Immune-related biomarkers in liquid biopsy for cancer: emerging tools for non-invasive precision oncology

MRD

By: Lai Wen · Xinhui Wang · Jinming Liu · Xinxin Pan · Yixin Zhang · Shuang Li · Mengying Tong · Yuankuan Jiang · Hewen Guan

29 September 2026 at 18:00

Front Cell Dev Biol. 2026 Sep 14;14:1878092. doi: 10.3389/fcell.2026.1878092. eCollection 2026.

ABSTRACT

Liquid biopsy has emerged as a powerful non-invasive tool in precision oncology, providing real-time insights into tumor evolution, host immune responses, and dynamic changes in the tumor immune microenvironment. By enabling minimally invasive sampling, it can overcome several limitations of conventional tissue biopsy. This review summarizes the major biological sources and components of liquid biopsy, including circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, and circulating immune cells, and discusses their value as dynamic indicators of interactions during cancer immunotherapy. Particular attention is given to immune-related biomarkers associated with immune checkpoints, immunosuppressive mechanisms, and immune escape, including circulating immune cell populations, and inflammatory cytokine profiles. We further examine their potential applications in predicting treatment response, monitoring immune-related adverse events, assessing minimal residual disease, and detecting acquired resistance. In addition, recent technological advances that are accelerating the clinical translation of liquid biopsy are highlighted, including multi-omics integration, microfluidic platforms. These approaches have improved the sensitivity, accuracy, and multidimensional characterization of tumor- and immune-derived biomarkers. Nevertheless, biological heterogeneity, limited assay standardization, and the lack of large-scale prospective validation studies continue to restrict widespread clinical implementation. Overall, immune-related biomarkers detected through liquid biopsy offer considerable potential for the longitudinal monitoring of the tumor immune microenvironment and may improve non-invasive cancer diagnosis, therapeutic monitoring, and personalized immunotherapy in the era of precision oncology.

PMID:42807637 | PMC:PMC13617286 | DOI:10.3389/fcell.2026.1878092

Toward Robust Personalized Alignment for LLMs: Mitigating Persona Drift in Multi-Turn Dialogue

cs.AI, q-bio.NC updates on arXiv.org

By: Youyuan Zhang · Siyuan Li · Fangming Liu · Jing Li

14 September 2026 at 12:00

arXiv:2609.12373v1 Announce Type: new Abstract: Persona drift remains a central challenge for personalized language models, as user profiles evolve over long interactions rather than remain permanently fixed. Models must therefore revise persistent persona states when preferences genuinely change, while avoiding updates driven by transient, ambiguous, or unresolved observations. We propose CORE, which separates turn-local evidence from persistent persona-state revision and selectively updates grounded user preferences through uncertainty-aware belief revision. We also introduce PERSIST, a held-out post-anchor benchmark for persona-state robustness under sequential interaction stress, covering ambiguity, conflict, and controlled social influence. Across ALOE, PersonaChat, and PERSIST, CORE improves personalized alignment and robustness, with complementary gains in normalized closed-slot state fidelity. Human evaluation and mechanistic controls further support explicit update control beyond stronger generation or persistent memory alone.

