Cumulative HIV viral load and lower CD4 cell count are associated with incident venous thromboembolism in people with HIV.

Background: People with HIV (PWH) have benefited greatly from antiretroviral therapy, but face additional challenges from age-related comorbid conditions, particularly cardiovascular disease including venous thromboembolism (VTE). Little is known about the effect of HIV viremia and immunodeficiency on VTE risk in this population.

Methods: We assessed incident, centrally adjudicated VTE among 21,507 PWH in care between 1/2009-12/2019 within the Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) cohort.

Adaptable and comprehensive approaches for long-read nanopore sequencing of polyadenylated and non-polyadenylated RNAs.

The advent of long-read (LR) sequencing technologies has provided a direct opportunity to determine the structure of transcripts with potential for end-to-end sequencing of full-length RNAs. LR methods that have been described to date include commercial offerings from Oxford Nanopore Technologies (ONT) and Pacific Biosciences. These kits are based on selection of polyadenylated (polyA+) RNAs and/or oligo-dT priming of reverse transcription.

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation.

Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer. To resolve genome dysregulation associated with HPV integration, we performed Oxford Nanopore long-read sequencing on 72 cervical cancer genomes from an Ugandan dataset that was previously characterized using short-read sequencing. We found recurrent structural rearrangement patterns at HPV integration events, which we categorized as: del(etion)-like, dup(lication)-like, translocation, multibreakpoint, or repeat region integrations.

"You know, it feels like you can trust them": mixed methods implementation research to inform the scale up of a health disparities-responsive COVID-19 school testing program.

Background: Health disparities lead to negative COVID-19 outcomes for Hispanic/Latino communities. Rapid antigen testing was an important mitigation tool for protecting schools and their communities as in-person learning resumed. Within the context of a 3-middle-school non-inferiority trial we assessed acceptability and appropriateness of at-home and school-based COVID-19 antigen testing and implementation barriers and facilitators to facilitate district-wide scale up.

The NF-κB-HE4 axis: A novel regulator of HE4 secretion in ovarian cancer.

Ovarian cancer is the leading cause of death among gynecologic malignancies. Despite recent advancements in targeted therapies such as PARP inhibitors, recurrence is common and frequently resistant to existing therapies. A powerful diagnostic tool, coupled with a comprehensive understanding of its implications, is crucial.

Mapping in silico genetic networks of the KMT2D tumour suppressor gene to uncover novel functional associations and cancer cell vulnerabilities.

Background: Loss-of-function (LOF) alterations in tumour suppressor genes cannot be directly targeted. Approaches characterising gene function and vulnerabilities conferred by such mutations are required.

Methods: Here, we computationally map genetic networks of KMT2D, a tumour suppressor gene frequently mutated in several cancer types.

Severity and Number of Substances Used are Independently Associated with Antiretroviral Therapy Adherence Over Time among People with HIV in the Current Treatment Era.

Substance use is associated with decreased antiretroviral therapy (ART) adherence among people with HIV (PWH). Adherence plays a significant role in mediating the negative effects of substance use on HIV suppression and is a principal modifiable patient-level factor in improving HIV suppression and reducing ART drug resistance. Understanding substance use and ART adherence, particularly with rapidly changing substance use epidemiology and ART regimens, is vital to improving HIV care.

The impact of Medicaid expansion under the Affordable Care Act on HIV care continuum outcomes across the United States.

HIV care continuum outcome disparities by health insurance status have been noted among people with HIV (PWH). We therefore examined associations between state Medicaid expansion and HIV outcomes in the United States. Adults (≥18 years) with ≥1 visit in NA-ACCORD clinical cohorts from 2012-2017 contributed person-time annually between first and final visit or death; in each calendar year, clinical retention was ≥2 completed visits > 90 days apart, antiretroviral therapy (ART) receipt was receipt of ≥3 antiretroviral agents, and viral suppression was last measured HIV-1 RNA < 200 copies/mL.

The Contribution of Socioeconomic Factors to HIV RNA Suppression in Persons With HIV Engaged in Care in the NA-ACCORD.

Introduction: Socioeconomic status (SES) influences well-being among people living with HIV (people with HIV [PWH]); when individual-level SES information is not available, area-level SES indicators may be a suitable alternative. We hypothesized that (1) select ZIP code-level SES indicators would be associated with viral suppression and (2) accounting for ZIP code-level SES would attenuate racial disparities in viral suppression among PWH.

Setting: The NA-ACCORD, a collaboration of clinical and interval cohorts of PWH, was used.

Cediranib and Olaparib Combination Compared With Cediranib or Olaparib Alone, or Chemotherapy in Platinum-Resistant or Primary Platinum-Refractory Ovarian Cancer: NRG-GY005.

Purpose: We assessed the efficacy of cediranib, olaparib, and cediranib/olaparib compared with standard-of-care chemotherapy (SOC) in platinum-resistant or platinum-refractory epithelial ovarian cancer (PROC).

