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Pan-cancer analysis identifies KANSL2 as a cell-cycle-associated regulator of tumor progression and immunity in liver hepatocellular carcinoma

Clin Exp Med. 2026 Jul 26;26(1):329. doi: 10.1007/s10238-026-02264-7.

ABSTRACT

KANSL2, a core component of the NSL histone acetyltransferase complex, has been implicated in tumorigenesis. However, its pan-cancer relevance and functional role in liver hepatocellular carcinoma (LIHC) remain unclear. Multi-omics data from TCGA, GEO, and HPA were integrated to systematically evaluate KANSL2 expression, clinical significance, genomic alterations, and immune associations across cancers. Functional enrichment, immune infiltration analyses, and single-cell transcriptomics were performed. In vitro assays were conducted to validate the biological effects of KANSL2 in LIHC cells. KANSL2 is broadly upregulated across cancers and exhibits strong diagnostic performance. Elevated KANSL2 expression correlates with unfavorable prognosis, particularly in LIHC. Mechanistically, KANSL2 and its co-expressed genes are enriched in cell-cycle progression. KANSL2 expression is also closely associated with immune infiltration and immunoregulatory signaling within the tumor microenvironment, with single-cell data indicating preferential expression in proliferative T-cell subsets. Functional experiments demonstrate that KANSL2 silencing suppresses proliferation, migration, and invasion, and induces G2/M phase arrest in LIHC cells. Notably, its effects on apoptosis are limited, suggesting that KANSL2 primarily drives tumor progression through cell-cycle-dependent mechanisms. This study identifies KANSL2 as a key regulator of tumor progression and immune remodeling in LIHC. By promoting malignancy predominantly via cell-cycle control, KANSL2 represents a promising biomarker for diagnosis and prognosis, and a potential therapeutic target.

PMID:42726304 | PMC:PMC13569553 | DOI:10.1007/s10238-026-02264-7

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Pan-cancer analysis identifies KANSL2 as a cell-cycle-associated regulator of tumor progression and immunity in liver hepatocellular carcinoma

Clin Exp Med. 2026 Jul 26;26(1):329. doi: 10.1007/s10238-026-02264-7.

ABSTRACT

KANSL2, a core component of the NSL histone acetyltransferase complex, has been implicated in tumorigenesis. However, its pan-cancer relevance and functional role in liver hepatocellular carcinoma (LIHC) remain unclear. Multi-omics data from TCGA, GEO, and HPA were integrated to systematically evaluate KANSL2 expression, clinical significance, genomic alterations, and immune associations across cancers. Functional enrichment, immune infiltration analyses, and single-cell transcriptomics were performed. In vitro assays were conducted to validate the biological effects of KANSL2 in LIHC cells. KANSL2 is broadly upregulated across cancers and exhibits strong diagnostic performance. Elevated KANSL2 expression correlates with unfavorable prognosis, particularly in LIHC. Mechanistically, KANSL2 and its co-expressed genes are enriched in cell-cycle progression. KANSL2 expression is also closely associated with immune infiltration and immunoregulatory signaling within the tumor microenvironment, with single-cell data indicating preferential expression in proliferative T-cell subsets. Functional experiments demonstrate that KANSL2 silencing suppresses proliferation, migration, and invasion, and induces G2/M phase arrest in LIHC cells. Notably, its effects on apoptosis are limited, suggesting that KANSL2 primarily drives tumor progression through cell-cycle-dependent mechanisms. This study identifies KANSL2 as a key regulator of tumor progression and immune remodeling in LIHC. By promoting malignancy predominantly via cell-cycle control, KANSL2 represents a promising biomarker for diagnosis and prognosis, and a potential therapeutic target.

PMID:42726304 | PMC:PMC13569553 | DOI:10.1007/s10238-026-02264-7

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Key Experimental Therapeutics and Knowledge Gaps in Metabolic Dysfunction-Associated Steatohepatitis (MASH)

Drug Des Devel Ther. 2026 Sep 5;20:543657. doi: 10.2147/DDDT.S543657. eCollection 2026.