Right Family, Wrong Skill: Evaluating Risk Exposure in Agent Skill Retrieval

cs.AI, q-bio.NC updates on arXiv.org

By: Jiandong Ding · Honglei Ji · Ming Liu · Tao Duan

14 September 2026 at 12:00

arXiv:2606.10388v3 Announce Type: replace-cross Abstract: Agent skill libraries are becoming routable software assets: a retrieved skill can contribute instructions, scripts, resource bindings, and execution assumptions to an agent. This makes retrieval failures more specific than broad irrelevance. A system can find the right capability family yet expose the wrong same-capability representative. We study this failure as same-capability risk-exposure retrieval. Each benchmark unit pairs a helpful skill with a query-specific risky sibling that shares the capability family but differs on an execution-controlling contract, such as the required resource, precondition, procedure, or artifact. We introduce SameCapRisk-Bench, an auditable benchmark with 1,190 skill-risk units and 1,686 evaluation query cases: 694 marked-sibling units under public library pressure and 496 hard role-flip units where the same two skills swap helpful/risky roles across paired queries. The release records admission evidence, cue/leakage checks, source hashes, family relations, and fixed candidate pools. The benchmark reports helpful ranking together with harmful sibling rate (HSR@K), the top-K exposure of the marked risky sibling. On this benchmark, public SkillRouter, SkillRet, and R3-Skill retrieve helpful skills at high Recall@3 (0.848--0.888) but also expose marked risky siblings frequently (HSR@3 0.346--0.372). A fully public score-and-cluster pipeline lowers HSR@3 to 0.128--0.182, with Recall@3 of 0.713--0.776. Under a benchmark-trained reference scorer, public text-cluster and controlled resolvers reach HSR@3 0.012 and 0.007; the latter attains Recall@3 0.833. Skill retrieval should therefore report both capability matching and same-family risk exposure, with HSR serving as a targeted exposure certificate for fixed skill libraries.

JarvisGUI: Towards Cross-Device GUI Agents with Dynamic Task Composition

cs.AI, q-bio.NC updates on arXiv.org

By: Zixiang Chen · Yuheng Lu · Zihao Cheng · Zeming Liu · Jizeng Bai · Ziye Huang · Zhiyin Lin · Zihan Li · Yuhang Guo · Yunhong Wang · Haifeng Wang

10 September 2026 at 12:00

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' readiness for real-world usage. We introduce JarvisGUI, a dynamic benchmark that evaluates GUI agents on cross-device workflows requiring coordinated interaction across heterogeneous platforms, including Android, Windows, and Ubuntu. Specifically, JarvisGUI formulates GUI tasks as input-output transformations under a lightweight type system, which allows us to automatically compose multi-step, cross-device workflows and dynamically evaluate agent performance within a unified framework. By evaluating agents in virtual environments spanning multiple operating systems, JarvisGUI reveals that state-of-the-art open-source GUI agents struggle with the state-transfer awareness, cross-platform contextual reasoning, and long-horizon dependency management required for real-world workflows, exposing a critical capability gap invisible to existing benchmarks.

MOSAIC: A Universal Agent-Level Interface for Cross-Paradigm Agent Mixing and Human-AI Collaboration

cs.AI, q-bio.NC updates on arXiv.org

By: Abdulhamid M. Mousa · Rakhmonberdi Khajiev · Jalaledin M. Azzabi · Abdulkarim M. Mousa · Peng Yong · Yunusa Haruna · Ming Liu

10 September 2026 at 12:00

arXiv:2603.01260v2 Announce Type: replace-cross Abstract: Existing infrastructure cannot deploy agents from different decision-making paradigms within the same environment, making fair cross-paradigm comparison under identical conditions impossible. We present MOSAIC, an open-source platform that enables heterogeneous agents (RL policies, LLMs, VLMs, and human operators) to act within shared reinforcement learning environments in ad-hoc team settings with reproducible results. MOSAIC introduces three contributions. (i) IPC-based worker protocol that wraps native and third-party frameworks as isolated subprocess workers, each executing its own training and inference logic unmodified and communicating through a versioned inter-process protocol. (ii) An operator abstraction that forms an agent-level interface by mapping workers to agent slots: each operator, regardless of whether it is backed by an RL policy, an LLM, or a human, conforms to a minimal universal interface. (iii) A deterministic cross-paradigm evaluation framework with two complementary modes: a manual mode that advances up to $N$ operators in lock-step under shared seeds for fine-grained visual inspection of behavioural differences; and a script mode that drives automated, long-running evaluation via declarative Python scripts for reproducible experiments. Our documentation is released at: https://mosaic-platform.readthedocs.io.

Parameter Efficient Multi-Class Intelligent Scheduling for Multimodal Online Distributed Industrial Anomaly Detection

cs.AI, q-bio.NC updates on arXiv.org

By: Heqiang Wang · Weihong Yang · Zheyuan Yang · Jia Zhou · Xiaoxiong Zhong · Fangming Liu · Weizhe Zhang

