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cs.AI, q-bio.NC updates on arXiv.org
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CyberGym: Evaluating AI Agents' Real-World Cybersecurity Capabilities at Scale
arXiv:2506.02548v3 Announce Type: replace-cross Abstract: AI agents have significant potential to reshape cybersecurity, making a thorough assessment of their capabilities critical. However, existing evaluations fall short, because they are based on small-scale benchmarks and only measure static outcomes, failing to capture the full, dynamic range of real-world security challenges. To address these limitations, we introduce CyberGym, a large-scale benchmark featuring 1,507 real-world vulnerabil
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cs.AI, q-bio.NC updates on arXiv.org
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From Noisy Labels to Intrinsic Structure: A Geometric-Structural Dual-Guided Framework for Noise-Robust Medical Image Segmentation
arXiv:2509.02419v2 Announce Type: replace-cross Abstract: The effectiveness of convolutional neural networks in medical image segmentation relies on large-scale, high-quality annotations, which are costly and time-consuming to obtain. Even expert-labeled datasets inevitably contain noise arising from subjectivity and coarse delineations, which disrupt feature learning and adversely impact model performance. To address these challenges, this study propose a Geometric-Structural Dual-Guided Netwo
From Noisy Labels to Intrinsic Structure: A Geometric-Structural Dual-Guided Framework for Noise-Robust Medical Image Segmentation
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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NUP85 as a Pan-Cancer Immune Biomarker: Integrated Multi Omics and Functional Analyses Reveal Its Role in Tumor Prognosis
Immunotargets Ther. 2026 Mar 17;15:541852. doi: 10.2147/ITT.S541852. eCollection 2026.ABSTRACTPURPOSE: NUP85 encodes protein components of the Nup107-160 subunit of the nuclear pore complex, belonging to the Nucleoporins (NUPs) family, potentially implicating its role in human cancer. This study aims to elucidate the potential involvement of NUP85 in cancer pathogenesis.METHODS: Leveraging data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analy
NUP85 as a Pan-Cancer Immune Biomarker: Integrated Multi Omics and Functional Analyses Reveal Its Role in Tumor Prognosis
Immunotargets Ther. 2026 Mar 17;15:541852. doi: 10.2147/ITT.S541852. eCollection 2026.
ABSTRACT
PURPOSE: NUP85 encodes protein components of the Nup107-160 subunit of the nuclear pore complex, belonging to the Nucleoporins (NUPs) family, potentially implicating its role in human cancer. This study aims to elucidate the potential involvement of NUP85 in cancer pathogenesis.
METHODS: Leveraging data from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Cancer Cell Line Encyclopedia (CCLE), Human Protein Atlas (HPA), Gene Expression Profiling Interactive Analysis (GEPIA), CellMiner, and GeneMANIA databases, we investigated the role of NUP85 across various tumors. Correlations between NUP85 expression and pathological stage, histological grade, survival, immune infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), drug resistance, DNA methylation, copy number variation (CNV), and single-cell expression were analyzed. Gene functional enrichment analysis was conducted to explore NUP85-associated pathways. Molecular biology experiments including Western blotting, flow cytometry, trans-well migration, and invasion assays were performed to validate NUP85's oncogenic role in lung adenocarcinoma (LUAD) and oral squamous cell carcinoma (OSCC) cell lines.
RESULTS: Our findings reveal up-regulated expression of NUP85 in most tumor tissues, with significant correlations observed with pathological stage, survival, immune infiltration, TMB, MSI, drug resistance, DNA methylation, and CNV. Molecular biology experiments confirm NUP85's tumor-promoting role in LUAD and OSCC cell lines. Single-cell sequencing data suggest elevated NUP85 expression primarily in proliferative T cells (Tprolif).
CONCLUSION: NUP85 emerges as a potential tumor marker associated with tumor immunity and poor prognosis. These insights offer avenues for the development of novel therapeutic targets and anti-neoplastic drugs.
PMID:41869435 | PMC:PMC13005628 | DOI:10.2147/ITT.S541852
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Omics in Hepatocellular
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Hypoxia-related and immune phenotype-related fusion model for non-invasive prognostication of hepatocellular carcinoma treated by TACE: a multicentre study
Gut. 2026 Mar 30:gutjnl-2025-337938. doi: 10.1136/gutjnl-2025-337938. Online ahead of print.ABSTRACTBACKGROUND: Survival outcomes after transarterial chemoembolisation (TACE) vary in hepatocellular carcinoma (HCC) patients, and existing prognostic scores and imaging models often lack generalisability and biological interpretability.OBJECTIVE: To develop and validate a multimodal prognostication model for HCC that allows for a precise assessment of survival outcomes of HCC patients receiving TACE
Hypoxia-related and immune phenotype-related fusion model for non-invasive prognostication of hepatocellular carcinoma treated by TACE: a multicentre study
Gut. 2026 Mar 30:gutjnl-2025-337938. doi: 10.1136/gutjnl-2025-337938. Online ahead of print.
ABSTRACT
BACKGROUND: Survival outcomes after transarterial chemoembolisation (TACE) vary in hepatocellular carcinoma (HCC) patients, and existing prognostic scores and imaging models often lack generalisability and biological interpretability.
OBJECTIVE: To develop and validate a multimodal prognostication model for HCC that allows for a precise assessment of survival outcomes of HCC patients receiving TACE therapy.
DESIGN: This study enrolled 1448 HCC patients, including a TACE cohort (n=1349), a biomarker subset from a randomised trial (n=41), a single-cell RNA sequencing cohort and The Cancer Genome Atlas (TCGA) HCC cohort (n=50). Pre-treatment contrast-enhanced CT images were used to construct deep learning and conventional radiomic models. The early-fusion and late-fusion models (LFMs) were compared, and a clinical-radiologic model (CRM) was formed by integrating the better-performing LFM with clinical variables. Using TCGA data and single-cell transcriptomic profiles, the differences between high-score and low-score groups in tumour immune microenvironment, cellular functional states and key signalling pathways were investigated.
RESULTS: The CRM effectively stratified patients' survival across multiple independent cohorts and achieved more granular risk stratification than the existing clinical models. Multi-omic analyses revealed that in the LFM high-score group, myelocytomatosis oncogene was activated, epithelial-mesenchymal transition enhanced, glycolysis upregulated and hypoxia pathway activated. Single-cell transcriptomic data confirmed that virtually all cell types in high-risk patients scored high in hypoxia, and cytotoxic T cells had a reduced cytotoxic activity.
CONCLUSION: The CRM model can non-invasively predict the prognosis of HCC patients treated by TACE therapy.
PMID:41856522 | DOI:10.1136/gutjnl-2025-337938
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Cell
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β-hydroxybutyrate enhances the metabolic fitness of CAR T cells in cancer
β-hydroxybutyrate (BHB), the ketone body associated with a ketogenic diet, metabolically reprograms and fuels CAR T cells to achieve proliferation, cytokine production, and superior tumor control. These findings suggest that BHB supplementation may be a practical way to boost adoptive cancer immunotherapy.