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A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.
Virus Evol
November 2024
Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.
Hypermutated proviruses, which arise in a single Human Immunodeficiency Virus (HIV) replication cycle when host antiviral APOBEC3 proteins introduce extensive guanine to adenine mutations throughout the viral genome, persist in all people living with HIV receiving antiretroviral therapy (ART). However, hypermutated sequences are routinely excluded from phylogenetic trees because their extensive mutations complicate phylogenetic inference, and as a result, we know relatively little about their within-host evolutionary origins and dynamics. Using >1400 longitudinal single-genome-amplified HIV sequences isolated from six women over a median of 18 years of follow-up-including plasma HIV RNA sequences collected over a median of 9 years between seroconversion and ART initiation, and >500 proviruses isolated over a median of 9 years on ART-we evaluated three approaches for masking hypermutation in nucleotide alignments.
View Article and Find Full Text PDFModel selection and model robustness for population size estimation in two-sample capture-recapture studies.
Am J Epidemiol
January 2025
Department of Mathematics and Statistics, University of Victoria, Victoria, British Columbia, Canada.
Two-sample capture-recapture studies are commonly used in the epidemiological and ecological literature. Most of these studies have been limited to analysis using the Lincoln-Petersen estimator, especially in epidemiological studies. We examine the use of the Lincoln-Petersen estimator and two alternative closed-population methods: Huggins' conditional likelihood method and Pledger's likelihood method with mixtures.
View Article and Find Full Text PDFImpact of age-related changes in buccal epithelial cells on pediatric epigenetic biomarker research.
Nat Commun
January 2025
British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.
Cheek swabs, heterogeneous samples consisting primarily of buccal epithelial cells, are widely used in pediatric DNA methylation studies and biomarker creation. However, the decrease in buccal proportion with age in adults remains unexamined in childhood. We analyzed cheek swabs from 4626 typically developing children 2-months to 20-years-old.
View Article and Find Full Text PDFObjectives: Numerous studies have examined the effects of physical activity on cognitive performance and executive function in people with Alzheimer's disease (AD), although the findings are not entirely consistent. There are also insufficient study reviews for specific workout and assessment tool types. Therefore, the purpose of this study was to systematically investigate the effects of aerobic exercise on the quality of life, cognitive performance and depressive symptoms in people with AD.
View Article and Find Full Text PDFBackground: The rupture of intracranial aneurysms (IAs) leads to aneurysmal subarachnoid hemorrhage (aSAH), which is associated with significant disability and mortality rates. This study aims to identify metabolic markers causally linked to the occurrence of IAs and aSAH through Mendelian randomization (MR), thereby offering novel predictive and therapeutic targets.
Methods: We conducted a genome-wide association study (GWAS) on IAs and aSAH, analyzing 1,400 metabolomic indices from the Canadian Longitudinal Study on Aging (CLSA) cohort (n = 8,299).
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