Rank discriminants for predicting phenotypes from RNA expression

Statistical methods for analyzing large-scale biomolecular data are commonplace in computational biology. A notable example is phenotype prediction from gene expression data, for instance, detecting human cancers, differentiating subtypes and predicting clinical outcomes. Still, clinical applications remain scarce. One reason is that the complexity of the decision rules that emerge from standard statistical learning impedes biological understanding, in particular, any mechanistic interpretation. Here we explore decision rules for binary classification utilizing only the ordering of expression among several genes; the basic building blocks are then two-gene expression comparisons. The simplest example, just one comparison, is the TSP classifier, which has appeared in a variety of cancer-related discovery studies. Decision rules based on multiple comparisons can better accommodate class heterogeneity, and thereby increase accuracy, and might provide a link with biological mechanism. We consider a general framework ("rank-in-context") for designing discriminant functions, including a data-driven selection of the number and identity of the genes in the support ("context"). We then specialize to two examples: voting among several pairs and comparing the median expression in two groups of genes. Comprehensive experiments assess accuracy relative to other, more complex, methods, and reinforce earlier observations that simple classifiers are competitive.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS738 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

On the Impact of Helium Content on the RR Lyrae Distance Scale

Indexación: Scopus.We constructed new sets of He-enhanced (Y = 0.30, Y = 0.40) nonlinear, time-dependent convective hydrodynamical models of RR Lyrae (RRL) stars covering a broad range in metal abundances (Z = 0.0001-0.02). The increase in He content from the canonical value (Y = 0.245) to Y = 0.30-0.40 causes a simultaneous increase in stellar luminosity and in pulsation period. To investigate the dependence of the RRL distance scale on the He abundance, we computed new optical (RI) and near-infrared (JHK) Period-luminosity-metallicity-helium relations. Interestingly enough, the increase in He content causes a minimal change in the coefficients of both period and metallicity terms, since canonical and He-enhanced models obey similar PLZ relations. On the contrary, the classical B-And V-band mean magnitude metallicity relations and the R-band PLZ relation display a significant dependence on the He content. The He-enhanced models are, at fixed metal content, 0.2-0.5 mag brighter than canonical ones. This variation is only marginally affected by evolutionary effects. The quoted distance diagnostics once calibrated with trigonometric parallaxes (Gaia) will provide the opportunity to estimate the He content of field and cluster RRLs. Moreover, the use of either spectroscopic or photometric metal abundances will pave the way to new empirical constraints on the universality of the helium-To-metal enrichment ratio in old (t10 Gyr) stellar tracers. © 2018. The American Astronomical Society. All rights reserved.https://iopscience.iop.org/article/10.3847/2041-8213/aada1

Superspace Formulation for the BRST Quantization of the Chiral Schwinger Model

It has recently been shown that the Field Antifield quantization of anomalous irreducible gauge theories with closed algebra can be represented in a BRST superspace where the quantum action at one loop order, including the Wess Zumino term, and the anomalies show up as components of the same superfield. We show here how the Chiral Schwinger model can be represented in this formulation.Comment: 11 pages, Late

Characterization of the CBC2 readout ASIC for the CMS strip-tracker high-luminosity upgrade

The CMS Binary Chip 2 (CBC2) is a full-scale prototype ASIC developed for the front-end readout of the high-luminosity upgrade of the CMS silicon strip tracker. The 254-channel, 130 nm CMOS ASIC is designed for the binary readout of double-layer modules, and features cluster-width discrimination and coincidence logic for detecting high-PT track candidates. The chip was delivered in January 2013 and has since been bump-bonded to a dual-chip hybrid and extensively tested. The CBC2 is fully functional and working to specification: we present the result of electrical characterization of the chip, including gain, noise, threshold scan and power consumption, together with the performance of the stub finding logic. Finally we will outline the plan for future developments towards the production version

Holographic model for heavy vector meson masses

The experimentally observed spectra of heavy vector meson radial excitations show a dependence on two different energy parameters. One is associated with the quark mass and the other with the binding energy levels of the quark anti-quark pair. The first is present in the large mass of the first state while the other corresponds to the small mass splittings between radial excitations. In this article we show how to reproduce such a behavior with reasonable precision using a holographic model. In the dual picture, the large energy scale shows up from a bulk mass and the small scale comes from the position of anti-de Sitter (AdS) space where field correlators are calculated. The model determines the masses of four observed S-wave states of charmonium and six S-wave states of bottomonium with , 6.1 % rms error. In consistency with the physical picture, the large energy parameter is flavor dependent, while the small parameter, associated with quark anti-quark interaction is the same for charmonium and bottomonium states.Comment: In V5 we just added some clarifying explanations about the model. 5 tables, no figure. Version published in Europhysics Letter

The Oblate Schwarzschild Approximation for Light Curves of Rapidly Rotating Neutron Stars

We present a simple method for including the oblateness of a rapidly rotating neutron star when fitting X-ray light curves. In previous work we showed that the oblateness induced by rotation at frequencies above 300 Hz produces a geometric effect which needs to be accounted for when modelling light curves to extract constraints on the neutron star's mass and radius. In our model X-rays are emitted from the surface of an oblate neutron star and propagate to the observer along geodesics of the Schwarzschild metric for a spherical neutron star. Doppler effects due to rotation are added in the same manner as in the case of a spherical neutron star. We show that this model captures the most important effects due to the neutron star's rotation. We also explain how the geometric oblateness effect can rival the Doppler effect for some emission geometries.Comment: 8 pages, 4 figures. v2: minor changes. Accepted by the Astrophysical Journa