Normal view
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Molecular Therapy
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Pan-cancer oncolytic virotherapy through disruption of tumor cell mitochondrial dynamics
Li and colleagues identified RhoA as a “redox rheostat” governing mitochondrial dynamics during oncolytic virotherapy and thereby engineered rNDV-RHOA, an NDV-based oncolytic virus overexpressing RhoA. This tumor-targeted RhoA overexpression synergizes oxidative stress and viral oncolysis, transcending conventional oncolysis by surmounting tumor heterogeneity through exploiting inherent tumor redox dependency.
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cs.AI, q-bio.NC updates on arXiv.org
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JarvisGUI: Towards Cross-Device GUI Agents with Dynamic Task Composition
arXiv:2609.10451v1 Announce Type: new Abstract: Real-world GUI usage frequently involves workflows that span multiple devices and platforms, requiring the transfer of intermediate results, maintenance of shared state, and coordination across heterogeneous environments. However, existing GUI benchmarks overwhelmingly evaluate agents on single-device, statically defined tasks, thus leaving such cross-device capabilities largely unexamined, resulting in an overly optimistic assessment of agents' r
JarvisGUI: Towards Cross-Device GUI Agents with Dynamic Task Composition
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cs.AI, q-bio.NC updates on arXiv.org
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Harbor Adapters and Harbor-Index: Infrastructure and a Curated Meta-Dataset for Large-Scale Agentic Evaluation
arXiv:2609.04298v2 Announce Type: replace Abstract: Evaluating agents on the growing number of agentic benchmarks is challenging because they often require complex environments and agent integrations. We introduce Harbor Adapters, a unified evaluation infrastructure for agentic benchmarks. Our work makes three contributions. First, we develop benchmark adapters that port more than 80 benchmarks to evaluate arbitrary agents, and validate them through rigorous code review and parity experiments.
Harbor Adapters and Harbor-Index: Infrastructure and a Curated Meta-Dataset for Large-Scale Agentic Evaluation
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cs.AI, q-bio.NC updates on arXiv.org
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RAU: Reference-based Anatomical Understanding with Vision Language Models
arXiv:2509.22404v2 Announce Type: replace-cross Abstract: Anatomical understanding, which is the ability to identify, localize, or segment anatomical structures, is critical in medical image analysis; however, its progress is constrained by the scarcity of expert-labeled data. A promising remedy is to leverage an annotated reference image to guide the interpretation of an unlabeled target. Although recent vision-language models (VLMs) exhibit non-trivial visual reasoning, their reference-based
RAU: Reference-based Anatomical Understanding with Vision Language Models
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Omics in Hepatocellular
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S1P-TREM2 axis protects immunosuppressive neutrophils from ferroptosis to promote tumour progression in hepatocellular carcinoma
Gut. 2026 Sep 7:gutjnl-2025-337414. doi: 10.1136/gutjnl-2025-337414. Online ahead of print.ABSTRACTBACKGROUND: Neutrophils are increasingly recognised as immunosuppressive drivers of hepatocellular carcinoma (HCC), yet their persistence in the oxidative, lipid-rich tumour microenvironment remains poorly understood.OBJECTIVE: To elucidate the metabolic and molecular programmes that enable tumour-associated neutrophils (TANs) to resist ferroptosis and sustain immunosuppression in HCC.DESIGN: We em
S1P-TREM2 axis protects immunosuppressive neutrophils from ferroptosis to promote tumour progression in hepatocellular carcinoma
Gut. 2026 Sep 7:gutjnl-2025-337414. doi: 10.1136/gutjnl-2025-337414. Online ahead of print.
ABSTRACT
BACKGROUND: Neutrophils are increasingly recognised as immunosuppressive drivers of hepatocellular carcinoma (HCC), yet their persistence in the oxidative, lipid-rich tumour microenvironment remains poorly understood.
OBJECTIVE: To elucidate the metabolic and molecular programmes that enable tumour-associated neutrophils (TANs) to resist ferroptosis and sustain immunosuppression in HCC.
DESIGN: We employed human HCC samples, multiple murine HCC models, transcriptomic and lipidomic profiling, genetic loss-of-function systems and therapeutic interventions. Ferroptosis sensitivity, lipid metabolic rewiring and immunological consequences of TANs were systematically evaluated across models and validated in patient datasets and biospecimens.
