bioRxiv

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Transforming Esogastric Cancer Surgery Integrating SpiderMass Mass Spectrometry with Clinical and Microbiome Data for Margin Delineation and Prognosis

bioRxiv Jan 1, 2025
Esophageal-gastric cancers (EC) represent a significant global health concern, with esophageal cancer ranking seventh in terms of incidence and mortality worldwide. Gastric cancer is especially concerning, with an estimated one million new cases and ...
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HypoAD: volumetric and single-cell analysis reveals changes in the human hypothalamus in aging and Alzheimer’s disease

bioRxiv Jan 1, 2025
Alterations in metabolism, stress response, sleep, circadian rhythms, and neuroendocrine processes are key features of aging and neurodegeneration. These fundamental processes are regulated by the hypothalamus, yet how its functionally distinct subre...
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Systematic Review of Over A Century of Global Bioscience Research

bioRxiv Jan 1, 2025
Bioscience encompasses studies on living organisms, their components, and their interactions, with the main aim of translating research into useful applications for medical, clinical, industrial, and environmental uses. The broad field of bioscience ...
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Cancer target discovery enabled by transcriptome-based virtual CRISPR screening

bioRxiv Jan 1, 2025
Functional genetic screens have uncovered dependencies in many cancers, but experimentally screened models for most cancers are far outnumbered by molecularly-profiled tumors, particularly for rare cancers. We used machine learning to infer gene depe...
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Automated Specimen Triage for Dark Taxa: Deep Learning Enables Orientation, Sex Identification, and Anatomical Segmentation from Robotic Imaging

bioRxiv Jan 1, 2025
Robotic specimen processing is transforming biodiversity discovery by replacing labor-intensive handling with scalable systems that can simultaneously generate high-quality specimen images. We demonstrate that these images can be leveraged by deep le...
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Gradual proactive regulation of body state by reinforcement learning of homeostasis

bioRxiv Jan 1, 2025
Living systems maintain physiological variables such as temperature, blood pressure, and glucose within narrow ranges—a process known as homeostasis. Homeostasis involves not only reactive feedback but also anticipatory adjustments shaped by experien...
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Spatially varying cell-specific gene regulation network inference

bioRxiv Jan 1, 2025
Gene regulatory networks (GRNs), involving interactions between large numbers of genes, govern expression levels of mRNA and their resulting proteins to control cell functions. As many new sequencing technologies in single-cell and spatial resolution...
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Finetuning Foundation Models for Temporal Clinical Transcriptomics Data

bioRxiv Jan 1, 2025
Timeseries clinical transcriptomic datasets offer the opportunity to gain insights into the dynamics of disease mechanisms/treatment responses. However, their utility in uncovering temporal patterns is often limited by high noise levels and small sam...
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The Liver is an Inflammatory Mediator of Pulmonary Arterial Hypertension

bioRxiv Jan 1, 2025
Inflammation is central to pulmonary arterial hypertension (PAH) pathogenesis. The liver regulates systemic immunity, yet its contribution to PAH remains unclear. To characterize hepatic involvement in experimental and human PAH. We hypothesized the ...
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Quantum Deep Learning Pipeline for Next Generation Network Biology

bioRxiv Jan 1, 2025
Module discovery in omics networks is central to interpretation. Classical pipelines capture broad community structure, but exact search for small, connected, topology aware modules is combinatorial, making exhaustive solutions impractical at genome ...
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