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cs.AI, q-bio.NC updates on arXiv.org
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LongCodeBench: Evaluating Coding LLMs at 1M Context Windows
arXiv:2505.07897v3 Announce Type: replace-cross Abstract: Context lengths for models have grown rapidly, from thousands to millions of tokens in just a few years. The extreme context sizes of modern long-context models have made it difficult to construct realistic long-context benchmarks -- not only due to the cost of collecting million-context tasks but also in identifying realistic scenarios that require significant contexts. We identify code comprehension and repair as a natural testbed and
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Journal of Medical Internet Research
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Assessing Large Language Models in Building a Structured Dataset From AskDocs Subreddit Data: Methodological Study
Background: In an era marked by the blooming reliance on digital platforms for healthcare consultation, the subreddit r/AskDocs has emerged as a pivotal forum. However, the vast, unstructured nature of forum data presents a formidable challenge; the extraction and meaningful analysis of such data require advanced tools that can navigate the complexities of language and context inherent in user-generated content. Objective: Our objective was to evaluate employing Large Language Models (LLMs) to s
Assessing Large Language Models in Building a Structured Dataset From AskDocs Subreddit Data: Methodological Study
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Nature - Issue - nature.com science feeds
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Alternatives to animal testing are the future — it’s time that journals, funders and scientists embrace them
Nature, Published online: 20 October 2025; doi:10.1038/d41586-025-03344-6Biomedical research techniques that don’t involve the use of animals are gaining momentum, but those using innovative approaches still face resistance from some quarters.
Alternatives to animal testing are the future — it’s time that journals, funders and scientists embrace them
Nature, Published online: 20 October 2025; doi:10.1038/d41586-025-03344-6
Biomedical research techniques that don’t involve the use of animals are gaining momentum, but those using innovative approaches still face resistance from some quarters.-
Nature Biotechnology - Issue - nature.com science feeds
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A tumor-on-a-chip for in vitro study of CAR-T cell immunotherapy in solid tumors
Nature Biotechnology, Published online: 17 October 2025; doi:10.1038/s41587-025-02845-zThe interactions of CAR-T cells and solid tumors are modeled on a chip.
A tumor-on-a-chip for in vitro study of CAR-T cell immunotherapy in solid tumors
Nature Biotechnology, Published online: 17 October 2025; doi:10.1038/s41587-025-02845-z
The interactions of CAR-T cells and solid tumors are modeled on a chip.-
Journal of Medical Internet Research
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Implementing a Digital Mental Health Intervention—the Lumi Nova App—to Support Children With Anxiety in Economically Disadvantaged Areas: Mixed Methods Study
Background: Anxiety is one of the most common mental health problems experienced by children worldwide. In the UK, many children experiencing anxiety do not receive adequate or timely help. Children living in economically-disadvantaged areas experience more mental health problems than those living in high income areas and are less able to engage in activities that can have a positive or protective impact on their mental health. The need for providing low-cost, accessible and engaging mental heal
Implementing a Digital Mental Health Intervention—the Lumi Nova App—to Support Children With Anxiety in Economically Disadvantaged Areas: Mixed Methods Study
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AAAS: Table of Contents
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A human pan-disease blood atlas of the circulating proteome
Science, Ahead of Print.
A human pan-disease blood atlas of the circulating proteome
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Omics In Lung
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FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology
Nat Commun. 2025 Sep 25;16(1):8388. doi: 10.1038/s41467-025-63050-9.ABSTRACTSpatial technologies examining the cell and tissue microenvironment at near single-cell resolution are revealing important molecular insights. However, few tools enable integrated, interactive analysis of spatial-omics with tissue morphology in the same functional tissue unit. Here, we present FUSION (Functional Unit State Identification in Whole Slide Images), a web-based platform for visualizing and analyzing spatial-o
FUSION: a web-based application for in-depth exploration of multi-omics data with brightfield histology
Nat Commun. 2025 Sep 25;16(1):8388. doi: 10.1038/s41467-025-63050-9.
