Quantifying DNA point mutations in commercially available AAV reporter vectors and plasmids.

To compare the accuracy of three sequencing methods for quantifying point mutations in AAV products, we sequenced the green fluorescent protein (GFP) transgene from two AAV9 reporter vectors (three lots each) and their respective plasmids, using three sequencing approaches: single-template amplification (STA) followed by Sanger sequencing (STA-Sanger) and two next-generation sequencing (NGS) platforms (Illumina and Oxford Nanopore Technologies [ONT]). Similar vector per-base mutation rates were found for both STA-Sanger (0.016%) and Illumina (0.

Indicators for Increased Likelihood of Epidemic Kaposi Sarcoma Progression After Antiretroviral Therapy Initiation.

Kaposi sarcoma (KS) is a common malignancy for people living with HIV (PLWH), despite antiretroviral therapy (ART). Curiously, even with improved CD4 T-cell counts and low viral loads following ART, some PLWH with KS may still experience KS progression or even death and require adjuvant chemotherapy to manage their KS. The factors associated with persistent or unresponsive KS after ART initiation remain poorly characterized, and biomarkers to identify patients at risk of KS progression are needed, particularly in resource-limited areas where access to chemotherapy is limited.

Infants' organization of pull-to-stand behaviors during play: A longitudinal investigation.

Pulling-to-stand (PTS) is an important transitional posture which may facilitate the shift to walking, but infants still frequently PTS even after learning to walk. Using a group of 13 infants who had learned to PTS about three weeks prior, we aimed to track how gains in PTS, standing, and walking experience contributed to infants' selection of more skilled PTS strategies and reorganized how infants used PTS to facilitate free play. We tracked spontaneous PTS over 10 biweekly laboratory sessions and video-coded functional measures of PTS skill, including hand-, knee-, and foot-use (e.

Monitoring and management of hemolytic disease of the fetus and newborn based on an international expert Delphi consensus.

The study aimed to develop structured, expert-based clinical guidance on the prenatal and postnatal management of hemolytic disease of the fetus and newborn. A Delphi procedure was conducted among an international panel of experts in fetal medicine, neonatology, and hematology. Experts were selected based on their expertise, relevant publications, and affiliations.

Decreasing early invasive mechanical ventilation exposure in preterm infants: a quality improvement initiative.

Objective: To decrease invasive mechanical ventilation exposure in the neonatal intensive care unit (NICU) in the first week of life for preterm infants with the global aim of decreasing bronchopulmonary dysplasia (BPD).

Methods: We created a quality improvement (QI) initiative to optimize early non-invasive respiratory support which launched in August 2021. Patients born at <32 weeks gestation and admitted to the NICU on non-invasive respiratory support were included.

Comparing Gold-Standard Sanger Sequencing with Two Next-Generation Sequencing Platforms of HIV-1 Single Genome Amplicons.

Our goal was to assess the accuracy of next generation sequencing (NGS) compared with Sanger. We performed single genome amplification (SGA) of HIV-1 on extracted tissue DNA from two HIV+ individuals. Amplicons ( = 30) were sequenced with Sanger or reamplified with barcoded primers and pooled before sequencing using Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PB).

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population.

Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8 epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.

Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen.

Background: The principal barrier to an HIV cure is the presence of the latent viral reservoir (LVR), which has been understudied in African populations. From 2018 to 2019, Uganda instituted a nationwide rollout of ART consisting of Dolutegravir (DTG) with two NRTI, which replaced the previous regimen of one NNRTI and the same two NRTI.

Methods: Changes in the inducible replication-competent LVR (RC-LVR) of ART-suppressed Ugandans with HIV (n = 88) from 2015 to 2020 were examined using the quantitative viral outgrowth assay.

Evaluating real-world emissions from in-use buses and taxis using on-road remote sensing.

Assessing real-world emissions from buses and taxis is vital to comprehend their impact on urban air quality. Such vehicles differ significantly from the majority of the fleet owing to their higher mileage rates. However, few studies have focused on specifically assessing the emissions from this segment of the vehicle fleet.