RESULTS: TANs in human HCC and mouse models exhibit pronounced lipid accumulation and oxidative stress compared with peripheral neutrophils. Multi-omic profiling revealed that TANs are enriched for lipid-binding gene programmes and undergo rewiring towards sphingolipid and unsaturated fatty acid metabolism. We identified triggering receptor expressed on myeloid cells 2 (TREM2) as a key lipid-sensing receptor selectively expressed in TANs. Functional deletion of TREM2 reprogrammed the tumour immune microenvironment, restoring CD8+ T cell activity and suppressing HCC progression. Mechanistically, tumour-derived sphingosine-1-phosphate (S1P) activates TREM2, triggering nuclear factor erythroid 2-related factor 2 (NRF2)-mediated transcription of glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11 (SLC7A11), thereby promoting ferroptosis resistance. TREM2 expression is transcriptionally induced by granulocyte-macrophage colony-stimulating factor-signal transducer and activator of transcription 3 (GM-CSF-STAT3) signalling. Genetic deletion of TREM2, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout of sphingosine kinase 1/2 (SPHK1/2) in tumour cells, or pharmacological inhibition of S1P synthesis disrupts this protective lipid-immune circuit, sensitises TANs to ferroptosis and restricts tumour growth. Therapeutically, a peptide-based TREM2 inhibitor reprogrammes TANs, restores CD8+ T cell function and enhances anti-programmed cell death protein 1 (PD-1) immunotherapy efficacy. Clinically, TREM2+ polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) are enriched in HCC tumours, correlate with SPHK1/2 expression and T cell dysfunction and associate with poor patient prognosis.
CONCLUSION: Our study uncovers the S1P-TREM2-NRF2 axis as a critical metabolic-immune circuit that preserves neutrophil survival and immunosuppressive function in HCC. Targeting this lipid-dependent ferroptosis resistance pathway offers a promising therapeutic strategy to overcome immunotherapy resistance in liver cancer.
PMID:42705697 | DOI:10.1136/gutjnl-2025-337414
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(Multiomics OR Omics) AND (Pancreatic)
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S1P-TREM2 axis protects immunosuppressive neutrophils from ferroptosis to promote tumour progression in hepatocellular carcinoma
Gut. 2026 Sep 7:gutjnl-2025-337414. doi: 10.1136/gutjnl-2025-337414. Online ahead of print.ABSTRACTBACKGROUND: Neutrophils are increasingly recognised as immunosuppressive drivers of hepatocellular carcinoma (HCC), yet their persistence in the oxidative, lipid-rich tumour microenvironment remains poorly understood.OBJECTIVE: To elucidate the metabolic and molecular programmes that enable tumour-associated neutrophils (TANs) to resist ferroptosis and sustain immunosuppression in HCC.DESIGN: We em
S1P-TREM2 axis protects immunosuppressive neutrophils from ferroptosis to promote tumour progression in hepatocellular carcinoma
Gut. 2026 Sep 7:gutjnl-2025-337414. doi: 10.1136/gutjnl-2025-337414. Online ahead of print.
ABSTRACT
BACKGROUND: Neutrophils are increasingly recognised as immunosuppressive drivers of hepatocellular carcinoma (HCC), yet their persistence in the oxidative, lipid-rich tumour microenvironment remains poorly understood.
OBJECTIVE: To elucidate the metabolic and molecular programmes that enable tumour-associated neutrophils (TANs) to resist ferroptosis and sustain immunosuppression in HCC.
DESIGN: We employed human HCC samples, multiple murine HCC models, transcriptomic and lipidomic profiling, genetic loss-of-function systems and therapeutic interventions. Ferroptosis sensitivity, lipid metabolic rewiring and immunological consequences of TANs were systematically evaluated across models and validated in patient datasets and biospecimens.
