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Factor IX Padua AAV gene therapy in adolescents with hemophilia B: a phase 1 trial

Nature Medicine, Published online: 16 September 2026; doi:10.1038/s41591-026-04636-8

In this single-arm phase 1 trial, an AAV gene therapy carrying the Padua variant of factor IX was well tolerated in 11 adolescents with hemophilia B and led to reductions in annualized bleeding rate.
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Graph-of-Skills: Dependency-Aware Structural Retrieval for Massive Agent Skills

arXiv:2604.05333v4 Announce Type: replace Abstract: As LLM agents act across personal applications, web browsers, and other interfaces, their reusable skill libraries can scale to thousands of skills. This scale introduces two challenges. First, loading the full library saturates the context window, driving up token costs, hallucination, and latency. Second, semantic retrieval surfaces topically relevant skills but can miss upstream and downstream prerequisite skills, creating a prerequisite gap that leaves the retrieved bundle insufficient for execution. We present Graph-of-Skills (GoS), an inference-time structural retrieval layer for large skill libraries. GoS constructs an executable skill graph offline from skill packages, then retrieves a bounded, dependency-aware bundle through hybrid semantic-lexical seeding, reverse-aware Personalized PageRank, and context-budgeted hydration. Across SkillsBench and ALFWorld, with three model families (Claude Sonnet 4.5, MiniMax M2.7, and GPT-5.2 Codex), GoS attains the highest average reward in all six model-benchmark blocks, at a fraction of the token cost of loading the full library. On SkillsBench with GPT-5.2 Codex it raises average reward by 7.0 absolute points over full skill loading, a 25.6% relative gain, while cutting total tokens by 56.7%. Ablations isolate the mechanism: replacing reverse traversal with forward propagation costs 9.1 reward points, a larger loss than removing the graph altogether. The gain thus comes from traversing dependencies backwards, not from graph diffusion as such. A budget-matched retrieval study holding seeding, reranking, hydration, and context budget fixed reproduces the same ordering, with dependency-pair co-recovery falling from 0.654 to 0.362. Code is available at https://github.com/davidliuk/graph-of-skills
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VBVR-Pro: A Scalable and Verifiable Suite for Native Visual Reasoning

arXiv:2608.26105v2 Announce Type: replace-cross Abstract: Native visual reasoning treats visual generation as the medium of reasoning itself: visual states (i.e. images and videos) are not merely inputs to be understood or outputs to be rendered, but first-class substrates for problem solving beyond language. Yet progress remains bottlenecked by the lack of scalable training tasks, reliable feedback, and controlled comparisons across generative substrates. In this work, we introduce VBVR-Pro, a closed-loop testbed that makes native visual reasoning through generation trainable, verifiable, optimizable, and experimentally controllable. 1) Task scaling. VBVR-Pro turns visual reasoning into a controlled task space of 300 procedurally generated tasks. Models trained on VBVR-Pro show strong transfer beyond the proposed suite across seven external visual reasoning benchmarks such as RISE-Video, MME-CoF-Pro, and BabyVision. 2) Verifiable rewards. VBVR-Pro provides verifiable reward scorers for task-grounded evaluation. Through a systematic study of leading MLLMs as judges, we identify recurring failure modes of the prevalent VLM-as-a-judge paradigm. In contrast, the proposed scorers are grounded in deterministic, task-specific rules, achieve fine-grained alignment with human judgments. Importantly, they serve as reliable reward signals for large-scale multi-task reinforcement learning and demonstrate stronger post-RL performance across visual reasoning tasks. 3) Mechanism study. VBVR-Pro enables controlled modality studies across more than 30 image, video, and interleaved generators. Our analysis shows that video generation remains strongest for tasks requiring persistent spatiotemporal state tracking, while interleaved generation provides a compute-efficient alternative. Critically, ablations and probing suggest the presence of vision-native trajectories that are crucial to visual reasoning. We release all data, models, scorers, and code.
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Reliable Near-Field Multi-User Positioning Informed by Two-Stage MUSIC

