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cs.AI, q-bio.NC updates on arXiv.org
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CXReasonBench: A Benchmark for Evaluating Structured Diagnostic Reasoning in Chest X-rays
arXiv:2505.18087v2 Announce Type: replace-cross Abstract: Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the public
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Nature - Issue - nature.com science feeds
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Parity and lactation induce T cell mediated breast cancer protection
Nature, Published online: 20 October 2025; doi:10.1038/s41586-025-09713-5Parity and lactation induce T cell mediated breast cancer protection
Parity and lactation induce T cell mediated breast cancer protection
Nature, Published online: 20 October 2025; doi:10.1038/s41586-025-09713-5
Parity and lactation induce T cell mediated breast cancer protection-
Nature Medicine
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Clinical validation of an AI-based blood testing device for diagnosis and prognosis of acute infection and sepsis
Nature Medicine, Published online: 30 September 2025; doi:10.1038/s41591-025-03933-yIn a prospective study enrolling 1,222 patients from 22 emergency departments, a device using a machine-learning-based signature of blood mRNAs demonstrated clinically acceptable performance to diagnose bacterial and viral infections and to predict the all-cause need for critical care interventions within 7 days, with benchmark to established biomarkers and risk scores.
Clinical validation of an AI-based blood testing device for diagnosis and prognosis of acute infection and sepsis
Nature Medicine, Published online: 30 September 2025; doi:10.1038/s41591-025-03933-y
In a prospective study enrolling 1,222 patients from 22 emergency departments, a device using a machine-learning-based signature of blood mRNAs demonstrated clinically acceptable performance to diagnose bacterial and viral infections and to predict the all-cause need for critical care interventions within 7 days, with benchmark to established biomarkers and risk scores.-
(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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A statistical physics approach to integrating multi-omics data for disease-module detection
Cell Rep Methods. 2025 Sep 19:101183. doi: 10.1016/j.crmeth.2025.101183. Online ahead of print.ABSTRACTGenes associated with the same disease frequently engage in mutual biological interactions, e.g., perturbation within a specific neighborhood in the molecular interactome, often referred to as the disease module. This has propelled the advancement of network-based approaches toward elucidating the molecular bases of human diseases. Although many computational methods have been developed to inte
A statistical physics approach to integrating multi-omics data for disease-module detection
Cell Rep Methods. 2025 Sep 19:101183. doi: 10.1016/j.crmeth.2025.101183. Online ahead of print.
ABSTRACT
Genes associated with the same disease frequently engage in mutual biological interactions, e.g., perturbation within a specific neighborhood in the molecular interactome, often referred to as the disease module. This has propelled the advancement of network-based approaches toward elucidating the molecular bases of human diseases. Although many computational methods have been developed to integrate the molecular interactome and omics profiles to extract such context-dependent disease modules, approaches that leverage multi-omics for disease-module detection are still lacking. Here, we developed a statistical physics approach based on the random-field O(n) model (RFOnM) to fill this gap. We applied the RFOnM approach to integrate gene-expression data and genome-wide association studies or mRNA data and DNA methylation for several complex diseases with the human interactome. We found that the RFOnM approach outperforms existing single omics methods in most of the complex diseases considered in this study.
PMID:40975055 | DOI:10.1016/j.crmeth.2025.101183
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Nature - Issue - nature.com science feeds
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Functional evaluation and clinical classification of <i>BRCA2</i> variants
Nature, Published online: 08 January 2025; doi:10.1038/s41586-024-08388-8Results from a comprehensive evaluation of the function of BRCA2 variants, particularly variants of uncertain significance, provide a useful resource to improve the clinical management of individuals who carry such genetic variants.
Functional evaluation and clinical classification of <i>BRCA2</i> variants
Nature, Published online: 08 January 2025; doi:10.1038/s41586-024-08388-8
Results from a comprehensive evaluation of the function of BRCA2 variants, particularly variants of uncertain significance, provide a useful resource to improve the clinical management of individuals who carry such genetic variants.-
Nature - Issue - nature.com science feeds
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Label-free detection and profiling of individual solution-phase molecules
Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07370-8Enhanced light–molecule interactions in high-finesse fibre-based Fabry–Pérot microcavities are used to detect and profile individual unlabelled solution-phase biomolecules, leading to potential applications in the life and chemical sciences.
Label-free detection and profiling of individual solution-phase molecules
Nature, Published online: 08 May 2024; doi:10.1038/s41586-024-07370-8
Enhanced light–molecule interactions in high-finesse fibre-based Fabry–Pérot microcavities are used to detect and profile individual unlabelled solution-phase biomolecules, leading to potential applications in the life and chemical sciences.-
Cell
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A pan-cancer analysis of the microbiome in metastatic cancer
Characterization of microbiome genomes at the species level in over 4,000 metastatic tumor biopsies identifies the distribution and diversity features of tumor-resident bacterial DNA at a pan-cancer scale, highlighting the associations between microbial community dynamics and tumor immunity and immunotherapy efficacy.
A pan-cancer analysis of the microbiome in metastatic cancer
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Nature - Issue - nature.com science feeds
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Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer
Nature, Published online: 08 April 2024; doi:10.1038/s41586-024-07379-zTumor-selective activity of RAS-GTP inhibition in pancreatic cancer
Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer
Nature, Published online: 08 April 2024; doi:10.1038/s41586-024-07379-z
Tumor-selective activity of RAS-GTP inhibition in pancreatic cancer-
Cell
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Pan-cancer proteogenomics characterization of tumor immunity
Immunotherapy holds strong promise for cancer treatment but at present benefits only a small proportion of cases. A pan-cancer analysis of the immune landscape in more than 1,000 tumors across ten cancer types reveals immune surveillance and immune evasion mechanisms as well as potential molecular target that could augment future immunotherapy and precision medicine strategies.