RESULTS: TANs in human HCC and mouse models exhibit pronounced lipid accumulation and oxidative stress compared with peripheral neutrophils. Multi-omic profiling revealed that TANs are enriched for lipid-binding gene programmes and undergo rewiring towards sphingolipid and unsaturated fatty acid metabolism. We identified triggering receptor expressed on myeloid cells 2 (TREM2) as a key lipid-sensing receptor selectively expressed in TANs. Functional deletion of TREM2 reprogrammed the tumour immune microenvironment, restoring CD8+ T cell activity and suppressing HCC progression. Mechanistically, tumour-derived sphingosine-1-phosphate (S1P) activates TREM2, triggering nuclear factor erythroid 2-related factor 2 (NRF2)-mediated transcription of glutathione peroxidase 4 (GPX4) and solute carrier family 7 member 11 (SLC7A11), thereby promoting ferroptosis resistance. TREM2 expression is transcriptionally induced by granulocyte-macrophage colony-stimulating factor-signal transducer and activator of transcription 3 (GM-CSF-STAT3) signalling. Genetic deletion of TREM2, clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout of sphingosine kinase 1/2 (SPHK1/2) in tumour cells, or pharmacological inhibition of S1P synthesis disrupts this protective lipid-immune circuit, sensitises TANs to ferroptosis and restricts tumour growth. Therapeutically, a peptide-based TREM2 inhibitor reprogrammes TANs, restores CD8+ T cell function and enhances anti-programmed cell death protein 1 (PD-1) immunotherapy efficacy. Clinically, TREM2+ polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) are enriched in HCC tumours, correlate with SPHK1/2 expression and T cell dysfunction and associate with poor patient prognosis.
CONCLUSION: Our study uncovers the S1P-TREM2-NRF2 axis as a critical metabolic-immune circuit that preserves neutrophil survival and immunosuppressive function in HCC. Targeting this lipid-dependent ferroptosis resistance pathway offers a promising therapeutic strategy to overcome immunotherapy resistance in liver cancer.
PMID:42705697 | DOI:10.1136/gutjnl-2025-337414
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Omics in Gastric
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Integrative Multi-Omics Analysis Identifies Thrombosis-Associated Molecular Features Linked to Germline Susceptibility and Immune Cell Communication in Gastric Cancer
Chem Biol Drug Des. 2026 Sep;108(3):e70386. doi: 10.1111/cbdd.70386.ABSTRACTEmerging evidence indicates that coagulation-related molecular programs are associated with thrombosis, tumor progression, and molecular dysregulation in gastric cancer (GC). However, thrombosis-associated molecular features in GC and their potential links to inherited susceptibility remain insufficiently understood. Integrated analyses of transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibu
Integrative Multi-Omics Analysis Identifies Thrombosis-Associated Molecular Features Linked to Germline Susceptibility and Immune Cell Communication in Gastric Cancer
Chem Biol Drug Des. 2026 Sep;108(3):e70386. doi: 10.1111/cbdd.70386.
ABSTRACT
Emerging evidence indicates that coagulation-related molecular programs are associated with thrombosis, tumor progression, and molecular dysregulation in gastric cancer (GC). However, thrombosis-associated molecular features in GC and their potential links to inherited susceptibility remain insufficiently understood. Integrated analyses of transcriptomic data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were performed to identify thrombosis-associated genes and establish a machine learning-based prognostic signature. Genome-wide association study (GWAS), expression quantitative trait loci (eQTL), transcriptome-wide association study (TWAS), and Mendelian randomization (MR) analyses were conducted to investigate susceptibility-associated transcriptional programs in GC. Functional assays were used to evaluate candidate genes associated with malignant phenotypes. Single-cell RNA sequencing (scRNA-seq) and cell-cell communication analyses were further performed to characterize cell-type-specific expression patterns and potential intercellular interactions. A total of 22 differentially expressed thrombosis-associated genes were identified, and a prognostic signature comprising 14 genes was established. The signature stratified patients into high- and low-risk groups and showed prognostic performance in both the training and validation cohorts. Integrative GWAS, eQTL, and TWAS analyses identified susceptibility-associated transcriptional programs that were positively correlated with the thrombosis-associated risk score. Silencing ACTN2 and CRYAB significantly reduced GC cell migration and invasion. scRNA-seq analysis revealed relatively high CRYAB expression in neutrophils, and CellChat analysis suggested potential neutrophil-B cell interactions involving COLLAGEN-related signaling. This integrative multi-omics study identified a thrombosis-associated molecular signature linked to prognosis and germline susceptibility-associated transcriptional programs in GC. ACTN2 and CRYAB may represent candidate genes associated with GC cell migration and invasion, while single-cell analysis suggested potential immune-related communication features.
