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aiXiv: A Next-Generation Open Access Ecosystem for Scientific Discovery Generated by AI Scientists
Systems pharmacology approaches decipher the anti-cancer efficacy of ethnopharmacological agents in hepatocellular carcinoma
Sci Rep. 2025 Dec 17;15(1):43996. doi: 10.1038/s41598-025-27744-w.
ABSTRACT
Hepatocellular carcinoma (HCC) poses a significant global health burden with limited therapeutic efficacy. Chinese herbal medicines (CHMs) offer multi-target potential, yet their systematic screening and mechanistic elucidation remain challenging. We established a high-throughput multi-omics platform integrating transcriptomics, proteomics, and deep learning (autoencoder and multiple kernel learning) to screen 187 medicinal plants. Five CHMs candidates were identified and shown to modulate hub genes (e.g., AKR1B10, HMGCR, THBS1) and key pathways (TNF/IL-17/MAPK, apoptosis, ferroptosis). Proteomic validation and functional assays confirmed their roles in suppressing proliferation, migration, and inducing apoptosis in HCC cells. This study provides a robust, data-driven pipeline for natural anti-HCC drug discovery, linking specific hub genes to CHM efficacy and offering novel insights into precision ethnopharmacology.
PMID:41408124 | DOI:10.1038/s41598-025-27744-w
Leveraging LLMs for Structured Data Extraction from Unstructured Patient Records
ValuePilot: A Two-Phase Framework for Value-Driven Decision-Making
Enhancing Transparency and Traceability in Healthcare AI: The AI Product Passport
Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems
Complex Mathematical Expression Recognition: Benchmark, Large-Scale Dataset and Strong Baseline
TF-MCL: Time-frequency Fusion and Multi-domain Cross-Loss for Self-supervised Depression Detection
Assessing High-Risk Systems: An EU AI Act Verification Framework
A data-physics hybrid generative model for patient-specific post-stroke motor rehabilitation using wearable sensor data
A Multicenter Benchmark of Multiple Instance Learning Models for Lymphoma Subtyping from HE-stained Whole Slide Images
COMMA: A Communicative Multimodal Multi-Agent Benchmark
A Knowledge Graph-based Retrieval-Augmented Generation Framework for Algorithm Selection in the Facility Layout Problem
Two-stage prompting framework with predefined verification steps for evaluating diagnostic reasoning tasks on two datasets
npj Digital Medicine, Published online: 16 December 2025; doi:10.1038/s41746-025-02146-4
Two-stage prompting framework with predefined verification steps for evaluating diagnostic reasoning tasks on two datasetsSingle-cell and spatial transcriptomic characterization of pulmonary pleomorphic carcinoma
Commun Biol. 2025 Dec 16;8(1):1773. doi: 10.1038/s42003-025-09162-w.
ABSTRACT
Pulmonary pleomorphic carcinoma (PPC) is a rare subtype of lung cancer that comprises both epithelial and sarcomatoid components. The molecular basis of PPC, including the cellular dynamics of its components, remains largely unknown. To elucidate potential therapeutic targets for PPC, we perform a multi-omics analysis incorporating digital spatial profiling and single-cell RNA sequencing (scRNA-seq). PPC exhibits diverse driver gene alterations, including MET exon 14 skipping mutation (METex14) and ALK fusion. In spatial transcriptomics, MET gene and protein are overexpressed exclusively within the epithelial component and not in the sarcomatoid component, even in patients harboring METex14. Epithelial-mesenchymal transition (EMT)-related transcriptional changes, along with extracellular matrix (ECM) remodeling between the epithelial and sarcomatoid components, are observed. scRNA-seq identifies cell populations within the epithelial component that contribute to the malignant transformation and differentiation of the sarcomatoid component. They are characterized by an intermediate EMT state with ECM remodeling signature, suggesting their potential as novel therapeutic targets for PPC.
PMID:41402584 | PMC:PMC12708732 | DOI:10.1038/s42003-025-09162-w
New Perspectives on Gastric Inflammaging: Integrating Multi-Omics Mechanisms and Gerotherapeutic Strategies in Chronic Gastritis
Aging Dis. 2025 Dec 15. doi: 10.14336/AD.2025.1444. Online ahead of print.
ABSTRACT
Chronic gastritis (CG) is a highly prevalent, age-associated inflammatory disorder of gastric mucosa and a key precursor of gastric cancer in older adults. Beyond Helicobacter pylori infection and environmental insults, accumulating evidence indicates that chronic, low-grade inflammation coupled with aging biology, "gastric inflammaging", plays a central role in driving mucosal degeneration, atrophy, and malignant transformation. Here, we synthesize current mechanistic and multi-omics evidence to conceptualize CG as a tractable model of organ-specific inflammaging. We first summarize how hallmarks of aging-including cellular senescence and the senescence-associated secretory phenotype (SASP), mitochondrial dysfunction, impaired autophagy, immune exhaustion, and microbiome dysbiosis-converge to create a self-perpetuating inflammatory microenvironment in the stomach. We then review emerging single-cell and spatial multi-omics studies that delineate senescence-inflammation niches and reveal how these molecular neighborhoods relate to disease stage and cancer risk. Finally, we discuss therapeutic implications, highlighting geroscience-guided interventions such as senolytics/senomorphics, inflammasome and cGAS-STING pathway modulators, microbiota- and metabolite-targeted strategies, lifestyle interventions, and natural products, and propose a precision framework linking inflammaging biomarkers to patient stratification and clinical endpoints. Reframing CG as a gastric inflammaging model may provide a prototype for organ-specific healthy aging strategies and near-term gerotherapeutic trials aimed at extending healthspan.
PMID:41400573 | DOI:10.14336/AD.2025.1444
Opinion: We crunched the numbers on drug discovery in the U.S. vs. China. The results were alarming
This essay is part of a First Opinion series on the future of the National Institutes of Health and American science.
Around the world, nations with robust research and development infrastructure race to create therapeutics that meet the needs of their residents. Simply put, they dictate research priorities based on need. During the Covid pandemic, the United States was one of the first countries to gain access to vaccines to protect its citizens.


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