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cs.AI, q-bio.NC updates on arXiv.org
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A Multi-faceted Analysis of Cognitive Abilities: Evaluating Prompt Methods with Large Language Models on the CONSORT Checklist
arXiv:2510.19139v1 Announce Type: new Abstract: Despite the rapid expansion of Large Language Models (LLMs) in healthcare, the ability of these systems to assess clinical trial reporting according to CONSORT standards remains unclear, particularly with respect to their cognitive and reasoning strategies. This study applies a behavioral and metacognitive analytic approach with expert-validated data, systematically comparing two representative LLMs under three prompt conditions. Clear differences
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cs.AI, q-bio.NC updates on arXiv.org
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MSC-Bench: A Rigorous Benchmark for Multi-Server Tool Orchestration
arXiv:2510.19423v1 Announce Type: new Abstract: We introduce MSC-Bench, a large-scale benchmark for evaluating multi-hop, end-to-end tool orchestration by LLM agents in a hierarchical Model-Context Protocol (MCP) ecosystem. Existing benchmarks often evaluate tools in isolation, ignoring challenges such as functional overlap and cross-server orchestration, leading to overly optimistic assessments. MSC-Bench addresses these gaps by constructing ground truth through 'equal function sets', allowing
MSC-Bench: A Rigorous Benchmark for Multi-Server Tool Orchestration
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cs.AI, q-bio.NC updates on arXiv.org
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KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge
arXiv:2510.19484v1 Announce Type: cross Abstract: The molecular large language models have garnered widespread attention due to their promising potential on molecular applications. However, current molecular large language models face significant limitations in understanding molecules due to inadequate textual descriptions and suboptimal molecular representation strategies during pretraining. To address these challenges, we introduce KnowMol-100K, a large-scale dataset with 100K fine-grained mo
KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge
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cs.AI, q-bio.NC updates on arXiv.org
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RoboGPT-R1: Enhancing Robot Planning with Reinforcement Learning
arXiv:2510.14828v2 Announce Type: replace Abstract: Improving the reasoning capabilities of embodied agents is crucial for robots to complete complex human instructions in long-view manipulation tasks successfully. Despite the success of large language models and vision language models based on Supervised Fine-Tuning (SFT) in planning tasks, they continue facing challenges in performing long-horizon manipulation tasks in complex real-world environments, owing to their restricted common sense an
RoboGPT-R1: Enhancing Robot Planning with Reinforcement Learning
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cs.AI, q-bio.NC updates on arXiv.org
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ScholaWrite: A Dataset of End-to-End Scholarly Writing Process
arXiv:2502.02904v4 Announce Type: replace-cross Abstract: Writing is a cognitively demanding activity that requires constant decision-making, heavy reliance on working memory, and frequent shifts between tasks of different goals. To build writing assistants that truly align with writers' cognition, we must capture and decode the complete thought process behind how writers transform ideas into final texts. We present ScholaWrite, the first dataset of end-to-end scholarly writing, tracing the mul
ScholaWrite: A Dataset of End-to-End Scholarly Writing Process
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Omics in Hepatocellular
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Landscape of T-cell exhaustion heterogeneity and HBV integration in virus-related HCC revealed by whole-exome, transcriptome, and single-cell sequencing
JHEP Rep. 2025 Jul 10;7(11):101518. doi: 10.1016/j.jhepr.2025.101518. eCollection 2025 Nov.ABSTRACTBACKGROUND & AIMS: To enhance our understanding of the tumor immune microenvironment (TIME) in hepatocellular carcinoma (HCC), we investigated the heterogeneity of T-cell exhaustion and its association with HBV integrations and direct oncogenic potential in HCC.METHODS: We conducted a multi-omics analysis, including single-cell RNA sequencing, whole-exome sequencing, whole-transcriptome sequenc
Landscape of T-cell exhaustion heterogeneity and HBV integration in virus-related HCC revealed by whole-exome, transcriptome, and single-cell sequencing
JHEP Rep. 2025 Jul 10;7(11):101518. doi: 10.1016/j.jhepr.2025.101518. eCollection 2025 Nov.
ABSTRACT
BACKGROUND & AIMS: To enhance our understanding of the tumor immune microenvironment (TIME) in hepatocellular carcinoma (HCC), we investigated the heterogeneity of T-cell exhaustion and its association with HBV integrations and direct oncogenic potential in HCC.
METHODS: We conducted a multi-omics analysis, including single-cell RNA sequencing, whole-exome sequencing, whole-transcriptome sequencing, and next-generation sequencing (NGS)-based HBV integration analysis, in eight patients with virus-related HCC. For validation, bulk RNA sequencing and NGS-based HBV integration analysis were performed in an independent cohort (n = 106).
