Integrated probability of coronary heart disease subject to the -308 tumor necrosis factor-alpha SNP: a Bayesian meta-analysis

We present a meta-analysis of independent studies on the potential implication in the occurrence of coronary heart disease (CHD) of the single-nucleotide polymorphism (SNP) at the -308 position of the tumor necrosis factor alpha (TNF-alpha) gene. We use Bayesian analysis to integrate independent data sets and to infer statistically robust measurements of correlation. Bayesian hypothesis testing indicates that there is no preference for the hypothesis that the -308 TNF-alpha SNP is related to the occurrence of CHD, in the Caucasian or in the Asian population, over the null hypothesis. As a measure of correlation, we use the probability of occurrence of CHD conditional on the presence of the SNP, derived as the posterior probability of the Bayesian meta-analysis. The conditional probability indicates that CHD is not more likely to occur when the SNP is present, which suggests that the -308 TNF-alpha SNP is not implicated in the occurrence of CHD.Comment: 21 pages, 7 figures, Published in PeerJ (2015

Nonparametric tests of structure for high angular resolution diffusion imaging in Q-space

High angular resolution diffusion imaging data is the observed characteristic function for the local diffusion of water molecules in tissue. This data is used to infer structural information in brain imaging. Nonparametric scalar measures are proposed to summarize such data, and to locally characterize spatial features of the diffusion probability density function (PDF), relying on the geometry of the characteristic function. Summary statistics are defined so that their distributions are, to first-order, both independent of nuisance parameters and also analytically tractable. The dominant direction of the diffusion at a spatial location (voxel) is determined, and a new set of axes are introduced in Fourier space. Variation quantified in these axes determines the local spatial properties of the diffusion density. Nonparametric hypothesis tests for determining whether the diffusion is unimodal, isotropic or multi-modal are proposed. More subtle characteristics of white-matter microstructure, such as the degree of anisotropy of the PDF and symmetry compared with a variety of asymmetric PDF alternatives, may be ascertained directly in the Fourier domain without parametric assumptions on the form of the diffusion PDF. We simulate a set of diffusion processes and characterize their local properties using the newly introduced summaries. We show how complex white-matter structures across multiple voxels exhibit clear ellipsoidal and asymmetric structure in simulation, and assess the performance of the statistics in clinically-acquired magnetic resonance imaging data.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS441 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Analysis of Modulated Multivariate Oscillations

The concept of a common modulated oscillation spanning multiple time series is formalized, a method for the recovery of such a signal from potentially noisy observations is proposed, and the time-varying bias properties of the recovery method are derived. The method, an extension of wavelet ridge analysis to the multivariate case, identifies the common oscillation by seeking, at each point in time, a frequency for which a bandpassed version of the signal obtains a local maximum in power. The lowest-order bias is shown to involve a quantity, termed the instantaneous curvature, which measures the strength of local quadratic modulation of the signal after demodulation by the common oscillation frequency. The bias can be made to be small if the analysis filter, or wavelet, can be chosen such that the signal's instantaneous curvature changes little over the filter time scale. An application is presented to the detection of vortex motions in a set of freely-drifting oceanographic instruments tracking the ocean currents

On the Analytic Wavelet Transform

An exact and general expression for the analytic wavelet transform of a real-valued signal is constructed, resolving the time-dependent effects of non-negligible amplitude and frequency modulation. The analytic signal is first locally represented as a modulated oscillation, demodulated by its own instantaneous frequency, and then Taylor-expanded at each point in time. The terms in this expansion, called the instantaneous modulation functions, are time-varying functions which quantify, at increasingly higher orders, the local departures of the signal from a uniform sinusoidal oscillation. Closed-form expressions for these functions are found in terms of Bell polynomials and derivatives of the signal's instantaneous frequency and bandwidth. The analytic wavelet transform is shown to depend upon the interaction between the signal's instantaneous modulation functions and frequency-domain derivatives of the wavelet, inducing a hierarchy of departures of the transform away from a perfect representation of the signal. The form of these deviation terms suggests a set of conditions for matching the wavelet properties to suit the variability of the signal, in which case our expressions simplify considerably. One may then quantify the time-varying bias associated with signal estimation via wavelet ridge analysis, and choose wavelets to minimize this bias

Generalized Morse Wavelets as a Superfamily of Analytic Wavelets

The generalized Morse wavelets are shown to constitute a superfamily that essentially encompasses all other commonly used analytic wavelets, subsuming eight apparently distinct types of analysis filters into a single common form. This superfamily of analytic wavelets provides a framework for systematically investigating wavelet suitability for various applications. In addition to a parameter controlling the time-domain duration or Fourier-domain bandwidth, the wavelet {\em shape} with fixed bandwidth may be modified by varying a second parameter, called $\gamma$. For integer values of $\gamma$, the most symmetric, most nearly Gaussian, and generally most time-frequency concentrated member of the superfamily is found to occur for $\gamma=3$. These wavelets, known as "Airy wavelets," capture the essential idea of popular Morlet wavelet, while avoiding its deficiencies. They may be recommended as an ideal starting point for general purpose use