arXiv:2609.09409v1 Announce Type: cross Abstract: Near-field localization is a promising technique for high-resolution multi-user positioning in future wireless systems, but its performance is often degraded by scattering-induced coherent propagation. Existing near-field localization methods, which require separate parameter estimation and path/source association, suffer from high computation overhead and accumulated errors, and usually do not provide any guarantee on reliability. In this paper, we propose \emph{MUSIC-Net}, an end-to-end near-field positioning deep learning (DL) framework informed by two-stage MUltiple SIgnal Classification (MUSIC) in mixed line-of-sight (LoS) and non-LoS (NLoS) multi-path scenarios, which embeds the two-stage MUSIC objects into training to isolate the LoS-related signal subspace and to identify a surrogate distance. The proposed framework directly recovers multi-user positions without the need for involved NLoS parameter estimation or path/source association. Furthermore, we introduce split conformal prediction (SCP) to move beyond point-estimation-based positioning towards statistically guaranteed (confidence) set estimation for all users. Numerical results show that the proposed MUSIC-Net achieves lower mean positioning error (MPER) than existing benchmarks and yields tighter SCP-calibrated prediction regions, demonstrating both accurate LoS localization and efficient uncertainty quantification (UQ) in coherent multi-path environments.
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An operational perturbation proteomics-based virtual cell model

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-11001-9

Temporal protein-abundance measurements from systematically perturbed breast cancer cell lines were generated to develop ProteinTalks, a virtual cell model that functions as an operational tool for diverse drug discovery tasks.
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CAFs shape the immunosuppressive microenvironment of pancreatic cancer through the Lin28b-STING Axis

Nat Commun. 2026 Aug 7;17(1):9491. doi: 10.1038/s41467-026-76495-3.

ABSTRACT

Cancer-associated fibroblasts comprise diverse functionally distinct cellular subsets, with certain subpopulations exerting pivotal influence in shaping the pancreatic cancer immune microenvironment. Here we show that Lin28b+ cancer-associated fibroblasts contribute to establishing an immunologically cold tumor microenvironment in pancreatic ductal adenocarcinoma. Mechanistically, Lin28b directly binds to STING mRNA and promotes its degradation, thereby suppressing STING expression and downstream type I interferon signaling. Loss of Lin28b in cancer-associated fibroblasts activates the cGAS-STING-interferon signaling cascade, enhancing dendritic cell antigen presentation and CD8+ T cell cytotoxic function. Importantly, genetic inhibition of Lin28b in cancer-associated fibroblasts enhances sensitivity to anti-PD-L1 immune checkpoint blockade therapy. These findings reveal that targeting the Lin28b-STING axis represents a promising therapeutic strategy for overcoming the intrinsic resistance of pancreatic ductal adenocarcinoma to immunotherapy.

PMID:42693143 | PMC:PMC13542369 | DOI:10.1038/s41467-026-76495-3

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The RNA-binding protein La/SSB is associated with HNSCC progression and TFAP2C/FSCN1-linked transcriptional regulation

Oncogene, Published online: 03 September 2026; doi:10.1038/s41388-026-03959-7

The RNA-binding protein La/SSB is associated with HNSCC progression and TFAP2C/FSCN1-linked transcriptional regulation
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SimuWoB: Simulating Real-World Mobile Apps for Fast and Faithful GUI Agent Benchmarking

arXiv:2605.25160v1 Announce Type: new Abstract: Mobile GUI agents powered by large language models have progressed rapidly, creating urgent needs for realistic and comprehensive evaluation. Existing benchmarks prioritize reproducibility but are often limited to open-source apps or file-operation tasks for the difficulty of constructing rewards on real applications, leaving a gap between benchmark settings and real-world usage. Moreover, most benchmarks focus on basic grounding and navigation, with limited coverage of complex, long-horizon interactions. To address these limitations, we introduce SimuWoB, a fully synthetic benchmark for mobile GUI agents with 120 challenging tasks spanning diverse types and difficulty levels. We build a robust virtual environment generation framework that synthesizes high-fidelity tasks and environments, and automatically provides valid rewards for each task. Each environment is deployed as a backend-free webpage accessible via URL, enabling efficient and reproducible evaluation. We conduct comprehensive experiments on several state-of-the-art mobile GUI agents. The average success rate is only 27.92%, dropping to 17.82% on long-horizon tasks, which reveals substantial weaknesses in current agents under complex scenarios. Evaluation result comparison with real-world sample tasks demonstrate that agent assessments based on our synthetic environment generalize well. We further provide diagnostic insights across key capability dimensions and discuss implications for future mobile GUI agent development.
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SSDAU: Structured Semantic Data Augmentation for Joint Entity and Relation Extraction

