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

Pyrite-induced hydroxyl radical formation and its effect on nucleic acids

BACKGROUND: Pyrite, the most abundant metal sulphide on Earth, is known to spontaneously form hydrogen peroxide when exposed to water. In this study the hypothesis that pyrite-induced hydrogen peroxide is transformed to hydroxyl radicals is tested. RESULTS: Using a combination of electron spin resonance (ESR) spin-trapping techniques and scavenging reactions involving nucleic acids, the formation of hydroxyl radicals in pyrite/aqueous suspensions is demonstrated. The addition of EDTA to pyrite slurries inhibits the hydrogen peroxide-to-hydroxyl radical conversion, but does not inhibit the formation of hydrogen peroxide. Given the stability of EDTA chelation with both ferrous and ferric iron, this suggests that the addition of the EDTA prevents the transformation by chelation of dissolved iron species. CONCLUSION: While the exact mechanism or mechanisms of the hydrogen peroxide-to-hydroxyl radical conversion cannot be resolved on the basis of the experiments reported in this study, it is clear that the pyrite surface promotes the reaction. The formation of hydroxyl radicals is significant because they react nearly instantaneously with most organic molecules. This suggests that the presence of pyrite in natural, engineered, or physiological aqueous systems may induce the transformation of a wide range of organic molecules. This finding has implications for the role pyrite may play in aquatic environments and raises the question whether inhalation of pyrite dust contributes to the development of lung diseases

Detection of receptors for polymerised human albumin by immunoperoxidase and immunoadherence in liver tissue of HBsAg chronic carriers.

Receptors for polymerised human albumin (pHSA-Rs) were detected in unfixed cryostat sections from HBsAg chronic carriers using direct immunoperoxidase and immunoadherence methods. Although pHSA-Rs were detected by both methods, the receptors detected by immunoperoxidase were associated with HBV and showed properties different from the receptors detected by immunoadherence. The double immunocytochemical staining which detected contemporaneously pHSA-Rs and HBsAg in the same cell showed that there are two types of infected hepatocytes: one capable of synthesizing pHSA-Rs and HBsAg and the other capable of synthesizing only HBsAg. The intrahepatocyte synthesis of pHSA-Rs does not correlate with the severity of chronic liver disease or with the presence of tissue HB core antigen

A generalization of the Thickened Flame model for stretched flames

The Thickened Flame (TF) model is a widely used approach for Large Eddy Simulation of premixed flames. It is based on a “mapping” transformation where all diffusivities are multiplied by a thickening factor F while reaction terms are divided by F. Theory shows and 1D flame simulations confirm that this mapping preserves the unstretched laminar flame speed s0L while increasing its thickness δ0L by F, allowing to resolve the flame on a coarse grid. However this property is not satisfied anymore when the TF model is applied to stretched flames: the burning velocity sc(k) of a thickened flame submitted to a stretch k is not conserved compared to the non-thickened solution. A new diffusion-reaction transformation, named Stretched-Thickened Flame (S-TF) model, is developed here to conserve the burning velocity of stretched flames, proposing a generalization of the classical diffusion-reaction transformation which the TF model is based on. Thermal and mass diffusion zones are thickened differently and the laminar unstretched properties are preserved by modifying the chemical source terms. The S-TF model is applied on canonical 1D strained flames and validated for a cylindrical expanding flame configuration to prove its applicability to recover both strain and curvature effects. Results show that the Stretched-Thickened Flame model is an effective solution to correct the deficiency of the classical approach for stretched flames and can be easily implemented in CFD codes relying on the TF model. s0

Antibodies to glutaraldehyde-polymerized human albumin (anti-pHSA) in viral hepatitis.

The antibody to polymerized human albumin (anti-pHSA) was studied in normal subjects and in the course of infection from hepatitis A virus, hepatitis B virus, and hepatitis non-A, non-B virus. Results show that anti-pHSA antibody was never found in normal subjects, but it appeared during virus liver pathologies. The behavior of anti-pHSA differs in acute type A hepatitis that does not change to chronic form and in those forms which tend to become chronic (B and nonA, nonB). In the type-A infection anti-pHSA disappears after the acute phase; in the other two forms it persists all along as the infection develops. Specifically in non-A, non-B infection only the IgM type anti-pHSA is produced

Correlation between hepatitis B virus deoxyribonucleic acid and receptors for polymerized human albumin in HBV chronic infection.

This study indicates that hepatitis B virus deoxyribonucleic acid (HBV DNA) is actually the most sensitive marker for the identification of HBV-related pathologies in active replication phase and does not correlate with serum receptor activity for polymerized human serum albumin which can be found in absence of either HBV DNA or HBeAg in HBV chronic infection

Serum binding activity for human albumin polymers in acute and chronic virus hepatitis.

We considered the serum binding activity for human albumin polymerized with glutaraldehyde in 346 serum samples of 205 subjects with acute and chronic type A, B and non-A, non-B virus hepatitis. We showed that the binding activity for pHSA in the control groups did not have a titer higher than 2(-6). All sera from patients with HAV and HBV acute infection showed a high binding titer that returned to below the threshold in the former after the peak of hepatocytolysis, and in the latter after the seroconversion of HBsAg to anti-HBs. In the subjects who became HBsAg chronic carriers after the acute episode of HBV infection, the pHSA binding activity showed a decrement of the titer in relation to the seroconversion of HBeAg to anti-HBe. Furthermore, 92% of HBsAg chronic carriers who were HBeAg positive had a high titer of pHSA binding, while only 14.3% of the anti-HBe positives showed a high titer. Acute and chronic hepatitis non-A, non-B virus showed a pHSA binding titer similar to that of the control group. The results indicate that the non-A, non-B virus does not seem to be correlated to pHSA or related factors