Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Tasks over Application Manuals: Revealing Gaps in Long-Horizon Procedural Reasoning for Language Models
arXiv:2609.13005v1 Announce Type: cross Abstract: Large language models (LLMs) have achieved strong performance on a wide range of natural language tasks, and recent benchmarks suggest that they are increasingly adept at multi-hop reasoning. However, these benchmarks are typically short-horizon, requiring only a small number of retrieval or inference steps, and provide limited evidence of reliability on real-world tasks that involve following manuals spanning hundreds of pages with complex, int
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Omics in Gastric
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CDO1 as a prognostic biomarker and therapeutic target in gastric cancer: Mechanistic insights into the PI3K/AKT-THBS1 axis and epigenetic reactivation by decitabine
Clin Transl Med. 2026 Sep;16(9):e70784. doi: 10.1002/ctm2.70784.ABSTRACTBACKGROUND: As a pivotal metabolic enzyme, cysteine dioxygenase type 1 (CDO1) exerts tumour-suppressive effects across diverse tumour types, and its expression is strongly correlated with clinical prognosis. However, the molecular mechanisms underlying CDO1-mediated tumour suppression in gastric cancer (GC), its relationship with the tumour-associated immune microenvironment, and pharmacological strategies to restore its exp
CDO1 as a prognostic biomarker and therapeutic target in gastric cancer: Mechanistic insights into the PI3K/AKT-THBS1 axis and epigenetic reactivation by decitabine
Clin Transl Med. 2026 Sep;16(9):e70784. doi: 10.1002/ctm2.70784.
ABSTRACT
BACKGROUND: As a pivotal metabolic enzyme, cysteine dioxygenase type 1 (CDO1) exerts tumour-suppressive effects across diverse tumour types, and its expression is strongly correlated with clinical prognosis. However, the molecular mechanisms underlying CDO1-mediated tumour suppression in gastric cancer (GC), its relationship with the tumour-associated immune microenvironment, and pharmacological strategies to restore its expression remain poorly understood.
METHODS: CDO1 expression and prognosis were evaluated by multi-omics and tissue microarray analyses. Tumour microenvironment and immune infiltration were analyzed using ESTIMATE and ssGSEA. Downstream pathways and interacting proteins were identified by transcriptomics, co-immunoprecipitation, and GST pull-down. CDO1 function was assessed by proliferation, apoptosis, and migration assays in gain- and loss-of-function models. In vivo tumorigenesis and CDO1-dependent decitabine efficacy were evaluated by subcutaneous xenografts. Patient-derived organoids were used to assess decitabine sensitivity and 5-FU synergy.
RESULTS: Compared with normal controls, CDO1 expression was notably decreased in GC tissues, and its low expression was strongly linked to unfavourable prognosis, supporting its utility as a biomarker for prognosis. Elevated CDO1 levels correlated with an immune-active tumour microenvironment and reduced metastatic signatures. Mechanistically, CDO1 directly bound to PI3K p85α, disrupting p85α-p110α dimerization, thereby attenuating PI3K/AKT phosphorylation and downregulating THBS1 expression. CDO1 overexpression led to reduced proliferation, invasiveness, and EMT, accompanied by increased apoptosis. These effects were reversed by PI3K activation or THBS1 co-overexpression. Decitabine was identified as an agent that epigenetically restores CDO1 expression. Critically, CDO1 knockdown significantly attenuated the anti-tumour efficacy of decitabine in vivo, confirming that decitabine acts primarily through CDO1 reactivation. Decitabine synergized with 5-FU in both organoids and xenografts.
CONCLUSIONS: Our data identify CDO1 as both a biomarker for prognosis and a tumour suppressor in gastric cancer. They reveal a CDO1-PI3K/AKT-THBS1 signalling axis and support the epigenetic reactivation of CDO1 by decitabine as a translatable therapeutic strategy.
KEY POINTS: CDO1 is frequently downregulated in gastric cancer and serves as an independent favourable prognostic biomarker. CDO1 directly binds PI3K p85α, disrupting p85α-p110α dimerization to suppress the PI3K/AKT-THBS1 signalling axis. Decitabine epigenetically restores CDO1 expression, and its anti-tumour activity is critically CDO1-dependent in vivo. Combining decitabine with 5-FU synergistically overcomes gastric cancer growth in patient-derived organoids and subcutaneous xenograft models.
