GLM permutation - nonparametric inference for arbitrary general linear models

Introduction: Permutation methods are finding growing use in neuroimag- ing data analyses (e.g. randomise in FSL, SnPM in SPM, XBAMM/BAMM/CAMBA, etc). These methods provide ex- act control of false positives, make only weak assumptions, and allow nonstandard types of statistics (e.g. smoothed variance t- test). With fast and inexpensive computing, there would seem few reasons not to use nonparametric methods. A significant limitation of these methods, however, is the lack of flexibility with respect to the experimental design and nuisance variables. Each specific design dictates the type of exchange- ability of null data, and hence how to permute. Nuisance effects (e.g. age) render data non-exchangeable even when the effect of interest is null. Hence, even something as simple as ANCOVA has no exact permutation test. Recently there has been an active literature on approximate– but accurate–permutation tests for 2-variable regression, one effect of interest, one nuisance (see review by Anderson & Robinson [1]). Here we extend and evaluate these methods for use with an arbitrary General Linear Model (GLM)

Development of novel multiplex microsatellite polymerase chain reactions to enable high-throughput population genetic studies of Schistosoma haematobium

© 2015 Webster et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. The attached file is the published version of the article

Projection on Segre varieties and determination of holomorphic mappings between real submanifolds

It is shown that a germ of a holomorphic mapping sending a real-analytic generic submanifold of finite type into another is determined by its projection on the Segre variety of the target manifold. A necessary and sufficient condition is given for a germ of a mapping into the Segre variety of the target manifold to be the projection of a holomorphic mapping sending the source manifold into the target. An application to the biholomorphic equivalence problem is also given.Comment: 16 page

Characterization of the complications associated with plasma exchange for thrombotic thrombocytopaenic purpura and related thrombotic microangiopathic anaemias: a single institution experience.

Plasma exchange (PEX) is a life-saving therapeutic procedure in patients with thrombotic thrombocytopaenic purpura (TTP) and other thrombotic microangiopathic anaemias (TMAs). However, it may be associated with significant complications, exacerbating the morbidity and mortality in this patient group

Circuit QED with a Flux Qubit Strongly Coupled to a Coplanar Transmission Line Resonator

We propose a scheme for circuit quantum electrodynamics with a superconducting flux-qubit coupled to a high-Q coplanar resonator. Assuming realistic circuit parameters we predict that it is possible to reach the strong coupling regime. Routes to metrological applications, such as single photon generation and quantum non-demolition measurements are discussed.Comment: 8 pages, 5 figure

Wiener Reconstruction of Large-Scale Structure from Peculiar Velocities

We present an alternative, Bayesian method for large-scale reconstruction from observed peculiar velocity data. The method stresses a rigorous treatment of the random errors and it allows extrapolation into poorly sampled regions in real space or in k-space. A likelihood analysis is used to determine the fluctuation power spectrum, followed by a Wiener Filter (WF) analysis to obtain the minimum-variance mean fields of velocity and mass density. Constrained Realizations (CR) are then used to sample the statistical scatter about the WF mean field. The WF/CR method is applied as a demonstration to the Mark III data with 1200 km/s, 900 km/s, and 500 km/s resolutions. The main reconstructed structures are consistent with those extracted by the POTENT method. A comparison with the structures in the distribution of IRAS 1.2Jy galaxies yields a general agreement. The reconstructed velocity field is decomposed into its divergent and tidal components relative to a cube of +/-8000 km/s centered on the Local Group. The divergent component is very similar to the velocity field predicted from the distribution of IRAS galaxies. The tidal component is dominated by a bulk flow of 194 +/- 32 km/s towards the general direction of the Shapley concentration, and it also indicates a significant quadrupole.Comment: 28 pages and 8 GIF figures, Latex (aasms4.sty), submitted to ApJ. Postscript version of the figures can be obtained by anonymous ftp from: ftp://alf.huji.ac.il/pub/saleem

Simple manipulation of a microwave dressed-state ion qubit

Many schemes for implementing quantum information processing require that the atomic states used have a non-zero magnetic moment, however such magnetically sensitive states of an atom are vulnerable to decoherence due to fluctuating magnetic fields. Dressing an atom with an external field is a powerful method of reducing such decoherence [N. Timoney et al., Nature 476, 185], even if the states being dressed are strongly coupled to the environment. We introduce an experimentally simpler method of manipulating such a dressed-state qubit, which allows the implementation of general rotations of the qubit, and demonstrate this method using a trapped ytterbium ion

The rate of convergence for approximate Bayesian computation

Approximate Bayesian Computation (ABC) is a popular computational method for likelihood-free Bayesian inference. The term “likelihood-free” refers to problems where the likelihood is intractable to compute or estimate directly, but where it is possible to generate simulated data X relatively easily given a candidate set of parameters θ simulated from a prior distribution. Parameters which generate simulated data within some tolerance δ of the observed data x* are regarded as plausible, and a collection of such θ is used to estimate the posterior distribution θ |X=x*. Suitable choice of δ is vital for ABC methods to return good approximations to θ in reasonable computational time. While ABC methods are widely used in practice, particularly in population genetics, rigorous study of the mathematical properties of ABC estimators lags behind practical developments of the method. We prove that ABC estimates converge to the exact solution under very weak assumptions and, under slightly stronger assumptions, quantify the rate of this convergence. In particular, we show that the bias of the ABC estimate is asymptotically proportional to δ2 as δ ↓ 0. At the same time, the computational cost for generating one ABC sample increases like δ−q where q is the dimension of the observations. Rates of convergence are obtained by optimally balancing the mean squared error against the computational cost. Our results can be used to guide the choice of the tolerance parameter δ

Role of the exchange and correlation potential into calculating the x-ray absorption spectra of half-metallic alloys: the case of Mn and Cu K-edge XANES in Cu2_2MnM (M = Al, Sn, In) Heusler alloys

This work reports a theoretical study of the x-ray absorption near-edge structure spectra at both the Cu and the Mn K-edge in several Cu$_2$MnM (M= Al, Sn and In) Heusler alloys. Our results show that {\it ab-initio} single-channel multiple-scattering calculations are able of reproducing the experimental spectra. Moreover, an extensive discussion is presented concerning the role of the final state potential needed to reproduce the experimental data of these half-metallic alloys. In particular, the effects of the cluster-size and of the exchange and correlation potential needed in reproducing all the experimental XANES features are discussed.Comment: 15 pages, 5 figure