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CASTER: Direct species tree inference from whole-genome alignments.
Science
January 2025
Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the current practice leaves out large chunks of genomes. As more high-quality genomes become available, we urgently need discordance-aware methods to infer the tree directly from a multiple genome alignment.
View Article and Find Full Text PDFIntegrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis.
Ann Med
December 2025
Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, PR China.
Objective: This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.
Methods: Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes.
Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover.
Theor Appl Genet
January 2025
Grasslands Research Centre, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand.
Genomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone. Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.
View Article and Find Full Text PDFNon-parametric Bayesian deep learning approach for whole-body low-dose PET reconstruction and uncertainty assessment.
Med Biol Eng Comput
January 2025
Faculty of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel.
Positron emission tomography (PET) imaging plays a pivotal role in oncology for the early detection of metastatic tumors and response to therapy assessment due to its high sensitivity compared to anatomical imaging modalities. The balance between image quality and radiation exposure is critical, as reducing the administered dose results in a lower signal-to-noise ratio (SNR) and information loss, which may significantly affect clinical diagnosis. Deep learning (DL) algorithms have recently made significant progress in low-dose (LD) PET reconstruction.
View Article and Find Full Text PDFAfter the storm, the calm never came: Hurricane Maria-related stressors and PTSD symptoms among Puerto Rican youth.
Psychol Trauma
January 2025
Medical University of South Carolina, Department of Psychiatry and Behavioral Sciences.
Objective: Youth may develop posttraumatic stress disorder (PTSD) following a hurricane. Triaging of mental health services is crucial to effectively deliver trauma-focused interventions following natural disasters. Given the increased likelihood of hurricanes due to the current climate crisis, this study sought to examine the dose-response effect between hurricane-related stressors and PTSD, identify a cumulative stressor cutoff score based on the number of hurricane-related stressors experienced, and identify important individual hurricane-related stressors in explaining PTSD symptoms among youth.
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