PMID:42670236 | PMC:PMC13527532 | DOI:10.1002/ctm2.70784
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Pulmonary nodule
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Protein glycosylation profiling in lung adenocarcinoma and precursor lesions: analysis of FFPE tissue sections
Anal Bioanal Chem. 2026 Jul 27. doi: 10.1007/s00216-026-06702-z. Online ahead of print.ABSTRACTProtein glycosylation is a major post-translational modification that regulates tumor initiation and progression; however, its dynamic modeling during multistep evolution of lung adenocarcinoma (LUAD) remains poorly understood, particularly in clinically archived tissues. Here, we established an integrated multi-omics workflow combining global proteomes, N-glycans, and site-specific intact N-glycopepti
Protein glycosylation profiling in lung adenocarcinoma and precursor lesions: analysis of FFPE tissue sections
Anal Bioanal Chem. 2026 Jul 27. doi: 10.1007/s00216-026-06702-z. Online ahead of print.
ABSTRACT
Protein glycosylation is a major post-translational modification that regulates tumor initiation and progression; however, its dynamic modeling during multistep evolution of lung adenocarcinoma (LUAD) remains poorly understood, particularly in clinically archived tissues. Here, we established an integrated multi-omics workflow combining global proteomes, N-glycans, and site-specific intact N-glycopeptides to comprehensively characterize glycosylation in formalin-fixed paraffin-embedded (FFPE) specimens spanning four pathological stages of LUAD progression: inflammatory nodules (IN), atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), and invasive adenocarcinoma (IAC). Using optimized protein extraction, hydrophilic interaction liquid chromatography (HILIC)-based glycopeptide enrichment, and high-resolution LC-MS/MS, we achieved large-scale identification of proteins, N-glycans, and intact glycopeptides from archival clinical samples. Integrated analyses revealed progressive remodeling of site-specific N-glycosylation during malignant transformation, characterized by increased glycan branching, fucosylation, and sialylation during the transition from premalignant lesions to invasive cancer. Sialylated glycans reached their highest abundance in the premalignant AAH stage, whereas highly branched and fucosylated complex N-glycans predominated in invasive adenocarcinoma, indicating stage-dependent glycan remodeling throughout disease progression. Functional enrichment analyses linked these glycosylation alterations to extracellular matrix organization, neutrophil degranulation, and immune-associated pathways, while representative glycoproteins, including CEACAM6 and FGB, exhibited coordinated changes in protein abundance and site-specific glycoform micro-heterogeneity across pathological stages. Collectively, this study demonstrates the feasibility of deep glycoproteomic profiling using archived FFPE tissues and provides a comprehensive molecular atlas of glycosylation remodeling during LUAD progression. These findings establish a valuable resource for elucidating disease mechanisms and identifying stage-specific glycosylation biomarkers and potential glycan-targeted therapeutic candidates for early lung adenocarcinoma.
PMID:42509285 | DOI:10.1007/s00216-026-06702-z
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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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(Multiomics OR Omics) AND (Pancreatic)
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Kaempferol functionally reprograms CD47 signaling to promote cytoprotection and attenuate oxeiptosis in severe acute pancreatitis
Phytomedicine. 2026 May 15;157:158305. doi: 10.1016/j.phymed.2026.158305. Online ahead of print.ABSTRACTBACKGROUND: Severe acute pancreatitis (SAP) lacks targeted therapies, and massive loss of functional pancreatic acinar cells (PAC) drives mortality. Kaempferol (KA) possesses well-established anti-inflammatory and cytoprotective activities and is derived from herbal medicinal plants, but its direct molecular targets and mechanism of action in SAP remain undefined.PURPOSE: To evaluate the prote
Kaempferol functionally reprograms CD47 signaling to promote cytoprotection and attenuate oxeiptosis in severe acute pancreatitis
Phytomedicine. 2026 May 15;157:158305. doi: 10.1016/j.phymed.2026.158305. Online ahead of print.
ABSTRACT
BACKGROUND: Severe acute pancreatitis (SAP) lacks targeted therapies, and massive loss of functional pancreatic acinar cells (PAC) drives mortality. Kaempferol (KA) possesses well-established anti-inflammatory and cytoprotective activities and is derived from herbal medicinal plants, but its direct molecular targets and mechanism of action in SAP remain undefined.
PURPOSE: To evaluate the protective effects of KA against SAP and to elucidate its molecular mechanism of specific action, with a focus on identifying the direct cellular target through which KA exerts its cytoprotective effects.