26 May 2026 at 12:00

arXiv:2605.23984v1 Announce Type: cross Abstract: Industrial anomaly detection has attracted significant attention as a fundamental challenge in industrial systems. The rapid advancement of heterogeneous industrial sensors has driven industrial anomaly detection from unimodal to multimodal paradigms. However, existing methods are primarily designed for centralized and offline settings, overlooking the distributed and continuously generated data characteristic of real-world industrial environments. With the advancement of edge intelligence, modern edge devices are increasingly capable of not only data acquisition but also distributed model training, enabling collaborative intelligence across the system. Industrial anomaly detection represents a critical application in this context. Motivated by these challenges, we propose a novel framework termed Multimodal Online Distributed Industrial Anomaly Detection (MODIAD). We first present a comprehensive workflow for MODIAD and then formulate a Multi-class Intelligent Scheduling (MIS) problem to coordinate cross class model updates by balancing data sufficiency and class update frequency. To efficiently solve this problem, we design a Sequential Marginal Gain Greedy (SMG) algorithm that enables effective multi-class training under resource constraints. Furthermore, to improve the computational and communication efficiency during training, we propose an Resource Efficient Class-Wise Low Rank Adaptation (REC-LoRA) strategy, which significantly reduces system overhead while preserving detection performance. Extensive experiments on two representative multimodal industrial anomaly detection datasets, MVTec 3D-AD and Eyecandies demonstrate that the proposed approach achieves superior performance and efficiency under the MODIAD scenario.

A World Model of Radiologist Reading for Medical Image Representation Learning

cs.AI, q-bio.NC updates on arXiv.org

By: Yiwei Li · Zihao Wu · Huaqin Zhao · Yifan Zhou · Chao Cao · Dajiang Zhu · Tianming Liu · Lin Zhao

26 May 2026 at 12:00

arXiv:2605.23992v1 Announce Type: cross Abstract: Radiologist eye-tracking data provide a rich record of how experts search, compare, and accumulate evidence during image reading; yet, existing methods exploit this signal only partially, either as a static spatial prior or as an auxiliary prediction target decoupled from diagnosis. We propose GazeWorld, a medical imaging world model that treats the image as the world and the radiologist's fixation sequence as a trajectory through it. GazeWorld autoregressively predicts the latent representation of the next fixated patch from all previously visited ones, while a spatial-completion branch covers unvisited regions. At inference, GazeWorld generates a sequence of patch representations from the image alone without requiring real gaze data. Frozen GazeWorld features achieve state-of-the-art diagnostic accuracy across all nine supervised settings on CheXpert, RSNA Pneumonia, and SIIM-ACR Pneumothorax, as well as the highest zero-shot accuracy on all three benchmarks. On the GazeSearch benchmark, a generic decoder trained on the same frozen features outperforms the purpose-built LogitGaze-Med by over 16\% in ScanMatch and 22\% in SED, despite not being explicitly trained to predict gaze. GazeWorld demonstrates that modeling how experts read, not just what they conclude, offers a promising pretraining paradigm for medical imaging AI.

Correcting Visual Blur Induced by Attention Distraction to Reduce Hallucinations: Algorithm and Theory

cs.AI, q-bio.NC updates on arXiv.org

By: Quanjiang Li · Zhiming Liu · Wei Luo · Tingjin Luo · Chenping Hou

26 May 2026 at 12:00

arXiv:2605.24602v1 Announce Type: cross Abstract: Multimodal large language models (MLLMs) frequently suffer from object hallucinations, yet the visual perceptual mechanism underlying this failure remains poorly understood. In this work, we reveal that hallucinations are strongly associated with a human-like attention distraction phenomenon, where humans under divided focus experience degraded visual clarity and produce inaccurate descriptions, while in models the same mechanism manifests as spatial inconsistency in multi-head attention and temporal fading of attention to image tokens during decoding. We further provide theoretical insights that attention dispersion increases model complexity and degrades classification generalization. Motivated by these findings, we propose an Attention-Focused Approach for Improved Image Perception (AFIP), which corrects attention distraction via cross-head attention enrichment and reinforces visual grounding through dynamic historical attention enhancement. Extensive experiments on multiple benchmarks and models validate the effectiveness of AFIP without additional training.