RESULTS: Based on the expression scores of exhaustion markers in effector CD8+ T cells, patients were classified into high (n = 2) and low (n = 6) exhaustion groups (p <0.001). The high-exhaustion group exhibited higher clonal expansion (Gini index: 0.83 vs. 0.48, p = 0.006) and sharing of CD8+ T effector memory and cycling T cells with elevated exhaustion markers. This group also showed increased clonal expansion of CD4+ regulatory T cells and follicular helper T cells (p <0.001) with higher PDCD1 expression. In addition, the high-exhaustion group had higher TP53 mutation rates and signature scores for proliferation subtypes compared with the low-exhaustion group, who predominantly harbored TERT mutations. Moreover, the high-exhaustion group demonstrated more pronounced HBV integrations with elevated intrahepatic covalently closed circular DNA (cccDNA) and pregenomic (pg)RNA levels. Similarly, in the validation cohort, the high-exhaustion group (n = 28) demonstrated stronger proliferation subtype signatures (p <0.001), along with higher HBV integrations, S-fusion transcripts, and an increased intrahepatic viral reservoir (cccDNA/pgRNA) (p <0.05) compared with the low-exhaustion group (n = 78).
CONCLUSIONS: Our study revealed the heterogeneity in T-cell exhaustion in the TIME of HCC, along with differences in HBV integrations and molecular subtypes. These findings provide insight into the intricate relationship between high exhaustion, proliferation subtype, increased HBV integrations, and enhanced HBV-induced oncogenic potential in virus-related HCC.
IMPACT AND IMPLICATIONS: This study provides a comprehensive immune landscape of T-cell exhaustion using multi-omics analysis, offering critical insights into T cell heterogeneity in virus-related HCC. It establishes a strong association between higher HBV integration, enhanced oncogenic potential, T-cell exhaustion, and proliferation subtypes in HCC. Our results also establish a basis for personalized therapies tailored to the immune-exhaustion status within the TIME of each patient with HCC.
PMID:41113120 | PMC:PMC12529496 | DOI:10.1016/j.jhepr.2025.101518
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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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Exploring Patient Perspectives, Engagement, and Output Quality in Doctor-Supervised Use of Artificial Intelligence During Informed Consent Consultation With ChatGPT and Retrieval Augmented Generation (RAG): Quantitative Exploratory Study
Background: Comprehensive preoperative education is essential for optimizing outcomes and ensuring informed consent in patients undergoing total hip arthroplasty (THA). Emerging artificial intelligence (AI) tools, such as ChatGPT, offer scalable support for patient education, but their clinical application requires rigorous evaluation to ensure accuracy, safety, and trust. Objective: This study assessed patients’ preferences and satisfaction with AI-assisted informed consent in THA, comparing tr
Exploring Patient Perspectives, Engagement, and Output Quality in Doctor-Supervised Use of Artificial Intelligence During Informed Consent Consultation With ChatGPT and Retrieval Augmented Generation (RAG): Quantitative Exploratory Study
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Journal of Medical Internet Research
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Assessing Large Language Models in Building a Structured Dataset From AskDocs Subreddit Data: Methodological Study
Background: In an era marked by the blooming reliance on digital platforms for healthcare consultation, the subreddit r/AskDocs has emerged as a pivotal forum. However, the vast, unstructured nature of forum data presents a formidable challenge; the extraction and meaningful analysis of such data require advanced tools that can navigate the complexities of language and context inherent in user-generated content. Objective: Our objective was to evaluate employing Large Language Models (LLMs) to s
Assessing Large Language Models in Building a Structured Dataset From AskDocs Subreddit Data: Methodological Study
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Oncogene - Issue - nature.com science feeds
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Meflin is a druggable target using antibody-drug conjugates in progressive osteosarcoma
Oncogene, Published online: 21 October 2025; doi:10.1038/s41388-025-03605-8Meflin is a druggable target using antibody-drug conjugates in progressive osteosarcoma
Meflin is a druggable target using antibody-drug conjugates in progressive osteosarcoma
Oncogene, Published online: 21 October 2025; doi:10.1038/s41388-025-03605-8
Meflin is a druggable target using antibody-drug conjugates in progressive osteosarcoma-
Nature Biotechnology - Issue - nature.com science feeds
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Integrated epigenetic and genetic programming of primary human T cells
Nature Biotechnology, Published online: 21 October 2025; doi:10.1038/s41587-025-02856-wMultiplexed editing in primary human T cells generates enhanced immune cell therapies.