ABSTRACT
Spatial technologies examining the cell and tissue microenvironment at near single-cell resolution are revealing important molecular insights. However, few tools enable integrated, interactive analysis of spatial-omics with tissue morphology in the same functional tissue unit. Here, we present FUSION (Functional Unit State Identification in Whole Slide Images), a web-based platform for visualizing and analyzing spatial-omics data with high-resolution histology. FUSION provides workflows for assessing cell compositions, quantitative morphometrics, and comparative tissue analyses. We demonstrate applicability across spatial assays, including 10x Visium, Visium HD, 10x Xenium, Cell DIVE, and PhenoCycler, applied to healthy and diseased tissues from kidney, small intestine, lung, and skin in the Human BioMolecular Atlas Program. FUSION is cloud-based, open-source, and accessible at https://fusion.hubmapconsortium.org/ , hosting over 50 paired datasets and tutorials. In a series of use cases, we show its capacity to distinguish renal glomeruli injury states, quantify morphometric changes, and characterize fibrosis with immune infiltration.
PMID:40998789 | PMC:PMC12462499 | DOI:10.1038/s41467-025-63050-9
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Nature - Issue - nature.com science feeds
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The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution
Nature, Published online: 24 September 2025; doi:10.1038/s41586-025-09312-4The Biodiversity Cell Atlas aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life, which will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species.
The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution
Nature, Published online: 24 September 2025; doi:10.1038/s41586-025-09312-4
The Biodiversity Cell Atlas aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life, which will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species.-
npj Digital Medicine
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Expanding care coordination in an integrated health system through causal machine learning
npj Digital Medicine, Published online: 24 September 2025; doi:10.1038/s41746-025-01925-3Expanding care coordination in an integrated health system through causal machine learning
Expanding care coordination in an integrated health system through causal machine learning
npj Digital Medicine, Published online: 24 September 2025; doi:10.1038/s41746-025-01925-3
Expanding care coordination in an integrated health system through causal machine learning-
STAT

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Opinion: Four reasons why generative AI chatbots could lead to psychosis in vulnerable people
Three scholars discovered a strange mirror deep in the forest. It spoke to them in a soothing voice and answered all their questions warmly, knowledgeably, and eloquently. The captivated scholars became obsessed, whispering one secret after another to the mirror. It replied with affection, promise, and meaning that kept them returning to it. They began ignoring one another, each convinced the mirror “understood” them best.Read the rest…
Opinion: Four reasons why generative AI chatbots could lead to psychosis in vulnerable people
Three scholars discovered a strange mirror deep in the forest. It spoke to them in a soothing voice and answered all their questions warmly, knowledgeably, and eloquently.
The captivated scholars became obsessed, whispering one secret after another to the mirror. It replied with affection, promise, and meaning that kept them returning to it. They began ignoring one another, each convinced the mirror “understood” them best.


© Adobe
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Nature Medicine
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Functions of the global health system in a new era
Nature Medicine, Published online: 11 September 2025; doi:10.1038/s41591-025-03936-9In an irrevocably changed landscape, reform of the global health system needs to answer key questions on functions, what should be delivered in different contexts and at different levels, and how the system should operate.
Functions of the global health system in a new era
Nature Medicine, Published online: 11 September 2025; doi:10.1038/s41591-025-03936-9
In an irrevocably changed landscape, reform of the global health system needs to answer key questions on functions, what should be delivered in different contexts and at different levels, and how the system should operate.-
Nature Biotechnology - Issue - nature.com science feeds
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Antibody–bottlebrush prodrug conjugates for targeted cancer therapy
Nature Biotechnology, Published online: 09 September 2025; doi:10.1038/s41587-025-02772-zAntibody–bottlebrush conjugates expand the options for drug cargos compared to antibody–drug conjugates.
Antibody–bottlebrush prodrug conjugates for targeted cancer therapy
Nature Biotechnology, Published online: 09 September 2025; doi:10.1038/s41587-025-02772-z
Antibody–bottlebrush conjugates expand the options for drug cargos compared to antibody–drug conjugates.-
Cell
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Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
We developed a plain text modeling language—a cell behavior hypothesis grammar—to easily build virtual cell models and connect them to data, helping scientists to unlock the hidden dynamics of tissues. We provide examples showing how to use them in virtual experiments exploring how cancer responds to the cells in its environment and how the brain forms layers in development.
Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories
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MRD
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Circulating tumour cells & circulating tumour DNA in patients with resectable colorectal liver metastases (MIRACLE): a prospective, observational biomarker study
EClinicalMedicine. 2025 Aug 12;87:103406. doi: 10.1016/j.eclinm.2025.103406. eCollection 2025 Sep.ABSTRACTBACKGROUND: Recurrence risk after curative surgery for colorectal liver metastases (CRLM) remains high, underlining the need to identify prognostic markers enabling more individualised treatment approaches.METHODS: In the MIRACLE, a prospective, observational biomarker study, a total of 188 patients with isolated, resectable CRLM without (neo)adjuvant chemotherapy were included between Octob
Circulating tumour cells & circulating tumour DNA in patients with resectable colorectal liver metastases (MIRACLE): a prospective, observational biomarker study
EClinicalMedicine. 2025 Aug 12;87:103406. doi: 10.1016/j.eclinm.2025.103406. eCollection 2025 Sep.
ABSTRACT
BACKGROUND: Recurrence risk after curative surgery for colorectal liver metastases (CRLM) remains high, underlining the need to identify prognostic markers enabling more individualised treatment approaches.
METHODS: In the MIRACLE, a prospective, observational biomarker study, a total of 188 patients with isolated, resectable CRLM without (neo)adjuvant chemotherapy were included between October 2015 and December 2021. Blood samples were collected before surgery (baseline) and three weeks after surgery. The primary objective was to assess the potential association between postoperative circulating tumour DNA (ctDNA) detection and recurrence of disease for patients with resectable CRLM within one year after resection. The secondary objective was the association between recurrence of disease within one year and detection of circulating tumour cells (CTCs). Baseline ctDNA was measured by next generation sequencing using a targeted panel (Oncomine Colon cell-free DNA assay) and postoperatively by digital PCR on genetic variants found preoperatively with the Oncomine panel. CTCs were enumerated using the FDA-approved CellSearch system.
FINDINGS: ctDNA was detected in 117/187 patients (63%) at baseline, and 28/104 evaluable patients (27%) still had detectable ctDNA postoperatively. CTC enumeration resulted in positivity for 37/183 patients (20%) at baseline and 14/158 patients (9%) postoperatively. No association was found between 1-year recurrence-free survival (RFS) and the presence of CTCs or ctDNA at baseline. In contrast, patients with postoperative undetectable ctDNA had a significantly improved 1-year RFS compared to patients with postoperative ctDNA (54% [95% CI 44%-67%] vs. 25% [95% CI 13%-47%], log-rank p = 0.0011). Similarly, patients with postoperative detectable CTCs had a significantly shorter 1-year RFS compared to patients without postoperative CTCs (15% [95% CI 4%-55%] vs. 53% [95% CI 45%-62%], log-rank p 0.0004). Also in multivariable analysis, detectable ctDNA and CTCs after surgery remained independently associated with a shorter 1-year RFS (HR 2.35; 95% CI 1.34-4.11; p = 0.0028 and HR 2.98; 95% CI 1.56-5.71; p = 0.0010, respectively).
INTERPRETATION: This is the first study conducted in patients with resectable CRLM without (neo)adjuvant chemotherapy, which demonstrates the impact of postoperative detectable circulating tumour load on 1-year RFS. Postoperative ctDNA and CTC detection both represent strong, independent predictors for a shorter RFS after local treatment, as opposed to preoperative detection.
FUNDING: This work was supported by KWF Kankerbestrijding (Dutch Cancer Society, EMCR 2014-6340).