STUDY DESIGN: Gain‑/loss‑of‑function in vitro and PAC‑specific CD47 SAP mouse models, combined with multi‑omics screening and biophysical assays.
METHODS: CD47 manipulation (siRNA/overexpression) was performed in primary PACs and cell lines, combined with WT/CD47-/-/Mist1‑CD47‑iOE (PAC‑specific) mouse models. Network pharmacology, transcriptomics and proteomics were integrated to screen and validate KA's protective effects. Computational‑experimental approaches (molecular docking/dynamics, CETSA, SPR, co‑IP, pharmacological epistasis) characterized KA's allosteric modulation of CD47 signaling.
RESULTS: CD47 was upregulated in SAP; its knockout reduced PAC death via KEAP1/PGAM5/AIFM1-driven oxeiptosis. KA reduced PAC death across genotypes, afforded no extra benefit in CD47-KO, and was not overridden by CD47‑OE. Mechanistically, KA allosterically binds CD47 ectodomain, stabilizes the CD47‑ UBQLN1 complex, and redirects signaling from Gαi‑mediated death to Gβγ/ ERK/NRF2‑mediated survival. ERK inhibition attenuated KA's protection. KA's action was CD47‑dependent.
CONCLUSION: This study identifies anti-oxeiptosis as a novel pharmacological activity of KA in SAP. This is achieved through allosteric modulation of CD47, redirecting its signaling from death‑promoting to a protective axis via activating Gβγ/ERK/NRF2 to suppress oxeiptosis. These findings reveal the CD47‑oxeiptosis axis as a therapeutic target and position KA as a promising candidate for SAP therapy, adding a new mechanistic dimension to KA's known pharmacological profile.
PMID:42184499 | DOI:10.1016/j.phymed.2026.158305
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cs.AI, q-bio.NC updates on arXiv.org
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AEGIS: Scaling Long-Sequence Homomorphic Encrypted Transformer Inference via Hybrid Parallelism on Multi-GPU Systems
arXiv:2604.03425v1 Announce Type: cross Abstract: Fully Homomorphic Encryption (FHE) enables privacy-preserving Transformer inference, but long-sequence encrypted Transformers quickly exceed single-GPU memory capacity because encoded weights are already large and encrypted activations grow rapidly with sequence length. Multi-GPU execution therefore becomes unavoidable, yet scaling remains challenging because communication is jointly induced by application-level aggregation and encryption-level
AEGIS: Scaling Long-Sequence Homomorphic Encrypted Transformer Inference via Hybrid Parallelism on Multi-GPU Systems
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cs.AI, q-bio.NC updates on arXiv.org
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AromaGen: Interactive Generation of Rich Olfactory Experiences with Multimodal Language Models
arXiv:2604.01650v1 Announce Type: cross Abstract: Smell's deep connection with food, memory, and social experience has long motivated researchers to bring olfaction into interactive systems. Yet most olfactory interfaces remain limited to fixed scent cartridges and pre-defined generation patterns, and the scarcity of large-scale olfactory datasets has further constrained AI-based approaches. We present AromaGen, an AI-powered wearable interface capable of real-time, general-purpose aroma genera
AromaGen: Interactive Generation of Rich Olfactory Experiences with Multimodal Language Models
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cs.AI, q-bio.NC updates on arXiv.org
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DR-LoRA: Dynamic Rank LoRA for Fine-Tuning Mixture-of-Experts Models
arXiv:2601.04823v5 Announce Type: replace Abstract: Mixture-of-Experts (MoE) has become a prominent paradigm for scaling Large Language Models (LLMs). Parameter-efficient fine-tuning methods, such as LoRA, are widely adopted to adapt pretrained MoE LLMs to downstream tasks. However, existing approaches typically assign identical LoRA ranks to all expert modules, ignoring the heterogeneous specialization of pretrained experts. This uniform allocation leads to a resource mismatch: task-relevant e
DR-LoRA: Dynamic Rank LoRA for Fine-Tuning Mixture-of-Experts Models
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cs.AI, q-bio.NC updates on arXiv.org
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Scalable AI-assisted Workflow Management for Detector Design Optimization Using Distributed Computing
arXiv:2603.30014v1 Announce Type: cross Abstract: The Production and Distributed Analysis (PanDA) system, originally developed for the ATLAS experiment at the CERN Large Hadron Collider (LHC), has evolved into a robust platform for orchestrating large-scale workflows across distributed computing resources. Coupled with its intelligent Distributed Dispatch and Scheduling (iDDS) component, PanDA supports AI/ML-driven workflows through a scalable and flexible workflow engine. We present an AI-as
Scalable AI-assisted Workflow Management for Detector Design Optimization Using Distributed Computing
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cs.AI, q-bio.NC updates on arXiv.org
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QuestA: Expanding Reasoning Capacity in LLMs via Question Augmentation
