Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy

Adherence to clinical follow-up recommendations for liver function tests: A cross-sectional study of patients with HCV and their associated risk behaviors

This study examined whether patients with Hepatitis C virus (HCV) infection adhered to their physicians\u27 recommendation and HCV clinical guidelines for obtaining a regular liver function test (LFT), and whether high-risk behaviors are associated with behavioral adherence. A cross-sectional survey was administered to 101 eligible patients with HCV who were recruited from health centers in New Jersey and Washington, DC. Adherence outcomes were defined as the patients\u27 self-report of two consecutive receipts of LFTs in accordance with their physicians\u27 recommended interval or the clinical guidelines for a LFT within 3-6 months. 67.4% of patients (66/98) reported a receipt of their physicians\u27 recommendation for a LFT. The rate of adherence to physician recommendation was about 70% (46/66), however over 50% (52/101) of patients with HCV did not obtain regular LFTs. 15.8% (16/101) of patients continued to use injection drugs. Patients who used injection drugs had 0.87 (adjusted odds ratio (aOR) = 0.13, 95% confidence interval 0.03-0.59) times lower odds adhering to their physician recommendation, relative to non-users. Patients with HIV co-infection had increased odds of adhering to the clinical guidelines (odds ratio 3.41, 95% confidence interval 1.34-8.70) vs. patients who did not report HIV co-infection. Additionally, patients who had received a physician\u27s recommendation had 7.21 times (95% confidence interval of 2.36-22.2) greater odds adhering to the clinical guidelines than those who had not. Overall, promoting HCV patient-provider communication regarding regular LFTs and reduction of risk behaviors is essential for preventing patients from HCV-related liver disease progression

Plasma Biomarkers of Alzheimer Disease in Women With and Without HIV

IMPORTANCE: Blood-based biomarkers associated with increased risk of Alzheimer disease (AD) are understudied in people living with and without HIV, particularly women. OBJECTIVES: To determine whether baseline or 1-year changes in plasma amyloid-β40 (Aβ40), Aβ42, ratio of Aβ42 to Aβ40, total tau (t-tau), phosphorylated tau 231 (p-tau231), glial fibrillary acidic protein (GFAP), and/or neurofilament light chain (NFL) are associated with neuropsychological performance (NP) among women living with HIV (WLWH) and women living without HIV (WLWOH). To determine whether baseline or 1-year changes in plasma amyloid-β40 (Aβ40), Aβ42, ratio of Aβ42 to Aβ40, total tau (t-tau), phosphorylated tau 231 (p-tau231), glial fibrillary acidic protein (GFAP), and/or neurofilament light chain (NFL) are associated with neuropsychological performance (NP) among women living with HIV (WLWH) and women living without HIV (WLWOH). DESIGN, SETTING, AND PARTICIPANTS: This longitudinal, prospective, cohort study with 1-year repeated clinical measures (NP only measured once) and biospecimen collection occurred between 2017 and 2019. Participants were women aged 40 years or older from 10 clinical research sites in cities across the US that were part of the Women’s Interagency HIV Study. Data analysis was conducted from April to December 2022. EXPOSURE: Laboratory-confirmed HIV status and AD biomarkers. MAIN OUTCOMES AND MEASURES: Sociodemographically adjusted NP T-scores (attention and working memory, executive function, processing speed, memory, learning, verbal fluency, motor function, and global performance) were the primary outcomes. Baseline and 1-year fasting plasma Aβ40, Aβ42, t-tau, p-tau231, GFAP, and NFL levels were measured and analyzed using multivariable linear regression. RESULTS: The study consisted of 307 participants (294 aged ≥50 years [96%]; 164 African American or Black women [53%]; 214 women with a high school education or higher [70%]; 238 women who were current or former smokers [78%]; and 236 women [77%] who were overweight or obese [body mass index >25]) including 209 WLWH and 98 WLWOH. Compared with WLWOH at baseline, WLWH performed worse on learning (mean [SD] T-score 47.8 [11.3] vs 51.4 [10.5]), memory (mean [SD] T-score 48.3 [11.6] vs 52.4 [10.2]), verbal fluency (mean [SD] T-score 48.3 [9.8] vs 50.7 [8.5]), and global (mean [SD] T-score 49.2 [6.8] vs 51.1 [5.9]) NP assessments. Baseline median Aβ40, GFAP, and NFL levels were higher among WLWH vs WLWOH. There were no differences in 1-year biomarker change by HIV serostatus. Lower learning, memory, and motor NP were associated with 1-year Aβ40 increase; lower learning and motor with Aβ42 increase; lower motor with p-tau231 increase; and lower processing speed, verbal fluency and motor with NFL increase in the entire sample. Among WLWH, a 1-year increase in Aβ40 from baseline to follow-up was associated with worse learning, memory, and global NP; a 1-year increase in t-tau with worse executive function; and a 1-year increase in NFL with worse processing speed. Among WLWOH, a 1-year increase in Aβ40 and Aβ42 were associated with poorer memory performance and NFL was associated with poorer motor performance. CONCLUSIONS AND RELEVANCE: These findings suggest that increases in certain plasma AD biomarkers are associated with NP in WLWH and WLWOH and may be associated with later onset of AD, and measuring these biomarkers could be a pivotal advancement in monitoring aging brain health and development of AD among women with and without HIV