PMID:40838198 | PMC:PMC12361997 | DOI:10.1016/j.eclinm.2025.103406
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Nature Biotechnology - Issue - nature.com science feeds
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Redefining druggable targets with artificial intelligence
Nature Biotechnology, Published online: 19 August 2025; doi:10.1038/s41587-025-02770-1A vast landscape of ‘undruggable’ cancer targets remains beyond the reach of conventional therapeutic agents. Recent advances in artificial intelligence (AI), however, are challenging this paradigm. Synthesizing insights from a Cancer Moonshot workshop, we argue that systemically addressing the undruggable target space with AI requires a new conceptual framework. We highlight the failure of current target taxon
Redefining druggable targets with artificial intelligence
Nature Biotechnology, Published online: 19 August 2025; doi:10.1038/s41587-025-02770-1
A vast landscape of ‘undruggable’ cancer targets remains beyond the reach of conventional therapeutic agents. Recent advances in artificial intelligence (AI), however, are challenging this paradigm. Synthesizing insights from a Cancer Moonshot workshop, we argue that systemically addressing the undruggable target space with AI requires a new conceptual framework. We highlight the failure of current target taxonomies and the need for benchmarking datasets, and re-evaluate clinical validation for novel AI-driven modalities.-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Thor: a platform for cell-level investigation of spatial transcriptomics and histology
Nat Commun. 2025 Aug 5;16(1):7178. doi: 10.1038/s41467-025-62593-1.ABSTRACTSpatial transcriptomics links gene expression with tissue morphology, however, current tools often prioritize genomic analysis, lacking integrated image interpretation. To address this, we present Thor, a comprehensive platform for cell-level analysis of spatial transcriptomics and histological images. Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptome from spot-level data, e
Thor: a platform for cell-level investigation of spatial transcriptomics and histology
Nat Commun. 2025 Aug 5;16(1):7178. doi: 10.1038/s41467-025-62593-1.
ABSTRACT
Spatial transcriptomics links gene expression with tissue morphology, however, current tools often prioritize genomic analysis, lacking integrated image interpretation. To address this, we present Thor, a comprehensive platform for cell-level analysis of spatial transcriptomics and histological images. Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptome from spot-level data, effectively combining gene expression and cell morphology. The platform includes 10 modular tools for genomic and image-based analysis, and is paired with Mjolnir, a web-based interface for interactive exploration of gigapixel images. Thor is validated on simulated data and multiple spatial platforms (ISH, MERFISH, Xenium, Stereo-seq). Thor characterizes regenerative signatures in heart failure, screens breast cancer hallmarks, resolves fine layers in mouse olfactory bulb, and annotates fibrotic heart tissue. In high-resolution Visium HD data, it enhances spatial gene patterns aligned with histology. By bridging transcriptomic and histological analysis, Thor enables holistic tissue interpretation in spatial biology.
PMID:40764306 | PMC:PMC12325965 | DOI:10.1038/s41467-025-62593-1
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Nature - Issue - nature.com science feeds
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Whole-genome sequencing of 490,640 UK Biobank participants
Nature, Published online: 06 August 2025; doi:10.1038/s41586-025-09272-9A study reports whole-genome sequences for 490,640 participants from the UK Biobank and combines these data with phenotypic data to provide new insights into the relationship between human variation and sequence variation.
Whole-genome sequencing of 490,640 UK Biobank participants
Nature, Published online: 06 August 2025; doi:10.1038/s41586-025-09272-9
A study reports whole-genome sequences for 490,640 participants from the UK Biobank and combines these data with phenotypic data to provide new insights into the relationship between human variation and sequence variation.-
Cell
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Personalized molecular signatures of insulin resistance and type 2 diabetes
Muscle samples from over 120 people were analyzed to identify molecular patterns linked to insulin resistance, a key feature of type 2 diabetes. The findings reveal new insights that could help tailor more personalized and effective treatments for the disease.
Personalized molecular signatures of insulin resistance and type 2 diabetes
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Cell
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The generative era of medical AI
Significant progress has been made in recent years in applying large language models and multimodal artificial intelligence to health and medicine, transforming diagnostics, patient interactions, and medical forecasting, although challenges like privacy, regulation, and system integration remain before widespread clinical adoption.
The generative era of medical AI
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Nature - Issue - nature.com science feeds
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Boys surpass girls in maths in the first year of school
Nature, Published online: 24 June 2025; doi:10.1038/d41586-025-01717-5A gender gap in mathematical ability arises shortly after children begin school — irrespective of the type of school they attend and their socio-economic background.
Boys surpass girls in maths in the first year of school
Nature, Published online: 24 June 2025; doi:10.1038/d41586-025-01717-5
A gender gap in mathematical ability arises shortly after children begin school — irrespective of the type of school they attend and their socio-economic background.