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Tongyi DeepResearch Technical Report
Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
Integrating deep learning and multi-omics features in radiation pneumonitis prediction for lung cancer patients using PET/CT
BMC Med Imaging. 2025 Oct 27;25(1):426. doi: 10.1186/s12880-025-01971-z.
ABSTRACT
BACKGROUND: To investigate the feasibility and accuracy of PET radiomics features, along with their combination with CT radiomics, dosiomics, and deep learning (DL) features, in predicting radiation pneumonitis (RP) in lung cancer patients treated with volumetric modulated arc therapy (VMAT).
METHODS: A total of 206 and 27 lung cancer patients who underwent VMAT with pre-treatment PET/CT imaging were enrolled from Hospital One and Hospital Two for model training and external validation, respectively. Four machine learning (ML) methods were applied to build radiomics models with features extracted from CT (R_CT), PET (R_PET), radiomics features fused PET/CT (R_fFU) and fused PET/CT images (R_ iFU), as well dosiomics features (D). Three DL models were built to extract features from PET (DL_PET), CT (DL_CT), and fused PET/CT images (DL_FU). The best-performing radiomics and DL models were combined with dosiomics to create the final joint model. ROC curves with AUC, accuracy, sensitivity, and specificity evaluated the performance. A nomogram was constructed using top-performing model features, parameters, and relevant clinical factors.
RESULTS: The extreme gradient boosting (XGBoost) and 18-layer residual neural network (Resnet-18) achieved the best performance. The R+D+DL model combined radiomics, dosiomics, and DL features achieved AUCs of 0.93, 0.92 and 0.89 in the training, internal validaiton and external validation cohorts, respectively. A nomogram constructed with gender, Adaptive RT, SUVp90, and XGBoost-score achieved an AUC of 0.94 for RP prediction in VMAT-treated lung cancer patients using PET/CT.
CONCLUSION: Integrating radiomics, DL, dosiomics features and SUVp90 is promising in the RP prediction for lung cancer patients underwent VMAT using PET/CT images.
PMID:41146084 | DOI:10.1186/s12880-025-01971-z
Learned, Lagged, LLM-splained: LLM Responses to End User Security Questions
Multimodal 3D Genome Pre-training
A full life cycle biological clock based on routine clinical data and its impact in health and diseases
Nature Medicine, Published online: 27 October 2025; doi:10.1038/s41591-025-04006-w
The biological clock model LifeClock predicts biological age across all life stages from routine clinical data, revealing distinct pediatric and adult disease risk patterns.MedAlign: A Synergistic Framework of Multimodal Preference Optimization and Federated Meta-Cognitive Reasoning
Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
Benchmarking GPT-5 for biomedical natural language processing
VaultGemma: A Differentially Private Gemma Model
MSC-Bench: A Rigorous Benchmark for Multi-Server Tool Orchestration
R-loops in hepatocellular carcinoma: Bridging genomic instability and therapeutic opportunity (Review)
Mol Med Rep. 2026 Jan;33(1):6. doi: 10.3892/mmr.2025.13716. Epub 2025 Oct 17.
ABSTRACT
R‑loops, three‑stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced single‑stranded DNA, have emerged as important regulators of gene expression and genome maintenance. Although physiological R‑loops participate in normal cellular processes, their dysregulation can threaten genomic integrity by inducing DNA damage and replication stress. The present review explores the role of R‑loops in hepatocellular carcinoma (HCC), a malignancy characterized by marked genomic instability. In the present review, the formation mechanisms of R‑loops, their dual functions in transcriptional regulation and DNA damage, and their specific implications for HCC pathophysiology were discussed. HCC cells exhibit altered R‑loop homeostasis with aberrant accumulation linked to hepatitis B virus infection, inflammatory signaling and oncogene activation. The present review highlighted how HCC cells exploit or manage R‑loops to promote tumor progression, particularly through the epigenetic silencing of differentiation genes and modulation of replication stress responses. Furthermore, emerging therapeutic strategies targeting R‑loop biology were examined, including small molecules that induce synthetic lethality, gene‑based interventions and combination approaches that exploit R‑loop vulnerabilities. Challenges in targeting R‑loops and future directions, including multi‑omics profiling and biomarker development, were also addressed. Understanding the complex interplay between R‑loops and HCC offers promising avenues for novel diagnostic and therapeutic approaches for this malignancy.
PMID:41104860 | DOI:10.3892/mmr.2025.13716
Scaling DNA synthesis with a microchip-based massively parallel synthesis system
Nature Biotechnology, Published online: 01 October 2025; doi:10.1038/s41587-025-02844-0
A microchip-based DNA synthesis method enables scalable production of complex DNA constructs.Scalable generation and functional classification of genetic variants in inborn errors of immunity to accelerate clinical diagnosis and treatment
Protein lipoylation in cancer: metabolic reprogramming and therapeutic potential
Cell Death Discovery, Published online: 02 September 2025; doi:10.1038/s41420-025-02718-z
Protein lipoylation in cancer: metabolic reprogramming and therapeutic potentialAn eyecare foundation model for clinical assistance: a randomized controlled trial
Nature Medicine, Published online: 28 August 2025; doi:10.1038/s41591-025-03900-7
Trained and validated on multimodal data from 14.5 million images from multicountry datasets, a foundation model is shown to increase diagnostic and referral accuracy of clinicians when used as an assistant in a trial involving 16 ophthalmologists and 668 patients.Multiomics Insights into the Mechanism and Enhanced Efficacy of Tumor Treating Fields (TTFields) Therapy in Glioblastoma
J Proteome Res. 2025 Sep 1. doi: 10.1021/acs.jproteome.5c00424. Online ahead of print.
