Software Carpentry lesson that teaches how to use databases and SQL In …
Software Carpentry lesson that teaches how to use databases and SQL In the late 1920s and early 1930s, William Dyer, Frank Pabodie, and Valentina Roerich led expeditions to the Pole of Inaccessibility in the South Pacific, and then onward to Antarctica. Two years ago, their expeditions were found in a storage locker at Miskatonic University. We have scanned and OCR the data they contain, and we now want to store that information in a way that will make search and analysis easy. Three common options for storage are text files, spreadsheets, and databases. Text files are easiest to create, and work well with version control, but then we would have to build search and analysis tools ourselves. Spreadsheets are good for doing simple analyses, but they don’t handle large or complex data sets well. Databases, however, include powerful tools for search and analysis, and can handle large, complex data sets. These lessons will show how to use a database to explore the expeditions’ data.
Background and Purpose—Preclinical research using animals often informs clinical trials. However, its …
Background and Purpose—Preclinical research using animals often informs clinical trials. However, its value is dependent on its scientific validity and reproducibility, which are, in turn, dependent on rigorous study design and reporting. In 2011, Stroke introduced a Basic Science Checklist to enhance the reporting and methodology of its preclinical studies. Except for Nature and Science journals, few others have implemented similar initiatives. We sought to estimate the impact of these journal interventions on the quality of their published reports.Methods—All articles published in Stroke, Nature Medicine, and Science Translational Medicine over 9 to 18 years and in 2 control journals without analogous interventions over a corresponding 11.5 years were reviewed to identify reports of experiments in nonhuman mammals with proposed clinical relevance. The effect of journal interventions on the reporting and use of key study design elements was estimated via interrupted time-series analyses.Results—Of 33 009 articles screened, 4162 studies met inclusion criteria. In the 3.5 to 12 years preceding each journal’s intervention, the proportions of studies reporting and using key study design elements were stable except for blinding in Stroke and randomization in Science Translational Medicine, which were both increasing. Post-intervention, abrupt and often marked increases were seen in the reporting of randomization status (level change: +17% to +44%, P≤0.005), blinding (level change: +20% to +40%, P≤0.008), and sample size estimation (level change: 0% to +40%, P≤0.002 in 2 journals). Significant but more modest improvements in the use of these study design elements were also observed. These improvements were not seen in control journals.Conclusions—Journal interventions such as Stroke’s author submission checklist can meaningfully improve the quality of published preclinical research and should be considered to enhance study transparency and design. However, such interventions are alone insufficient to fully address widespread shortcomings in preclinical research practices.
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