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We present a model of directed investigation of KEGG pathway analysis, beginning with discrete correlate summation (DCS) clustering of Swiss-Prot sets. Dopamine and angiotensin related proteins define the boundary for pathway analyses upon a network of proteins also associated with a compositely defined matrix of Swiss-Prot keywords to provide a framework for their biological indices (Figure 1).
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http://dx.doi.org/10.1101/2024.06.22.600163 | DOI Listing |
PLoS Comput Biol
September 2025
Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.
Simulation of realistic omics data is a key input for benchmarking studies that help users obtain optimal computational pipelines. Omics data involves large numbers of measured features on each sample and these measures are generally correlated with each other. However, simulation too often ignores these correlations, perhaps due to computational and statistical hurdles of doing so.
View Article and Find Full Text PDFAnal Chem
September 2025
Interdisciplinary Laboratories for Advanced Materials Physics (i-LAMP) & Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, via della Garzetta 48, 25133 Brescia, Italy.
Optical recognition and identification of nanoplastics such as polystyrene nanobeads (PSbs), a widely used polymer and an actual source of environmental pollution, is a challenging task relying on knowledge of the PSbs' refractive index (RI) and its relation to the PSbs' morphology. This is, however, lacking for PSbs' sizes lower than 1 μm. Here, we bridge this gap by measuring UV-vis spectra of PSbs deposited on a sapphire substrate via spin coating and by connecting the experimental data to the RI, PSbs' morphology, and optical transitions through a new optical model based on the Mie theory.
View Article and Find Full Text PDFCytotechnology
October 2025
Core Facilities, Zhejiang University School of Medicine, Hangzhou, 310058 China.
Super-resolution fluorescence microscopy (SRM) has enabled visualization of nanoscale cellular structures, but systematic evaluation of resolution assessment methods across diverse biological structures and SRM modalities remains lacking. Here, we comparatively assessed three resolution metrics-Full Width at Half Maximum (FWHM), decorrelation analysis, and Fourier Ring Correlation (FRC)-across two SRM techniques (Super-resolution Radial Fluctuation, SRRF; Stimulated Emission Depletion, STED) using key subcellular structures: microtubules (filaments), mitochondria (membranes), and nuclear pore protein Nup98 (single particles) in HeLa/U2OS cells. Our results showed decorrelation analysis provided robust resolution estimates across all structures and modalities (confocal/SRRF/STED), exhibiting superior performance for dense nuclear pore complexes where FWHM failed due to overlapping point spread functions.
View Article and Find Full Text PDFBayesian Anal
November 2024
Department of Statistical Science, Duke University.
We propose a class of nonstationary processes to characterize space- and time-varying directional associations in point-referenced data. We are motivated by spatiotemporal modeling of air pollutants in which local wind patterns are key determinants of the pollutant spread, but information regarding prevailing wind directions may be missing or unreliable. We propose to map a discrete set of wind directions to edges in a sparse directed acyclic graph (DAG), accounting for uncertainty in directional correlation patterns across a domain.
View Article and Find Full Text PDFAdv Orthop
August 2025
Surgery Department, CHU de Québec-Université Laval, Québec, Canada.
Multiple biomechanical models have been suggested to quantify lower limb joint contact stress distributions, with varying results. Among others, the choice of cartilage morphology and gait loading patterns can significantly affect simulation results. Moreover, there is currently no consensus on simulating the input and output data needed to obtain reliable results and enable a comprehensive analysis.
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