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)

Surfactant mixtures at the oil–water interface

NOTICE: this is the author’s version of a work that was accepted for publication in Journal of Colloid and Interface Science. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in JOURNAL OF COLLOID AND INTERFACE SCIENCE, VOL 398, (2013) DOI 10.1016/j.jcis.2013.01.06

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

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

The Optical Emission from Gamma-ray Quasars

We present photometric observations of six radio-loud quasars that were detected by the COMPTEL gamma-ray telescope. The data encompasses seven wavebands in the optical and near-infrared. After correction for Galactic extinction, we find a wide range in optical slopes. Two sources are as blue as optically-selected quasars, and are likely to be dominated by the accretion disc emission, while three others show colours consistent with a red synchrotron component. We discuss the properties of the COMPTEL sample of quasars, as well as the implications our observations have for multi-wavelength modelling of gamma-ray quasars.Comment: 12 pages, 3 figures, accepted for publication in P.A.S.A; minor typos correcte

Unravelling Active Galactic Nuclei

A complete flat-spectrum radio-loud sample of AGN includes a significant fraction of Seyfert-like AGN including a NLS1. Analysis of their optical spectra suggests that the reddest continuum colours are either associated with AGN in nearby resolved galaxies, or distant quasars showing relatively narrow permitted emission lines.Comment: Poster contribution presented at the Joint MPE,AIP,ESO workshop on NLS1s, Bad Honnef, Dec. 1999, to appear in New Astronomy Reviews; also available at http://wave.xray.mpe.mpg.de/conferences/nls1-worksho

Compartmental Bone Morphometry in the Mouse Femur: Reproducibility and Resolution Dependence of Microtomographic Measurements

Microcomputed tomography (μCT) is widely used for nondestructive bone phenotyping in small animals, especially in the mouse. Here, we investigated the reproducibility and resolution dependence of μCT analysis of microstructural parameters in three different compartments in the mouse femur. Reproducibility was assessed with respect to precision error (PE%CV) and intraclass correlation coefficient (ICC). We examined 14 left femurs isolated postmortem from two strains of mice (seven per group). Measurements and analyses were repeated five times on different days. In a second step, analysis was repeated again five times for a single measurement. Resolution dependence was assessed by high-resolution measurements (10μm) in one strain and subsequent image degrading. Reproducibility was better in full bone compartment and in cortical bone compartment in the diaphysis (PE%CV = 0.06-2.16%) than in trabecular compartment in the distal metaphysis (PE%CV = 0.59-5.24%). Nevertheless, ICC (0.92-1.00) showed a very high reliability of the assessed parameters in all regions, indicating very small variances within repeated measurements compared to the population variances. Morphometric indices computed from lower- and higher-resolution images displayed in general only weak dependence and were highly correlated with each other (R2 = 0.91-0.99). The results show that parameters in the full and cortical compartments were very reproducible, whereas precision in the trabecular compartment was somewhat lower. Nevertheless, all compartmental analysis methods were very robust, as shown by the high ICC values, demonstrating high suitability for application in inbred strains, where highest precision is needed due to small population variance

Width dependence of inherent TM-mode lateral leakage loss in silicon-on-insulator ridge waveguides

We report the first experimental observation in the optical domain of a dramatic width-dependent lateral leakage loss behavior for the TM-like mode of tight vertical confinement ridge waveguides formed in silicon-on-insulator. The lateral leakage loss displays a series of sharp cyclic minima at precise waveguide widths, and appears to be inherent to waveguide geometries of central importance to a wide variety of active devices in silicon photonics requiring lateral electrical access. This behavior is not predicted by the often-used effective-index-based methods, but is understood phenomenologically and also compared to prior numerical analysis and predictions of leaky mode behavior. It is shown that TM-like mode operation, critical to the operation of some active component designs, will require precision control of waveguide dimensions to achieve high performance