ABSTRACT

Metabolic dysfunction-associated steatohepatitis (MASH) is not solely a disorder of hepatocellular lipid accumulation, but a multicellular disease driven by coordinated metabolic stress, sterile inflammation, fibrogenesis, and niche remodeling. Recent therapeutic progress with the provisional approval of resmetirom and semaglutide has validated MASH as a tractable clinical target. However, many experimental agents have shown limited or inconsistent efficacy, particularly for regression of hepatic fibrosis or cirrhosis, reflecting the biological heterogeneity and dynamic cellular architecture of the disease. Distinct from conventional pathway- or drug class-based reviews, we summarize emerging therapeutics through a liver cell-centered framework, integrating hepatocyte-directed metabolic therapies, immune-cell modulation, hepatic stellate cell-targeted antifibrotic strategies, niche-directed approaches involving liver sinusoidal endothelial cells and cholangiocytes, systemic multi-cell modulators, and precision-delivery technologies. We further compare how these interventions reshape pathogenic communication among hepatic and extrahepatic compartments, while emphasizing unresolved challenges in drug target selection, cellular specificity, disease-stage dependency, safety, and patient stratification. This perspective emphasizes the need to move from isolated pathway targeting toward cell- and network-informed therapeutic strategies supported by spatial multi-omics, human-relevant models, and precision delivery.

PMID:42719321 | PMC:PMC13557022 | DOI:10.2147/DDDT.S543657

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Multi-Omics-Enabled Precision Strategies for Overcoming CAR-T Therapy Limitations in Gastrointestinal Malignancies

Biofactors. 2026 Sep-Oct;52(5):e70150. doi: 10.1002/biof.70150.

ABSTRACT

Gastrointestinal malignancies, including gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic ductal adenocarcinoma, remain major causes of cancer-related morbidity and mortality worldwide. Although chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the treatment of hematologic malignancies, its efficacy in gastrointestinal solid tumors remains limited by antigen heterogeneity, insufficient trafficking and infiltration, immunosuppressive tumor microenvironments, on-target off-tumor toxicity, and adaptive resistance. In this review, we summarize the current landscape of CAR-T therapy in gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic cancer, with a focus on representative target antigens and emerging biomarker strategies. We further discuss two major categories of biomarkers: target antigen-related biomarkers and conventional dynamic biomarkers, including serum tumor markers, cytokine changes, CAR-T expansion kinetics, and antigen-loss monitoring. In addition, we highlight how single-cell ribonucleic acid sequencing and spatial transcriptomics provide complementary insights into cellular states, immune exhaustion, stromal barriers, and spatially restricted immune exclusion. By integrating these multi-omics approaches with biomarker-guided patient stratification and next-generation CAR-T engineering, gastrointestinal solid tumor CAR-T therapy may evolve from empirical optimization toward mechanism-driven and precision-guided clinical translation.

PMID:42717494 | PMC:PMC13558850 | DOI:10.1002/biof.70150

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Multi-Omics-Enabled Precision Strategies for Overcoming CAR-T Therapy Limitations in Gastrointestinal Malignancies

Biofactors. 2026 Sep-Oct;52(5):e70150. doi: 10.1002/biof.70150.

ABSTRACT

Gastrointestinal malignancies, including gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic ductal adenocarcinoma, remain major causes of cancer-related morbidity and mortality worldwide. Although chimeric antigen receptor T-cell (CAR-T) therapy has revolutionized the treatment of hematologic malignancies, its efficacy in gastrointestinal solid tumors remains limited by antigen heterogeneity, insufficient trafficking and infiltration, immunosuppressive tumor microenvironments, on-target off-tumor toxicity, and adaptive resistance. In this review, we summarize the current landscape of CAR-T therapy in gastric cancer, colorectal cancer, hepatocellular carcinoma, and pancreatic cancer, with a focus on representative target antigens and emerging biomarker strategies. We further discuss two major categories of biomarkers: target antigen-related biomarkers and conventional dynamic biomarkers, including serum tumor markers, cytokine changes, CAR-T expansion kinetics, and antigen-loss monitoring. In addition, we highlight how single-cell ribonucleic acid sequencing and spatial transcriptomics provide complementary insights into cellular states, immune exhaustion, stromal barriers, and spatially restricted immune exclusion. By integrating these multi-omics approaches with biomarker-guided patient stratification and next-generation CAR-T engineering, gastrointestinal solid tumor CAR-T therapy may evolve from empirical optimization toward mechanism-driven and precision-guided clinical translation.

