Association of Environmental Injustice and Cardiovascular Diseases and Risk Factors in the United States.

BACKGROUND: While the impacts of social and environmental exposure on cardiovascular risks are often reported individually, the combined effect is poorly understood. METHODS AND RESULTS: Using the 2022 Environmental Justice Index, socio-environmental justice index and environmental burden module ranks of census tracts were divided into quartiles (quartile 1, the least vulnerable census tracts; quartile 4, the most vulnerable census tracts). Age-adjusted rate ratios (RRs) of coronary artery disease, strokes, and various health measures reported in the Prevention Population-Level Analysis and Community Estimates data were compared between quartiles using multivariable Poisson regression. The quartile 4 Environmental Justice Index was associated with a higher rate of coronary artery disease (RR, 1.684 [95% CI, 1.660-1.708]) and stroke (RR, 2.112 [95% CI, 2.078-2.147]) compared with the quartile 1 Environmental Justice Index. Similarly, coronary artery disease 1.057 [95% CI,1.043-1.0716] and stroke (RR, 1.118 [95% CI, 1.102-1.135]) were significantly higher in the quartile 4 than in the quartile 1 environmental burden module. Similar results were observed for chronic kidney disease, hypertension, diabetes, obesity, high cholesterol, lack of health insurance, sleep <7 hours per night, no leisure time physical activity, and impaired mental and physical health >14 days. CONCLUSIONS: The prevalence of CVD and its risk factors is highly associated with increased social and environmental adversities, and environmental exposure plays an important role independent of social factors.

Deep Nonnegative Matrix Factorization Using a Variational Autoencoder With Application to Single-Cell RNA Sequencing Data.

Single-cell RNA sequencing is used to analyze the gene expression data of individual cells, thereby adding to existing knowledge of biological phenomena. Accordingly, this technology is widely used in numerous biomedical studies. Recently, the variational autoencoder has emerged and has been adopted for the analysis of single-cell data owing to its high capacity to manage large-scale data. Many different variants of the variational autoencoder have been applied, and have yielded superior results. However, because it is nonlinear, the model does not provide parameters that can be used to explain the underlying biological patterns. In this paper, we propose an interpretable nonnegative matrix factorization method that decomposes parameters into those shared across cells and those that are cell-specific. Effective nonlinear dimension reduction was achieved via a variational autoencoder applied to the cell-specific parameters. In addition to achieving nonlinear dimension reduction, our model could estimate the cell-type-specific gene expression. To improve the estimation accuracy, we introduced log-regularization, which reflects the single-cell property. Overall, our approach displayed excellent performance in a simulation study and in real data analyses, while maintaining good biological interpretability.

A zero-inflated non-negative matrix factorization for the deconvolution of mixed signals of biological data.

A latent factor model for count data is popularly applied in deconvoluting mixed signals in biological data as exemplified by sequencing data for transcriptome or microbiome studies. Due to the availability of pure samples such as single-cell transcriptome data, the accuracy of the estimates could be much improved. However, the advantage quickly disappears in the presence of excessive zeros. To correctly account for this phenomenon in both mixed and pure samples, we propose a zero-inflated non-negative matrix factorization and derive an effective multiplicative parameter updating rule. In simulation studies, our method yielded the smallest bias. We applied our approach to brain gene expression as well as fecal microbiome datasets, illustrating the superior performance of the approach. Our method is implemented as a publicly available R-package, iNMF.