Altered N170 Response in a Facial Oddball Task in Persons with High Depressive Symptoms

Psycholog

Type II Superstring Field Theory: Geometric Approach and Operadic Description

We outline the construction of type II superstring field theory leading to a geometric and algebraic BV master equation, analogous to Zwiebach's construction for the bosonic string. The construction uses the small Hilbert space. Elementary vertices of the non-polynomial action are described with the help of a properly formulated minimal area problem. They give rise to an infinite tower of superstring field products defining a $\mathcal{N}=1$ generalization of a loop homotopy Lie algebra, the genus zero part generalizing a homotopy Lie algebra. Finally, we give an operadic interpretation of the construction.Comment: 37 pages, 1 figure, corrected typos and added reference

Partial Least Squares: A Versatile Tool for the Analysis of High-Dimensional Genomic Data

Partial Least Squares (PLS) is a highly efficient statistical regression technique that is well suited for the analysis of high-dimensional genomic data. In this paper we review the theory and applications of PLS both under methodological and biological points of view. Focusing on microarray expression data we provide a systematic comparison of the PLS approaches currently employed, and discuss problems as different as tumor classification, identification of relevant genes, survival analysis and modeling of gene networks

Chemical investigation of light induced DNA bipyrimidine damage and repair

In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine–pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(a-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature’s repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided

Modular operads and the quantum open-closed homotopy algebra

We verify that certain algebras appearing in string field theory are algebras over Feynman transform of modular operads which we describe explicitly. Equivalent description in terms of solutions of generalized BV master equations are explained from the operadic point of view.Comment: 56 pages, v2: substantially revised expositio

Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks

We present a procedure for effective estimation of entropy and mutual information from small-sample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically as well as computationally. Despite its simplicity, we show that it outperforms eight other entropy estimation procedures across a diverse range of sampling scenarios and data-generating models, even in cases of severe undersampling. We illustrate the approach by analyzing E. coli gene expression data and computing an entropy-based gene-association network from gene expression data. A computer program is available that implements the proposed shrinkage estimator.Comment: 18 pages, 3 figures, 1 tabl

Gene ranking and biomarker discovery under correlation

Biomarker discovery and gene ranking is a standard task in genomic high throughput analysis. Typically, the ordering of markers is based on a stabilized variant of the t-score, such as the moderated t or the SAM statistic. However, these procedures ignore gene-gene correlations, which may have a profound impact on the gene orderings and on the power of the subsequent tests. We propose a simple procedure that adjusts gene-wise t-statistics to take account of correlations among genes. The resulting correlation-adjusted t-scores ("cat" scores) are derived from a predictive perspective, i.e. as a score for variable selection to discriminate group membership in two-class linear discriminant analysis. In the absence of correlation the cat score reduces to the standard t-score. Moreover, using the cat score it is straightforward to evaluate groups of features (i.e. gene sets). For computation of the cat score from small sample data we propose a shrinkage procedure. In a comparative study comprising six different synthetic and empirical correlation structures we show that the cat score improves estimation of gene orderings and leads to higher power for fixed true discovery rate, and vice versa. Finally, we also illustrate the cat score by analyzing metabolomic data. The shrinkage cat score is implemented in the R package "st" available from URL http://cran.r-project.org/web/packages/st/Comment: 18 pages, 5 figures, 1 tabl

Construction and Test of New Precision Drift-Tube Chambers for the ATLAS Muon Spectrometer

ATLAS muon detector upgrades aim for increased acceptance for muon triggering and precision tracking and for improved rate capability of the muon chambers in the high-background regions of the detector with increasing LHC luminosity. The small-diameter Muon Drift Tube (sMDT) chambers have been developed for these purposes. With half of the drift-tube diameter of the MDT chambers and otherwise unchanged operating parameters, sMDT chambers share the advantages of the MDTs, but have an order of magnitude higher rate capability and can be installed in detector regions where MDT chambers do not fit in. The chamber assembly methods have been optimized for mass production, minimizing construction time and personnel. Sense wire positioning accuracies of 5 ?micons have been achieved in serial production for large-size chambers comprising several hundred drift tubes. The construction of new sMDT chambers for installation in the 2016/17 winter shutdown of the LHC and the design of sMDT chambers in combination with new RPC trigger chambers for replacement of the inner layer of the barrel muon spectrometer are in progress