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cs.AI, q-bio.NC updates on arXiv.org
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Digital Twin AI: Opportunities and Challenges from Large Language Models to World Models
arXiv:2601.01321v1 Announce Type: new Abstract: Digital twins, as precise digital representations of physical systems, have evolved from passive simulation tools into intelligent and autonomous entities through the integration of artificial intelligence technologies. This paper presents a unified four-stage framework that systematically characterizes AI integration across the digital twin lifecycle, spanning modeling, mirroring, intervention, and autonomous management. By synthesizing existing
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cs.AI, q-bio.NC updates on arXiv.org
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AI Deception: Risks, Dynamics, and Controls
arXiv:2511.22619v2 Announce Type: replace Abstract: As intelligence increases, so does its shadow. AI deception, in which systems induce false beliefs to secure self-beneficial outcomes, has evolved from a speculative concern to an empirically demonstrated risk across language models, AI agents, and emerging frontier systems. This project provides a comprehensive and up-to-date overview of the AI deception field, covering its core concepts, methodologies, genesis, and potential mitigations. Fir
AI Deception: Risks, Dynamics, and Controls
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cs.AI, q-bio.NC updates on arXiv.org
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Large Language Model Benchmarks in Medical Tasks
arXiv:2410.21348v3 Announce Type: replace-cross Abstract: With the increasing application of large language models (LLMs) in the medical domain, evaluating these models' performance using benchmark datasets has become crucial. This paper presents a comprehensive survey of various benchmark datasets employed in medical LLM tasks. These datasets span multiple modalities including text, image, and multimodal benchmarks, focusing on different aspects of medical knowledge such as electronic health r
Large Language Model Benchmarks in Medical Tasks
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Nanomaterial-assisted immunodiagnostic profiling and therapeutic targeting of hepatocellular carcinoma: from molecular biomarkers to clinical applications
Front Immunol. 2025 Oct 14;16:1668630. doi: 10.3389/fimmu.2025.1668630. eCollection 2025.ABSTRACTAIMS AND OBJECTIVES: This study aimed to identify immunologically relevant transcriptomic and proteomic biomarkers in hepatocellular carcinoma (HCC) and to characterize their B-cell epitopes for potential integration into nanomaterial-based biosensors and immunomodulatory platforms for early diagnosis and targeted therapy.METHODS: We conducted a comprehensive multi-omics analysis by integrating trans
Nanomaterial-assisted immunodiagnostic profiling and therapeutic targeting of hepatocellular carcinoma: from molecular biomarkers to clinical applications
Front Immunol. 2025 Oct 14;16:1668630. doi: 10.3389/fimmu.2025.1668630. eCollection 2025.
ABSTRACT
AIMS AND OBJECTIVES: This study aimed to identify immunologically relevant transcriptomic and proteomic biomarkers in hepatocellular carcinoma (HCC) and to characterize their B-cell epitopes for potential integration into nanomaterial-based biosensors and immunomodulatory platforms for early diagnosis and targeted therapy.
METHODS: We conducted a comprehensive multi-omics analysis by integrating transcriptomic (TCGA-LIHC) and proteomic data to identify differentially expressed genes (DEGs) in HCC. Protein-protein interaction networks and pathway enrichment were used to prioritize hub genes. Five candidate biomarkers, RFC2, HSP90AB1, YWHAZ, CYP2E1, and ADH4, were selected for qRT-PCR and serum ELISA validation in clinical cohorts comprising 85 HCC patients and 50 healthy controls. B-cell epitope prediction was performed using BepiPred 2.0 and validated through synthetic peptide-based ELISA in the same cohort to assess immunoreactivity. Diagnostic performance was evaluated using ROC curve analysis.
RESULTS: RFC2, HSP90AB1, and YWHAZ were significantly upregulated (|log2FC|>0.2) and showed high serological expression, whereas CYP2E1 and ADH4 were consistently downregulated. Predicted B-cell epitopes from RFC2, HSP90AB1, and YWHAZ exhibited strong immunoreactivity (AUC>0.84), indicating their diagnostic potential. Enrichment analysis revealed that upregulated DEGs were involved in cell cycle and mitotic progression, while downregulated genes were linked to immune suppression and metabolic dysfunction. These validated immunogenic epitopes offer promising anchors for nanomaterial-functionalized biosensors, such as gold nanoparticle-conjugated ELISA, graphene-based electrochemical platforms, and peptide-coated quantum dots, for ultrasensitive and multiplexed HCC detection.
CONCLUSION: By integrating transcriptomic and proteomic screening with epitope-level validation, we identified a novel panel of immunogenic biomarkers suitable for nanomaterial-enabled diagnostics in HCC. These findings support the translational potential of peptide-nano scaffold conjugates in developing minimally invasive, immune-responsive biosensing and therapeutic tools tailored for early-stage liver cancer management.
PMID:41164201 | PMC:PMC12558944 | DOI:10.3389/fimmu.2025.1668630
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Journal of Medical Internet Research
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Using Large Language Models to Assess the Consistency of Randomized Controlled Trials on AI Interventions With CONSORT-AI: Cross-Sectional Survey
Background: Chatbots based on large language models (LLMs) have shown promise in evaluating the consistency of research. Previously, researchers used LLM to assess if randomized controlled trial (RCT) abstracts adhered to the CONSORT-Abstract guidelines. However, the consistency of artificial intelligence (AI) interventional RCTs align with the CONSORT-AI standards by LLMs remains unclear. Objective: The aim of this study is to identify the consistency of randomized controlled trials on AI inter
Using Large Language Models to Assess the Consistency of Randomized Controlled Trials on AI Interventions With CONSORT-AI: Cross-Sectional Survey
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Nature - Issue - nature.com science feeds
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A fully open AI foundation model applied to chest radiography
Nature, Published online: 11 June 2025; doi:10.1038/s41586-025-09079-8Ark+, a fully open artificial intelligence foundation model, demonstrates exceptional capabilities in diagnosing common, rare and novel thoracic diseases.
