Detecting differential usage of exons from RNA-Seq data

RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package

Inelastic Confinement-Induced Resonances in Low-Dimensional Quantum Systems

A theoretical model is presented describing the confinement-induced resonances observed in the recent loss experiment of Haller et al. [Phys. Rev. Lett. 104, 153203 (2010)]. These resonances originate from possible molecule formation due to the coupling of center-of-mass and relative motion. A corresponding model is verified by ab initio calculations and predicts the resonance positions in 1D as well as in 2D confinement in agreement with the experiment. This resolves the contradiction of the experimental observations to previous theoretical predictions.Comment: 5 pages, 4 figure

Alignment-Dependent Ionization of N2_2, O2_2, and CO2_2 in Intense Laser Fields

The ionization probability of N$_2$, O$_2$, and CO$_2$ in intense laser fields is studied theoretically as a function of the alignment angle by solving the time-dependent Schr\"odinger equation numerically assuming only the single-active-electron approximation. The results are compared to recent experimental data [D.~Pavi{\v{c}}i{\'c} et al., Phys.\,Rev.\,Lett.\ {\bf 98}, 243001 (2007)] and good agreement is found for N$_2$ and O$_2$. For CO$_2$ a possible explanation is provided for the failure of simplified single-active-electron models to reproduce the experimentally observed narrow ionization distribution. It is based on a field-induced coherent core-trapping effect.Comment: 5 pages, 2 figure

Human peritoneal mesothelial cell death induced by high-glucose hypertonic solution involves Ca2+ and Na+ ions and oxidative stress with the participation of PKC/NOX2 and PI3K/Akt pathways

Indexación: Web of Science; Scopus.Chronic peritoneal dialysis (PD) therapy is equally efficient as hemodialysis while providing greater patient comfort and mobility. Therefore, PD is the treatment of choice for several types of renal patients. During PD, a high-glucose hyperosmotic (HGH) solution is administered into the peritoneal cavity to generate an osmotic gradient that promotes water and solutes transport from peritoneal blood to the dialysis solution. Unfortunately, PD has been associated with a loss of peritoneal viability and function through the generation of a severe inflammatory state that induces human peritoneal mesothelial cell (HPMC) death. Despite this deleterious effect, the precise molecular mechanism of HPMC death as induced by HGH solutions is far from being understood. Therefore, the aim of this study was to explore the pathways involved in HGH solution-induced HPMC death. HGH-induced HPMC death included influxes of intracellular Ca2+ and Na+. Furthermore, HGH-induced HPMC death was inhibited by antioxidant and reducing agents. In line with this, HPMC death was induced solely by increased oxidative stress. In addition to this, the cPKC/NOX2 and PI3K/Akt intracellular signaling pathways also participated in HGH-induced HPMC death. The participation of PI3K/Akt intracellular is in agreement with previously shown in rat PMC apoptosis. These findings contribute toward fully elucidating the underlying molecular mechanism mediating peritoneal mesothelial cell death induced by high-glucose solutions during peritoneal dialysis.https://www.frontiersin.org/articles/10.3389/fphys.2017.00379/ful