Patients And Methods: NRG-GY005 is an open-label, four-arm, phase II/III superiority trial enrolling patients with high-grade serous/endometrioid PROC and one to three previous therapies. Key exclusion criteria included previous receipt of poly(ADP-ribose) polymerase inhibitor or receipt of antiangiogenic therapy in the recurrent setting.

Cohort profile update: the Johns Hopkins HIV clinical cohort, 1989-2023.

The Johns Hopkins HIV Clinical Cohort, established in 1989, links comprehensive, longitudinal clinical data for adults with HIV receiving care in the Johns Hopkins John G. Bartlett Specialty Practice in Baltimore, Maryland, USA, to aid in understanding HIV care and treatment outcomes. Data include demographics, laboratory results, inpatient and outpatient visit information and clinical diagnoses, and prescribed and dispensed medications abstracted from medical records.

Gasdermin D and Gasdermin E Are Dispensable for Silica-Mediated IL-1β Secretion from Mouse Macrophages.

Silica crystals activate the NLRP3 inflammasome in macrophages, resulting in the caspase-1-dependent secretion of the proinflammatory cytokine IL-1β. Caspase-1-mediated cleavage of gasdermin D (GSDMD) triggers the formation of GSDMD pores, which drive pyroptotic cell death and facilitate the rapid release of IL-1β. However, the role of GSDMD in silica-induced lung injury is unclear.

Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing.

Accurate assessment of fragment abundance within a genome is crucial in clinical genomics applications such as the analysis of copy number variation (CNV). However, this task is often hindered by biased coverage in regions with varying guanine-cytosine (GC) content. These biases are particularly exacerbated in hybridization capture sequencing due to GC effects on probe hybridization and polymerase chain reaction (PCR) amplification efficiency.

Smoking and Type 1 Versus Type 2 Myocardial Infarction Among People With HIV in the United States: Results from the Center for AIDS Research Network Integrated Clinical Systems Cohort.

Smoking is a myocardial infarction (MI) risk factor among people with HIV (PWH). Questions persist regarding the role of smoking behaviors and measurements (e.g.

Internalized HIV stigma and viral suppression: examining the mediating and moderating roles of substance use and social support.

Objective: To examine the effects of internalized HIV stigma on viral non-suppression via depressive symptoms, alcohol use, illicit drug use, and medication adherence and investigate whether social support moderates these effects.

Design: Longitudinal observational clinical cohort of patients in HIV care in the US.Methods: Data from the CFAR Network for Integrated Clinical Systems (2016-2019) were used to conduct structural equation models (SEM) to test the indirect effects of internalized HIV stigma on viral non-suppression through depressive symptoms, illicit drug use, alcohol use, and medication adherence.

The origin of great ape gestural forms.

Two views claim to account for the origins of great ape gestural forms. On the Leipzig view, gestural forms are ontogenetically ritualised from action sequences between pairs of individuals. On the St Andrews view, gestures are the product of natural selection for shared gestural forms.

The HIV Index Is Associated With Retention in Care Among Latinx Persons Living With HIV in the CFAR Network of Integrated Clinical Systems Cohort.

The HIV Index is a validated self-report scale of engagement in HIV care previously correlated with future retention and virologic suppression. However, its performance in a monoethnic Latinx population has not been studied. We evaluated the HIV Index among Latinx persons living with HIV in the Centers for AIDS Research Network of Integrated Clinical Systems cohort and performed multivariable logistic regression to estimate its association with primary outcomes of suboptimal retention (not keeping 100% of HIV clinic appointments) and virologic suppression (HIV viral load <200 copies/mL).

Identification of circulating tumor cells captured by the FDA-cleared Parsortix PC1 system from the peripheral blood of metastatic breast cancer patients using immunofluorescence and cytopathological evaluations.

Circulating Tumor Cells (CTCs) may serve as a non-invasive source of tumor material to investigate an individual's disease in real-time. The Parsortix PC1 System, the first FDA-cleared medical device for the capture and harvest of CTCs from peripheral blood of metastatic breast cancer (MBC) patients for use in subsequent user-validated downstream analyses, enables the epitope-independent capture of CTCs with diverse phenotypes based on cell size and deformability. The aim of this study was to determine the proportion of MBC patients and self-declared female healthy volunteers (HVs) that had CTCs identified using immunofluorescence (IF) or Wright-Giemsa (WG) staining.

DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.

Phytophthora sansomeana is an emerging oomycete pathogen causing root rot in many agricultural species including soybean. However, as of now, only one potential resistance gene has been identified in soybean, and our understanding of how genetic and epigenetic regulation in soybean contributes to responses against this pathogen remains largely unknown. In this study, we performed whole genome bisulfite sequencing (WGBS) on two soybean lines, Colfax (resistant) and Williams 82 (susceptible), in response to P.