ABSTRACT
Glioma is an aggressive brain tumor that requires challenging treatments. Tumor Treating Fields (TTFields), an FDA-approved therapy for glioblastoma (GBM), pleural mesothelioma, and platinum-refractory metastatic nonsmall cell lung cancer (in combination with PD-1/PD-L1 inhibitors or docetaxel), employs specific frequency electric fields to disrupt cell division and enhance treatment efficacy. However, their molecular mechanisms remain unclear. This study aimed to elucidate these mechanisms and optimize the therapeutic potential of TTFields through quantitative proteomics, phosphoproteomics, and glycoproteomics. Pathway analysis of the proteomics revealed that TTFields impact the cell cycle, DNA repair, autophagy, and DNA replication. Phosphoproteomic studies further demonstrated a marked decline in the activity of key kinases ABL1 and PDK1, while glycoproteomics highlighted disruptions in cell adhesion and ECM-receptor interactions. Notably, proteomic analysis identified an upregulation of PARP1 and BRD4 protein levels, suggesting a previously unrecognized resistance mechanism. Consistently, combining TTFields with inhibitors targeting these proteins significantly enhanced the treatment efficacy in U87 cells. Thus, this study uncovers comprehensive molecular mechanisms underlying TTFields' effects on GBM cells and supports the development of concomitant therapies to enhance treatment efficacy.
PMID:40889189 | DOI:10.1021/acs.jproteome.5c00424
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Cell. 2025 Aug 22:S0092-8674(25)00922-5. doi: 10.1016/j.cell.2025.08.008. Online ahead of print.
ABSTRACT
Performing total RNA profiling on formalin-fixed, paraffin-embedded (FFPE) samples, the predominant sample conservation method in clinical practice, remains challenging for current spatial transcriptomics techniques. Here, we introduce Stereo-seq V2, which employs random primers to capture and sequence RNAs in situ on FFPE sections and provides single-cell resolution. The random-priming-based strategy offers unbiased transcript capturing and uniform gene body coverage, which increase the sensitivity to marker genes, the efficiency of non-polyadenylation (poly(A)) RNA profiling, and immune repertoire coverage. We demonstrated the robust performance of Stereo-seq V2 on clinical FFPE samples using triple-negative breast cancer (TNBC) sections and identified tumor-specific alternative splicing events. In a Mycobacterium tuberculosis (Mtb)-infected mouse model, we monitored gene expression dynamics of host and pathogen transcriptomes simultaneously by utilizing Stereo-seq V2. We also assembled immune repertoires and identified Mtb-specific BCR clones, which could also be observed in human tuberculous lung samples. These results highlight Stereo-seq V2's potential in biomedical research and personalized medicine.
PMID:40882628 | DOI:10.1016/j.cell.2025.08.008
The emerging role of microbiota in lung cancer: a new perspective on lung cancer development and treatment
Cell Oncol (Dordr). 2025 Aug 26. doi: 10.1007/s13402-025-01103-3. Online ahead of print.
ABSTRACT
Lung cancer remains the leading cause of cancer-related mortality worldwide, with limited treatment efficacy and frequent resistance to conventional therapies. Recent advances have uncovered the critical influence of the human microbiota-complex communities of bacteria, viruses, fungi, and other microorganisms-on lung cancer pathogenesis and therapeutic responses. This review synthesizes current knowledge on the compositional and functional roles of microbiota across multiple body sites, including the gut, lung, tumor microenvironment, circulation, and oral cavity, highlighting their contributions to tumor initiation, progression, metastasis, and immune regulation. We emphasize the bidirectional communication between microbial metabolites and host immune pathways, particularly the gut-lung axis, which modulates systemic and local antitumor immunity. Importantly, microbiota composition has been linked to differential responses and toxicities in chemotherapy, radiotherapy, targeted therapy, and immune checkpoint blockade. Microbiota-targeted interventions, such as probiotics, fecal microbiota transplantation, and selective antibiotics, show promising potential to enhance treatment efficacy and mitigate adverse effects. However, challenges remain in clinical translation due to interindividual microbiome variability, mechanistic complexities, and limited longitudinal data. Future research integrating multi-omics, microbial functional profiling, and controlled clinical trials is essential to harness the microbiome as a precision medicine tool in lung cancer management. This review provides a comprehensive overview of the emerging role of microbiota in lung cancer development and therapy, offering new perspectives for innovative therapeutic strategies.
PMID:40856929 | DOI:10.1007/s13402-025-01103-3