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Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.
bioRxiv
November 2024
Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia.
A DNA sequence pattern, or "motif", is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications.
View Article and Find Full Text PDFAdministration Route Differentiation of Altrenogest via the Metabolomic LC-HRMS Analysis of Equine Urine.
Molecules
October 2024
Centre for Forensic Science, University of Technology Sydney, Sydney, NSW 2007, Australia.
Altrenogest, also known as allyltrenbolone, is a synthetic form of progesterone used therapeutically to suppress unwanted symptoms of estrus in female horses. Altrenogest affects the system by decreasing levels of endogenous gonadotrophin and luteinizing and follicle-stimulating hormones, which in turn decreases estrogen and mimics the increase of progesterone production. This results in more manageable mares for training and competition alongside male horses while improving the workplace safety of riders and handlers.
View Article and Find Full Text PDFThe ant and the grasshopper: Contrasting responses and behaviors to water stress of riparian trees along a hydroclimatic gradient.
Sci Total Environ
November 2024
Université Claude Bernard Lyon 1, LEHNA UMR 5023, CNRS, ENTPE, F-69622, Villeurbanne, France.
Riparian trees are particularly vulnerable to drought because they are highly dependent on water availability for their survival. However, the response of riparian tree species to water stress varies depending on regional hydroclimatic conditions, making them unevenly vulnerable to changing drought patterns. Understanding this spatial variability in stress responses requires a comprehensive assessment of water stress across broader spatial and temporal scales.
View Article and Find Full Text PDFAn integrated multitool analysis contributes elements to interpreting unclassified factor IX missense variants associated with hemophilia B.
J Thromb Haemost
October 2024
Department of Translational Medicine and Surgery, Catholic University of the Sacred Heart, Rome, Italy; Center for Hemorrhagic and Thrombotic Diseases, Foundation University Hospital "A. Gemelli" IRCCS, Rome, Italy. Electronic address:
Background: Dissection of genotype-phenotype relationships in hemophilia B (HB) is particularly relevant for challenging (mild HB) or for HB-associated but unclassified factor (F)IX missense variants.
Objective: To contribute elements to interpret unclassified HB-associated FIX missense variants by a multiple-level approach upon identification of a reported, but uncharacterized, FIX missense variant associated with mild HB.
Methods: Molecular modeling of wild-type and V92A FIX variants, expression studies in HEK293 cells with evaluation of protein (ELISA, western blotting) and activity (activated partial thromboplastin time-based/chromogenic assays) levels after recombinant expression, and multiple prediction tools.
suMRak: a multi-tool solution for preclinical brain MRI data analysis.
Front Neuroinform
March 2024
Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia.
Introduction: Magnetic resonance imaging (MRI) is invaluable for understanding brain disorders, but data complexity poses a challenge in experimental research. In this study, we introduce suMRak, a MATLAB application designed for efficient preclinical brain MRI analysis. SuMRak integrates brain segmentation, volumetry, image registration, and parameter map generation into a unified interface, thereby reducing the number of separate tools that researchers may require for straightforward data handling.
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