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Site-specific DNA insertion into the human genome with engineered recombinases
Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02895-3
Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.Improving dataset transparency in dermatologic Artificial Intelligence using a dataset nutrition label
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02125-9
Biased and poorly documented dermatology datasets pose risks to the development of safe and generalizable artificial intelligence (AI) tools. We created a Dataset Nutrition Label (DNL) for multiple dermatology datasets to support transparent and responsible data use. The DNL offers a structured, digestible summary of key attributes, including metadata, limitations, and risks, enabling data users to better assess suitability and proactively address potential sources of bias in datasets.Evaluating clinical AI summaries with large language models as judges
npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02005-2
Evaluating clinical AI summaries with large language models as judgesLiquid biopsy in gastrointestinal oncology: clinical applications and translational integration of ctDNA, CTCs, and sEVs
Oncol Rev. 2025 Oct 20;19:1702932. doi: 10.3389/or.2025.1702932. eCollection 2025.
ABSTRACT
BACKGROUND AND AIMS: Liquid biopsy offers a minimally invasive tool to detect actionable mutations, monitor minimal residual disease (MRD), and guide therapy in gastrointestinal (GI) cancers. We critically review the clinical utility of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and small extracellular vesicles (sEVs) across GI malignancies and propose a framework for their integration into clinical practice.
METHODS: We synthesized evidence from over 200 studies, including prospective trials and translational research, to assess diagnostic accuracy, prognostic value, and clinical actionability of each biomarker type in esophageal, gastric, colorectal, pancreatic, hepatocellular, and biliary cancers.
RESULTS: ctDNA has shown strong potential for MRD detection and treatment monitoring, particularly in colorectal and pancreatic cancer. CTCs offer insights into metastatic risk and therapeutic resistance, while sEVs provide molecular cargo relevant to immunomodulation and disease progression. Emerging microfluidics and AI-driven multi-omics approaches may overcome current limitations.
CONCLUSION: The integration of liquid biopsy technologies into GI oncology holds promise for early detection and precision therapy. We propose a five-phase clinical roadmap and outine the key research gaps that need to be addressed before widespread implementation in routine care.
PMID:41190015 | PMC:PMC12580207 | DOI:10.3389/or.2025.1702932
Combining International Standards to Develop Clinical Decision Support for Parent Smoking Cessation in Pediatrics
A multimodal whole-slide foundation model for pathology
Nature Medicine, Published online: 05 November 2025; doi:10.1038/s41591-025-03982-3
Pretrained using 335,645 whole-slide images, a foundation model is developed to provide representations for slide- and patient-level tasks. It is capable of performing clinical tasks and generating reports even in data-scarce scenarios, such as rare cancer diagnosis and survival prediction, without requiring further fine-tuning.Fair human-centric image dataset for ethical AI benchmarking
Nature, Published online: 05 November 2025; doi:10.1038/s41586-025-09716-2
The Fair Human-Centric Image Benchmark (FHIBE, pronounced ‘Feebee’)—an image dataset that implements best practices for consent, privacy, compensation, safety, diversity and utility—can be used responsibly as a fairness evaluation dataset for many human-centric computer vision applications.How can we assess human-agent interactions? Case studies in software agent design
Digital Twin based Automatic Reconfiguration of Robotic Systems in Smart Environments
Will Humanity Be Rendered Obsolete by AI?
The Denario project: Deep knowledge AI agents for scientific discovery
Frame Semantic Patterns for Identifying Underreporting of Notifiable Events in Healthcare: The Case of Gender-Based Violence
A Systematic Literature Review of Spatio-Temporal Graph Neural Network Models for Time Series Forecasting and Classification
Deep Learning-based Prediction of Clinical Trial Enrollment with Uncertainty Estimates
A Process Mining-Based System For The Analysis and Prediction of Software Development Workflows
On the limitation of evaluating machine unlearning using only a single training seed
International expert consensus on the clinical integration of circulating tumor cells in solid tumors
Eur J Cancer. 2025 Dec 9;231:116050. doi: 10.1016/j.ejca.2025.116050. Epub 2025 Oct 20.
ABSTRACT
BACKGROUND: Circulating tumor cells (CTCs) are a versatile biomarker in solid tumors. Extensive research supports their clinical relevance and led to regulatory approval in breast, prostate, and colorectal cancers. However, clinical adoption remains limited mainly due to the lack of consensus and standardized technologies. Additionally, CTC research lacks unified direction. To address these gaps, an international expert panel was established to assess the current and future clinical utility of CTCs.
METHODS: A panel of 11 CTC experts identified key areas of controversy, informing a structured survey distributed to 55 international multidisciplinary experts. Consensus was predefined as ≥ 70 % agreement. Areas without consensus were discussed in a virtual meeting, leading to final statements on the clinical integration of CTCs.
RESULTS: Thirty-seven experts completed the survey. Consensus was reached on the clinical utility of CTCs for prognosis and treatment monitoring in metastatic breast (BC) and prostate (PC) cancers, including AR-V7 testing in metastatic castration-resistant PC for therapy selection. In other tumors, CTCs remain investigational. Experts agreed that while clinical utility is not yet established in early-stage disease, CTCs show promise in early BC, especially combined with cell-free DNA (cfDNA) for minimal residual disease detection. CellSearch® is currently the only platform with high-level evidence for clinical use, though emerging technologies are promising. Key challenges include improving detection sensitivity/specificity, standardizing workflows, generating robust data, and clinician education. Experts emphasized shifting from enumeration to phenotypic and molecular characterization, particularly for treatment guidance, and highlighted the complementary role of CTCs and cfDNA, advocating for integrated liquid biopsy approaches.
CONCLUSIONS: This consensus offers practical guidance for clinical integration of CTCs and outlines strategic research priorities to unlock their full potential in precision oncology.
PMID:41172567 | DOI:10.1016/j.ejca.2025.116050
Animal models in tuberculosis metabolomics: a systematic review of current evidence and the road to translational relevance
Front Mol Biosci. 2025 Oct 15;12:1688882. doi: 10.3389/fmolb.2025.1688882. eCollection 2025.
ABSTRACT
BACKGROUND: Animal models are important for tuberculosis (TB) research, offering controlled settings to study disease mechanisms. However, their ability to replicate TB-induced metabolic responses in humans is uncertain. This systematic review evaluated the current use of animal models in metabolomics studies aimed at characterising active pulmonary TB.
METHODS: PubMed, Scopus, and Web of Science were systematically searched for metabolomics studies of pulmonary TB in humans and animal models, following PRISMA guidelines. Eligible studies were screened, and quality was assessed using QUDOMICS and STAIR tools. Data were synthesised by species, sample matrix, experimental design, and reported differential metabolites. Differential metabolite names were compared between species and subjected to pathway analysis in MetaboAnalyst 6.0.
RESULTS: Of the 80 eligible studies, nine involved animal models, predominantly mice. These models captured only 4.7% of human TB-associated differential metabolites, with the highest overlap (3.8%) in mouse lung tissue. Despite low concordance at metabolite level, conserved disruptions were observed in amino acid, glutathione, and one-carbon metabolism pathways. Interspecies variation was evident, influenced by host species, sample matrix, infection protocol, and analytical method.
CONCLUSION: Animal models partially replicated key metabolic features of human TB, particularly at the pathway level. However, variability across studies hampers current translational interpretation. Broader model use, standardised protocols, and integrated multi-platform omics approaches are needed to improve the relevance and comparability of animal models in TB metabolomics research.
PMID:41169614 | PMC:PMC12568366 | DOI:10.3389/fmolb.2025.1688882