arXiv:2605.23440v2 Announce Type: replace-cross Abstract: Joint Entity and Relation Extraction (JERE) is highly susceptible to weak generalization due to low-quality training data. Data augmentation is a common strategy to enhance model generalization across different domains. However, existing data augmentation methods often overlook text relevance and may disrupt semantic structures and dependencies, making it difficult to generate effective augmented data for improving model generalization. In this paper, we propose Structured Semantic Data Augmentation (SSDAU), a novel method designed to preserve the semantic structure of text during augmentation. SSDAU segments text based on entity labels and employs an encoder to capture semantic features of entities through context awareness. It then performs entity semantic restructuring to generate augmented data. To distinguish semantically similar entities, SSDAU fuses contextualized embeddings with traditional similarity scores. To mitigate potential topic ambiguity and information loss, we apply the BERTTopic model to filter out irrelevant topics, ensuring topic consistency. We evaluate SSDAU on datasets with different annotation types and compare its performance on five representative JERE models against seven popular data augmentation baselines. Experiments demonstrate that SSDAU generates semantically consistent data with superior robustness against ambiguity (8.26% F1 decrease vs. 31.91% for baselines), significantly outperforming all existing methods across all metrics.
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Clinical and translational roles of circulating tumor cells in non-small cell and small cell lung cancer: a narrative review

J Thorac Dis. 2026 Apr 30;18(4):415. doi: 10.21037/jtd-2026-1-0025. Epub 2026 Apr 24.

ABSTRACT

BACKGROUND AND OBJECTIVE: Circulating tumor cells (CTCs) are malignant cells shed into blood that enable noninvasive, longitudinal assessment of lung cancer. Increasing evidence frames CTCs within a circulating tumor microenvironment (cTME) and broader circulating tumor-associated cell (CTAC) ecosystems that include multicellular clusters and circulating tumor endothelial cells (CTECs). We summarize definitions, detection approaches, and clinical applications of CTC-centered liquid biopsy in non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC).

METHODS: A comprehensive literature search was conducted in PubMed, Embase, Web of Science, and Google Scholar using the terms "non-small cell lung cancer", "small cell lung cancer", and "circulating tumor cells". Relevant clinical, basic, and translational studies were selected and synthesized to outline current knowledge and future directions.

KEY CONTENT AND FINDINGS: CTCs can be enriched by immunoaffinity, size, or microfluidic platforms, enabling enumeration and downstream profiling. In both NSCLC and SCLC, CTC positivity and higher burden are associated with worse survival, with the strongest effects in SCLC and with circulating tumor emboli (CTE). Serial monitoring provides early signals of response or failure; and post-treatment supports minimal residual disease (MRD) detection and relapse prediction. Molecular and phenotypic profiling enables driver and resistance tracking, including epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK), while CTECs may add vascular and immune-relevant information.

CONCLUSIONS: CTC-based assays have the potential to complement imaging and tissue biopsy across screening research, prognostication, therapeutic monitoring, MRD assessment, and personalized care. Clinical translation requires standardized preanalytical workflows, harmonized thresholds, and prospective trials testing CTC-guided management.

PMID:42182710 | PMC:PMC13190041 | DOI:10.21037/jtd-2026-1-0025

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Machine learning-driven multi-omics integration uncovers a senescence associated molecular axis in HCC

Front Immunol. 2026 May 8;17:1762222. doi: 10.3389/fimmu.2026.1762222. eCollection 2026.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) exhibits profound molecular heterogeneity and aberrant cellular senescence. This study systematically dissects the senescence-associated molecular landscape to identify key regulators driving HCC progression and immune evasion.

