Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Asking the Right Questions: Benchmarking Large Language Models in the Development of Clinical Consultation Templates
arXiv:2508.01159v2 Announce Type: replace-cross Abstract: This study evaluates the capacity of large language models (LLMs) to generate structured clinical consultation templates for electronic consultation. Using 145 expert-crafted templates developed and routinely used by Stanford's eConsult team, we assess frontier models -- including o3, GPT-4o, Kimi K2, Claude 4 Sonnet, Llama 3 70B, and Gemini 2.5 Pro -- for their ability to produce clinically coherent, concise, and prioritized clinical qu
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cs.AI, q-bio.NC updates on arXiv.org
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SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
arXiv:2511.08151v1 Announce Type: new Abstract: Recent advances in large language models have enabled AI systems to achieve expert-level performance on domain-specific scientific tasks, yet these systems remain narrow and handcrafted. We introduce SciAgent, a unified multi-agent system designed for generalistic scientific reasoning-the ability to adapt reasoning strategies across disciplines and difficulty levels. SciAgent organizes problem solving as a hierarchical process: a Coordinator Agent
SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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MemSearcher: Training LLMs to Reason, Search and Manage Memory via End-to-End Reinforcement Learning
arXiv:2511.02805v1 Announce Type: cross Abstract: Typical search agents concatenate the entire interaction history into the LLM context, preserving information integrity but producing long, noisy contexts, resulting in high computation and memory costs. In contrast, using only the current turn avoids this overhead but discards essential information. This trade-off limits the scalability of search agents. To address this challenge, we propose MemSearcher, an agent workflow that iteratively maint
MemSearcher: Training LLMs to Reason, Search and Manage Memory via End-to-End Reinforcement Learning
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cs.AI, q-bio.NC updates on arXiv.org
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Beyond Accuracy: Rethinking Hallucination and Regulatory Response in Generative AI
arXiv:2509.13345v2 Announce Type: replace-cross Abstract: Hallucination in generative AI is often treated as a technical failure to produce factually correct output. Yet this framing underrepresents the broader significance of hallucinated content in language models, which may appear fluent, persuasive, and contextually appropriate while conveying distortions that escape conventional accuracy checks. This paper critically examines how regulatory and evaluation frameworks have inherited a narrow
Beyond Accuracy: Rethinking Hallucination and Regulatory Response in Generative AI
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Omics In Lung
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Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications
Cell Death Dis. 2025 Oct 21;16(1):746. doi: 10.1038/s41419-025-08060-7.ABSTRACTThe regulatory mechanisms governing transcriptional programs in the cancer genome remain elusive, particularly those concerning cell-type specificity. We carefully curated single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) data from eight distinct carcinoma tissues, including breast, skin, colon, endometrium, lung, ovary, liver, and kidney. Using s
Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications
Cell Death Dis. 2025 Oct 21;16(1):746. doi: 10.1038/s41419-025-08060-7.
ABSTRACT
The regulatory mechanisms governing transcriptional programs in the cancer genome remain elusive, particularly those concerning cell-type specificity. We carefully curated single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) and single-cell RNA sequencing (scRNA-seq) data from eight distinct carcinoma tissues, including breast, skin, colon, endometrium, lung, ovary, liver, and kidney. Using single-cell multi-omics analysis, we identified extensive open chromatin regions and constructed peak-gene link networks, which can reveal distinct cancer gene regulation and genetic risks. We further explored conserved epigenetic regulation across cell types within cancer and elucidated their functional implications. Moreover, we identified cell-type-associated transcription factors (TFs) that regulate key cellular functions, such as the TEAD family of TFs, which widely control cancer-related signaling pathways in tumor cells. In colon cancer, we further identified tumor-specific TFs that are more highly activated in tumor cells than in normal epithelial cells, including CEBPG, LEF1, SOX4, TCF7, and TEAD4, which are pivotal in driving malignant transcriptional programs and represent potential therapeutic targets, as corroborated by single-cell sequencing data from multiple sources and in vitro experiments. Our findings provide a comprehensive understanding of the regulatory dynamics underlying carcinomas and offer valuable insights into potential therapeutic interventions.
PMID:41120274 | PMC:PMC12541060 | DOI:10.1038/s41419-025-08060-7
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Journal of Medical Internet Research
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Behavior Change Strategies in Digital Exercise Interventions for Adolescent Idiopathic Scoliosis: Scoping Review
Background: Adolescent idiopathic scoliosis is a common spinal deformity typically treated with exercise therapy. Despite the increasing use of digital technologies in interventions, there remains a gap in understanding how to effectively integrate behavior change techniques (BCTs) and behavior theories within these digital solutions. Objective: This review aims to identify the digital characteristics of interventions and the BCTs used, and to analyze potential theoretical mechanisms with the Th
Behavior Change Strategies in Digital Exercise Interventions for Adolescent Idiopathic Scoliosis: Scoping Review
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Cell Death Discovery nature.com science feeds
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Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential
Cell Death Discovery, Published online: 02 September 2025; doi:10.1038/s41420-025-02718-zProtein lipoylation in cancer: metabolic reprogramming and therapeutic potential
Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential
Cell Death Discovery, Published online: 02 September 2025; doi:10.1038/s41420-025-02718-z
Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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An organoid co-culture model for probing systemic anti-tumor immunity in lung cancer
Cell Stem Cell. 2025 Jun 6:S1934-5909(25)00191-2. doi: 10.1016/j.stem.2025.05.011. Online ahead of print.ABSTRACTDeciphering interactions between tumor micro- and systemic immune macroenvironments is essential for developing more effective cancer diagnosis and therapeutic strategies. Here, we established a gel-liquid interface (GLI) co-culture model of lung cancer organoids (LCOs) and paired peripheral-blood mononuclear cells (PBMCs), featuring enhanced interactions between immune cells and tumo
An organoid co-culture model for probing systemic anti-tumor immunity in lung cancer
Cell Stem Cell. 2025 Jun 6:S1934-5909(25)00191-2. doi: 10.1016/j.stem.2025.05.011. Online ahead of print.
