical data, but are generally not descriptive enough in their design to be reproduced in subsequent publications and were not expected to contain reproducibility characteristics [11].…”

Section: Data Extractionmentioning

confidence: 99%

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

Evans

Fladie

Anderson

et al. 2019

Preprint

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Disclosures:The authors report no conflicts of interest. Word count: 2,978Author contributions: MV and DT conceived the study and designed the protocol. MV and DT supervised the study. MV received research funding. SE and IF extracted data. SE and IF conducted data analysis and organization. MA conducted the final data analysis. SE, IF, MA, DT, and MV drafted the manuscript. All authors provided critical feedback, ideas, and editing for the manuscript and have approved the final version. SE assumes responsibility for this manuscript. Abstract: Background:In 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.Purpose: Our 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. Study Design: Cross-sectional reviewMethods: Using 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. Results:Of 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.Conclusion: Reproducibility 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.

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Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

Cited by 215 publications

References 35 publications

Genomic features of parthenogenetic animals

Genomic features of parthenogenetic animals

Can Orthopaedics become the Gold Standard for Reproducibility? A Roadmap to Success

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

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