METHODS: Integrating multi-cohort transcriptomic datasets, we developed a robust prognostic signature using 101 machine-learning models, identifying prognostic signature. We employed preliminary proteomic, exploratory metabolomic, and single-cell RNA sequencing (scRNA-seq) analyses to explore multi-omics alterations. The functional senescence status and MCM7 were validated in a clinical HCC cohort by RT-qPCR, Western blotting, immunohistochemistry, and multiplex immunofluorescence (mIF). Causality was established using in vitro functional assays in HepG2 cells.

RESULTS: A 12-gene random survival forest (RSF) signature accurately predicted patient survival across independent cohorts. MCM7 emerged as a central senescence-associated driver. ScRNA-seq and mIF confirmed MCM7 characterizes a highly proliferative, clonally expanding subset of CD8+ T cells within the tumor microenvironment. In vitro, MCM7 knockdown significantly inhibited HepG2 cell proliferation and upregulated senescence enforcers p16 and p21, whereas overexpression facilitated evasion. Additionally, TIDE analysis revealed that high-risk patients exhibited elevated immune evasion potential, predicting poor immunotherapy response.

CONCLUSION: This integrative multi-omics framework uncovers an MCM7 MCM7-driven senescence-associated axis promising HCC progression and immune dysfunction, offering a robust tool for prognostic stratification and novel therapeutic insights.

PMID:42183188 | PMC:PMC13195000 | DOI:10.3389/fimmu.2026.1762222

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Machine learning-driven multi-omics integration uncovers a senescence associated molecular axis in HCC

Front Immunol. 2026 May 8;17:1762222. doi: 10.3389/fimmu.2026.1762222. eCollection 2026.

ABSTRACT

BACKGROUND: Hepatocellular carcinoma (HCC) exhibits profound molecular heterogeneity and aberrant cellular senescence. This study systematically dissects the senescence-associated molecular landscape to identify key regulators driving HCC progression and immune evasion.

METHODS: Integrating multi-cohort transcriptomic datasets, we developed a robust prognostic signature using 101 machine-learning models, identifying prognostic signature. We employed preliminary proteomic, exploratory metabolomic, and single-cell RNA sequencing (scRNA-seq) analyses to explore multi-omics alterations. The functional senescence status and MCM7 were validated in a clinical HCC cohort by RT-qPCR, Western blotting, immunohistochemistry, and multiplex immunofluorescence (mIF). Causality was established using in vitro functional assays in HepG2 cells.

RESULTS: A 12-gene random survival forest (RSF) signature accurately predicted patient survival across independent cohorts. MCM7 emerged as a central senescence-associated driver. ScRNA-seq and mIF confirmed MCM7 characterizes a highly proliferative, clonally expanding subset of CD8+ T cells within the tumor microenvironment. In vitro, MCM7 knockdown significantly inhibited HepG2 cell proliferation and upregulated senescence enforcers p16 and p21, whereas overexpression facilitated evasion. Additionally, TIDE analysis revealed that high-risk patients exhibited elevated immune evasion potential, predicting poor immunotherapy response.

CONCLUSION: This integrative multi-omics framework uncovers an MCM7 MCM7-driven senescence-associated axis promising HCC progression and immune dysfunction, offering a robust tool for prognostic stratification and novel therapeutic insights.

PMID:42183188 | PMC:PMC13195000 | DOI:10.3389/fimmu.2026.1762222

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A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10572-x

A fungal long non-coding RNA from Magnaporthe oryzae translocates into rice cells to sequester a host microRNA that normally represses PKR1, a negative immunity regulator, thereby facilitating infection and revealing a widespread RNA-based pathogen–host interaction mechanism.
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High-salt diet in macrophage-associated metabolic disorders: Mechanisms and therapeutic implications

Chin Med J (Engl). 2026 May 19. doi: 10.1097/CM9.0000000000004098. Online ahead of print.

