Normal view
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Molecular Therapy
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Targeting the MNK1-MYH9 axis blocks YAP1 recruitment to prevent thrombosis and platelet activation-induced NETosis
MNK1 acts as a structural shield on MYH9, preventing YAP1-mediated platelet activation. Developing MD2 to lock this MNK1-MYH9 complex introduces a safe antithrombotic strategy, shifting the therapeutic paradigm from kinase inhibition to stabilizing protein-protein interactions against immunothrombosis.
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Molecular Therapy
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Synchronized latency reversal and immune clearance by a multifunctional fusion protein enables HIV-1 reservoir reduction
Latent HIV reservoirs evade both antiviral therapy and immune surveillance. Luo and colleagues develop a multifunctional fusion protein that couples reservoir reactivation with targeted immune engagement and clearance, offering a coordinated strategy to expose and eliminate persistent HIV-infected cells.
Synchronized latency reversal and immune clearance by a multifunctional fusion protein enables HIV-1 reservoir reduction
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Nature Biomedical Engineering
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Engineering inflammation-responsive proteins through nitric oxide-caged amino acids
Nature Biomedical Engineering, Published online: 31 August 2026; doi:10.1038/s41551-026-01782-9A protein engineering strategy enables nitric oxide-triggered reactivation of proteins using genetically encoded caged amino acids, allowing inflammation-localized control of protein activity, viral gene delivery and biosensing in vivo.
Engineering inflammation-responsive proteins through nitric oxide-caged amino acids
Nature Biomedical Engineering, Published online: 31 August 2026; doi:10.1038/s41551-026-01782-9
A protein engineering strategy enables nitric oxide-triggered reactivation of proteins using genetically encoded caged amino acids, allowing inflammation-localized control of protein activity, viral gene delivery and biosensing in vivo.-
cs.AI, q-bio.NC updates on arXiv.org
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Structural Process Supervision for Latent Chain-of-Thought Reasoning
arXiv:2609.09928v1 Announce Type: new Abstract: Latent reasoning approaches enhance token-level efficiency and robustness by replacing verbose, explicit chain-of-thought (CoT) tokens with compact continuous-space embeddings. However, existing methods lack direct process supervision over these latent embeddings, which often leads to representation collapse and uneven information distribution. To address this, we propose Prototype-Mediated Process Supervision (PMPS), which introduces learnable re
Structural Process Supervision for Latent Chain-of-Thought Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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VANTAGE-Bench: Evaluating the Infrastructure AI Gap in Vision-Language Models
arXiv:2609.09396v1 Announce Type: cross Abstract: As Vision-Language Models (VLMs) advance toward physical deployment, the focus has remained on action-oriented Embodied AI evaluated on subject-centric consumer video. This overlooks a pervasive class of Physical AI: Infrastructure AI, which relies on fixed cameras for open-loop insights like safety monitoring and operational logging. We introduce VANTAGE-Bench, a benchmark measuring this "Infrastructure AI Gap." It spans three operational domai
VANTAGE-Bench: Evaluating the Infrastructure AI Gap in Vision-Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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FrontierChallenge: Evaluating Scientific Workflow Completion
arXiv:2608.24979v2 Announce Type: replace Abstract: Scientific agents increasingly analyze data, execute code, and produce research artifacts, yet most benchmarks emphasize final answers, isolated programs, or a single domain. We introduce FrontierChallenge, a cross-domain benchmark comprising 300 end-to-end scientific workflows. In this paper, we release and evaluate 97 of these tasks, spanning quantum chemistry, molecular dynamics, materials characterization, analytical chemistry, life scienc
FrontierChallenge: Evaluating Scientific Workflow Completion
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cs.AI, q-bio.NC updates on arXiv.org
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LightNav-0: Eliciting VLM Spatial Intelligence for Generalist Embodied Navigation
arXiv:2608.30935v2 Announce Type: replace-cross Abstract: Embodied navigation requires agents to translate heterogeneous goals and visual observations into actions across tasks, environments, and robot embodiments. Modern vision-language models (VLMs) already encode spatial priors for visual grounding, spatial reasoning, and pointing, but these capabilities are rarely elicited directly for robot control. Existing navigation systems instead rely on task- or embodiment-specific components, fragme
LightNav-0: Eliciting VLM Spatial Intelligence for Generalist Embodied Navigation
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development
Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.ABSTRACTLung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datas
A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development
Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.
ABSTRACT
Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.
PMID:42189071 | DOI:10.1002/advs.75839
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension
J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.ABSTRACT(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 4
Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension
J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.