PMID:42681916 | PMC:PMC13534880 | DOI:10.1111/cbdd.70386
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cs.AI, q-bio.NC updates on arXiv.org
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DRIVE: Modeling Skills at the Reasoning and Interaction Levels for Web Agents under Continual Learning
arXiv:2605.23939v1 Announce Type: new Abstract: Web agents require both high-level reasoning (for task decomposition) and low-level interactions (for page elements manipulation) to conduct different tasks. However, these knowledge types differ fundamentally: reasoning knowledge (e.g., booking a flight requires first searching for routes) is abstract and transferable across websites, while interaction knowledge (e.g., clicking the Search button at a specific coordinate on Site A) depends heavily
DRIVE: Modeling Skills at the Reasoning and Interaction Levels for Web Agents under Continual Learning
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cs.AI, q-bio.NC updates on arXiv.org
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SPACE: Unifying Symmetric and Asymmetric Routing Problems for Generalist Neural Solver
arXiv:2605.24484v1 Announce Type: new Abstract: Generalist neural routing solvers have shown great potential in solving diverse vehicle routing problems (VRPs) with a unified model. However, existing solvers are typically limited to symmetric settings or degrade in performance when switching to asymmetric settings due to input inconsistencies or inherent structural differences, substantially limiting their practicality in real-world scenarios that encompass both scenarios. To address this limit
SPACE: Unifying Symmetric and Asymmetric Routing Problems for Generalist Neural Solver
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cs.AI, q-bio.NC updates on arXiv.org
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NeurIPS: Neuro-anatomical Inductive Priors for Sphere-based Brain Decoding
arXiv:2605.24993v1 Announce Type: new Abstract: Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a S
NeurIPS: Neuro-anatomical Inductive Priors for Sphere-based Brain Decoding
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cs.AI, q-bio.NC updates on arXiv.org
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Agent-Centric Social Trajectory Prediction: A Free Energy Principle Perspective
arXiv:2605.25748v1 Announce Type: new Abstract: Trajectory prediction methods have demonstrated remarkable capabilities in capturing complex motion patterns. However, existing methods rely on global state assumptions, suffer from insufficient belief inference under partial observability, and lack cognitive behavioral constraints in prediction. These limitations severely compromise both deployment feasibility and physical plausibility in real-world settings. In this work, we propose FEP-Diff, an
Agent-Centric Social Trajectory Prediction: A Free Energy Principle Perspective
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cs.AI, q-bio.NC updates on arXiv.org
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CITYREP: A Unified Benchmark for Urban Representations Across Cities, Tasks, and Modalities
arXiv:2605.26036v1 Announce Type: new Abstract: Urban representation learning encodes complex urban environments into general-purpose embeddings for diverse downstream tasks and emerging urban foundation models. However, current evaluations are limited, typically focusing on one or two cities and tasks and relying on random splits that introduce spatial leakage, leading to inflated performance and weak support for cross-location generalization and fair comparison. To address this, we propose Ci
CITYREP: A Unified Benchmark for Urban Representations Across Cities, Tasks, and Modalities
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cs.AI, q-bio.NC updates on arXiv.org
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ActQuant: Sub-4-bit Action-Guided Quantization for Vision-Language-Action Models
arXiv:2605.24011v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models exhibit remarkable action generation for embodied intelligence, but their heavy compute make deployment on edge platforms impractical. Aggressive, sub-4-bit weight quantization is the natural solution, yet existing post-training quantization (PTQ) methods suffer severe performance degradation in this regime. To address this, we introduce ActQuant, an action-guided mixed-precision PTQ framework that operates in
ActQuant: Sub-4-bit Action-Guided Quantization for Vision-Language-Action Models
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cs.AI, q-bio.NC updates on arXiv.org
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Rethinking Federated Unlearning via the Lens of Memorization
arXiv:2605.24545v1 Announce Type: cross Abstract: Federated learning (FL) increasingly needs machine unlearning to comply with privacy regulations. However, existing federated unlearning approaches may overlook the overlapping information between the unlearning and remaining data, leading to ineffective unlearning and unfairness between clients. In this work, we revisit federated unlearning through the lens of memorization. We argue that unlearning should mainly remove the unique memorized info