PMID:42717494 | PMC:PMC13558850 | DOI:10.1002/biof.70150

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Inhaled nanosilica orchestrates a pulmonary macrophage-NK cell axis for memory-like NK programming toward synergistic cancer immunotherapy

Yuan and colleagues demonstrate that inhaled biodegradable nanosilica activates an alveolar macrophage–NK axis, triggering an IL-12/15/18 triad that programs memory-like NK cells. This non-fibrotic, cell-free strategy suppresses melanoma growth, prevents postsurgical recurrence, and synergizes with anti-PD-1, establishing a robust framework for in vivo NK cell immunotherapy.
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ACC1 inhibition enhances BCG-induced trained immunity by reprogramming acetyl-CoA metabolism

The efficacy of vaccines remains suboptimal in many settings, underscoring the need for new strategies. Baydemir and colleagues show that modulation of acetyl-CoA metabolism reshapes metabolic and epigenetic programs underlying Bacille Calmette-Guérin-induced trained immunity, enhancing cellular innate immune responses and identifying immunometabolic targeting as a promising approach to improve vaccine efficacy.
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Developmental deviations of association-network structural connectivity in youths with ADHD predict symptom and treatment outcomes

Nature Biomedical Engineering, Published online: 31 August 2026; doi:10.1038/s41551-026-01779-4

This large-scale study of white matter structural connectivity during development reveals biomarkers associated with attention deficit hyperactivity disorder in youth that track symptom trajectories and predict differential treatment response.
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Publisher Correction: Edge-sharing RuO<sub>2</sub> single layer for stable and low overpotential acidic water electrolysis

Nature Nanotechnology, Published online: 08 September 2026; doi:10.1038/s41565-026-02288-w

Publisher Correction: Edge-sharing RuO2 single layer for stable and low overpotential acidic water electrolysis
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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 reasoning prototypes as semantic anchors to provide structural process-level supervision for latent reasoning. PMPS projects latent embeddings and explicit CoT embeddings into a shared prototype space, achieving many-to-many soft alignment between unequal-length representations through prototype assignment. Meanwhile, we introduce a Progressive Sequential Alignment (PSA) module to further guide training: positional priors initially encourage sequential alignment structure, then gradually relax to permit adaptive matching. Experimental results show that PMPS compresses output token length to under 50% of explicit CoT on GSM8K-Aug. Compared to leading baseline SIM-CoT, our method achieves average accuracy gains of 2.08% across different model families. On GPT-2, PMPS even surpasses CoT-SFT. On larger models and a more challenging task, PMPS consistently attains the highest accuracy among all latent reasoning methods with comparable output length.
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CS-Guard: Benchmarking LLM Guardrails for Code Generation Security

arXiv:2609.09798v1 Announce Type: cross Abstract: Large language models (LLMs) have been ex- ploited to generate malware, but the effective- ness of guardrails for code generation secu- rity remains unclear. We introduce CS-Guard, the first benchmark to systematically evalu- ate guardrails for code generation security. It covers 1) text-to-code generation with 1000 high-quality malware-generation prompts, 7 jailbreak attacks, and a novel fictional scenario attack (FSA) that embeds malicious intent in a legitimate fictional software-development sce- nario; and 2) code-to-code generation with 331 code prompts spanning code infilling, code completion, and code translation. We empiri- cally evaluate 9 guardrails across seven LLMs. We find that current guardrails perform poorly against malicious code-generation re- quests: for text-to-code, the average attack success rate (ASR) after jailbreaks reaches about 50% for many guardrails; for code-to- code, average ASR approaches 100% on base LLMs and remains high across many guardrails (14.4% to nearly 100%). Our FSA also achieves ASR close to 100% across many guardrails, raising major reliability concerns for real-world software development. To sup- port future research, CS-Guard uses a modular three-layer guardrail taxonomy that lets devel- opers register guardrails for evaluation. We release the benchmark and data to enable fur- ther community evaluation.
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A Trust-Network-Based Federated Learning Framework for Multi-Center Aging Clock Prediction

