Matrix eQTL: Ultra fast eQTL analysis via large matrix operations

Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex diseases such as cancer, diabetes, and cystic fibrosis. A modern eQTL dataset contains millions of SNPs and thousands of transcripts measured for hundreds of samples. This makes the analysis computationally complex as it involves independent testing for association for every transcript-SNP pair. The heavy computational burden makes eQTL analysis less popular, often forces analysts to restrict their attention to just a subset of transcripts and SNPs. As larger genotype and gene expression datasets become available, the demand for fast tools for eQTL analysis increases. We present a new method for fast eQTL analysis via linear models, called Matrix eQTL. Matrix eQTL can model and test for association using both linear regression and ANOVA models. The models can include covariates to account for such factors as population structure, gender, and clinical variables. It also supports testing of heteroscedastic models and models with correlated errors. In our experiment on large datasets Matrix eQTL was thousands of times faster than the existing popular software for QTL/eQTL analysis. Matrix eQTL is implemented as both Matlab and R packages and thus can easily be run on Windows, Mac OS, and Linux systems. The software is freely available at the following address: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTLComment: 9 pages, 1 figur

CP violation in K±→π0π0π±K^{\pm}\to\pi^0\pi^0\pi^{\pm} decay

CP violation leads to a difference between the parameters $g^+$ and $g^-$ describing the energy distributions of the charged pions produced in the $K^+ \to\pi^0 \pi^0 \pi^+$ and $K^- \to \pi^0\pi^0 \pi^-$ decays. We study the difference $(g^+ - g^-)$ as a function of the relative contributions from the QCD-penguin and the electroweak-penguin diagrams. We find that the combination of these contributions in $(g^+ - g^-)$ is very similar to the corresponding one defining the parameter $\epsilon'$ in the $K_L \to 2\pi$ decays. This observation allows a determination of the value of $(g^+ - g^-)$, using data on $\epsilon'$

Loop-Less Electric Dipole Moment of the Nucleon in the Standard Model

We point out that the electric dipole moment of the neutron in the Standard Model is generated already at tree level to the second order in the weak interactions due to bound-state effects, without short-distance Penguin loops. The related contribution has a regular nonvanishing chiral limit and does not depend on the mass splitting between s and d quarks. We estimate it to be roughly 10^(-31)e*cm and expect a more accurate evaluation in the future. We comment on the connection between d_n and the direct CP-violation in D decays.Comment: 10 pages, 2 figure

On CP-Odd Effects in K_L \to 2\pi and K^{\pm} \to \pi^{\pm} \pi^{\pm} \pi^{\mp} Decays Generated by Direct CP Violation

The amplitudes of the K^{\pm} \to 3\pi and K \to 2\pi decays are expressed in terms of different combinations of one and the same set of CP-conserving and CP-odd parameters. Extracting the magnitudes of these parameters from the data on K \to 2\pi decays, we estimate an expected CP-odd difference between the values of the slope parameters g^+ and g^- of the energy distributions of "odd" pions in K^+ \to \pi^+\pi^+\pi^- and K^- \to \pi^-\pi^-\pi^+ decays.Comment: 12 pages, no figure

An Empirical Bayes Approach for Multiple Tissue eQTL Analysis

Expression quantitative trait loci (eQTL) analyses, which identify genetic markers associated with the expression of a gene, are an important tool in the understanding of diseases in human and other populations. While most eQTL studies to date consider the connection between genetic variation and expression in a single tissue, complex, multi-tissue data sets are now being generated by the GTEx initiative. These data sets have the potential to improve the findings of single tissue analyses by borrowing strength across tissues, and the potential to elucidate the genotypic basis of differences between tissues. In this paper we introduce and study a multivariate hierarchical Bayesian model (MT-eQTL) for multi-tissue eQTL analysis. MT-eQTL directly models the vector of correlations between expression and genotype across tissues. It explicitly captures patterns of variation in the presence or absence of eQTLs, as well as the heterogeneity of effect sizes across tissues. Moreover, the model is applicable to complex designs in which the set of donors can (i) vary from tissue to tissue, and (ii) exhibit incomplete overlap between tissues. The MT-eQTL model is marginally consistent, in the sense that the model for a subset of tissues can be obtained from the full model via marginalization. Fitting of the MT-eQTL model is carried out via empirical Bayes, using an approximate EM algorithm. Inferences concerning eQTL detection and the configuration of eQTLs across tissues are derived from adaptive thresholding of local false discovery rates, and maximum a-posteriori estimation, respectively. We investigate the MT-eQTL model through a simulation study, and rigorously establish the FDR control of the local FDR testing procedure under mild assumptions appropriate for dependent data.Comment: accepted by Biostatistic

