A varying threshold method for ChIP peak-calling using multiple sources of information

Motivation: Gene regulation commonly involves interaction among DNA, proteins and biochemical conditions. Using chromatin immunoprecipitation (ChIP) technologies, protein–DNA interactions are routinely detected in the genome scale. Computational methods that detect weak protein-binding signals and simultaneously maintain a high specificity yet remain to be challenging. An attractive approach is to incorporate biologically relevant data, such as protein co-occupancy, to improve the power of protein-binding detection. We call the additional data related with the target protein binding as supporting tracks

Target mass number dependence of subthreshold antiproton production in proton-, deuteron- and alpha-particle-induced reactions

Data from KEK on subthreshold \bar{\mrm{p}} as well as on $\pi^\pm$ and \mrm{K}^\pm production in proton-, deuteron- and $\alpha$-induced reactions at energies between 2.0 and 12.0 A GeV for C, Cu and Pb targets are described within a unified approach. We use a model which considers a nuclear reaction as an incoherent sum over collisions of varying numbers of projectile and target nucleons. It samples complete events and thus allows for the simultaneous consideration of all final particles including the decay products of the nuclear residues. The enormous enhancement of the \bar{\mrm{p}} cross section, as well as the moderate increase of meson production in deuteron and $\alpha$ induced compared to proton-induced reactions, is well reproduced for all target nuclei. In our approach, the observed enhancement near the production threshold is mainly due to the contributions from the interactions of few-nucleon clusters by simultaneously considering fragmentation processes of the nuclear residues. The ability of the model to reproduce the target mass dependence may be considered as a further proof of the validity of the cluster concept.Comment: 9 pages, 4 figure

Ferromagnetic Kondo-Lattice Model

We present a many-body approach to the electronic and magnetic properties of the (multiband) Kondo-lattice model with ferromagnetic interband exchange. The coupling between itinerant conduction electrons and localized magnetic moments leads, on the one hand, to a distinct temperature-dependence of the electronic quasiparticle spectrum and, on the other hand, to magnetic properties, as e.~g.the Curie temperature T_C or the magnon dispersion, which are strongly influenced by the band electron selfenergy and therewith in particular by the carrier density. We present results for the single-band Kondo-lattice model in terms of quasiparticle densities of states and quasiparticle band structures and demonstrate the density-dependence of the self-consistently derived Curie temperature. The transition from weak-coupling (RKKY) to strong-coupling (double exchange) behaviour is worked out. The multiband model is combined with a tight-binding-LMTO bandstructure calculation to describe real magnetic materials. As an example we present results for the archetypal ferromagnetic local-moment systems EuO and EuS. The proposed method avoids the double counting of relevant interactions and takes into account the correct symmetry of atomic orbitals.Comment: 15 pages, 10 figure

Localization Properties of Two Interacting Electrons in a Disordered Quasi One-Dimensional Potential

We study the transport properties of two electrons in a quasi one-dimensional disordered wire. The electrons are subject to both, a disorder potential and a short range two-body interaction. Using the approach developed by Iida et al. [ Ann. Phys. (N.Y.) 200 (1990) 219 ], the supersymmetry technique, and a suitable truncation of Hilbert space, we work out the two-point correlation function in the framework of a non-linear sigma model. We study the loop corrections to arbitrary order. We obtain a remarkably simple and physically transparent expression for the change of the localization length caused by the two-body interaction.Comment: 10 page

The BioGRID Interaction Database: 2011 update

The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans (http://www.thebiogrid.org). BioGRID currently holds 347 966 interactions (170 162 genetic, 177 804 protein) curated from both high-throughput data sets and individual focused studies, as derived from over 23 000 publications in the primary literature. Complete coverage of the entire literature is maintained for budding yeast (Saccharomyces cerevisiae), fission yeast (Schizosaccharomyces pombe) and thale cress (Arabidopsis thaliana), and efforts to expand curation across multiple metazoan species are underway. The BioGRID houses 48 831 human protein interactions that have been curated from 10 247 publications. Current curation drives are focused on particular areas of biology to enable insights into conserved networks and pathways that are relevant to human health. The BioGRID 3.0 web interface contains new search and display features that enable rapid queries across multiple data types and sources. An automated Interaction Management System (IMS) is used to prioritize, coordinate and track curation across international sites and projects. BioGRID provides interaction data to several model organism databases, resources such as Entrez-Gene and other interaction meta-databases. The entire BioGRID 3.0 data collection may be downloaded in multiple file formats, including PSI MI XML. Source code for BioGRID 3.0 is freely available without any restrictions

Computed tomography-osteoabsorptiometry for assessing the density distribution of subchondral bone as a measure of long-term mechanical adaptation in individual joints

To estimate subchondral mineralisation patterns which represent the long-term loading history of individual joints, a method has been developed employing computed tomography (CT) which permits repeated examination of living joints. The method was tested on 5 knee, 3 sacroiliac, 3 ankle and 5 shoulder joints and then investigated with X-ray densitometry. A CT absorptiometric presentation and maps of the area distribution of the subchondral bone density areas were derived using an image analyser. Comparison of the results from both X-ray densitometry and CT-absorptiometry revealed almost identical pictures of distribution of the subchondral bone density. The method may be used to examine subchondral mineralisation as a measure of the mechanical adaptability of joints in the living subject

Organization of Multinational Activities and Ownership Structure

We develop a model in which multinational investors decide about the modes of organization, the locations of production, and the markets to be served. Foreign investments are driven by market-seeking and cost-reducing motives. We further assume that investors face costs of control that vary among sectors and increase in distance. The results show that (i) production intensive sectors are more likely to operate a foreign business independent of the investment motive, (ii) that distance may have a non-monotonous effect on the likelihood of horizontal investments, and (iii) that globalization, if understood as reducing distance, leads to more integration

β- and α-Cell Dysfunction in Subjects Developing Impaired Glucose Tolerance: Outcome of a 12-Year Prospective Study in Postmenopausal Caucasian Women

OBJECTIVE— This study assessed insulin and glucagon secretion in relation to insulin sensitivity in Caucasian women who develop impaired glucose tolerance (IGT) versus those who maintain normal glucose tolerance (NGT) over a 12-year period

Collusion through Joint R&D: An Empirical Assessment

This paper tests whether upstream R&D cooperation leads to downstream collusion. We consider an oligopolistic setting where firms enter in research joint ventures (RJVs) to lower production costs or coordinate on collusion in the product market. We show that a sufficient condition for identifying collusive behavior is a decline in the market share of RJV-participating firms, which is also necessary and sufficient for a decrease in consumer welfare. Using information from the US National Cooperation Research Act, we estimate a market share equation correcting for the endogeneity of RJV participation and R&D expenditures. We find robust evidence that large networks between direct competitors – created through firms being members in several RJVs at the same time – are conducive to collusive outcomes in the product market which reduce consumer welfare. By contrast, RJVs among non-competitors are efficiency enhancing

Review of the k-Body Embedded Ensembles of Gaussian Random Matrices

The embedded ensembles were introduced by Mon and French as physically more plausible stochastic models of many--body systems governed by one--and two--body interactions than provided by standard random--matrix theory. We review several approaches aimed at determining the spectral density, the spectral fluctuation properties, and the ergodic properties of these ensembles: moments methods, numerical simulations, the replica trick, the eigenvector decomposition of the matrix of second moments and supersymmetry, the binary correlation approximation, and the study of correlations between matrix elements.Comment: Final version. 29 pages, 4 ps figures, uses iopart.st