arXiv:2609.10108v1 Announce Type: cross Abstract: Aging clocks quantify biological aging and help characterize individual health status. What protein interactions are important for accurate aging clocks, and are they zeroth-order or higher-order? Addressing these questions requires learning from large molecular datasets distributed across medical centers, where privacy constraints prevent centralized data sharing. Federated learning offers a natural solution but faces four challenges in this setting: limited local sample sizes, sparse and directional inter-center trust, the need to retain discriminative age prediction while supporting interpretation, and model drift and forgetting under heterogeneous cross-center data. We propose TNFL, a trust-network-based federated learning framework that progressively propagates models along directed pairwise trust relations without centralized aggregation. TNFL combines an age-aware mixture-of-experts model with generative replay to preserve previously learned information and reduce forgetting and drift. Experiments across multiple molecular datasets show that TNFL enables effective aging-clock prediction with limited local data, provides interpretable age-dependent prediction patterns, and maintains stable performance across interaction orders. To investigate the biological questions, we analyze TNFL-identified pairwise protein interactions and their higher-order organization through functional and network analyses. The identified interactions repeatedly form coordinated higher-order subnetworks spanning multiple aging-related biological systems, with several proteins recurring across subnetworks. These findings suggest that TNFL captures molecular relationships beyond isolated pairwise associations and reveals coherent higher-order biological organization associated with aging.
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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, fragmenting perception, reasoning, and action while offering limited generalization. Here we present LightNav-0, a compact generalist embodied navigation model that elicits the spatial intelligence of a pretrained VLM and aligns it with navigation, without task-specific prediction heads. LightNav-0 represents diverse navigation tasks through a unified token interface: dual-channel pointing expresses task-, scene-, and embodiment-agnostic spatial intent, while a residual vector-quantized action tokenizer maps this intent to precise, embodiment-specific trajectories. Together with temporally aware visual history compression, ER mid-training, supervised fine-tuning, and reinforcement learning, this formulation supports instruction following, open-vocabulary object navigation, and visual tracking within a single model. The navigation training corpus spans 2K+ scenes and 4K+ hours of embodied navigation data. LightNav-ER, the embodied-reasoning checkpoint used to initialize LightNav-0, attains the highest complete-set average across 8 embodied-reasoning benchmarks, while LightNav-0 achieves state-of-the-art monocular success rates across all 10 public navigation simulation settings. Real-world evaluations further demonstrate zero-shot generalization across robot embodiments, diverse scenes, and static and dynamic targets. These results establish compact VLMs as a unified and transferable backbone for generalist embodied navigation.
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Galanin impairs tumor immunity in glioblastoma by promoting infiltration and ferroptosis resistance of myeloid-derived suppressor cells

Nature Cancer, Published online: 25 August 2026; doi:10.1038/s43018-026-01221-3

Chen and colleagues report that the neuropeptide galanin impairs antitumor immunity in glioblastoma by interacting with its receptor GALR3 on monocytic myeloid-derived suppressor cells, promoting their infiltration and ferroptosis resistance.
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BODHI: Precise OS Kernel Specification Inference