CollectionLoRA: Collecting 50 Effects in 1 LoRA via Multi-Teacher On-Policy Distillation

cs.AI, q-bio.NC updates on arXiv.org

By: Fangtai Wu · Hailong Guo · Shijie Huang · Jiayi Song · Yubo Huang · Mushui Liu · Zhao Wang · Yunlong Yu · Jiaming Liu · Ruihua Huang

26 May 2026 at 12:00

arXiv:2605.25378v1 Announce Type: cross Abstract: Customized image editing aims to equip pre-trained diffusion models with specific visual effects using limited paired data, typically via Low-Rank Adaptation (LoRA). As the number of desired effects grows, storing and dynamically loading numerous these effect LoRAs significantly increases deployment overhead. Furthermore, current pipelines typically cascade these effect LoRAs with acceleration modules for fast generation, which triggers severe parameter interference and results in concept bleeding and style degradation. We propose CollectionLoRA, a multi-teacher on-policy distillation framework capable of distilling the concepts of up to 50 different effect LoRAs along with few-step generation capabilities into a single LoRA. This fundamentally resolves the feature interference issue and significantly reduces deployment costs. Specifically, the method introduces (i) a Probabilistic Dual-Stream Routing mechanism that enables the model to randomly switch between data sources during training, effectively enhancing its generalization in unseen scenarios; (ii) an Asymmetric Orthogonal Prompting strategy to achieve concept isolation within the prompt space; (iii) a Coarse-to-Fine Distillation Objective to mitigate the distribution gap between the teacher and student models. Extensive evaluations show that CollectionLoRA distills all customized effects and few-step generation into a single LoRA, reducing deployment overhead while achieving concept fidelity comparable to or better than independently trained teacher models.

Multi-omics biomarkers for predicting resistance, hyperprogression, and immune-related toxicity during PD-1/PD-L1 therapy in lung cancer: a literature review

(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)

By: Na Hu · Ziyue Wang · Ming Liu · Dong Guo · Chenxue Jiang · Yun Chen · Zhenshan Zhang · Menglin Bai · Bo Cheng · Jessica C Hsu · Leilei Wu · Xiujie Sui

25 May 2026 at 18:00

Front Immunol. 2026 May 8;17:1780459. doi: 10.3389/fimmu.2026.1780459. eCollection 2026.

ABSTRACT

Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and its ligand programmed death-ligand 1 (PD-L1) have transformed the management of advanced lung cancer, yet most patients experience primary resistance, hyperprogressive disease (HPD), or clinically significant immune-related adverse events (irAEs). Multi-omics technologies now enable integrated interrogation of tumor, microenvironmental, host, and clinical determinants of these divergent outcomes. In this review, we first discuss the biological and clinical foundations of PD-1/PD-L1 blockade in non-small cell and small cell lung cancer, and summarize the spectrum of resistance, HPD, and irAEs observed in trials and real-world practice. We then describe multi-omics study frameworks that connect genomics, transcriptomics, epigenomics, proteomics, metabolomics, radiomics, and microbiome profiling with these outcome phenotypes. Building on this foundation, we synthesize evidence for composite biomarkers of primary and acquired resistance, delineate emerging multi-omics signatures of HPD, and examine host- and tumor-derived multi-omics correlates of organ-specific and systemic irAEs. We further propose an efficacy-risk quadrant framework to guide clinical decision-making when favorable efficacy predictors coexist with elevated risk of severe adverse outcomes, and outline a three-step approach for high-efficacy/high-risk patients: joint probability reporting, multi-omics guided mitigation, and dynamic reassessment. Finally, we evaluate translational strategies that integrate multi-omics scores into baseline risk stratification, dynamic monitoring with attention to technical challenges such as distinguishing true progression from ctDNA pseudoprogression, and biomarker-driven trial design, while assessing the evidence level and translational readiness of candidate assays from retrospective discovery to clinical implementation. A clinical case illustrates how multi-omics can link baseline risk stratification, regimen selection, and longitudinal monitoring into a coherent action plan, while acknowledging that artificial intelligence-driven models remain investigational and real-world application still relies on clinician judgment. Collectively, this review defines how integrated multi-omics biomarkers can be leveraged to predict resistance, HPD, and immune-related toxicity, and to refine patient selection and management during PD-1/PD-L1 therapy in lung cancer.

