Pneumoproteins are associated with pulmonary function in HIV-infected persons.

BACKGROUND: COPD is a common HIV comorbidity, and HIV-infected individuals have a higher incidence and earlier onset of COPD compared to HIV-uninfected individuals. While the pathogenesis of HIV-associated COPD is largely unknown, chronic inflammation may contribute. Four pneumoproteins known to be markers of lung injury and inflammation have been associated with COPD in HIV-uninfected individuals: PARC/CCL-18, SP-D, CC-16, and sRAGE. OBJECTIVE: To determine whether these pneumoproteins are also associated with pulmonary function and COPD Assessment Test (CAT) scores in HIV-infected individuals. METHODS: Associations between plasma pneumoprotein levels and pulmonary function were determined in a cross-sectional study of otherwise healthy HIV-infected individuals enrolled between September 2016 and June 2017. Covariates included HIV-associated (antiretroviral therapy, CD4 count, and viral load) and COPD-associated (smoking and BMI) covariates. RESULTS: Among 65 participants, 78.5% were male, 50.8% had undetectable viral load, and 76.9% were ever-smokers. Mean post-bronchodilator FEV1/FVC was 0.71, and mean DLco%predicted was 61%. Higher PARC/CCL-18 was associated with lower DLco%predicted and higher CAT score. Higher CC-16 was associated with lower DLco%predicted and lower FVC%predicted. CONCLUSIONS: This exploratory analysis is the first to characterize associations between these four pneumoproteins and pulmonary function in an HIV-infected cohort. Our findings suggest the pathogenesis of HIV-associated COPD may differ from that of non-HIV-associated COPD due to HIV-specific inflammatory changes affecting DLco. PARC/CCL-18 is associated with structural and functional pulmonary abnormalities and may be an important COPD biomarker candidate in HIV infection. Our study is a preliminary step toward finding clinically relevant COPD biomarkers in high-risk populations.

Concordance of Text Message Ecological Momentary Assessment and Retrospective Survey Data Among Substance-Using Men Who Have Sex With Men: A Secondary Analysis of a Randomized Controlled Trial.

BACKGROUND: Alcohol and illicit drug use is more prevalent among men who have sex with men (MSM) compared to the general population and has been linked to HIV transmission in this population. Research assessing individual patterns of substance use often utilizes questionnaires or interviews that rely on retrospective self-reported information, which can be subject to recall bias. Ecological momentary assessment (EMA) is a set of methods developed to mitigate recall bias by collecting data about subjects' mental states and behaviors on a near real-time basis. EMA remains underutilized in substance use and HIV research. OBJECTIVE: To assess the concordance between daily reports of substance use collected by EMA text messages (short message service, SMS) and retrospective questionnaires and identify predictors of daily concordance in a sample of MSM. METHODS: We conducted a secondary analysis of EMA text responses (regarding behavior on the previous day) and audio computer-assisted self-interview (ACASI) survey data (14-day recall) from June 2013 to September 2014 as part of a randomized controlled trial assessing a pharmacologic intervention to reduce methamphetamine and alcohol use among nondependent MSM in San Francisco, California. Reports of daily methamphetamine use, alcohol use, and binge alcohol use (5 or more drinks on one occasion) were collected via EMA and ACASI and compared using McNemar's tests. Demographic and behavioral correlates of daily concordance between EMA and ACASI were assessed for each substance, using separate multivariable logistic regression models, fit with generalized estimating equations. RESULTS: Among 30 MSM, a total of 994 days were included in the analysis for methamphetamine use, 987 for alcohol use, and 981 for binge alcohol use. Methamphetamine (EMA 20%, ACASI 11%, P<.001) and alcohol use (EMA 40%, ACASI 35%, P=.001) were reported significantly more frequently via EMA versus ACASI. In multivariable analysis, text reporting of methamphetamine (adjusted odds ratio 0.06, 95% CI 0.04-0.10), alcohol (0.48, 0.33-0.69), and binge alcohol use (0.27, 0.17-0.42) was negatively associated with daily concordance in the reporting of each respective substance. Compared to white participants, African American participants were less likely to have daily concordance in methamphetamine (0.15, 0.05-0.43) and alcohol (0.2, 0.05-0.54) reporting, and other participants of color (ie, Asian, Hispanic, multi-racial) were less likely to have daily concordance in methamphetamine reporting (0.34, 0.12-1.00). College graduates were more likely to have daily concordance in methamphetamine reporting (6.79, 1.84-25.04) compared to those with no college experience. CONCLUSIONS: We found that methamphetamine and alcohol use were reported more frequently with daily EMA texts compared to retrospective ACASI, concordance varied among different racial/ethnic subgroups and education levels, and reported substance use by EMA text was associated with lower daily concordance with retrospective ACASI. These findings suggest that EMA methods may provide more complete reporting of frequent, discrete behaviors such as substance use.

De novo characterization of the Timema cristinae transcriptome facilitates marker discovery and inference of genetic divergence.

Adaptation to different ecological environments can promote speciation. Although numerous examples of such 'ecological speciation' now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study, we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84,937 contigs representing approximately 18,282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multilocus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.