ABSTRACT

High-salt diet (HSD) has emerged as a prevalent environmental factor that exacerbates chronic inflammation and insulin resistance in obesity-associated type 2 diabetes (T2D) by modulating macrophage polarization, metabolic reprogramming, and epigenetic imprinting. Current evidence demonstrates that HSD activates p38/mitogen-activated protein kinase (MAPK), nuclear factor kappa-B (NF-κB), and NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways, by which it drives macrophage polarization toward a proinflammatory M1 phenotype while inducing a glycolysis-dominant metabolic shift, thereby establishing a persistent "metabolic memory". Moreover, HSD orchestrates metabolic memory in macrophages through coordinated epigenetic machinery, including histone modifications (Trimethylation of histone H3 at lysine 4 [H3K4me3] and Acetylation of histone H3 at lysine 27 [H3K27ac]), DNA methylation, and noncoding RNAs (e.g., long non-coding RNA MALAT1 and miR-155), leading to sustained inflammatory phenotypes. In multiple metabolic organs (e.g., adipose tissue, liver, pancreas, and gut), the HSD-macrophage axis aggravates systemic insulin resistance through shared proinflammatory signaling and other tissue-specific mechanisms. Most importantly, therapeutic strategies targeting the NLRP3 inflammasome, metabolic pathways, and epigenetic alterations offer novel approaches for managing metabolic inflammation. Future investigations are encouraged to leverage lineage tracing, single-cell sequencing, and spatial multi-omics technologies to advance the development of precision medicine for macrophage-associated metabolic disorders.

PMID:42156155 | DOI:10.1097/CM9.0000000000004098

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Imaging interface-controlled bulk oxygen spillover

Nature, Published online: 15 April 2026; doi:10.1038/s41586-026-10324-x

In situ microscopic single-particle imaging demonstrates the significance of rationally engineered metal–support interfaces for activating the oxygen in bulk catalyst, helping elucidate reaction pathways in catalytic conversions.
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FileGram: Grounding Agent Personalization in File-System Behavioral Traces

arXiv:2604.04901v1 Announce Type: cross Abstract: Coworking AI agents operating within local file systems are rapidly emerging as a paradigm in human-AI interaction; however, effective personalization remains limited by severe data constraints, as strict privacy barriers and the difficulty of jointly collecting multimodal real-world traces prevent scalable training and evaluation, and existing methods remain interaction-centric while overlooking dense behavioral traces in file-system operations; to address this gap, we propose FileGram, a comprehensive framework that grounds agent memory and personalization in file-system behavioral traces, comprising three core components: (1) FileGramEngine, a scalable persona-driven data engine that simulates realistic workflows and generates fine-grained multimodal action sequences at scale; (2) FileGramBench, a diagnostic benchmark grounded in file-system behavioral traces for evaluating memory systems on profile reconstruction, trace disentanglement, persona drift detection, and multimodal grounding; and (3) FileGramOS, a bottom-up memory architecture that builds user profiles directly from atomic actions and content deltas rather than dialogue summaries, encoding these traces into procedural, semantic, and episodic channels with query-time abstraction; extensive experiments show that FileGramBench remains challenging for state-of-the-art memory systems and that FileGramEngine and FileGramOS are effective, and by open-sourcing the framework, we hope to support future research on personalized memory-centric file-system agents.
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A Review of the Role of Zeqi Decoction in the Treatment of Non-Small Cell Lung Cancer

J Multidiscip Healthc. 2026 Mar 11;19:584071. doi: 10.2147/JMDH.S584071. eCollection 2026.

