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Macrophage spatiotemporal plasticity in pulmonary diseases: decoding the niche at single-cell resolution

Front Immunol. 2026 Jun 18;17:1855906. doi: 10.3389/fimmu.2026.1855906. eCollection 2026.

ABSTRACT

Pulmonary gas exchange and host defense depend on the dynamic coordination of resident and recruited macrophage populations. Historically, macrophage functions have often been interpreted through the classic M1/M2 dichotomy; however, this binary framework does not capture the heterogeneity and context-dependent plasticity of macrophage states within the lung microenvironment. Advances in single-cell RNA sequencing and spatial multi-omics have substantially refined our understanding of this complex macrophage network. Here, we synthesize evidence from human studies and experimental models to summarize macrophage functional states in homeostasis and across chronic obstructive pulmonary disease, asthma, idiopathic pulmonary fibrosis, pulmonary hypertension, acute lung injury/acute respiratory distress syndrome, and lung cancer. We highlight how macrophage transcriptional programs are shaped by ontogeny, tissue niche, and epigenetic-metabolic regulation, and how these programs are linked to disease-specific remodeling of the pulmonary microenvironment. Across diverse respiratory diseases, persistent tissue injury and microenvironmental stress remodel resident macrophage programs and are frequently accompanied by the expansion and context-dependent differentiation of recruited monocyte-derived macrophages. These macrophage states are associated with inflammatory amplification, epithelial and endothelial barrier dysfunction, extracellular matrix remodeling, and tumor immune evasion. Ligand-receptor and spatial analyses further identify candidate communication axes linking macrophages with stromal, epithelial, endothelial, and immune cells, some of which appear partially conserved across disease contexts. Emerging macrophage-targeted strategies are increasingly being explored beyond broad depletion, with growing interest in context-specific reprogramming and niche modulation, including antibody-based, nanocarrier-mediated, and engineered-cell approaches. Decoding the spatiotemporal trajectories and cell-cell communication networks of specific macrophage subsets, while considering tissue context, species differences, and levels of experimental support, may help clarify mechanisms of tissue remodeling, therapeutic resistance, and macrophage-targeted intervention in complex pulmonary diseases.

PMID:42396453 | PMC:PMC13322945 | DOI:10.3389/fimmu.2026.1855906

Asymmetric selection of a rice immune module and rebuild of disease resistance

Nature, Published online: 08 April 2026; doi:10.1038/s41586-026-10361-6

Stacking XA48-mediated effector-triggered immunity with XA21-mediated pattern-triggered immunity in Oryza sativa japonica reconstitutes the broad-spectrum resistance from wild rice.

ContextBudget: Budget-Aware Context Management for Long-Horizon Search Agents

arXiv:2604.01664v1 Announce Type: new Abstract: LLM-based agents show strong potential for long-horizon reasoning, yet their context size is limited by deployment factors (e.g., memory, latency, and cost), yielding a constrained context budget. As interaction histories grow, this induces a trade-off between retaining past information and staying within the context limit. To address this challenge, we propose Budget-Aware Context Management (BACM), which formulates context management as a sequential decision problem with a context budget constraint. It enables agents to assess the available budget before incorporating new observations and decide when and how much of the interaction history to compress. We further develop BACM-RL, an end-to-end curriculum-based reinforcement learning approach that learns compression strategies under varying context budgets. Experiments on compositional multi-objective QA and long-horizon web browsing benchmarks show that BACM-RL consistently outperforms prior methods across model scales and task complexities, achieving over $1.6\times$ gains over strong baselines in high-complexity settings, while maintaining strong advantages as budgets shrink, where most methods exhibit a downward performance trend.

SecureVibeBench: Evaluating Secure Coding Capabilities of Code Agents with Realistic Vulnerability Scenarios

arXiv:2509.22097v2 Announce Type: replace-cross Abstract: Large language model-powered code agents are rapidly transforming software engineering, yet the security risks of their generated code have become a critical concern. Existing benchmarks have provided valuable insights, but they fail to capture scenarios in which vulnerabilities are actually introduced by human developers, making fair comparisons between humans and agents infeasible. We therefore introduce SecureVibeBench, a benchmark of 105 C/C++ secure coding tasks sourced from 41 projects in OSS-Fuzz for code agents. SecureVibeBench has the following features: (i) realistic task settings that require multi-file edits in large repositories, (ii)~aligned contexts based on real-world open-source vulnerabilities with precisely identified vulnerability introduction points, and (iii) comprehensive evaluation that combines functionality testing and security checking with both static and dynamic oracles. We evaluate 5 popular code agents like OpenHands, supported by 5 LLMs (e.g., Claude sonnet 4.5) on SecureVibeBench. Results show that current agents struggle to produce both correct and secure code, as even the best-performing one, produces merely 23.8\% correct and secure solutions on SecureVibeBench.

Risk-adaptive therapy guided by dynamic ctDNA in nasopharyngeal carcinoma

Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10244-w

A clinical trial testing whether monitoring ctDNA clearance during treatment for nasopharyngeal cancer could be used to inform decisions about an individual’s subsequent therapeutic programme shows promising results.
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