bioRxiv

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Normalized Raman Imaging for Studies of Tissue Physiology of the Kidney

bioRxiv Jan 1, 2025
Histology is the cornerstone of clinical pathology and an essential tool for many areas of medicine. Nevertheless, conventional histological methods, which rely on fixation, embedding, sectioning, and staining, distort cellular architecture, extract ...
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Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence

bioRxiv Jan 1, 2025
Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genetic diversity. We analyze how Prochlorococcus genomics relate to high vs. low light environment adaptations, applying traditional comparative genomics ...
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Decision Voting Based Multiscale Convolutional Learning of Brain Networks With Explainability

bioRxiv Jan 1, 2025
The diagnosis of neurological disorders requires comprehensive frameworks that incorporate multimodal neuroimaging data while ensuring clinical interpretability. Recent neuroimaging research is focusing on the integration of brain structure and funct...
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Comparison of dimensionality reduction and feature selection for cognitive task decoding in functional magnetic resonance imaging

bioRxiv Jan 1, 2025
Advances in functional magnetic resonance imaging (fMRI) have led to the ability to study the brain across many contexts. However, the large number of features generated by functional connectivity approaches may overfit the data. These problems can b...
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Linearizing and forecasting: a reservoir computing route to digital twins of the brain

bioRxiv Jan 1, 2025
Exploring the dynamics of a complex system, such as the human brain, poses significant challenges due to inherent uncertainties and limited data. In this study, we enhance the capabilities of noisy linear recurrent neural networks (lRNNs) within the ...
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Single-cell RNA sequencing and large-scale bulk combination with machine learning reveal gastric cancer-related macrophage heterogeneity

bioRxiv Jan 1, 2025
The tumor microenvironment (TME) significantly impacts cancer progression and overall patient survival. However, the complexity of tumor cell-TME interactions in gastric cancer (GC) and their underlying molecular basis remain to be systematically elu...
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Cingulate-centered flexible control: physiologic correlates and enhancement by internal capsule stimulation

bioRxiv Jan 1, 2025
The flexible deployment of cognitive control is essential for adaptive functioning in dynamic environments given limited cognitive resources. That flexibility depends on rapid detection and resolution of control- prediction errors (CPEs) when current...
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Multi-objective Evaluation and Optimization of Stochastic Gradient Boosting Machines for Genomic Prediction and Selection in Wheat (Triticum aestivum) Breeding

bioRxiv Jan 1, 2025
Machine learning (ML) models with stochastic and non-deterministic characteristics are increasingly used for genomic prediction in plant breeding, but evaluation often neglects important aspects like prediction stability and ranking performance. This...
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TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

bioRxiv Jan 1, 2025
High-throughput chromosome conformation capture sequencing (Hi-C) is a key technology for studying the three-dimensional (3D) structure of genomes and chromatin folding. Hi-C data reveals underlying patterns of genome organization, such as topologica...
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PARSEbp: Pairwise Agreement-based RNA Scoring with Emphasis on Base Pairings

bioRxiv Jan 1, 2025
High-fidelity scoring of RNA 3D structures remains a major challenge in RNA structure prediction and conformational sampling. While single-model methods for scoring RNA structures can capture individual structural features, they fail to capture the b...
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