PMID:42183274 | PMC:PMC13194140 | DOI:10.3389/fimmu.2026.1780459

Multi-omics biomarkers for predicting resistance, hyperprogression, and immune-related toxicity during PD-1/PD-L1 therapy in lung cancer: a literature review

Omics In Lung

By: Na Hu · Ziyue Wang · Ming Liu · Dong Guo · Chenxue Jiang · Yun Chen · Zhenshan Zhang · Menglin Bai · Bo Cheng · Jessica C Hsu · Leilei Wu · Xiujie Sui

25 May 2026 at 18:00

Front Immunol. 2026 May 8;17:1780459. doi: 10.3389/fimmu.2026.1780459. eCollection 2026.

ABSTRACT

Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and its ligand programmed death-ligand 1 (PD-L1) have transformed the management of advanced lung cancer, yet most patients experience primary resistance, hyperprogressive disease (HPD), or clinically significant immune-related adverse events (irAEs). Multi-omics technologies now enable integrated interrogation of tumor, microenvironmental, host, and clinical determinants of these divergent outcomes. In this review, we first discuss the biological and clinical foundations of PD-1/PD-L1 blockade in non-small cell and small cell lung cancer, and summarize the spectrum of resistance, HPD, and irAEs observed in trials and real-world practice. We then describe multi-omics study frameworks that connect genomics, transcriptomics, epigenomics, proteomics, metabolomics, radiomics, and microbiome profiling with these outcome phenotypes. Building on this foundation, we synthesize evidence for composite biomarkers of primary and acquired resistance, delineate emerging multi-omics signatures of HPD, and examine host- and tumor-derived multi-omics correlates of organ-specific and systemic irAEs. We further propose an efficacy-risk quadrant framework to guide clinical decision-making when favorable efficacy predictors coexist with elevated risk of severe adverse outcomes, and outline a three-step approach for high-efficacy/high-risk patients: joint probability reporting, multi-omics guided mitigation, and dynamic reassessment. Finally, we evaluate translational strategies that integrate multi-omics scores into baseline risk stratification, dynamic monitoring with attention to technical challenges such as distinguishing true progression from ctDNA pseudoprogression, and biomarker-driven trial design, while assessing the evidence level and translational readiness of candidate assays from retrospective discovery to clinical implementation. A clinical case illustrates how multi-omics can link baseline risk stratification, regimen selection, and longitudinal monitoring into a coherent action plan, while acknowledging that artificial intelligence-driven models remain investigational and real-world application still relies on clinician judgment. Collectively, this review defines how integrated multi-omics biomarkers can be leveraged to predict resistance, HPD, and immune-related toxicity, and to refine patient selection and management during PD-1/PD-L1 therapy in lung cancer.

PMID:42183274 | PMC:PMC13194140 | DOI:10.3389/fimmu.2026.1780459

PRXL2B facilitates the progression of hepatocellular carcinoma and the therapeutic efficacy of oncolytic adenovirus H101 through the PI3K/AKT/PD-L1 axis

Omics in Hepatocellular

By: Ziqi Zhang · Hongli Chen · Yangming Liu · Hao Wang · You Yan · Yanxi Yu · Zuotian Huang · Yanyao Liu · Wei Li · Zhongjun Wu · Meiqing Kang · Xiaoyong Luo · Ping Che · Rui Liao

20 May 2026 at 18:00

Biosci Trends. 2026 May 21. doi: 10.5582/bst.2026.01000. Online ahead of print.

ABSTRACT

Oncolytic adenovirus H101 has shown antitumor activity in hepatocellular carcinoma (HCC), but the molecular determinants of treatment response remain unclear. In this study, a Hepa1-6 subcutaneous tumor model was established in C57BL/6 mice and treated with intratumoral H101, followed by integrated transcriptomic and proteomic analyses to identify candidate genes associated with H101 response. PRXL2B was selected for further investigation using public multi-omics datasets, tissue microarray-based immunohistochemistry, in vitro functional assays, mechanistic analyses, and in vivo validation experiments. Integrated multi-omics analyses identified PRXL2B as a candidate gene downregulated after H101 treatment. Public datasets and tissue-based validation further showed that PRXL2B was upregulated in HCC tissues. In MHCC97H and HCCLM3 cells, PRXL2B knockdown inhibited proliferation, migration, and invasion, promoted apoptosis and cell-cycle arrest, and enhanced the antitumor effect of H101. Mechanistically, PRXL2B silencing reduced AKT phosphorylation and PD-L1 expression. In vivo, PRXL2B knockdown suppressed tumor growth, and the combination of PRXL2B knockdown and H101 produced the strongest antitumor effect. These findings indicate that PRXL2B promotes malignant phenotypes in HCC and may modulate H101 efficacy through the PI3K/AKT/PD-L1 axis. Targeting PRXL2B may therefore represent a potential strategy to enhance the therapeutic efficacy of oncolytic virus therapy in HCC.