Rethinking Federated Unlearning via the Lens of Memorization
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cs.AI, q-bio.NC updates on arXiv.org
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VaaWIT: Visual-Aware Adaptation of Large Language Models for Multilingual Web Image Translation
arXiv:2605.24675v1 Announce Type: cross Abstract: Translating text embedded in Web images is crucial for improving content accessibility and cross-lingual information retrieval, particularly within social media and e-commerce domains. Although Large Vision-Language Models (LVLMs) have advanced multimodal understanding, applying them to Web image translation remains challenging due to the visual representation gap: standard encoders often prioritize high-level semantics over the fine-grained vis
VaaWIT: Visual-Aware Adaptation of Large Language Models for Multilingual Web Image Translation
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cs.AI, q-bio.NC updates on arXiv.org
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RealBench: Benchmarking Data-Driven Numerical Weather Forecasting Under Operational Conditions and Extreme Event Challenges
arXiv:2605.24945v1 Announce Type: cross Abstract: Accurate evaluation of weather forecasting models is critical for their reliable deployment in real-world applications. However, existing benchmarks predominantly rely on reanalysis products such as ERA5, which are generated through delayed data assimilation and do not reflect the constraints of real-time operational forecasting, thereby resulting in a systematic mismatch between benchmark performance and real-world forecasting. In this work, we
RealBench: Benchmarking Data-Driven Numerical Weather Forecasting Under Operational Conditions and Extreme Event Challenges
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cs.AI, q-bio.NC updates on arXiv.org
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DeGRe: Dense-supervised Generative Reranking for Recommendation
arXiv:2605.25749v1 Announce Type: cross Abstract: In multi-stage recommender systems, reranking optimizes overall utility by capturing intra-list contextual dependencies, yet its central challenge lies in exploring optimal sequences within an exponentially large permutation space. Recent studies have shifted towards end-to-end generative frameworks, which typically leverage list-wise rewards or preference alignment to guide generator training. However, these methods still face two critical issu
DeGRe: Dense-supervised Generative Reranking for Recommendation
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cs.AI, q-bio.NC updates on arXiv.org
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Agent Learning via Early Experience
arXiv:2510.08558v3 Announce Type: replace Abstract: A long-term goal of language agents is to learn and improve through their own experience, ultimately outperforming humans in complex, real-world tasks. However, training agents from experience data with reinforcement learning remains difficult in many environments, which either lack verifiable rewards (e.g., websites) or require inefficient long-horizon rollouts (e.g., multi-turn tool use). As a result, most current agents rely on supervised f
Agent Learning via Early Experience
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cs.AI, q-bio.NC updates on arXiv.org
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PathMem: Toward Cognition-Aligned Memory Transformation for Pathology MLLMs
arXiv:2603.09943v2 Announce Type: replace Abstract: Computational pathology demands both visual pattern recognition and dynamic integration of structured domain knowledge, including taxonomy, grading criteria, and clinical evidence. In practice, diagnostic reasoning requires linking morphological evidence with formal diagnostic and grading criteria. Although multimodal large language models (MLLMs) demonstrate strong vision language reasoning capabilities, they lack explicit mechanisms for stru
PathMem: Toward Cognition-Aligned Memory Transformation for Pathology MLLMs
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cs.AI, q-bio.NC updates on arXiv.org
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UniToolCall: Unifying Tool-Use Representation, Data, and Evaluation for LLM Agents
arXiv:2604.11557v2 Announce Type: replace Abstract: Tool-use capability is a fundamental component of LLM agents, enabling them to interact with external systems through structured function calls. However, existing research exhibits inconsistent interaction representations, largely overlooks the structural distribution of tool-use trajectories, and relies on incompatible evaluation benchmarks. We present UniToolCall, a unified framework for tool learning that standardizes the entire pipeline fr