Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task

A cross-sectional investigation of regional patterns of diet and cardio-metabolic risk in India

<p>Abstract</p> <p>Background</p> <p>The role of diet in India's rapidly progressing chronic disease epidemic is unclear; moreover, diet may vary considerably across North-South regions.</p> <p>Methods</p> <p>The India Health Study was a multicenter study of men and women aged 35-69, who provided diet, lifestyle, and medical histories, as well as blood pressure, fasting blood, urine, and anthropometric measurements. In each region (Delhi, n = 824; Mumbai, n = 743; Trivandrum, n = 2,247), we identified two dietary patterns with factor analysis. In multiple logistic regression models adjusted for age, gender, education, income, marital status, religion, physical activity, tobacco, alcohol, and total energy intake, we investigated associations between regional dietary patterns and abdominal adiposity, hypertension, diabetes, and dyslipidemia.</p> <p>Results</p> <p>Across the regions, more than 80% of the participants met the criteria for abdominal adiposity and 10 to 28% of participants were considered diabetic. In Delhi, the "fruit and dairy" dietary pattern was positively associated with abdominal adiposity [highest versus lowest tertile, multivariate-adjusted OR and 95% CI: 2.32 (1.03-5.23); P_trend= 0.008] and hypertension [2.20 (1.47-3.31); P_trend< 0.0001]. In Trivandrum, the "pulses and rice" pattern was inversely related to diabetes [0.70 (0.51-0.95); P_trend= 0.03] and the "snacks and sweets" pattern was positively associated with abdominal adiposity [2.05 (1.34-3.14); P_trend= 0.03]. In Mumbai, the "fruit and vegetable" pattern was inversely associated with hypertension [0.63 (0.40-0.99); P_trend= 0.05] and the "snack and meat" pattern appeared to be positively associated with abdominal adiposity.</p> <p>Conclusions</p> <p>Cardio-metabolic risk factors were highly prevalent in this population. Across all regions, we found little evidence of a Westernized diet; however, dietary patterns characterized by animal products, fried snacks, or sweets appeared to be positively associated with abdominal adiposity. Conversely, more traditional diets in the Southern regions were inversely related to diabetes and hypertension. Continued investigation of diet, as well as other environmental and biological factors, will be needed to better understand the risk profile in this population and potential means of prevention.</p

Adsorption of carbon monoxide on the surfaces of polycrystalline transition metals and alloys: electron energy loss and ultraviolet photoelectron spectral studies1

Adsorption of CO has been investigated on the surfaces of polycrystalline transition metals as well as alloys by employing electron energy loss spectroscopy (eels) and ultraviolet photoelectron spectroscopy (ups). CO adsorbs on polycrystalline transition metal surfaces with a multiplicity of sites, each being associated with a characteristic CO stretching frequency; the relative intensities vary with temperature as well as coverage. Whilst at low temperatures (80- 120 K), low coordination sites are stabilized, the higher coordination sites are stabilized at higher temperatures (270-300 K). Adsorption on surfaces of polycrystalline alloys gives characteristic stretching frequencies due to the constituent metal sites. Alloying, however, causes a shift in the stretching frequencies, indicating the effect of the band structure on the nature of adsorption. The up spectra provide confirmatory evidence for the existence of separate metal sites in the alloys as well as for the high-temperature and low-temperature phases of adsorbed CO