PMID:42161529 | DOI:10.5582/bst.2026.01000

Schema-Aware Planning and Hybrid Knowledge Toolset for Reliable Knowledge Graph Triple Verification

7 April 2026 at 12:00

arXiv:2604.04190v1 Announce Type: new Abstract: Knowledge Graphs (KGs) serve as a critical foundation for AI systems, yet their automated construction inevitably introduces noise, compromising data trustworthiness. Existing triple verification methods, based on graph embeddings or language models, often suffer from single-source bias by relying on either internal structural constraints or external semantic evidence, and usually follow a static inference paradigm. As a result, they struggle with complex or long-tail facts and provide limited interpretability. To address these limitations, we propose SHARP (Schema-Hybrid Agent for Reliable Prediction), a training-free autonomous agent that reformulates triple verification as a dynamic process of strategic planning, active investigation, and evidential reasoning. Specifically, SHARP combines a Memory-Augmented Mechanism with Schema-Aware Strategic Planning to improve reasoning stability, and employs an enhanced ReAct loop with a Hybrid Knowledge Toolset to dynamically integrate internal KG structure and external textual evidence for cross-verification. Experiments on FB15K-237 and Wikidata5M-Ind show that SHARP significantly outperforms existing state-of-the-art baselines, achieving accuracy gains of 4.2% and 12.9%, respectively. Moreover, SHARP provides transparent, fact-based evidence chains for each judgment, demonstrating strong interpretability and robustness for complex verification tasks.

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation

(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)

By: Zhengyu Hu · Jiaqi Wang · Jialin Yu · Zheqing Hu · Jing Xue · Zhanbing Ma · Miaomiao Nian · Ruixin Qi · Tingting Zhao · Xia Cao · Hongxia Xin · Xiuyan Wang · Guilan Yang · Zhenzhen Gui · Xiaoming Liu · Juan Chen

6 April 2026 at 18:00

Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.

ABSTRACT

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.

METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.

RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.

CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.

PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289

Multi-omics integration and machine learning reveal gut-immune signatures in idiopathic pulmonary fibrosis: insights from bulk RNA-seq, single-cell profiles, spatial transcriptomics, and experimental validation

Omics In Lung

By: Zhengyu Hu · Jiaqi Wang · Jialin Yu · Zheqing Hu · Jing Xue · Zhanbing Ma · Miaomiao Nian · Ruixin Qi · Tingting Zhao · Xia Cao · Hongxia Xin · Xiuyan Wang · Guilan Yang · Zhenzhen Gui · Xiaoming Liu · Juan Chen

6 April 2026 at 18:00

Front Immunol. 2026 Mar 19;17:1730289. doi: 10.3389/fimmu.2026.1730289. eCollection 2026.

ABSTRACT

BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with limited treatment options and a poor prognosis. Recent studies suggest a critical role for the gut-immune-lung axis in IPF, yet the underlying molecular mechanisms remain unclear.

METHODS: The current study performed in silico multi-omics integration of publicly available datasets, including bulk RNA-seq, single-cell and spatial transcriptomics, as well as peripheral blood multi-omics data to uncover key molecular signatures in IPF. Furthermore, machine learning techniques were utilized to identify core genes, whereas functional analyses and Mendelian randomization were conducted to evaluate the causal relationships among gut microbiota, immune cells, and IPF. Additionally, experimental validation using qPCR and ELISA assays was conducted in vitro, in vivo, and in patient plasma to confirm the expression patterns of key genes.

