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 <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

The minimum information about a genome sequence (MIGS) specification

With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases

The Psychometric Modeling of Scientific Reasoning: a Review and Recommendations for Future Avenues

Psychometric modeling has become a frequently used statistical tool in research on scientific reasoning. We review psychometric modeling practices in this field, including model choice, model testing, and researchers’ inferences based on their psychometric practices. A review of 11 empirical research studies reveals that the predominant psychometric approach is Rasch modeling with a focus on itemfit statistics, applied in a way strongly similar to practices in national and international large-scale educational assessment programs. This approach is common in the educational assessment community and rooted in subtle philosophical views on measurement. However, we find that based on this approach, researchers tend to draw interpretations that are not within the inferential domain of this specific approach and not in accordance with the related practices and inferential purposes. In some of the reviewed articles, researchers put emphasis on item infit statistics for dimensionality assessment. Item infit statistics, however, cannot be regarded as a valid indicator of the dimensionality of scientific reasoning. Using simulations as illustration, we argue that this practice is limited in delivering psychological insights; in fact, various recent inferences about the structure, cognitive basis, and correlates of scientific reasoning might be unwarranted. In order to harness its full potential, we make suggestions towards adjusting psychometric modeling practices to the psychological and educational questions at hand