bioRxiv

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Deep Learning for Molecular and Genomic Characterization of Lung Cancer in Never-Smokers Using Hematoxylin and Eosin-Stained Images

bioRxiv Jan 1, 2025
Despite promising results in using deep learning to infer genetic features from histological whole-slide images (WSIs), no prior studies have specifically applied these methods to lung adenocarcinomas from subjects who have never smoked tobacco (NS-L...
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A structure-informed evolutionary model for predicting viral immune escape and evolution

bioRxiv Jan 1, 2025
Persistent emergence of viral variants capable of evading host immunity constitutes a significant threat to public health. This antigenic evolution frequently outpaces the development of vaccines and therapeutics, highlighting the necessity of predic...
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Close-Up of vesicular ER Exit Sites by Volume Electron Imaging using FIB-SEM

bioRxiv Jan 1, 2025
Volume electron microscopy by high-pressure freeze substitution combined with block-face focused ion beam scanning electron microscopy (FIB-SEM) provides comprehensive 3D views of subcellular architecture, essential for understanding cellular activit...
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Human CYP2C9 metabolism of organophosphorus pesticides and nerve agent surrogates

bioRxiv Jan 1, 2025
Of the Cytochrome P450 enzymes, the CYP2C9 variant is very important and is the cytochrome P450 (CYP) involved in the metabolism of several human drugs where it acts as a natural bioscavenger. Previously, CYP2C9 was demonstrated to remove sulfur from...
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Perceptual predictions track subjective, over objective, statistical structure

bioRxiv Jan 1, 2025
Predictive processes in cognition and the brain are usually modelled as tracking objective event probabilities. However, we know little about how our subjective representations of statistical structure may determine these functions, as they will like...
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Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii

bioRxiv Jan 1, 2025
Pneumocystis jirovecii is a fungal pathogen causing Pneumocystis pneumonia in humans, mainly in immunocompromised individuals. Infections by P. jirovecii are treated using the antifolate combination drug trimethoprim-sulfamethoxazole (TMP-SMX), targe...
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Improving Protein Interaction Prediction in GenPPi: A Novel Interaction Sampling Approach Preserving Network Topology

bioRxiv Jan 1, 2025
Computational prediction of protein-protein interactions (PPIs) is crucial for understanding cell biology and drug development, offering an alternative to costly experimental methods. The original GenPPi software advanced ab initio PPI network predic...
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Neuromodulation enhances dynamic sensory processing in spiking neural network models

bioRxiv Jan 1, 2025
Neuromodulators allow circuits to dynamically change their biophysical properties in a context-sensitive way. In addition to their role in learning, neuromodulators have been suggested to play a role in sensory processing at relatively fast timescale...
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Segmentation Matters: Recognizing the Cell Segmentation Challenge in Spatial Transcriptomics

bioRxiv Jan 1, 2025
Probe-based in situ hybridization spatial transcriptomics has emerged as a state-of-the-art for neuroscience research. Accurate segmentation of neurons and non-neuronal cells, a critical step for downstream analysis, remains a big challenge. Using hu...
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Topological spatial coding for rapid generalization in the hippocampal formation

bioRxiv Jan 1, 2025
The brain navigates complex environments by combining entorhinal grid codes with hippocampal place codes. Although grid codes effectively represent a current environment’s geometry, their capacity to generalize across topologically analogous environm...
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