bioRxiv

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Taguchi–Machine Learning Hybrid Framework for Optimization of Particulate Drug Delivery Systems

bioRxiv Jan 1, 2025
Optimizing particulate drug carrier systems requires balancing multiple formulation parameters to achieve target physicochemical properties while minimizing experimental burden. Here, we implement a hybrid optimization framework integrating a Taguchi...
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Drosophila Video-assisted Activity Monitor (DrosoVAM): a versatile method for behavior monitoring

bioRxiv Jan 1, 2025
Drosophila melanogaster has been a pioneering model system for investigations into the genetic bases of behavior. Studies of circadian activity were some of the first behaviors investigated in flies. The DAM system by TriKinetics played a key role in...
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The role of active mRNA-ribosome dynamics and closing constriction in daughter chromosome separation in Escherichia coli

bioRxiv Jan 1, 2025
The mechanisms by which two sister chromosomes separate and partition into daughter cells in bacteria remain poorly understood. A recent theoretical model has proposed that out-of-equilibrium central dogma reactions involving mRNA and ribosomes play ...
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Imagined Speech Reconstruction with 3D Neural Metabolism and Large Language Model Integration

bioRxiv Jan 1, 2025
Cognitive linguistics posits that language underpins human thought, and this principle has influenced the study and development of large language models (LLMs). In particular, several studies have investigated the metabolic costs of sentence formatio...
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A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy

bioRxiv Jan 1, 2025
Functional hyperaemia is a well-established hallmark of healthy brain function, whereby local brain blood flow adjusts in response to a change in the activity of the surrounding neurons. Although functional hyperemia has been extensively studied at t...
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Cumulative microscopy reveals cellular states in fibroblasts from patients with genetic disorders

bioRxiv Jan 1, 2025
Analysis of cellular states and signaling trajectories can provide insights into causes of disease. We developed cumulative microscopy, a method to perform cyclical imaging without elution or quenching steps. Cumulative microscopy computationally ext...
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Modeling differences in neurodevelopmental maturity of the reading network using support vector regression on functional connectivity data

bioRxiv Jan 1, 2025
The construction of growth charts trained to predict age or developmental deviation (the ‘brain-age index’) based on structural/functional properties of the brain may be informative of children’s neurodevelopmental trajectories. When applied to both ...
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ICEPIC: A Toolkit to Discover Ice Binding Proteins from Sequence

bioRxiv Jan 1, 2025
Ice binding proteins, such as antifreeze proteins (AFPs) and ice nucleation proteins (INPs), are critical for survival in subzero environments and have wide-ranging applications in biotechnology, agriculture, and materials science. Current discovery ...
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BioScientist Agent: Designing LLM-Biomedical Agents with KG-Augmented RL Reasoning Modules for Drug Repurposing and Mechanistic of Action Elucidation

bioRxiv Jan 1, 2025
Drug discovery is protracted, resource-intensive, and afflicted by attrition rates exceeding 90 %, which leaves most diseases, particularly rare or neglected indications, without effective therapies. Drug repurposing offers a cost effective alternati...
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Uncovering Developmental Lineages from Single-cell Data with Contrastive Poincaré Maps

bioRxiv Jan 1, 2025
Single-cell RNA-sequencing (scRNA-seq) enables the study of hierarchical and branching patterns in organismic development at high resolution. Analyzing such data requires visualization and analysis tools that faithfully represent the deep, tree-like ...
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