656 research outputs found
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 decay
CP violation leads to a difference between the parameters and
describing the energy distributions of the charged pions produced in the and decays. We study the
difference 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 is very similar to the corresponding
one defining the parameter in the decays. This
observation allows a determination of the value of , using data on
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
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
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
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
Emergency control algorithm for maintaining power stability based on newton's method
The problem of stability boundary evaluation for the current power system state is of paramount importance for power system operation. In addition, maintaining stability after large scale disturbances has come to the fore in recent years. This paper presents the algorithm, which allows us to both evaluate the stability boundary of a power system and to calculate emergency control actions for maintaining stability in the case of blackout. The algorithm is based on Newton's method for solving optimization problems. There are a number of emergency actions algorithms in literature, but most of them use heuristic rules. On the contrary, the proposed method has a reasonable analytical background. Thus, having an adequate power system model, the proposed method is able to calculate more accurate control actions. The paper demonstrates the very basic idea of the approach with the simplest example. © 2014 WIT Press.International Journal of Safety and Security Engineering;International Journal of Sustainable Development and Planning;WIT Transactions on Ecology and the Environmen
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