arXiv:2605.23931v1 Announce Type: new Abstract: The formal verification of operating system kernels requires precise specifications that capture the intended behavior of system calls. Writing these specifications manually demands deep domain expertise, motivating the use of large language models (LLMs) to automate the process. However, in OSV-Bench, a benchmark of 245 specification generation tasks derived from the Hyperkernel OS kernel, the best reported Pass@1 is 55.10%. We propose a domain knowledge prompting method (BODHI), which augments the standard few-shot prompt with a structured C-to-Python translation guide covering 15 categories of domain-specific translation patterns. Inspired by Structured Chain-of-Thought (SCoT) prompting, the guide organizes translation by separation of concerns, addressing pre-condition extraction and post-condition generation as distinct categories. Evaluated on nine models from six providers (Anthropic, Mistral, Amazon, DeepSeek, Meta, Alibaba), covering dense, mixture-of-experts and reasoning architectures, BODHI improves every model tested, with gains ranging from +11% to +32%. The best configuration (Claude Opus 4.6 + BODHI) reaches 96.73% Pass@1. BODHI reduces both syntax and semantic errors, with the strongest effect on models that have sufficient instruction-following capability to utilize structured reference material. These results demonstrate that domain knowledge injection is a model-agnostic technique that substantially bridges the gap between general-purpose code generation and formal specification synthesis.
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From Accuracy to Auditability: A Survey of Determinism in Financial AI Systems

arXiv:2605.23955v1 Announce Type: new Abstract: Deploying machine learning in regulated financial environments -- credit risk, fraud detection, and anti-money laundering -- exposes critical vulnerabilities in algorithmic reproducibility. While early financial ML addressed statistical challenges such as backtest overfitting, deep neural networks and Generative AI have introduced mechanical nondeterminism rooted in hardware and architecture. This survey provides a systems perspective on reproducibility failures across three modalities now dominant in financial AI: tabular models (post-hoc explanation variance), graph networks (stochastic sampling and temporal asynchrony), and LLM-based agentic workflows (batch-dependent divergence and trajectory drift). We supplement the literature analysis with first-party experiments on public financial datasets -- quantifying explanation rank instability in credit scoring, prediction flip rates in GNN-based fraud detection, and tensor-parallel-induced output divergence in LLM entity extraction. We propose a layered evaluation framework linking modality-specific metrics (RBO, D_cos, TDI, PSD) to audit readiness, and empirically validate the complementarity of logit-level and semantic-level determinism measures.
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Reasoning as an Attack Surface: Adaptive Evolutionary CoT Jailbreaks for LLMs

arXiv:2605.24497v1 Announce Type: new Abstract: Large Reasoning Models (LRMs) have demonstrated remarkable capabilities in reasoning and generation tasks and are increasingly deployed in real-world applications. However, their explicit chain-of-thought (CoT) mechanism introduces new security risks, making them particularly vulnerable to jailbreak attacks. Existing approaches often rely on static CoT templates to elicit harmful outputs, but such fixed designs suffer from limited diversity, adaptability, and effectiveness. To overcome these limitations, we propose an adaptive evolutionary CoT jailbreak framework, called AE-CoT. Specifically, the method first rewrites harmful goals into mild prompts with teacher role-play and decomposes them into semantically coherent reasoning fragments to construct a pool of CoT jailbreak candidates. Then, within a structured representation space, we perform multi-generation evolutionary search, where candidate diversity is expanded through fragment-level crossover and a mutation strategy with an adaptive mutation-rate control mechanism. An independent scoring model provides graded harmfulness evaluations, and high-scoring candidates are further enhanced with a harmful CoT template to induce more destructive generations. Extensive experiments across multiple models and datasets demonstrate the effectiveness of the proposed AE-CoT, consistently outperforming state-of-the-art jailbreak methods.
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ProActor: Timing-Aware Reinforcement Learning for Proactive Task Scheduling Agents

