bioRxiv

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Development of an EMT-related exosomal miRNA signature that can predict prognosis in hepatocellular carcinoma

bioRxiv Jan 1, 2025
Chemoresistance and epithelial-mesenchymal transition (EMT) are associated with failure of cancer chemotherapy and poor survival of patients. We have previously shown that chemoresistance and stemness in hepatocellular carcinoma (HCC) cells was accom...
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Detection of multiple per- and polyfluoroalkyl substances (PFAS) using a biological brain-based gas sensor

bioRxiv Jan 1, 2025
Per- and polyfluoroalkyl substances (PFAS) are man-made compounds that bioaccumulate in environments. Current PFAS detection technologies encounter difficulty in detecting trace concentrations and require complex data processing, limiting their on-si...
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Discovery of RdRp Thumb-1 as a novel broad-spectrum antiviral family of targets and MDL-001 as a potent broad-spectrum inhibitor thereof

bioRxiv Jan 1, 2025
Multiple positive-sense, single-stranded RNA (+ssRNA) viruses cause human diseases, ranging from mild colds to deadly pandemics. These viruses share a highly conserved RNA-dependent RNA polymerase (RdRp), but developing a non-nucleoside RdRp inhibito...
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Using Diffusion Transformers to Generate Synthetic Diffusion Scalar Maps for Data Augmentation

bioRxiv Jan 1, 2025
Generation of high-quality synthetic brain MRI data could be beneficial for advancing neuroimaging research, particularly when access to large-scale, labeled datasets is limited. In this work, we leverage a pretrained Diffusion Transformer (DiT) arch...
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Integrative Spatial Modelling of Cellular Plasticity using Graph Neural Networks and Geostatistics

bioRxiv Jan 1, 2025
Cellular plasticity - the ability of cells to change phenotype in response to intrinsic and environmental cues - is central to development, regeneration, and disease, but remains difficult to quantify due to its dynamic, context-dependent nature. Her...
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mBER: Controllable de novo antibody design with million-scale experimental screening

bioRxiv Jan 1, 2025
Recent machine learning approaches have achieved high success rates in designing protein binders that demonstrate in vitro binding to their targets. While open models for unconstrained “minibinder” design have shown great experimental promise, method...
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Learning local geometry and nonlinear topology of neural manifolds via spike-timing dependent plasticity

bioRxiv Jan 1, 2025
Neural manifolds are an indispensable framework for understanding information encoded by activity in neural populations. While some neural manifolds are linear and can be recovered from population activity using standard techniques, many neural manif...
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Evaluation of Deep Learning Algorithms to Predict Multiple Dementia-Related Neuropathologies from Brain MRI, Clinical and Genetic Data

bioRxiv Jan 1, 2025
Alzheimer’s disease and related dementias (ADRD) involve overlapping neurodegenerative and vascular pathologies—such as amyloid-β (Aβ), tau, cerebral amyloid angiopathy (CAA), TDP-43, and alpha-synuclein—that complicate diagnosis and treatment. While...
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GNN2Pfam: Integrating protein sequence and structure with graph neural networks for Pfam domain annotation

bioRxiv Jan 1, 2025
The challenge of establishing the relationship between protein sequences and their function cannot yet be considered completely solved. State-of-the-art annotation of Pfam domains is based on hidden Markov models (HMMs) built from hand-crafted sequen...
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Rationality self-organizes beyond subjective reasonings through the coupling of brain and internal organs

bioRxiv Jan 1, 2025
The somatic marker hypothesis proposes that internal bodily activity (IBA) is a prerequisite for rationality. However, the underlying mechanism remains unclear. First, we reveal that IBAs directly switch or lock the output of a neural circuit involve...
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