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Enhancing Research Through Image Analysis Workshops: Experiences and Best Practices.
Microsc Res Tech
December 2024
Advanced Light Microscopy Science Technology Platform, The Francis Crick Institute, London, UK.
Modern microscopy systems allow researchers to generate large volumes of image data with relative ease. However, the challenge of analyzing these data effectively is often hindered by a lack of computational skills. This bottleneck negatively impacts both research reproducibility and efficiency, as researchers frequently rely on manual or semi-automated analysis methods.
View Article and Find Full Text PDFDominant myosin storage myopathy mutations disrupt striated muscles in Drosophila and the myosin tail-tail interactome of human cardiac thick filaments.
Genetics
January 2025
Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Avenue, Baltimore, MD 21205, USA.
Myosin storage myopathy (MSM) is a rare skeletal muscle disorder caused by mutations in the slow muscle/β-cardiac myosin heavy chain (MHC) gene. MSM missense mutations frequently disrupt the tail's stabilizing heptad repeat motif. Disease hallmarks include subsarcolemmal hyaline-like β-MHC aggregates, muscle weakness, and, occasionally, cardiomyopathy.
View Article and Find Full Text PDFQuantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals.
Anal Chem
August 2024
RECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno 602 00, Czech Republic.
There is a lack of experimental electron ionization high-resolution mass spectra available to assist compound identification. The in silico generation of mass spectra by quantum chemistry can aid annotation workflows, in particular to support the identification of compounds that lack experimental reference spectra, such as environmental chemicals. We present an open-source, semiautomated workflow for the in silico prediction of electron ionization high-resolution mass spectra at 70 eV based on the QCxMS software.
View Article and Find Full Text PDFNon-negative matrix factorization-aided phase unmixing and trace element quantification of STEM-EDXS data.
Ultramicroscopy
September 2024
Electron Spectrometry and Microscopy Laboratory (LSME), Institute of Physics (IPHYS), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland. Electronic address:
Energy-dispersive X-ray spectroscopy (EDXS) mapping with a scanning transmission electron microscope (STEM) is commonly used for chemical characterization of materials. However, STEM-EDXS quantification becomes challenging when the phases constituting the sample under investigation share common elements and overlap spatially. In this paper, we present a methodology to identify, segment, and unmix phases with a substantial spectral and spatial overlap in a semi-automated fashion through combining non-negative matrix factorization with a priori knowledge of the sample.
View Article and Find Full Text PDFHandling of problematic ion chromatograms with the Automated Target Screening (ATS) workflow for unsupervised analysis of high-resolution mass spectrometry data.
Anal Bioanal Chem
May 2024
Department of Cell Toxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany.
Liquid chromatography (LC) or gas chromatography (GC) coupled to high-resolution mass spectrometry (HRMS) is a versatile analytical method for the analysis of thousands of chemical pollutants that can be found in environmental and biological samples. While the tools for handling such complex datasets have improved, there are still no fully automated workflows for targeted screening analysis. Here we present an R-based workflow that is able to cope with challenging data like noisy ion chromatograms, retention time shifts, and multiple peak patterns.
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