Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Learn to Relax with Large Language Models: Solving Constraint Optimization Problems via Bidirectional Coevolution
arXiv:2509.12643v3 Announce Type: replace Abstract: Large Language Model (LLM)-based optimization has recently shown promise for autonomous problem solving, yet most approaches still cast LLMs as passive constraint checkers rather than proactive strategy designers, limiting their effectiveness on complex Constraint Optimization Problems (COPs). To address this, we present AutoCO, an end-to-end Automated Constraint Optimization method that tightly couples operations-research principles of constr
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AAAS: Table of Contents
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A high-throughput selection system for fast-acting covalent protein drugs
Science, Ahead of Print.
A high-throughput selection system for fast-acting covalent protein drugs
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Omics in Gastric
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Integrated transcriptomic and proteomic analyses elucidate the stress tolerance network of <em>Saccharomyces boulardii</em> under gastrointestinal challenge
Food Funct. 2026 Mar 31. doi: 10.1039/d5fo04958j. Online ahead of print.ABSTRACTThe probiotic yeast Saccharomyces boulardii is renowned for its clinical efficacy, which is intrinsically linked to its exceptional ability to survive the harsh gastrointestinal (GI) environment. However, a comprehensive understanding of the molecular mechanisms and regulatory pathways underlying the stress tolerance of S. boulardii remains limited. This study employed an integrated transcriptomic and proteomic appro
Integrated transcriptomic and proteomic analyses elucidate the stress tolerance network of <em>Saccharomyces boulardii</em> under gastrointestinal challenge
Food Funct. 2026 Mar 31. doi: 10.1039/d5fo04958j. Online ahead of print.
ABSTRACT
The probiotic yeast Saccharomyces boulardii is renowned for its clinical efficacy, which is intrinsically linked to its exceptional ability to survive the harsh gastrointestinal (GI) environment. However, a comprehensive understanding of the molecular mechanisms and regulatory pathways underlying the stress tolerance of S. boulardii remains limited. This study employed an integrated transcriptomic and proteomic approach to systematically map the dynamic responses of S. boulardii to simulated GI transit. Our analysis revealed that the intestinal phase posed a significantly greater challenge than the gastric phase, triggering extensive molecular reprogramming. A core adaptive strategy was the marked upregulation of the central carbon metabolism, particularly glycolysis, as evidenced by the concerted overexpression of key enzymes at both transcriptional and translational levels, indicating a heightened demand for energy to fuel stress defence mechanisms. Furthermore, significant enrichment was observed in the pathways related to nitrogen and fatty acid metabolism. Integration of the multi-omics datasets highlighted the complexity of the regulatory response, with frequent discordance between mRNA and protein abundance underscoring the importance of post-transcriptional regulation. This study provides a detailed molecular profile of the stress tolerance network in S. boulardii, elucidating the strategic metabolic rewiring and multi-layered regulation that underpin its probiotic resilience. The findings offer valuable insights and a foundational resource for the future development of enhanced probiotic therapies.
PMID:41914832 | DOI:10.1039/d5fo04958j
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Integrated transcriptomic and proteomic analyses elucidate the stress tolerance network of <em>Saccharomyces boulardii</em> under gastrointestinal challenge
Food Funct. 2026 Mar 31. doi: 10.1039/d5fo04958j. Online ahead of print.ABSTRACTThe probiotic yeast Saccharomyces boulardii is renowned for its clinical efficacy, which is intrinsically linked to its exceptional ability to survive the harsh gastrointestinal (GI) environment. However, a comprehensive understanding of the molecular mechanisms and regulatory pathways underlying the stress tolerance of S. boulardii remains limited. This study employed an integrated transcriptomic and proteomic appro
Integrated transcriptomic and proteomic analyses elucidate the stress tolerance network of <em>Saccharomyces boulardii</em> under gastrointestinal challenge
Food Funct. 2026 Mar 31. doi: 10.1039/d5fo04958j. Online ahead of print.
ABSTRACT
The probiotic yeast Saccharomyces boulardii is renowned for its clinical efficacy, which is intrinsically linked to its exceptional ability to survive the harsh gastrointestinal (GI) environment. However, a comprehensive understanding of the molecular mechanisms and regulatory pathways underlying the stress tolerance of S. boulardii remains limited. This study employed an integrated transcriptomic and proteomic approach to systematically map the dynamic responses of S. boulardii to simulated GI transit. Our analysis revealed that the intestinal phase posed a significantly greater challenge than the gastric phase, triggering extensive molecular reprogramming. A core adaptive strategy was the marked upregulation of the central carbon metabolism, particularly glycolysis, as evidenced by the concerted overexpression of key enzymes at both transcriptional and translational levels, indicating a heightened demand for energy to fuel stress defence mechanisms. Furthermore, significant enrichment was observed in the pathways related to nitrogen and fatty acid metabolism. Integration of the multi-omics datasets highlighted the complexity of the regulatory response, with frequent discordance between mRNA and protein abundance underscoring the importance of post-transcriptional regulation. This study provides a detailed molecular profile of the stress tolerance network in S. boulardii, elucidating the strategic metabolic rewiring and multi-layered regulation that underpin its probiotic resilience. The findings offer valuable insights and a foundational resource for the future development of enhanced probiotic therapies.