Pan-cancer proteogenomics characterization of tumor immunity
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Nature - Issue - nature.com science feeds
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Organ aging signatures in the plasma proteome track health and disease
Nature, Published online: 06 December 2023; doi:10.1038/s41586-023-06802-1Blood plasma protein data was combined with machine learning models for a simple method to determine differences in organ-specific aging; the study provides a basis for the prediction of diseases and aging effects using plasma proteomics.
Organ aging signatures in the plasma proteome track health and disease
Nature, Published online: 06 December 2023; doi:10.1038/s41586-023-06802-1
Blood plasma protein data was combined with machine learning models for a simple method to determine differences in organ-specific aging; the study provides a basis for the prediction of diseases and aging effects using plasma proteomics.-
Cell
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Early career Latinas in STEM: Challenges and solutions
Mexican, Puerto Rican, and Central American Ancestry (MPRCA) individuals represent 82% of US Latinos. An intergenerational group of MPRCA women and allies met to discuss persistent underrepresentation of MPRCA women in STEM, identifying multi-level challenges and solutions. Implementation of these solutions is important and will benefit MPRCA and the entire academic community.
Early career Latinas in STEM: Challenges and solutions
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Oncogene - Issue - nature.com science feeds
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Metabolic control of cancer metastasis: role of amino acids at secondary organ sites
Oncogene, Published online: 18 October 2023; doi:10.1038/s41388-023-02868-3Metabolic control of cancer metastasis: role of amino acids at secondary organ sites
Metabolic control of cancer metastasis: role of amino acids at secondary organ sites
Oncogene, Published online: 18 October 2023; doi:10.1038/s41388-023-02868-3
Metabolic control of cancer metastasis: role of amino acids at secondary organ sites-
Nature - Issue - nature.com science feeds
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Why a blockbuster superconductivity claim met a wall of scepticism
Nature, Published online: 06 September 2023; doi:10.1038/d41586-023-02733-zPhysicist Ranga Dias and his colleagues have twice claimed to make a room-temperature superconductor. But many researchers question the evidence.
Why a blockbuster superconductivity claim met a wall of scepticism
Nature, Published online: 06 September 2023; doi:10.1038/d41586-023-02733-z
Physicist Ranga Dias and his colleagues have twice claimed to make a room-temperature superconductor. But many researchers question the evidence.-
Nature Biotechnology - Issue - nature.com science feeds
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Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
Nature Biotechnology, Published online: 22 August 2023; doi:10.1038/s41587-023-01952-zAuthor Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification
Nature Biotechnology, Published online: 22 August 2023; doi:10.1038/s41587-023-01952-z
Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification-
Oncogene - Issue - nature.com science feeds
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Editorial Expression of Concern: Overexpression of CEACAM6 promotes insulin-like growth factor I-induced pancreatic adenocarcinoma cellular invasiveness
Oncogene, Published online: 19 July 2023; doi:10.1038/s41388-023-02784-6Editorial Expression of Concern: Overexpression of CEACAM6 promotes insulin-like growth factor I-induced pancreatic adenocarcinoma cellular invasiveness
Editorial Expression of Concern: Overexpression of CEACAM6 promotes insulin-like growth factor I-induced pancreatic adenocarcinoma cellular invasiveness
Oncogene, Published online: 19 July 2023; doi:10.1038/s41388-023-02784-6
Editorial Expression of Concern: Overexpression of CEACAM6 promotes insulin-like growth factor I-induced pancreatic adenocarcinoma cellular invasiveness-
Nature - Issue - nature.com science feeds
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Organization of the human intestine at single-cell resolution
Nature, Published online: 19 July 2023; doi:10.1038/s41586-023-05915-xIntestinal cell types are organized into distinct neighbourhoods and communities within the healthy human intestine, with distinct immunological niches.
Organization of the human intestine at single-cell resolution
Nature, Published online: 19 July 2023; doi:10.1038/s41586-023-05915-x
Intestinal cell types are organized into distinct neighbourhoods and communities within the healthy human intestine, with distinct immunological niches.-
Nature - Issue - nature.com science feeds
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Pan-cancer whole-genome comparison of primary and metastatic solid tumours
Nature, Published online: 10 May 2023; doi:10.1038/s41586-023-06054-zThe genomic differences between primary and metastatic tumours are assessed across 23 cancer types using pan-cancer whole-genome analysis.
Pan-cancer whole-genome comparison of primary and metastatic solid tumours
Nature, Published online: 10 May 2023; doi:10.1038/s41586-023-06054-z
The genomic differences between primary and metastatic tumours are assessed across 23 cancer types using pan-cancer whole-genome analysis.-
Oncogene - Issue - nature.com science feeds
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Nuclear FGFR1 promotes pancreatic stellate cell-driven invasion through up-regulation of Neuregulin 1
Oncogene, Published online: 10 November 2022; doi:10.1038/s41388-022-02513-5Nuclear FGFR1 promotes pancreatic stellate cell-driven invasion through up-regulation of Neuregulin 1
Nuclear FGFR1 promotes pancreatic stellate cell-driven invasion through up-regulation of Neuregulin 1
Oncogene, Published online: 10 November 2022; doi:10.1038/s41388-022-02513-5
Nuclear FGFR1 promotes pancreatic stellate cell-driven invasion through up-regulation of Neuregulin 1