Two photon decay of neutral scalars below 1.5 GeV in a chiral model for bar{q}q and bar{q}bar{q}qq states

We study the two photon decay of neutral scalars below 1.5 GeV in the context of a recently proposed chiral model for bar{q}q and bar{q}bar{q}qq states. We find good agreement with experimental results for the a_{0}(980)->gamma gamma. Our calculations for f_{0}(980)->gamma gamma shows that further work is necessary in order to understand the structure of this meson. The model predicts Gamma(a_{0}(1450)->gamma gamma)=0.16+/-0.10KeV, Gamma(sigma->gamma gamma)=0.47+/-0.66 KeV, Gamma(f(1370)->gamma gamma)=0.07+/-0.15 KeV, Gamma(f(1500)->gamma gamma)=0.74+/-0.78 KeV.Comment: 6 pages, 1 figur

Intensity interferometry of single x-ray pulses from a synchrotron storage ring

We report on measurements of second-order intensity correlations at the high brilliance storage ring PETRA III using a prototype of the newly developed Adaptive Gain Integrating Pixel Detector (AGIPD). The detector recorded individual synchrotron radiation pulses with an x-ray photon energy of 14.4 keV and repetition rate of about 5 MHz. The second-order intensity correlation function was measured simultaneously at different spatial separations that allowed to determine the transverse coherence length at these x-ray energies. The measured values are in a good agreement with theoretical simulations based on the Gaussian Schell-model.Comment: 16 pages, 6 figures, 42 reference

Hanbury Brown and Twiss interferometry at a free-electron laser

We present measurements of second- and higher-order intensity correlation functions (so-called Hanbury Brown and Twiss experiment) performed at the free-electron laser (FEL) FLASH in the non-linear regime of its operation. We demonstrate the high transverse coherence properties of the FEL beam with a degree of transverse coherence of about 80% and degeneracy parameter of the order 10^9 that makes it similar to laser sources. Intensity correlation measurements in spatial and frequency domain gave an estimate of the FEL average pulse duration of 50 fs. Our measurements of the higher-order correlation functions indicate that FEL radiation obeys Gaussian statistics, which is characteristic to chaotic sources.Comment: 19 pages, 6 figures, 1 table, 40 reference

Flavor Structure of Warped Extra Dimension Models

We recently showed, in hep-ph/0406101, that warped extra dimensional models with bulk custodial symmetry and few TeV KK masses lead to striking signals at $B$-factories. In this paper, using a spurion analysis, we systematically study the flavor structure of models that belong to the above class. In particular we find that the profiles of the zero modes, which are similar in all these models, essentially control the underlying flavor structure. This implies that our results are robust and model independent in this class of models. We discuss in detail the origin of the signals in B-physics. We also briefly study other NP signatures that arise in rare K decays ($K \to \pi \nu \nu$), in rare top decays [$t \to c \gamma (Z, gluon)$] and the possibilty of CP asymmetries in $D^0$ decays to CP eigenstates such as $K_S \pi^0$ and others. Finally we demonstrate that with light KK masses, $\sim3$ TeV, the above class of models with anarchic $5D$ Yukawas has a ``CP problem'' since contributions to the neutron electric dipole moment are roughly 20 times larger than the current experimental bound. Using AdS/CFT correspondence, these extra-dimensional models are dual to a purely 4D strongly coupled conformal Higgs sector thus enhancing their appeal.Comment: 41 pages, 52 pages including appendice

Characterization of Spatial Coherence of Synchrotron Radiation with Non-Redundant Arrays of Apertures

We present a method to characterize the spatial coherence of soft X-ray radiation from a single diffraction pattern. The technique is based on scattering from non-redundant arrays (NRA) of slits and records the degree of spatial coherence at several relative separations from one to 15 microns, simultaneously. Using NRAs we measured the transverse coherence of the X-ray beam at the XUV X-ray beamline P04 of the PETRA III synchrotron storage ring as a function of different beam parameters. To verify the results obtained with the NRAs additional Young's double pinhole experiments were conducted and show good agreement.Comment: 15 pages, 6 figures, 2 tables, 42 reference