Integrated epigenetic and genetic programming of primary human T cells
Nature Biotechnology, Published online: 21 October 2025; doi:10.1038/s41587-025-02856-w
Multiplexed editing in primary human T cells generates enhanced immune cell therapies.-
(Multiomics OR Omics) AND (Pancreatic)
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Multi-omics analyses inform mechanisms of immunotherapy response in pancreatic cancer
Front Immunol. 2025 Oct 2;16:1673098. doi: 10.3389/fimmu.2025.1673098. eCollection 2025.ABSTRACTINTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) continues to exhibit resistance to immunotherapy. In this study, we evaluated the efficacy of combining immunotherapy with chemotherapy for the treatment of advanced pancreatic cancer. Additionally, we employed a multimodal analytical approach to elucidate the immune landscape and conduct transcriptomic profiling in PDAC.METHODS: A retrospective an
Multi-omics analyses inform mechanisms of immunotherapy response in pancreatic cancer
Front Immunol. 2025 Oct 2;16:1673098. doi: 10.3389/fimmu.2025.1673098. eCollection 2025.
ABSTRACT
INTRODUCTION: Pancreatic ductal adenocarcinoma (PDAC) continues to exhibit resistance to immunotherapy. In this study, we evaluated the efficacy of combining immunotherapy with chemotherapy for the treatment of advanced pancreatic cancer. Additionally, we employed a multimodal analytical approach to elucidate the immune landscape and conduct transcriptomic profiling in PDAC.
METHODS: A retrospective analysis was conducted on the clinical data of 52 patients diagnosed with advanced PDAC who underwent a combined treatment regimen of immunotherapy and chemotherapy. The study evaluated the objective response rate (ORR), disease control rate (DCR), and progression-free survival (PFS). To characterize the immune landscape in treatment-naive pancreatic ductal adenocarcinoma (PDAC) tumors and in the systemic circulation, flow cytometry, multiplex immunohistochemistry (mIHC), and whole transcriptome sequencing were employed.
RESULTS: The study reported an ORR of 32.7%, a DCR of 67.3%, and a 6-month PFS rate of 38.5%, with a median PFS of 5.5 months. Patients treated with a combination of immunotherapy and gemcitabine achieved the longest PFS. The first-line treatment cohort exhibited a significantly higher DCR (79.3% vs. 52.2%, P = 0.038) and a longer median PFS (6.6 vs. 3.5 months, P = 0.032) compared to the second-line treatment cohort. The efficacy of treatment varied depending on the drug combinations used. Flow cytometry analysis revealed a greater frequency of CD45- CD64+ cells in the peripheral blood of patients with progressive disease (PD) compared to those with a partial response (PR). Multiplex immunofluorescence (MIF) analysis indicated an increased intratumoral infiltration of CD8+ T cells and CD137+ CD8+ T cells in patients with PR. Whole transcriptome sequencing (WTSS) identified key genes involved in immune regulation, signal transduction, and digestive function. Hemopexin (HPX) and regulatory factor X-associated protein (RFXAP) were upregulated in PR patients and showed a positive correlation with survival, whereas Interleukin-6 (IL-6) expression was linked to poor prognosis.
CONCLUSIONS: These findings indicate that immunochemotherapy shows potential for the treatment of advanced PDAC. Our study elucidates the immune landscape associated with PDAC and provides critical insights for the identification of prospective therapeutic targets, which could guide the development of innovative combination immunotherapy strategies.
PMID:41112307 | PMC:PMC12528169 | DOI:10.3389/fimmu.2025.1673098
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Nature - Issue - nature.com science feeds
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Parity and lactation induce T cell mediated breast cancer protection
Nature, Published online: 20 October 2025; doi:10.1038/s41586-025-09713-5Parity and lactation induce T cell mediated breast cancer protection
Parity and lactation induce T cell mediated breast cancer protection
Nature, Published online: 20 October 2025; doi:10.1038/s41586-025-09713-5
Parity and lactation induce T cell mediated breast cancer protection-
Nature - Issue - nature.com science feeds
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Alternatives to animal testing are the future — it’s time that journals, funders and scientists embrace them
Nature, Published online: 20 October 2025; doi:10.1038/d41586-025-03344-6Biomedical research techniques that don’t involve the use of animals are gaining momentum, but those using innovative approaches still face resistance from some quarters.
Alternatives to animal testing are the future — it’s time that journals, funders and scientists embrace them
Nature, Published online: 20 October 2025; doi:10.1038/d41586-025-03344-6
Biomedical research techniques that don’t involve the use of animals are gaining momentum, but those using innovative approaches still face resistance from some quarters.-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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R-loops in hepatocellular carcinoma: Bridging genomic instability and therapeutic opportunity (Review)
Mol Med Rep. 2026 Jan;33(1):6. doi: 10.3892/mmr.2025.13716. Epub 2025 Oct 17.ABSTRACTR‑loops, three‑stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced single‑stranded DNA, have emerged as important regulators of gene expression and genome maintenance. Although physiological R‑loops participate in normal cellular processes, their dysregulation can threaten genomic integrity by inducing DNA damage and replication stress. The present review explores the role of R‑loops in
R-loops in hepatocellular carcinoma: Bridging genomic instability and therapeutic opportunity (Review)
Mol Med Rep. 2026 Jan;33(1):6. doi: 10.3892/mmr.2025.13716. Epub 2025 Oct 17.