ABSTRACT
(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 40 HAPH patients and 40 healthy controls in Yunnan's high-altitude regions to characterize molecular profiles, identify biomarkers, and develop a predictive model. (3) Results: Proteomic analysis identified four proteins (A2IPH7, K1C14, PSME2, SERPINE2) commonly dysregulated in HAPH patients from two high-altitude regions. SERPINE2 was notably downregulated and showed a negative correlation with clinical severity, which was further validated in HAPH rat lung tissues and supported by UK Biobank data for idiopathic PAH. Concurrent metabolomics uncovered 11 shared metabolites, largely acyl fatty acids, enriched in pathways such as unsaturated fatty acid synthesis. Integration of these multi-omics data enabled the development of a robust predictive model. (4) Conclusion: Our study identified key protein and metabolic biomarkers involved in HAPH development, which were validated in animal models. Based on these findings, a predictive model was developed, highlighting SERPINE2 and 11 metabolites as promising targets for the prediction and prevention of HAPH.
PMID:42188081 | DOI:10.3390/jcdd13050195
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Omics In Lung
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A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development
Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.ABSTRACTLung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datas
A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development
Adv Sci (Weinh). 2026 May 26:e75839. doi: 10.1002/advs.75839. Online ahead of print.
ABSTRACT
Lung squamous cell carcinoma (LUSC) lacks clearly defined key drivers and effective targeted therapies, reflecting an incomplete understanding of its molecular pathogenesis. Here, we identify SMAD4 as a critical regulator of three-dimensional (3D) genome organization in LUSC and uncover a mechanistic link between tumor suppressor loss and oncogenic transcriptional activation. By integrating clinical datasets, genetically engineered mouse models, human and murine LUSC cell lines, and multi-omics analyses, we demonstrate that SMAD4 deficiency promotes LUSC progression by unleashing EP300-mediated enhancer-promoter looping at the SOX2 locus. Mechanistically, SMAD4 does not directly bind SOX2 regulatory elements but instead constrains chromatin looping by sequestering EP300 away from loop anchor regions. Loss of SMAD4 leads to enhanced H3K27ac deposition, aberrant SOX2 activation, and increased LUSC tumor cell proliferation. Together, these findings reveal a non-canonical role for a transcription factor (e.g., SMAD4) in regulating dysregulated 3D genome architecture to inhibit tumor development.
PMID:42189071 | DOI:10.1002/advs.75839
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Omics In Lung
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Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension
J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.ABSTRACT(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 4
Multi-Omics Identification of Biomarkers for High-Altitude Pulmonary Hypertension
J Cardiovasc Dev Dis. 2026 Apr 30;13(5):195. doi: 10.3390/jcdd13050195.
ABSTRACT
(1) Aim: The incidence of high-altitude pulmonary hypertension (HAPH) has risen in recent years and is expected to continue increasing; however, its diagnosis remains challenging. In this study, we employed proteomics and metabolomics to identify the proteins and metabolic biomarkers that contribute to the development of HAPH. (2) Methods: We applied integrated proteomics and metabolomics to match blood samples from 40 HAPH patients and 40 healthy controls in Yunnan's high-altitude regions to characterize molecular profiles, identify biomarkers, and develop a predictive model. (3) Results: Proteomic analysis identified four proteins (A2IPH7, K1C14, PSME2, SERPINE2) commonly dysregulated in HAPH patients from two high-altitude regions. SERPINE2 was notably downregulated and showed a negative correlation with clinical severity, which was further validated in HAPH rat lung tissues and supported by UK Biobank data for idiopathic PAH. Concurrent metabolomics uncovered 11 shared metabolites, largely acyl fatty acids, enriched in pathways such as unsaturated fatty acid synthesis. Integration of these multi-omics data enabled the development of a robust predictive model. (4) Conclusion: Our study identified key protein and metabolic biomarkers involved in HAPH development, which were validated in animal models. Based on these findings, a predictive model was developed, highlighting SERPINE2 and 11 metabolites as promising targets for the prediction and prevention of HAPH.