The impact on passenger car emissions associated with the promotion and demise of diesel fuel.

The promotion and growth in the use of diesel fuel in passenger cars in the UK and Europe over the past two decades led to considerable adverse air quality impacts in urban areas and more widely. In this work, we construct a multi-decade analysis of passenger car emissions in the UK based on real driving emissions data. An important part of the study is the use of extensive vehicle emission remote sensing data covering multiple measurement locations, time periods, environmental conditions and consisting of over 600,000 measurements.

Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations.

Background: We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana.

Methods: Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp.

HIV-1 subtypes maintain distinctive physicochemical signatures in Nef domains associated with immunoregulation.

Background: HIV subtype is associated with varied rates of disease progression. The HIV accessory protein, Nef, continues to be present during antiretroviral therapy (ART) where it has numerous immunoregulatory effects. In this study, we analyzed Nef sequences from HIV subtypes A1, B, C, and D using a machine learning approach that integrates functional amino acid information to identify if unique physicochemical features are associated with Nef functional/structural domains in a subtype-specific manner.

Associations between neighborhood socioeconomic deprivation, IFNγ, and high-density lipoprotein particle size: Data from the Washington, D.C. cardiovascular health and needs assessment.

Introduction: Neighborhood socioeconomic deprivation is associated with increased cardiovascular risk factors, including inflammation. Inflammation plays an important role in modifying the cardioprotective function of high-density lipoprotein (HDL). Moreover, recent studies suggest that very high HDL is associated with adverse cardiovascular disease (CVD) outcomes.

Comparing antimicrobial resistant genes and phenotypes across multiple sequencing platforms and assays for Enterobacterales clinical isolates.

Introduction: Whole genome sequencing (WGS) of bacterial isolates can be used to identify antimicrobial resistance (AMR) genes. Previous studies have shown that genotype-based AMR has variable accuracy for predicting carbapenem resistance in carbapenem-resistant Enterobacterales (CRE); however, the majority of these studies used short-read platforms (e.g.

Temporary increase in circulating replication-competent latent HIV-infected resting CD4+ T cells after switch to an integrase inhibitor based antiretroviral regimen.

The principal barrier to an HIV cure is the presence of a latent viral reservoir (LVR) made up primarily of latently infected resting CD4+ (rCD4) T-cells. Studies in the United States have shown that the LVR decays slowly (half-life=3.8 years), but this rate in African populations has been understudied.

Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons.

To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model.

Assessing the impact of fire on spiders through a global comparative analysis.

In many regions fire regimes are changing due to anthropogenic factors. Understanding the responses of species to fire can help to develop predictive models and inform fire management decisions. Spiders are a diverse and ubiquitous group and can offer important insights into the impacts of fire on invertebrates and whether these depend on environmental factors, phylogenetic history or functional traits.

An Adjuvant Stem Cell Patch with Coronary Artery Bypass Graft Surgery Improves Diastolic Recovery in Porcine Hibernating Myocardium.

Diastolic dysfunction persists despite coronary artery bypass graft surgery (CABG) in patients with hibernating myocardium (HIB). We studied whether the adjunctive use of a mesenchymal stem cells (MSCs) patch during CABG improves diastolic function by reducing inflammation and fibrosis. HIB was induced in juvenile swine by placing a constrictor on the left anterior descending (LAD) artery, causing myocardial ischemia without infarction.

Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons.

To overcome the ethical and technical limitations of human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate of disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model.

Cannabidiol modulates excitatory-inhibitory ratio to counter hippocampal hyperactivity.

Cannabidiol (CBD), a non-euphoric component of cannabis, reduces seizures in multiple forms of pediatric epilepsies, but the mechanism(s) of anti-seizure action remain unclear. In one leading model, CBD acts at glutamatergic axon terminals, blocking the pro-excitatory actions of an endogenous membrane phospholipid, lysophosphatidylinositol (LPI), at the G-protein-coupled receptor GPR55. However, the impact of LPI-GPR55 signaling at inhibitory synapses and in epileptogenesis remains underexplored.