arXiv:2605.24900v1 Announce Type: new Abstract: Proactive task-oriented agents must autonomously anticipate user needs, identify actionable opportunities, and trigger software actions at appropriate moments - fundamentally shifting from reactive systems that await explicit instructions. However, existing approaches lack generalizable end-to-end solutions for measuring and optimizing such anticipatory behaviors. This paper introduces ProActor, a unified framework for conversational task scheduling that integrates: (1) a domain-agnostic automated annotation methodology that enables scalable proactiveness reinforcement learning (RL) by generating full opportunity time windows instead of rigid point labels, (2) systematic proactiveness metrics capturing both timing quality and reference action alignment, and (3) RL optimization using GRPO with various reward designs. Our insight is that RULER-based rewards with proactiveness rubrics are crucial for improving timing quality, and that proactiveness optimization enabled by stage-aware composite rewards is key to balancing timing quality and reference action alignment. Timing-aware RL requires extensive exploration, demanding efficient infrastructure. We develop ART-F, an adaptive framework combining request-adaptive inference clusters with DDP-based training on single-node multi-GPU systems, enabling LoRA training of 4-bit Qwen2.5-14B-ProActor-Q4 with 4-8x speedups. Experiments on two newly auto-annotated datasets demonstrate significant improvements in proactive timing while maintaining action consistency comparable to state-of-the-art (SOTA) baselines. Ablations validate the effectiveness of distinct composite reward variations.
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CODESKILL: Learning Self-Evolving Skills for Coding Agents

arXiv:2605.25430v1 Announce Type: new Abstract: Coding agents produce rich trajectories while solving software-engineering tasks. To enable agent self-evolution, these trajectories can be distilled into reusable procedural skills that compactly encode experience to guide future behavior. However, existing skill construction and maintenance methods often rely on fixed prompts and heuristic update rules, leaving it unclear how knowledge should be selected, abstracted, and maintained to best serve downstream agents. We propose CODESKILL, an LLM-based framework that reformulates skill extraction and skill-bank maintenance as a learnable management policy. CODESKILL extracts multi-granularity procedural skills from coding-agent trajectories, evolves skills with new experience, and maintains a compact skill bank for future task solving. We train CODESKILL with reinforcement learning, using a hybrid reward that combines dense rubric-based skill-quality feedback with sparse verifiable execution feedback from the frozen downstream agent. Experiments on EnvBench, SWE-Bench Verified, and Terminal-Bench 2 show that CODESKILL improves average pass rate by 9.69 over the no-skill baseline and by 4.01 over the strongest prompt-based or memory baseline, while maintaining the skill bank at a stable size during iterative construction.
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CUA-Gym: Scaling Verifiable Training Environments and Tasks for Computer-Use Agents

arXiv:2605.25624v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards (RLVR) has driven breakthroughs in domains such as math, tool-use, and software engineering, yet its extension to computer-use agents (CUAs) has been bottlenecked by the scarcity of scalable training data with deterministic rewards. Constructing such data for CUAs requires consistent task instruction, executable environment, and verifiable reward. However, hand-curated benchmarks achieve high reward fidelity but cover few applications and LLM-as-judge-based datasets scale broadly but lack reliable verification. We present CUA-Gym, a scalable pipeline that co-generates task instructions, environment states, and reward functions. Concretely, a Generator agent constructs the initial and golden environment states, and a separate Discriminator agent writes the reward function from the task specification. An orchestrator agent drives the two through iterative rounds upon execution. Generated tuples then pass a final filter combining LLM majority voting and agent rollouts, ensuring quality beyond the per-task adversarial loop. To address the scarcity of training environments, we further synthesize CUA-Gym-Hub, a broad suite of high-fidelity mock web applications grounded in real-world software-use distributions, expanding the scale of CUA RLVR data by magnitude. Using this pipeline, we construct CUA-Gym, a dataset of 32,112 verified RLVR training tuples grounded in 110 environments. Trained with GSPO on CUA-Gym, our CUA-Gym-A3B and CUA-Gym-A17B achieve 62.1% and 72.6% on OSWorld-Verified, outperforming prior open-source CUAs at comparable scales, with performance scaling smoothly in both data volume and environment diversity. The same checkpoints also improve on the held-out WebArena benchmark, indicating transfer beyond the training environments. We will open-source the full synthesis pipeline, dataset, CUA-Gym-Hub environments, and models.
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