arXiv:2507.13266v4 Announce Type: replace-cross Abstract: Reinforcement learning (RL) has emerged as a central paradigm for training large language models (LLMs) in reasoning tasks. Yet recent studies question RL's ability to incentivize reasoning capacity beyond the base model. This raises a key challenge: how can RL be adapted to solve harder reasoning problems more effectively? To address this challenge, we propose a simple yet effective strategy via Question Augmentation: introduce partial
QuestA: Expanding Reasoning Capacity in LLMs via Question Augmentation
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cs.AI, q-bio.NC updates on arXiv.org
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mAVE: A Watermark for Joint Audio-Visual Generation Models
arXiv:2603.07090v1 Announce Type: cross Abstract: As Joint Audio-Visual Generation Models see widespread commercial deployment, embedding watermarks has become essential for protecting vendor copyright and ensuring content provenance. However, existing techniques suffer from an architectural mismatch by treating modalities as decoupled entities, exposing a critical Binding Vulnerability. Adversaries exploit this via Swap Attacks by replacing authentic audio with malicious deepfakes while retain
mAVE: A Watermark for Joint Audio-Visual Generation Models
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cs.AI, q-bio.NC updates on arXiv.org
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Contextualized Privacy Defense for LLM Agents
arXiv:2603.02983v1 Announce Type: cross Abstract: LLM agents increasingly act on users' personal information, yet existing privacy defenses remain limited in both design and adaptability. Most prior approaches rely on static or passive defenses, such as prompting and guarding. These paradigms are insufficient for supporting contextual, proactive privacy decisions in multi-step agent execution. We propose Contextualized Defense Instructing (CDI), a new privacy defense paradigm in which an instru
Contextualized Privacy Defense for LLM Agents
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cs.AI, q-bio.NC updates on arXiv.org
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A Very Big Video Reasoning Suite
arXiv:2602.20159v1 Announce Type: cross Abstract: Rapid progress in video models has largely focused on visual quality, leaving their reasoning capabilities underexplored. Video reasoning grounds intelligence in spatiotemporally consistent visual environments that go beyond what text can naturally capture, enabling intuitive reasoning over spatiotemporal structure such as continuity, interaction, and causality. However, systematically studying video reasoning and its scaling behavior is hindere
A Very Big Video Reasoning Suite
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cs.AI, q-bio.NC updates on arXiv.org
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OmniVideoBench: Towards Audio-Visual Understanding Evaluation for Omni MLLMs
arXiv:2510.10689v2 Announce Type: replace Abstract: Recent advances in multimodal large language models (MLLMs) have demonstrated substantial potential in video understanding. However, existing benchmarks fail to comprehensively evaluate synergistic reasoning capabilities across audio and visual modalities, often neglecting either one of the modalities or integrating them in a logically inconsistent manner. To bridge this gap, we introduce OmniVideoBench, a large-scale and rigorously designed b
OmniVideoBench: Towards Audio-Visual Understanding Evaluation for Omni MLLMs
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cs.AI, q-bio.NC updates on arXiv.org
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Single Image Reflection Separation via Dual Prior Interaction Transformer
arXiv:2505.12641v3 Announce Type: replace-cross Abstract: Single image reflection separation aims to separate the transmission and reflection layers from a mixed image. Existing methods typically combine general priors from pre-trained models with task-specific priors such as text prompts and reflection detection. However, the transmission prior, as the most direct task-specific prior for the target transmission layer, has not been effectively modeled or fully utilized, limiting performance in
Single Image Reflection Separation via Dual Prior Interaction Transformer
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cs.AI, q-bio.NC updates on arXiv.org
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Kunlun: Establishing Scaling Laws for Massive-Scale Recommendation Systems through Unified Architecture Design
arXiv:2602.10016v2 Announce Type: replace-cross Abstract: Deriving predictable scaling laws that govern the relationship between model performance and computational investment is crucial for designing and allocating resources in massive-scale recommendation systems. While such laws are established for large language models, they remain challenging for recommendation systems, especially those processing both user history and context features. We identify poor scaling efficiency as the main barri