PMID:42188081 | DOI:10.3390/jcdd13050195
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cs.AI, q-bio.NC updates on arXiv.org
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Summoning the Oracle to Slay It: Mitigating Look-Ahead Bias in Financial Backtesting with Large Language Models
arXiv:2605.24564v1 Announce Type: new Abstract: Backtesting large language models (LLMs) on historical financial data is unreliable because pre-training cuts off after the events happened. An LLM trained in 2024 already "knows" which way 2018-2020 stocks moved. We name this failure parametric look-ahead bias and propose FinCAD, an inference-time adaptation of Context-Aware Decoding that suppresses an LLM's memory of historical outcomes without retraining. FinCAD pairs an adversarial bias-discov
Summoning the Oracle to Slay It: Mitigating Look-Ahead Bias in Financial Backtesting with Large Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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LipoAgent: Coordinating Fine-Tuned LLM Agents for Safer Lipid Design
arXiv:2605.25250v1 Announce Type: new Abstract: Lipid nanoparticles (LNPs) are among the most clinically mature platforms for nucleic acid delivery, yet designing lipids that are both effective and biologically safe remains a major bottleneck. In practical screening, toxicity is a decision-level constraint: if a lipid is toxic, its efficiency prediction is clinically irrelevant. We propose LipoAgent, a safety-aware multi-agent LLM framework for lipid discovery. LipoAgent combines domain-specifi
LipoAgent: Coordinating Fine-Tuned LLM Agents for Safer Lipid Design
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cs.AI, q-bio.NC updates on arXiv.org
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IPR-1: Interactive Physical Reasoner
arXiv:2511.15407v4 Announce Type: replace Abstract: Humans learn by observing, interacting with environments, and internalizing physics and causality. Here, we aim to ask whether an agent can similarly acquire human-like reasoning from interaction and keep improving with more experience. To study this, we introduce a Game-to-Unseen (G2U) benchmark of 1,000+ heterogeneous games that exhibit significant visual domain gaps. Existing approaches, including VLMs and world models, struggle to capture
IPR-1: Interactive Physical Reasoner
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cs.AI, q-bio.NC updates on arXiv.org
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Prism: Spectral-Aware Block-Sparse Attention
arXiv:2602.08426v2 Announce Type: replace-cross Abstract: Block-sparse attention is promising for accelerating long-context LLM pre-filling, yet identifying relevant blocks efficiently remains a bottleneck. Existing methods typically employ coarse-grained attention as a proxy for block importance estimation, but often resort to expensive token-level searching or scoring, resulting in significant selection overhead. In this work, we trace the inaccuracy of standard coarse-grained attention via m
Prism: Spectral-Aware Block-Sparse Attention
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Nature - Issue - nature.com science feeds
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Synthetic super-enhancers enable precision viral immunotherapy
Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10329-6Synthetic super-enhancers enable specific delivery of anticancer payloads, achieving tumour elimination after a single dose in a mouse model of aggressive glioblastoma.
Synthetic super-enhancers enable precision viral immunotherapy
Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10329-6
Synthetic super-enhancers enable specific delivery of anticancer payloads, achieving tumour elimination after a single dose in a mouse model of aggressive glioblastoma.-
cs.AI, q-bio.NC updates on arXiv.org
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TABQAWORLD: Optimizing Multimodal Reasoning for Multi-Turn Table Question Answering
arXiv:2604.03393v1 Announce Type: new Abstract: Multimodal reasoning has emerged as a powerful framework for enhancing reasoning capabilities of reasoning models. While multi-turn table reasoning methods have improved reasoning accuracy through tool use and reward modeling, they rely on fixed text serialization for table state readouts. This introduces representation errors in table encoding that significantly accumulate over multiple turns. Such accumulation is alleviated by tabular grounding
TABQAWORLD: Optimizing Multimodal Reasoning for Multi-Turn Table Question Answering
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cs.AI, q-bio.NC updates on arXiv.org
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FeynmanBench: Benchmarking Multimodal LLMs on Diagrammatic Physics Reasoning
arXiv:2604.03893v1 Announce Type: new Abstract: Breakthroughs in frontier theory often depend on the combination of concrete diagrammatic notations with rigorous logic. While multimodal large language models (MLLMs) show promise in general scientific tasks, current benchmarks often focus on local information extraction rather than the global structural logic inherent in formal scientific notations. In this work, we introduce FeynmanBench, the first benchmark centered on Feynman diagram tasks. I
FeynmanBench: Benchmarking Multimodal LLMs on Diagrammatic Physics Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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RDEx-CMOP: Feasibility-Aware Indicator-Guided Differential Evolution for Fixed-Budget Constrained Multiobjective Optimization
arXiv:2604.03708v1 Announce Type: cross Abstract: Constrained multiobjective optimisation requires fast feasibility attainment together with stable convergence and diversity preservation under strict evaluation budgets. This report documents RDEx-CMOP, the differential evolution variant used in the IEEE CEC 2025 numerical optimisation competition (C06 special session) constrained multiobjective track. RDEx-CMOP integrates an {\epsilon}-level feasibility schedule, a SPEA2-style indicator-driven
RDEx-CMOP: Feasibility-Aware Indicator-Guided Differential Evolution for Fixed-Budget Constrained Multiobjective Optimization
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cs.AI, q-bio.NC updates on arXiv.org
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CREBench: Evaluating Large Language Models in Cryptographic Binary Reverse Engineering
arXiv:2604.03750v1 Announce Type: cross Abstract: Reverse engineering (RE) is central to software security, particularly for cryptographic programs that handle sensitive data and are highly prone to vulnerabilities. It supports critical tasks such as vulnerability discovery and malware analysis. Despite its importance, RE remains labor-intensive and requires substantial expertise, making large language models (LLMs) a potential solution for automating the process. However, their capabilities fo