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

Seismotectonic setting at the North Anatolian Fault Zone after the 1999 Mw=7.4 Izmit earthquake based on high-resolution aftershock locations

The most recent devastating earthquakes that occurred along the North Anatolian Fault Zone (NAFZ) in northwestern Turkey were the 1999 Izmit (Mw=7.4) and Düzce (Mw=7.1) events. In this study we present a catalog of Izmit aftershock hypocenters that was deduced from a network covering the entire 140 km long rupture of the mainshock. 7348 events with a location accuracy better than 5 km are analysed. Aftershocks were observed along the entire ruptured segment along a 20 km wide band of activity. Events are clustered in distinct regions and dominantly occur at 5 to 15 km depth. The eastern termination of the Izmit rupture is characterized by a sharp and steeply dipping boundary exactly where the Düzce mainshock initiated 87 days after the Izmit event. Relocation of the events using double-difference technology results in 4696 high-resolution hypocenters that allow resolving the internal structure of the seismically active areas with a resolution of 300 m (horizontal) and 400m (vertical). Below the Akyazi Plain, representing a small pull-apart structure at a triple junction of the NAFZ, we identify planes of activity that can be correlated with nodal planes of EW extensional normal faulting aftershocks. Along the easternmost Karadere-Düzce segment we identify the down-dip extension of the Karadere fault that hosted about 1 m of right-lateral coseismic slip. At the easternmost rupture we correlate a cloud-type distribution of seismic activity with the largest aftershocks in this area, a subevent of the Izmit mainshock and the Düzce mainshock that all have an almost identical focal mechanism. This part of the NAFZ is interpreted as a classical example of a seismic barrier along the fault

Level of everyday life satisfaction of elderly from different socioeconomical backgrounds: Case of Ankara

Background and Aim: Getting older, level of life satisfaction of elderly is changed. The aim of the study is to determine the level of evereyday life satisfaction of elderly in Ankara. Materials and Method: The sample includes 1268 people who are older than 60 and from different socioeconomical levels. It is considered that their views about living place, neighbour and friend relationships, health and physical conditions, economic status, marriage, evaluation about occupation and family life in elder's life satisfaction. Level of satisfaction is measured using five point scale. Variance analysis and T test are used to analyze the data. Results: Its found that higher the economical status and educational level, higher the level of satisfaction (p<0.01). Those who are married are found to have higher levels of satisfaction. Men have higher levels of satisfaction than women. It is also found that younger ones have higher satisfaction levels than older ones (P<0.01). Conclusion: It is thought that the findings of the study can be useful for plans and politics toward elderly

Peripheral blood T cells in acute myeloid leukemia (AML) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with AML blasts

Understanding how the immune system in patients with cancer interacts with malignant cells is critical for the development of successful immunotherapeutic strategies. We studied peripheral blood from newly diagnosed patients with acute myeloid leukemia (AML) to assess the impact of this disease on the patients' T cells. The absolute number of peripheral blood T cells is increased in AML compared with healthy controls. An increase in the absolute number of CD3+56+ cells was also noted. Gene expression profiling on T cells from AML patients compared with healthy donors demonstrated global differences in transcription suggesting aberrant T-cell activation patterns. These gene expression changes differ from those observed in chronic lymphocytic leukemia (CLL), indicating the heterogeneous means by which different tumors evade the host immune response. However, in common with CLL, differentially regulated genes involved in actin cytoskeletal formation were identified, and therefore the ability of T cells from AML patients to form immunologic synapses was assessed. Although AML T cells could form conjugates with autologous blasts, their ability to form immune synapses and recruit phosphotyrosine signaling molecules to the synapse was significantly impaired. These findings identify T-cell dysfunction in AML that may contribute to the failure of a host immune response against leukemic blasts