Biology subjects

Weissgerber, T. L.

Publications and source records attributed to Weissgerber, T. L..

4 recordsLinked to original sources

bioRxiv2022

Taking shortcuts: Great for travel, but not for reproducible methods sections

Methods sections are often missing critical details needed to reproduce an experiment. Methodological shortcut citations, in which authors cite previous papers instead of describing the method in detail, may contribute to this problem. This meta-research study used three approaches to systematically examine the use of shortcut citations in neuroscience, biology and psychiatry. First, we examined papers to determine why authors use citations in the methods section and to assess how often shortcut citations were used. Common reasons for using citations in the methods section included explaining how something was done by citing a previous resource that used the method (methodological shortcut citation), giving credit or specifying what was used (who or what citation), and providing context or a justification (why citation). Next, we reviewed 15 papers to determine what can happen when readers follow shortcut citations to find methodological details. While shortcut citations can be used effectively, problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and chains of shortcut citations. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report methods that have been described previously or asking authors to explain modifications of previously described methods. We propose that methodological shortcut citations should meet three criteria; cited resources should describe a method very similar to the authors method, provide enough detail to allow others to implement the method, and be open access. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting.

neuroscience↗

bioRxiv2022

Blind spots on western blots: a meta-research study highlighting opportunities to improve figures and methods reporting

Western blotting is a standard laboratory method used to detect proteins and assess their expression levels. Unfortunately, poor western blot image display practices and a lack of detailed methods reporting can limit a readers ability to evaluate or reproduce western blot results. While several groups have studied the prevalence of image manipulation or provided recommendations for improving western blotting, data on the prevalence of common publication practices are scarce. We systematically examined 551 articles published in the top 25% of journals in neurosciences (n=151) and cell biology (n=400) that contained western blot images, focusing on practices that may omit important information. Our data show that most published western blots are cropped and blot source data are not made available to readers in the supplement. Publishing blots with visible molecular weight markers is rare, and many blots additionally lack molecular weight labels. Western blot methods sections often lack information on the amount of protein loaded on the gel, blocking steps and antibody labeling protocol. Important antibody identifiers like source, catalog number or RRID were omitted frequently for primary antibodies, and regularly for secondary antibodies. We present detailed descriptions and visual examples to help scientists, peer reviewers and editors to publish more informative western blot figures and methods. Additional resources include a toolbox to help scientists produce more reproducible western blot data, teaching slides in English and Spanish and an antibody reporting template.

cell biology↗

bioRxiv2022

Replacing bar graphs of continuous data with more informative graphics: Are we making progress?

Recent work has raised awareness about the need to replace bar graphs of continuous data with informative graphs showing the data distribution. The impact of these efforts is not known. This observational meta-research study examined how often scientists in different fields use various graph types, and assessed whether visualization practices have changed between 2010 and 2020. We developed and validated an automated screening tool, designed to identify bar graphs of counts or proportions, bar graphs of continuous data, bar graphs with dot plots, dot plots, box plots, violin plots, histograms, pie charts, and flow charts. Papers from 23 fields (approximately 1,000 papers/field/year) were randomly selected from PubMed Central and screened (n=227,998). F1 scores for different graphs ranged between 0.83 and 0.95 in the internal validation set. While the tool also performed well in external validation sets, F1 scores were lower for uncommon graphs. Bar graphs are more often used incorrectly to display continuous data than they are used correctly to display counts or proportions. The proportion of papers that use bar graphs of continuous data varies markedly across fields (range in 2020: 4%-58%), with high rates in biochemistry and cell biology, complementary and alternative medicine, physiology, genetics, oncology and carcinogenesis, pharmacology, microbiology and immunology. Visualization practices have improved in some fields in recent years. Fewer than 25% of papers use flow charts, which provide information about attrition and the risk of bias. This study highlights the need for continued interventions to improve visualization and identifies fields that would benefit most.

scientific communication and education↗

bioRxiv2020

Creating Clear and Informative Image-based Figures for Scientific Publications

Scientists routinely use images to display data. Readers often examine figures first; therefore, it is important that figures are accessible to a broad audience. Many resources discuss fraudulent image manipulation and technical specifications for image acquisition; however, data on the legibility and interpretability of images are scarce. We systematically examined these factors in non-blot images published in the top 15 journals in three fields; plant sciences, cell biology and physiology (n=580 papers). Common problems included missing scale bars, misplaced or poorly marked insets, images or labels that were not accessible to colorblind readers, and insufficient explanations of colors, labels, annotations, or the species and tissue or object depicted in the image. Papers that met all good practice criteria examined for all image-based figures were uncommon (physiology 16%, cell biology 12%, plant sciences 2%). We present detailed descriptions and visual examples to help scientists avoid common pitfalls when publishing images. Our recommendations address image magnification, scale information, insets, annotation, and color and may encourage discussion about quality standards for bioimage publishing.

bioinformatics↗