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cs.AI, q-bio.NC updates on arXiv.org
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From Efficiency to Adaptivity: A Deeper Look at Adaptive Reasoning in Large Language Models
arXiv:2511.10788v1 Announce Type: new Abstract: Recent advances in large language models (LLMs) have made reasoning a central benchmark for evaluating intelligence. While prior surveys focus on efficiency by examining how to shorten reasoning chains or reduce computation, this view overlooks a fundamental challenge: current LLMs apply uniform reasoning strategies regardless of task complexity, generating long traces for trivial problems while failing to extend reasoning for difficult tasks. Thi
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cs.AI, q-bio.NC updates on arXiv.org
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Mixture-of-Experts Meets In-Context Reinforcement Learning
arXiv:2506.05426v2 Announce Type: replace-cross Abstract: In-context reinforcement learning (ICRL) has emerged as a promising paradigm for adapting RL agents to downstream tasks through prompt conditioning. However, two notable challenges remain in fully harnessing in-context learning within RL domains: the intrinsic multi-modality of the state-action-reward data and the diverse, heterogeneous nature of decision tasks. To tackle these challenges, we propose T2MIR (Token- and Task-wise MoE for I
Mixture-of-Experts Meets In-Context Reinforcement Learning
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(Multiomics OR Omics) AND (Pancreatic)
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Long-read RNA sequencing dataset of human pancreatic cancer cell lines
Sci Data. 2025 Oct 20;12(1):1653. doi: 10.1038/s41597-025-05939-0.ABSTRACTLong-read RNA sequencing (RNA-seq) technologies have revolutionized transcriptomic research by enabling the sequencing of full-length RNA molecules, thus providing a more accurate characterization of complex transcript isoforms than traditional short-read approaches. In this study, we present a high-coverage long-read transcriptome dataset generated using Oxford Nanopore Technologies' PromethION platform from ten human pan
Long-read RNA sequencing dataset of human pancreatic cancer cell lines
Sci Data. 2025 Oct 20;12(1):1653. doi: 10.1038/s41597-025-05939-0.
ABSTRACT
Long-read RNA sequencing (RNA-seq) technologies have revolutionized transcriptomic research by enabling the sequencing of full-length RNA molecules, thus providing a more accurate characterization of complex transcript isoforms than traditional short-read approaches. In this study, we present a high-coverage long-read transcriptome dataset generated using Oxford Nanopore Technologies' PromethION platform from ten human pancreatic cancer cell lines, with two biological replicates per line. The dataset comprises approximately 189.8 million reads across 20 samples, providing a valuable resource for studying transcript structures in pancreatic cancer. We perform systematic quality assessments, including read length, base quality, and gene body coverage, and report high reproducibility between replicates. Processed files, including transcript annotations in GTF, FASTA, and BED formats, are publicly available to facilitate reuse. This resource supports a wide range of downstream applications such as isoform discovery, transcriptome annotation, and integration with other omics data, offering a foundation for further exploration of transcriptomic complexity in cancer biology.
PMID:41115920 | PMC:PMC12537988 | DOI:10.1038/s41597-025-05939-0
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(Multiomics OR Omics) AND (Pancreatic)
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Integrated spatial omics of metabolic reprogramming and the tumor microenvironment in pancreatic cancer
iScience. 2025 May 15;28(6):112681. doi: 10.1016/j.isci.2025.112681. eCollection 2025 Jun 20.ABSTRACTMetabolic reprogramming is a defining feature of pancreatic cancer, influencing tumor progression and the tumor microenvironment. By integrating single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics, this study visualized the spatial co-localization of metabolites and gene expression within tumor samples, uncovering metabolic heterogeneity and intercellular interactions.
Integrated spatial omics of metabolic reprogramming and the tumor microenvironment in pancreatic cancer
iScience. 2025 May 15;28(6):112681. doi: 10.1016/j.isci.2025.112681. eCollection 2025 Jun 20.
ABSTRACT
Metabolic reprogramming is a defining feature of pancreatic cancer, influencing tumor progression and the tumor microenvironment. By integrating single-cell transcriptomics, spatial transcriptomics, and spatial metabolomics, this study visualized the spatial co-localization of metabolites and gene expression within tumor samples, uncovering metabolic heterogeneity and intercellular interactions. Spatial transcriptomics identified distinct pathological regions, which were further characterized using single-cell transcriptomic data and pathologist annotations. Pseudotime trajectory analysis revealed metabolic shifts along the malignant progression, while single-cell Metabolism (scMetabolism) delineated metabolic differences between pathological regions, classifying them as hypermetabolic or hypometabolic. Notably, aberrant cell communication between cancer cells, macrophages, and fibroblasts was observed, with key receptor-ligand pairs significantly co-expressed in malignant regions and correlated with poor prognosis. Spatial metabolomics imaging identified signature metabolites, highlighting metabolic alterations in amino acid metabolism, polyamine metabolism, fatty acid synthesis, and phospholipid metabolism. This integrated analysis provides critical insights into pancreatic cancer metabolism, offering potential avenues for targeted therapeutic interventions.
PMID:40538442 | PMC:PMC12177182 | DOI:10.1016/j.isci.2025.112681
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Cell Death Discovery nature.com science feeds
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Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms
Cell Death Discovery, Published online: 11 May 2024; doi:10.1038/s41420-024-01994-5Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms
Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms
Cell Death Discovery, Published online: 11 May 2024; doi:10.1038/s41420-024-01994-5
Mono-ADP-ribosylation, a MARylationmultifaced modification of protein, DNA and RNA: characterizations, functions and mechanisms-
Nature Biotechnology - Issue - nature.com science feeds
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Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Nature Biotechnology, Published online: 28 August 2023; doi:10.1038/s41587-023-01909-2Simultaneous single-cell profiling of 5hmC and 5mC shows their unique regulatory roles.
Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects
Nature Biotechnology, Published online: 28 August 2023; doi:10.1038/s41587-023-01909-2
Simultaneous single-cell profiling of 5hmC and 5mC shows their unique regulatory roles.