New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Shortcut citations in the methods section: Frequency, problems, and strategies for responsible reuse.

Methods sections are often missing essential details. 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 3 approaches to examine shortcut citation use in neuroscience, biology, and psychiatry. First, we assessed current practices in more than 750 papers. More than 90% of papers used shortcut citations. Other common reasons for using citations in the methods included 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, they can also deprive readers of essential methodological details. Problems encountered included difficulty identifying or accessing the cited materials, missing or insufficient descriptions of the cited method, and shortcut citation chains. Third, we examined journal policies. Fewer than one quarter of journals had policies describing how authors should report previously described methods. We propose that methodological shortcut citations should meet 3 criteria; cited resources should provide (1) a detailed description of (2) the method used by the citing authors', and (3) be open access. Resources that do not meet these criteria should be cited to give credit, but not as shortcut citations. We outline actions that authors and journals can take to use shortcut citations responsibly, while fostering a culture of open and reproducible methods reporting

Age of the youngest, median, and oldest shortcut citations within a paper for each field.

This table shows summary statistics for Fig 3A. IQR, interquartile range. Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12]. (DOCX)</p

The level of methodological detail required depends on the reader.

All readers need an overview of the study design, methods used to answer the research question, and information needed to assess scientific rigor and the risk of bias. These details should always be presented in the methods section of the paper. While fewer readers need the details required to reproduce or reuse the method, these individuals are particularly important because they are most likely to perform follow-up experiments. Very simple methods that can be explained and reproduced easily may be described in the methods section. Protocol repositories or method or protocol journals are better for many methods, as it is difficult to provide the details needed to implement or reuse the method within the methods section.</p

Reasons for citing a resource in the methods section of a paper.

The box plots illustrate the number of times that each type of citation was used, per article, for neuroscience (yellow), biology (blue), and psychiatry (red). The horizontal line within each box shows the median, whereas the top and bottom of the box show the 25th and 75th percentiles. Whiskers represent the furthest datapoint that is within 1.5* the interquartile range from the box. Dots above the whiskers show outliers. Data are available at https://osf.io/d2sa3/, in the methodological citations study folder [12]. (TIF)</p

Flow diagram for journal policy study.

This flow chart illustrates the journal screening process and shows the number of observations excluded and reasons for exclusion at each phase of screening. Data are available at https://osf.io/d2sa3/, in the journal policy study folder [12]. (TIF)</p