PMID:41914832 | DOI:10.1039/d5fo04958j
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Nature Biotechnology - Issue - nature.com science feeds
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Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics
Nature Biotechnology, Published online: 31 March 2026; doi:10.1038/s41587-026-03068-6Simultaneous profiling of adenylated and non-adenylated RNAs reveals regulatory programs across diverse cell types.
Scalable single-cell total RNA sequencing unifies coding and noncoding transcriptomics
Nature Biotechnology, Published online: 31 March 2026; doi:10.1038/s41587-026-03068-6
Simultaneous profiling of adenylated and non-adenylated RNAs reveals regulatory programs across diverse cell types.-
Omics in Hepatocellular
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Integrated Machine Learning and Multi-Omics Identifies a Novel Molecular Signature for Improving the Prognosis of Hepatocellular Carcinoma
J Hepatocell Carcinoma. 2026 Mar 11;13:574690. doi: 10.2147/JHC.S574690. eCollection 2026.ABSTRACTBACKGROUND: Hepatocellular carcinoma (HCC) exhibits significant molecular heterogeneity and complex immune microenvironment, which to some extent limits the accuracy of prognosis assessment and the formulation of individualized treatment strategies. This study aims to identify immune-derived molecular signatures based on multi-omics data and machine learning methods for the prognosis prediction and
Integrated Machine Learning and Multi-Omics Identifies a Novel Molecular Signature for Improving the Prognosis of Hepatocellular Carcinoma
J Hepatocell Carcinoma. 2026 Mar 11;13:574690. doi: 10.2147/JHC.S574690. eCollection 2026.
ABSTRACT
BACKGROUND: Hepatocellular carcinoma (HCC) exhibits significant molecular heterogeneity and complex immune microenvironment, which to some extent limits the accuracy of prognosis assessment and the formulation of individualized treatment strategies. This study aims to identify immune-derived molecular signatures based on multi-omics data and machine learning methods for the prognosis prediction and risk stratification of HCC.
METHODS: Based on weighted gene co-expression network analysis(WGCNA) and differential gene analysis,immune-derived molecular signature (IDMS) were screened in both single-cell and bulk transcriptomes. Prognostic model was constructed by multi-machine learning approachs. Subsequently, we investigated the differences in mutations, biological functions, and immune cell infiltration within the tumor microenvironment between the high- and low-risk groups.In addition, we comprehensively analyzed the drug sensitivity of IDMS and predicted potential drugs.
RESULTS: We identified seven hub genes at the single-cell and bulk transcriptome levels. Based on multiple machine learning, we constructed a prognostic model that demonstrated excellent performance in predicting overall survival for patients with HCC. IDMS -integrated normograms provide a promising and quantitative tool for clinical risk management.Notably, a significant difference in microsatellite instability (MSI) was observed between the high- and low-risk groups. This indicates that patients in the high-risk group might have a better response to immunotherapy. Additionally, we predicted potential drugs targeting to these risk subgroups.
CONCLUSION: Our research developed an IDMS that could serve as an effective tool for patient stratification management and prognosis prediction. This signature could provide a reference for immunotherapy for patients with HCC and improve their prognosis.
PMID:41847219 | PMC:PMC12991065 | DOI:10.2147/JHC.S574690
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Cell
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Human-specific features of the cerebellum and ZP2-regulated synapse development
Human-specific transcriptomic and regulatory features are present in the cerebellum, with ZP2 playing a key role in synapse regulation. ZP2 expression is induced by pontine mossy fibers, leading to decreased synaptic proteins and neuronal activity, which provides insights into the evolutionary development of the human cerebellum.
Human-specific features of the cerebellum and ZP2-regulated synapse development
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cs.AI, q-bio.NC updates on arXiv.org
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AtomicVLA: Unlocking the Potential of Atomic Skill Learning in Robots
arXiv:2603.07648v1 Announce Type: cross Abstract: Recent advances in Visual-Language-Action (VLA) models have shown promising potential for robotic manipulation tasks. However, real-world robotic tasks often involve long-horizon, multi-step problem-solving and require generalization for continual skill acquisition, extending beyond single actions or skills. These challenges present significant barriers for existing VLA models, which use monolithic action decoders trained on aggregated data, res