ABSTRACT

Non-small cell lung cancer (NSCLC) is one of the malignant tumors with the highest incidence and mortality rates. Zeqi Decoction has the functions of "promoting diuresis and reducing swelling, resolving phlegm and dispersing nodules", embodying the unique approach of traditional Chinese medicine in treating lung cancer by "strengthening the body's resistance and eliminating pathogenic factors". Modern research shows that Zeqi Decoction exerts anti-NSCLC effects through multiple pathways and targets. In terms of the material basis of its efficacy, its active ingredients (such as diterpene esters and flavonoids contained in Zeqi) have the ability to directly inhibit the proliferation, invasion and migration of tumor cells and induce apoptosis. In terms of the mechanism of action, basic experiments have revealed that Zeqi Decoction can down-regulate the S100A9/STAT3 signaling pathway, inhibit the immunosuppressive activity of myelium-derived suppressor cells (MDSCs), reshape the tumor microenvironment, thereby enhancing the cytotoxic function of CD8⁺T cells, and can also regulate the EGFR/PI3K/Akt pathway to affect PD-L1 expression. Intervene in tumor immune escape; In terms of clinical transformation, the combination of Zexi Decoction with chemotherapy and targeted therapy can improve patients' symptoms such as cough and pleural effusion, prolong progression-free survival, and alleviate the toxic and side effects of Western medical treatment. In addition, Zexi Decoction also shows potential value in reversing drug resistance such as gemcitabine. At present, there are still problems such as the lack of standardized protocols and unclear molecular mechanisms in the research. In the future, it is necessary to combine new technologies such as network pharmacology and multi-omics analysis to deepen the research on the pharmacological material basis, dose-effect relationship and evidence-based medicine of Zeqi Decoction, so as to promote the clinical application and transformation of the combination of traditional Chinese and Western medicine in the treatment of NSCLC.

PMID:41847115 | PMC:PMC12991379 | DOI:10.2147/JMDH.S584071

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FedBPrompt: Federated Domain Generalization Person Re-Identification via Body Distribution Aware Visual Prompts

arXiv:2603.12912v1 Announce Type: cross Abstract: Federated Domain Generalization for Person Re-Identification (FedDG-ReID) learns domain-invariant representations from decentralized data. While Vision Transformer (ViT) is widely adopted, its global attention often fails to distinguish pedestrians from high similarity backgrounds or diverse viewpoints -- a challenge amplified by cross-client distribution shifts in FedDG-ReID. To address this, we propose Federated Body Distribution Aware Visual Prompt (FedBPrompt), introducing learnable visual prompts to guide Transformer attention toward pedestrian-centric regions. FedBPrompt employs a Body Distribution Aware Visual Prompts Mechanism (BAPM) comprising: Holistic Full Body Prompts to suppress cross-client background noise, and Body Part Alignment Prompts to capture fine-grained details robust to pose and viewpoint variations. To mitigate high communication costs, we design a Prompt-based Fine-Tuning Strategy (PFTS) that freezes the ViT backbone and updates only lightweight prompts, significantly reducing communication overhead while maintaining adaptability. Extensive experiments demonstrate that BAPM effectively enhances feature discrimination and cross-domain generalization, while PFTS achieves notable performance gains within only a few aggregation rounds. Moreover, both BAPM and PFTS can be easily integrated into existing ViT-based FedDG-ReID frameworks, making FedBPrompt a flexible and effective solution for federated person re-identification. The code is available at https://github.com/leavlong/FedBPrompt.
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GeoChemAD: Benchmarking Unsupervised Geochemical Anomaly Detection for Mineral Exploration

arXiv:2603.13068v1 Announce Type: cross Abstract: Geochemical anomaly detection plays a critical role in mineral exploration as deviations from regional geochemical baselines may indicate mineralization. Existing studies suffer from two key limitations: (1) single region scenarios which limit model generalizability; (2) proprietary datasets, which makes result reproduction unattainable. In this work, we introduce \textbf{GeoChemAD}, an open-source benchmark dataset compiled from government-led geological surveys, covering multiple regions, sampling sources, and target elements. The dataset comprises eight subsets representing diverse spatial scales and sampling conditions. To establish strong baselines, we reproduce and benchmark a range of unsupervised anomaly detection methods, including statistical models, generative and transformer-based approaches. Furthermore, we propose \textbf{GeoChemFormer}, a transformer-based framework that leverages self-supervised pretraining to learn target-element-aware geochemical representations for spatial samples. Extensive experiments demonstrate that GeoChemFormer consistently achieves superior and robust performance across all eight subsets, outperforming existing unsupervised methods in both anomaly detection accuracy and generalization capability. The proposed dataset and framework provide a foundation for reproducible research and future development in this direction.
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Author Correction: Gut stem cell necroptosis by genome instability triggers bowel inflammation

Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10302-3

Author Correction: Gut stem cell necroptosis by genome instability triggers bowel inflammation
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