A simple phylogenetic approach to analyze hypermutated HIV proviruses reveals insights into their dynamics and persistence during antiretroviral therapy.

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.

From the ocean to our kitchen table: anthropogenic particles in the edible tissue of U.S. West Coast seafood species.

Microplastics (MPs) and other anthropogenic particles (APs) are pervasive environmental contaminants found throughout marine and aquatic environments. We quantified APs in the edible tissue of black rockfish, lingcod, Chinook salmon, Pacific herring, Pacific lamprey, and pink shrimp, comparing AP burdens across trophic levels and between vessel-retrieved and retail-purchased individuals. Edible tissue was digested and analyzed under a microscope, and a subset of suspected APs was identified using spectroscopy (μFTIR).

Electrocardiographic Changes in Pregnant Patients With Congenital Heart Disease For the STORCC Investigators.

Background: Electrocardiograms (EKGs) are routinely performed in pregnant patients with pre-existing cardiovascular disease. However, in pregnant patients with congenital heart disease (CHD), EKG changes during gestation have not been explored.

Methods: We performed a retrospective study of pregnant patients with CHD enrolled in the STORCC initiative.

TraitTrainR: accelerating large-scale simulation under models of continuous trait evolution.

Motivation: The scale and scope of comparative trait data are expanding at unprecedented rates, and recent advances in evolutionary modeling and simulation sometimes struggle to match this pace. Well-organized and flexible applications for conducting large-scale simulations of evolution hold promise in this context for understanding models and more so our ability to confidently estimate them with real trait data sampled from nature.

Results: We introduce , an R package designed to facilitate efficient, large-scale simulations under complex models of continuous trait evolution.