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Abstract Background The increasing volume and complexity of genomic data pose significant challenges for effective data management and reuse. Public genomic data often undergo similar preprocessing across projects, leading to redundant or inconsistent datasets and inefficient use of computing resources. This is especially pertinent for bioinformaticians engaged in multiple projects. Tools have been created to address challenges in managing and accessing curated genomic datasets, however, the practical utility of such tools becomes especially beneficial for users who seek to work with specific types of data or are technically inclined toward a particular programming language. Currently, there exists a gap in the availability of an R-specific solution for efficient data management and versatile data reuse. Results Here we present ReUseData, an R software tool that overcomes some of the limitations of existing solutions and provides a versatile and reproducible approach to effective data management within R. ReUseData facilitates the transformation of ad hoc scripts for data preprocessing into Common Workflow Language (CWL)-based data recipes, allowing for the reproducible generation of curated data files in their generic formats. The data recipes are standardized and self-contained, enabling them to be easily portable and reproducible across various computing platforms. ReUseData also streamlines the reuse of curated data files and their integration into downstream analysis tools and workflows with different frameworks. Conclusions ReUseData provides a reliable and reproducible approach for genomic data management within the R environment to enhance the accessibility and reusability of genomic data. The package is available at Bioconductor ( https://bioconductor.org/packages/ReUseData/ ) with additional information on the project website ( https://rcwl.org/dataRecipes/ ).

Abstract Major depression is the most common neuropsychiatric disorder among people living with HIV (PLWH) and is predictive of high morbidity and mortality among them. This study estimated the prevalence and explored factors associated with depression among PLWH in two rural secondary health facilities providing anti-retroviral therapy (ART) services in Southwestern Nigeria between September and December 2020. The Patient Health Questionnaire-9 (PHQ-9) was used to screen and identify PLWH aged 18 years or older with depression. Descriptive statistics, bivariate and multivariate analyses were performed with SPSS version 23. A total of 172 respondents were screened. The prevalence of depression was 16.3% (95% CI 11.1%, 22.7%). Mild, moderate, and moderately severe depression was identified in 17 (9.9%), 8(4.7%) and 3(1.7%) of the participants, respectively. One (0.6%) respondent had suicidal ideation. Of PLWH with any depression, 20/28(71.4%) were within the 40–59 years of age range. None of the participants was on antidepressants. The factor most associated with depression was hypertension, with adjusted odd ratios of 9.8(95% CI 3.5–27.3, p

Abstract Rationale Due to the relatively short existence of alternative tobacco products, gaps exist in our current understanding of their long-term respiratory health effects. We therefore undertook the first-ever side-by-side comparison of the impact of chronic inhalation of aerosols emitted from electronic cigarettes (EC) and heated tobacco products (HTP), and combustible cigarettes (CC) smoke. Objectives To evaluate the potential differential effects of alternative tobacco products on lung inflammatory responses and efficacy of vaccination in comparison to CC. Methods Mice were exposed to emissions from EC, HTP, CC, or air for 8 weeks. BAL and lung tissue were analyzed for markers of inflammation, lung damage, and oxidative stress. Another group was exposed for 12 weeks and vaccinated and challenged with a bacterial respiratory infection. Antibody titers in BAL and sera and pulmonary bacterial clearance were assessed. Main results EC- and HTP-aerosols significantly augmented lung immune cell infiltrates equivalent to that achieved following CC-exposure. HTP and CC significantly increased neutrophil numbers compared to EC. All products augmented numbers of B cells, T cells, and pro-inflammatory IL17A+ T cells in the lungs. Decreased lung antioxidant activity and lung epithelial and endothelial damage was induced by all products. EC and HTP differentially augmented inflammatory cytokines/chemokines in the BAL. Generation of immunity following vaccination was impaired by EC and HTP but to a lesser extent than CC, with a CC > HTP > EC hierarchy of suppression of pulmonary bacterial clearance. Conclusions HTP and EC-aerosols induced a proinflammatory pulmonary microenvironment, lung damage, and suppressed efficacy of vaccination.