RESULTS: Across integrated public bulk, single-cell, spatial, and blood multi-omics, CXCL13, IL33, TLR4, and IGF1 were identified as core IPF genes consistently linked to immune infiltration and fibrotic remodeling. Deconvolution, scRNA-seq, and spatial mapping localized their dysregulation to fibroblasts and immune compartments (notably B-cell, macrophage, and mast-cell axes), highlighting fibroblast-immune crosstalk in fibrotic foci. A four-gene model robustly distinguished IPF from controls across cohorts. Mendelian randomization supported a gut-immune-lung axis, indicating causal effects of specific gut taxa on IPF risk via immune phenotypes. qPCR/ELISA in TGF-β1-stimulated fibroblasts, bleomycin mouse lungs, and patient plasma corroborated upregulation of IL33, CXCL13, IGF1 and downregulation of TLR4. Drug-signature reversal nominated cucurbitacin I and temsirolimus; molecular docking was performed as a preliminary in silico, computer-simulation-based assessment of potential ligand-protein interactions between these compounds and the four core targets.

CONCLUSION: This study provides new insights into the importance of gut-immune-lung axis in IPF and identifies CXCL13, IL33, TLR4, and IGF1 as diagnostic signatures and therapeutic targets. By integrating public multi-omics resources with experimental validation, our findings offer a foundation for future diagnostic and treatment strategies aimed at modulating the gut microbiota and immune system in IPF.

PMID:41939867 | PMC:PMC13043422 | DOI:10.3389/fimmu.2026.1730289

SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation

Oncogene - Issue - nature.com science feeds

By: Mengqing Xiao · Yanni Ma · Ganghua Zhang · Guanjun Chen · Yuxing Zhu · Xiaoming Liu · Yaxin Cheng · Ziyang Feng · Ke Cao

6 April 2026 at 08:00

Oncogene, Published online: 06 April 2026; doi:10.1038/s41388-026-03735-7

SRSF10 promotes cisplatin resistance in bladder cancer via BIN1 Exon 12 retention and ANXA1 activation

Hierarchical Memory Orchestration for Personalized Persistent Agents

cs.AI, q-bio.NC updates on arXiv.org

By: Junming Liu · Yifei Sun · Weihua Cheng · Haodong Lei · Yuqi Li · Yirong Chen · Ding Wang

3 April 2026 at 12:00

arXiv:2604.01670v1 Announce Type: new Abstract: While long-term memory is essential for intelligent agents to maintain consistent historical awareness, the accumulation of extensive interaction data often leads to performance bottlenecks. Naive storage expansion increases retrieval noise and computational latency, overwhelming the reasoning capacity of models deployed on constrained personal devices. To address this, we propose Hierarchical Memory Orchestration (HMO), a framework that organizes interaction history into a three-tiered directory driven by user-centric contextual relevance. Our system maintains a compact primary cache, coupling recent and pivotal memories with an evolving user profile to ensure agent reasoning remains aligned with individual behavioral traits. This primary cache is complemented by a high-priority secondary layer, both of which are managed within a global archive of the full interaction history. Crucially, the user persona dictates memory redistribution across this hierarchy, promoting records mapped to long-term patterns toward more active tiers while relegating less relevant information. This targeted orchestration surfaces historical knowledge precisely when needed while maintaining a lean and efficient active search space. Evaluations on multiple benchmarks achieve state-of-the-art performance. Real-world deployments in ecosystems like OpenClaw demonstrate that HMO significantly enhances agent fluidity and personalization.

Scaling Whole-Body Human Musculoskeletal Behavior Emulation for Specificity and Diversity

cs.AI, q-bio.NC updates on arXiv.org

By: Yunyue Wei · Chenhui Zuo · Shanning Zhuang · Haixin Gong · Yaming Liu · Yanan Sui