ABSTRACT
R‑loops, three‑stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced single‑stranded DNA, have emerged as important regulators of gene expression and genome maintenance. Although physiological R‑loops participate in normal cellular processes, their dysregulation can threaten genomic integrity by inducing DNA damage and replication stress. The present review explores the role of R‑loops in hepatocellular carcinoma (HCC), a malignancy characterized by marked genomic instability. In the present review, the formation mechanisms of R‑loops, their dual functions in transcriptional regulation and DNA damage, and their specific implications for HCC pathophysiology were discussed. HCC cells exhibit altered R‑loop homeostasis with aberrant accumulation linked to hepatitis B virus infection, inflammatory signaling and oncogene activation. The present review highlighted how HCC cells exploit or manage R‑loops to promote tumor progression, particularly through the epigenetic silencing of differentiation genes and modulation of replication stress responses. Furthermore, emerging therapeutic strategies targeting R‑loop biology were examined, including small molecules that induce synthetic lethality, gene‑based interventions and combination approaches that exploit R‑loop vulnerabilities. Challenges in targeting R‑loops and future directions, including multi‑omics profiling and biomarker development, were also addressed. Understanding the complex interplay between R‑loops and HCC offers promising avenues for novel diagnostic and therapeutic approaches for this malignancy.
PMID:41104860 | DOI:10.3892/mmr.2025.13716
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npj Digital Medicine
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When helpfulness backfires: LLMs and the risk of false medical information due to sycophantic behavior
npj Digital Medicine, Published online: 17 October 2025; doi:10.1038/s41746-025-02008-zWhen helpfulness backfires: LLMs and the risk of false medical information due to sycophantic behavior
When helpfulness backfires: LLMs and the risk of false medical information due to sycophantic behavior
npj Digital Medicine, Published online: 17 October 2025; doi:10.1038/s41746-025-02008-z
When helpfulness backfires: LLMs and the risk of false medical information due to sycophantic behavior-
npj Digital Medicine
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Semi-automated surveillance of surgical site infections using machine learning and rule-based classification models
npj Digital Medicine, Published online: 17 October 2025; doi:10.1038/s41746-025-01989-1Semi-automated surveillance of surgical site infections using machine learning and rule-based classification models
Semi-automated surveillance of surgical site infections using machine learning and rule-based classification models
npj Digital Medicine, Published online: 17 October 2025; doi:10.1038/s41746-025-01989-1
Semi-automated surveillance of surgical site infections using machine learning and rule-based classification models-
Journal of Medical Internet Research
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Use of Artificial Intelligence-Assisted Conversational Agents to Improve Patient Experience Related to Physicians: Cross-Sectional Study in China
Background: Artificial intelligence-assisted conversational agents have been applied and developed in outpatient departments to improve health services in China. However, there has been little research that evaluates the effect of artificial intelligence-assisted conversational agents on the patient experience related to physicians during outpatient visits. Objective: This aim of this study was to examine whether the use of artificial intelligence-assisted conversational agents improves the pati
Use of Artificial Intelligence-Assisted Conversational Agents to Improve Patient Experience Related to Physicians: Cross-Sectional Study in China
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Cell Death Discovery nature.com science feeds
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Evidence of fructose metabolism in colorectal cancer
Cell Death Discovery, Published online: 16 October 2025; doi:10.1038/s41420-025-02745-wEvidence of fructose metabolism in colorectal cancer
Evidence of fructose metabolism in colorectal cancer
Cell Death Discovery, Published online: 16 October 2025; doi:10.1038/s41420-025-02745-w
Evidence of fructose metabolism in colorectal cancer-
Nature Biotechnology - Issue - nature.com science feeds
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A tumor-on-a-chip for in vitro study of CAR-T cell immunotherapy in solid tumors
Nature Biotechnology, Published online: 17 October 2025; doi:10.1038/s41587-025-02845-zThe interactions of CAR-T cells and solid tumors are modeled on a chip.
A tumor-on-a-chip for in vitro study of CAR-T cell immunotherapy in solid tumors
Nature Biotechnology, Published online: 17 October 2025; doi:10.1038/s41587-025-02845-z
The interactions of CAR-T cells and solid tumors are modeled on a chip.