Association between BMI and periodontitis in women living with or at risk for HIV

Aims: Currently, there is no data available assessing the association between body mass index (BMI) and periodontitis among women living with HIV (WLWH). This study aims to investigate this association among WLWH and women at risk for HIV (WRH) in the United States. Methods and results: Data from 351 WLWH and 52 WRH participants from the Women's Interagency HIV Study having pocket depths and clinical periodontal attachment loss assessments in 2003–2004 were included. Multinomial logistic regression analyses in the full sample assessed the relationship between BMI (underweight/normal, overweight, or obese) and periodontitis by severity (mild, moderate, severe), adjusting for study sites, age, education, annual household income, smoking, alcohol consumption, and diabetes. Overall, 75.2% women (76.0% WLWH; 69.0% WRH) had periodontitis. Moreover, 75.0% obese and 75.3% overweight women were affected by periodontitis. In the full sample, adjusted odds ratio (aOR) of having mild, moderate, and severe periodontitis in obese women were: 1.14 (95% confidence interval [CI]: 0.51–2.52), 1.02 (95% CI: 0.46–2.29), and 0.24 (95% CI: 0.06–1.07), respectively, and in overweight women: 0.70 (95% CI: 0.31–1.58), 0.85 (95% CI: 0.38–1.90), and 0.31 (95% CI: 0.08–1.15), respectively. Conclusions: Even with high prevalence of periodontitis among women with or without HIV infection in this cohort, this study does not provide evidence of an association between BMI and periodontitis

Health Insurance Type and Control of Hypertension Among US Women Living With and Without HIV Infection in the Women’s Interagency HIV Study

BACKGROUND: Health care access is an important determinant of health. We assessed the effect of health insurance status and type on blood pressure control among US women living with (WLWH) and without HIV. METHODS: We used longitudinal cohort data from the Women's Interagency HIV Study (WIHS). WIHS participants were included at their first study visit since 2001 with incident uncontrolled blood pressure (BP) (i.e., BP ≥140/90 and at which BP at the prior visit was controlled (i.e., <135/85). We assessed time to regained BP control using inverse Kaplan-Meier curves and Cox proportional hazard models. Confounding and selection bias were accounted for using inverse probability-of-exposure-and-censoring weights. RESULTS: Most of the 1,130 WLWH and 422 HIV-uninfected WIHS participants who had an elevated systolic or diastolic measurement were insured via Medicaid, were African-American, and had a yearly income ≤$12,000. Among participants living with HIV, comparing the uninsured to those with Medicaid yielded an 18-month BP control risk difference of 0.16 (95% CI: 0.10, 0.23). This translates into a number-needed-to-treat (or insure) of 6; to reduce the caseload of WLWH with uncontrolled BP by one case, five individuals without insurance would need to be insured via Medicaid. Blood pressure control was similar among WLWH with private insurance and Medicaid. There were no differences observed by health insurance status on 18-month risk of BP control among the HIV-uninfected participants. CONCLUSIONS: These results underscore the importance of health insurance for hypertension control-especially for people living with HIV

Impact of Health Insurance, ADAP, and Income on HIV Viral Suppression Among US Women in the Womenʼs Interagency HIV Study, 2006–2009

Implementation of the Affordable Care Act motivates assessment of health insurance and supplementary programs, such as the AIDS Drug Assistance Program (ADAP) on health outcomes of HIV-infected people in the United States. We assessed the effects of health insurance, ADAP, and income on HIV viral load suppression