1 April 2026 at 12:00

arXiv:2603.29332v1 Announce Type: cross Abstract: The embodied learning of human motor control requires whole-body neuro-actuated musculoskeletal dynamics, while the internal muscle-driven processes underlying movement remain inaccessible to direct measurement. Computational modeling offers an alternative, but inverse dynamics methods struggled to resolve redundant control from observed kinematics in the high-dimensional, over-actuated system. Forward imitation approaches based on deep reinforcement learning exhibited inadequate tracking performance due to the curse of dimensionality in both control and reward design. Here we introduce a large-scale parallel musculoskeletal computation framework for biomechanically grounded whole-body motion reproduction. By integrating large-scale parallel GPU simulation with adversarial reward aggregation and value-guided flow exploration, the MS-Emulator framework overcomes key optimization bottlenecks in high-dimensional reinforcement learning for musculoskeletal control, which accurately reproduces a broad repertoire of motions in a whole-body human musculoskeletal system actuated by approximately 700 muscles. It achieved high joint angle accuracy and body position alignment for highly dynamic tasks such as dance, cartwheel, and backflip. The framework was also used to explore the musculoskeletal control solution space, identifying distinct musculoskeletal control policies that converge to nearly identical external kinematic and mechanical measurements. This work establishes a tractable computational route to analyzing the specificity and diversity underlying human embodied control of movement. Project page: https://lnsgroup.cc/research/MS-Emulator.

X-World: Controllable Ego-Centric Multi-Camera World Models for Scalable End-to-End Driving

cs.AI, q-bio.NC updates on arXiv.org

By: Chaoda Zheng · Sean Li · Jinhao Deng · Zhennan Wang · Shijia Chen · Liqiang Xiao · Ziheng Chi · Hongbin Lin · Kangjie Chen · Boyang Wang · Yu Zhang · Xianming Liu

1 April 2026 at 12:00

arXiv:2603.19979v2 Announce Type: replace-cross Abstract: Scalable and reliable evaluation is increasingly critical in the end-to-end era of autonomous driving, where vision--language--action (VLA) policies directly map raw sensor streams to driving actions. Yet, current evaluation pipelines still rely heavily on real-world road testing, which is costly, biased toward limited scenario coverage, and difficult to reproduce. These challenges motivate a real-world simulator that can generate realistic future observations under proposed actions, while remaining controllable and stable over long horizons. We present X-World, an action-conditioned multi-camera generative world model that simulates future observations directly in video space. Given synchronized multi-view camera history and a future action sequence, X-World generates future multi-camera video streams that follow the commanded actions. To ensure reproducible and editable scene rollouts, X-World further supports optional controls over dynamic traffic agents and static road elements, and retains a text-prompt interface for appearance-level control (e.g., weather and time of day). Beyond world simulation, X-World also enables video style transfer by conditioning on appearance prompts while preserving the underlying action and scene dynamics. At the core of X-World is a multi-view latent video generator designed to explicitly encourage cross-view geometric consistency and temporal coherence under diverse control signals. Experiments show that X-World achieves high-quality multi-view video generation with (i) strong view consistency across cameras, (ii) stable temporal dynamics over long rollouts, and (iii) high controllability with strict action following and faithful adherence to optional scene controls. These properties make X-World a practical foundation for scalable and reproducible evaluation.

EVA: Aligning Video World Models with Executable Robot Actions via Inverse Dynamics Rewards

cs.AI, q-bio.NC updates on arXiv.org

By: Ruixiang Wang · Qingming Liu · Yueci Deng · Guiliang Liu · Zhen Liu · Kui Jia

25 March 2026 at 12:00

arXiv:2603.17808v2 Announce Type: replace-cross Abstract: Video generative models are increasingly used as world models for robotics, where a model generates a future visual rollout conditioned on the current observation and task instruction, and an inverse dynamics model (IDM) converts the generated frames into executable robot actions. However, current video world models lack explicit executability constraints. As a result, visually coherent rollouts may still violate rigid-body and kinematic consistency, producing unstable or infeasible control commands when decoded by an IDM. We refer to this mismatch between visual generation and physically executable control as the executability gap. While this gap can be mitigated at inference time using techniques such as rejection sampling, such approaches are inefficient due to the high cost of video generation. In this paper, we leverage the executability gap as a training signal and introduce Executable Video Alignment (EVA), a reinforcement-learning post-training framework for aligning video world models. EVA trains an inverse dynamics model on real robot trajectories and repurposes it as a reward model that evaluates generated videos through the action sequences they induce, encouraging smooth motions measured by velocity, acceleration, and jerk while penalizing actions that violate embodiment constraints. Importantly, the reward remains informative even when generated videos contain severe visual artifacts, since such artifacts typically translate into unstable or out-of-bound actions. Experiments on the RoboTwin benchmark and a real bimanual robot show that EVA reduces embodiment-specific artifacts in generated rollouts and improves downstream task execution success.

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