ABSTRACT
Deciphering interactions between tumor micro- and systemic immune macroenvironments is essential for developing more effective cancer diagnosis and therapeutic strategies. Here, we established a gel-liquid interface (GLI) co-culture model of lung cancer organoids (LCOs) and paired peripheral-blood mononuclear cells (PBMCs), featuring enhanced interactions between immune cells and tumor organoids for optimized simulation of in vivo systemic anti-tumor immunity. By constructing a cohort of lung cancer patients, we demonstrated that the responses of GLI models under αPD1 treatment reflected the immunotherapy outcomes of the corresponding patients precisely. Furthermore, we dissected the various tumor immune processes mediated by PBMC-derived T cells within GLI models through functional multi-omics analyses, along with the characterization of circulating tumor-reactive T cells (GNLY+CD44+CD9+) with effector memory-like phenotypes as a potential indicator of immunotherapy efficacy. Our findings indicate that the GLI co-culture model can be used to develop diagnostic strategies for precision immunotherapies, as well as understanding the underlying mechanisms.
PMID:40513558 | DOI:10.1016/j.stem.2025.05.011
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Nat Comput Sci. 2025 Feb 7. doi: 10.1038/s43588-024-00764-8. Online ahead of print.ABSTRACTLarge-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limi
A statistical framework for multi-trait rare variant analysis in large-scale whole-genome sequencing studies
Nat Comput Sci. 2025 Feb 7. doi: 10.1038/s43588-024-00764-8. Online ahead of print.
ABSTRACT
Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally scalable analytical pipeline for functionally informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits in 61,838 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered and replicated new associations with lipid traits missed by single-trait analysis.
PMID:39920506 | DOI:10.1038/s43588-024-00764-8
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Oncogene - Issue - nature.com science feeds
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Identification of novel germline mutations in <i>FUT7</i> and <i>EXT1</i> linked with hereditary multiple exostoses
Oncogene, Published online: 17 December 2024; doi:10.1038/s41388-024-03254-3Identification of novel germline mutations in FUT7 and EXT1 linked with hereditary multiple exostoses
Identification of novel germline mutations in <i>FUT7</i> and <i>EXT1</i> linked with hereditary multiple exostoses
Oncogene, Published online: 17 December 2024; doi:10.1038/s41388-024-03254-3
Identification of novel germline mutations in FUT7 and EXT1 linked with hereditary multiple exostoses-
Nature - Issue - nature.com science feeds
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Synthesis of portimines reveals the basis of their anti-cancer activity
Nature, Published online: 20 September 2023; doi:10.1038/s41586-023-06535-1A scalable total synthesis of portimines enables structural reassignment of portimine B and in-depth functional evaluation of portimine A, revealing that portimine A induces translation inhibition selectively in human cancer cells and is efficacious in vivo tumour-clearance models.
Synthesis of portimines reveals the basis of their anti-cancer activity
Nature, Published online: 20 September 2023; doi:10.1038/s41586-023-06535-1
A scalable total synthesis of portimines enables structural reassignment of portimine B and in-depth functional evaluation of portimine A, revealing that portimine A induces translation inhibition selectively in human cancer cells and is efficacious in vivo tumour-clearance models.-
Nature - Issue - nature.com science feeds
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Scientific discovery in the age of artificial intelligence
Nature, Published online: 02 August 2023; doi:10.1038/s41586-023-06221-2The advances in artificial intelligence over the past decade are examined, with a discussion on how artificial intelligence systems can aid the scientific process and the central issues that remain despite advances.
Scientific discovery in the age of artificial intelligence
Nature, Published online: 02 August 2023; doi:10.1038/s41586-023-06221-2
The advances in artificial intelligence over the past decade are examined, with a discussion on how artificial intelligence systems can aid the scientific process and the central issues that remain despite advances.-
Nature Biotechnology - Issue - nature.com science feeds
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Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 13 July 2023; doi:10.1038/s41587-023-01884-8Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 13 July 2023; doi:10.1038/s41587-023-01884-8
Author Correction: An engineered influenza virus to deliver antigens for lung cancer vaccination-
Nature Biotechnology - Issue - nature.com science feeds
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An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 25 May 2023; doi:10.1038/s41587-023-01796-7A cancer vaccine is delivered to the lung by an engineered attenuated influenza virus.
An engineered influenza virus to deliver antigens for lung cancer vaccination
Nature Biotechnology, Published online: 25 May 2023; doi:10.1038/s41587-023-01796-7
A cancer vaccine is delivered to the lung by an engineered attenuated influenza virus.-
Most Recent Articles: Clinical Epigenetics
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Epigenetically regulated gene expression profiles decipher four molecular subtypes with prognostic and therapeutic implications in gastric cancer
Gastric cancer (GC) is one of the most common malignant tumors of the digestive tract which seriously endangers the health of human beings worldwide. Transcriptomic deregulation by epigenetic mechanisms plays ...
Epigenetically regulated gene expression profiles decipher four molecular subtypes with prognostic and therapeutic implications in gastric cancer
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Most Recent Articles: Clinical Epigenetics
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Predicting disease-free survival in colorectal cancer by circulating tumor DNA methylation markers
Recurrence represents a well-known poor prognostic factor for colorectal cancer (CRC) patients. This study aimed to establish an effective prognostic prediction model based on noninvasive circulating tumor DNA...