A fully open AI foundation model applied to chest radiography
Nature, Published online: 11 June 2025; doi:10.1038/s41586-025-09079-8
Ark+, a fully open artificial intelligence foundation model, demonstrates exceptional capabilities in diagnosing common, rare and novel thoracic diseases.-
Omics In Lung
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RMethyMD: An integrated platform for exploring RNA methylation in pan-cancer via a multiomics analysis
Cancer Lett. 2025 Jan 12;612:217462. doi: 10.1016/j.canlet.2025.217462. Online ahead of print.ABSTRACTA user-friendly integrated database, RMethyMD (http://www.tmliang.cn/rnamethy), was developed to provide a comprehensive analysis of methylation regulators aimed at facilitating the exploration of molecular features in tumorigenesis and clinical implications in cancer diagnosis and treatment via a multiomics approach. Subsequently, molecular landscapes and a robust constructed m6A-based prognost
RMethyMD: An integrated platform for exploring RNA methylation in pan-cancer via a multiomics analysis
Cancer Lett. 2025 Jan 12;612:217462. doi: 10.1016/j.canlet.2025.217462. Online ahead of print.
ABSTRACT
A user-friendly integrated database, RMethyMD (http://www.tmliang.cn/rnamethy), was developed to provide a comprehensive analysis of methylation regulators aimed at facilitating the exploration of molecular features in tumorigenesis and clinical implications in cancer diagnosis and treatment via a multiomics approach. Subsequently, molecular landscapes and a robust constructed m6A-based prognostic model using coxBoost + RSF algorithms in lung cancer highlighted m6A as a suitable marker to guide therapeutic strategy. RMethyMD provides a comprehensive resource and multiomics analysis to explore m6A-based prognostic and clinical values, thereby contributing to aiding personalized cancer therapy.
PMID:39809358 | DOI:10.1016/j.canlet.2025.217462
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Nature - Issue - nature.com science feeds
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Author Correction: π-HuB: the proteomic navigator of the human body
Nature, Published online: 23 December 2024; doi:10.1038/s41586-024-08555-xAuthor Correction: π-HuB: the proteomic navigator of the human body
Author Correction: π-HuB: the proteomic navigator of the human body
Nature, Published online: 23 December 2024; doi:10.1038/s41586-024-08555-x
Author Correction: π-HuB: the proteomic navigator of the human body-
Cell Death Discovery nature.com science feeds
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KDM5B promotes SMAD4 loss-driven drug resistance through activating DLG1/YAP to induce lipid accumulation in pancreatic ductal adenocarcinoma
Cell Death Discovery, Published online: 24 May 2024; doi:10.1038/s41420-024-02020-4KDM5B promotes SMAD4 loss-driven drug resistance through activating DLG1/YAP to induce lipid accumulation in pancreatic ductal adenocarcinoma
KDM5B promotes SMAD4 loss-driven drug resistance through activating DLG1/YAP to induce lipid accumulation in pancreatic ductal adenocarcinoma
Cell Death Discovery, Published online: 24 May 2024; doi:10.1038/s41420-024-02020-4
KDM5B promotes SMAD4 loss-driven drug resistance through activating DLG1/YAP to induce lipid accumulation in pancreatic ductal adenocarcinoma-
Nature - Issue - nature.com science feeds
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Genome-wide characterization of circulating metabolic biomarkers
Nature, Published online: 06 March 2024; doi:10.1038/s41586-024-07148-yA meta-analysis of genome-wide association studies for 233 circulating metabolites from 33 cohorts reveals more than 400 loci and suggests probable causal genes, providing insights into metabolic pathways and disease aetiology.
Genome-wide characterization of circulating metabolic biomarkers
Nature, Published online: 06 March 2024; doi:10.1038/s41586-024-07148-y
A meta-analysis of genome-wide association studies for 233 circulating metabolites from 33 cohorts reveals more than 400 loci and suggests probable causal genes, providing insights into metabolic pathways and disease aetiology.-
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.-
Cell Death Discovery nature.com science feeds
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The trigger for pancreatic disease: NLRP3 inflammasome
Cell Death Discovery, Published online: 14 July 2023; doi:10.1038/s41420-023-01550-7The trigger for pancreatic disease: NLRP3 inflammasome
The trigger for pancreatic disease: NLRP3 inflammasome
Cell Death Discovery, Published online: 14 July 2023; doi:10.1038/s41420-023-01550-7
The trigger for pancreatic disease: NLRP3 inflammasome-
Oncogenesis - nature.com science feeds
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ZNF655 accelerates progression of pancreatic cancer by promoting the binding of E2F1 and CDK1
Oncogenesis, Published online: 04 August 2022; doi:10.1038/s41389-022-00418-2ZNF655 accelerates progression of pancreatic cancer by promoting the binding of E2F1 and CDK1
ZNF655 accelerates progression of pancreatic cancer by promoting the binding of E2F1 and CDK1
Oncogenesis, Published online: 04 August 2022; doi:10.1038/s41389-022-00418-2
ZNF655 accelerates progression of pancreatic cancer by promoting the binding of E2F1 and CDK1