Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data

UNLABELLED: As the volume of patient-specific genome sequences increases the focus of biomedical research is switching from the detection of disease-mutations to their interpretation. To this end a number of techniques have been developed that use mutation data collected within a population to predict whether individual genes are likely to be disease-causing or not. As both sequence data and associated analysis tools proliferate, it becomes increasingly difficult for the community to make sense of these data and their implications. Moreover, no single analysis tool is likely to capture all relevant genomic features that contribute to the gene's pathogenicity. Here, we introduce Web-based Gene Pathogenicity Analysis (WGPA), a web-based tool to analyze genes impacted by mutations and rank them through the integration of existing prioritization tools, which assess different aspects of gene pathogenicity using population-level sequence data. Additionally, to explore the polygenic contribution of mutations to disease, WGPA implements gene set enrichment analysis to prioritize disease-causing genes and gene interaction networks, therefore providing a comprehensive annotation of personal genomes data in disease. AVAILABILITY AND IMPLEMENTATION: wgpa.systems-genetics.net

Differences in the Performance of Knowledge Transfer Across Projects: A Study of Gender and Role of Key Project Stakeholders

This investigation contributes empirical results of differences identified in key project stakeholders with respect to their use of knowledge transferred across projects. Gender and role were the two individual characteristics investigated. Project managers and members of project teams were the key stakeholders analyzed. Data was collected from 71 closed projects using a survey composed of closed-ended questions. The data collected was cross tabulated and statistically analyzed using Friedman\u27s test and Spearman\u27s correlation. The results provide evidence of the association of the performance of knowledge transfer across projects with (a) the individual factors of gender and role of key project stakeholders in projects, and (b) the project factor of importance of the project deliverables to the project-based organization. These results are important to engineering management researchers and practitioners because they provide evidence of the importance of considering individual and project factors in the enhancement, design, and operation of knowledge management systems in project-based organizations

Magnetic properties and critical behavior of disordered Fe_{1-x}Ru_x alloys: a Monte Carlo approach

We study the critical behavior of a quenched random-exchange Ising model with competing interactions on a bcc lattice. This model was introduced in the study of the magnetic behavior of Fe_{1-x}Ru_x alloys for ruthenium concentrations x=0%, x=4%, x=6%, and x=8%. Our study is carried out within a Monte Carlo approach, with the aid of a re-weighting multiple histogram technique. By means of a finite-size scaling analysis of several thermodynamic quantities, taking into account up to the leading irrelevant scaling field term, we find estimates of the critical exponents \alpha, \beta, \gamma, and \nu, and of the critical temperatures of the model. Our results for x=0% are in excellent agreement with those for the three-dimensional pure Ising model in the literature. We also show that our critical exponent estimates for the disordered cases are consistent with those reported for the transition line between paramagnetic and ferromagnetic phases of both randomly dilute and $\pm J$ Ising models. We compare the behavior of the magnetization as a function of temperature with that obtained by Paduani and Branco (2008), qualitatively confirming the mean-field result. However, the comparison of the critical temperatures obtained in this work with experimental measurements suggest that the model (initially obtained in a mean-field approach) needs to be modified

Nonminimal supersymmetric standard model with lepton number violation

We carry out a detailed analysis of the nonminimal supersymmetric standard model with lepton number violation. The model contains a unique trilinear lepton number violating term in the superpotential which can give rise to neutrino masses at the tree level. We search for the gauged discrete symmetries realized by cyclic groups which preserve the structure of the associated trilinear superpotential of this model, and which satisfy the constraints of the anomaly cancellation. The implications of this trilinear lepton number violating term in the superpotential and the associated soft supersymmetry breaking term on the phenomenology of the light neutrino masses and mixing is studied in detail. We evaluate the tree and loop level contributions to the neutrino mass matrix in this model. We search for possible suppression mechanism which could explain large hierarchies and maximal mixing angles.Comment: Latex file, 43 pages, 2 figure

Dynamical and spectral properties of complex networks

Dynamical properties of complex networks are related to the spectral properties of the Laplacian matrix that describes the pattern of connectivity of the network. In particular we compute the synchronization time for different types of networks and different dynamics. We show that the main dependence of the synchronization time is on the smallest nonzero eigenvalue of the Laplacian matrix, in contrast to other proposals in terms of the spectrum of the adjacency matrix. Then, this topological property becomes the most relevant for the dynamics.Comment: 14 pages, 5 figures, to be published in New Journal of Physic

Pair distribution function analysis of the reassembly step of the assembly-disassembly-organisation-reassembly (ADOR) process

The authors S. E. R and R. E. M. would like to thank the European Research Council for funding opportunities under the Advanced Grant 787073. We acknowledge Diamond Light Source for time on I15-1 under proposal CY26990.An in situ pair distribution function study assessing the reassembly of three IM-12 (UTL) intermediate materials to the corresponding fully connected materials. A greater level of atomic change is observed at higher temperatures for the reassembly of the fully disconnected intermediate, IPC-1P, compared to the two partially connected intermediates of IPC-2P and IPC-6P.Publisher PDFPeer reviewe

The Nuclear and Circum-nuclear Stellar Population in Seyfert 2 Galaxies: Implications for the Starburst-AGN Connection

We report the results of a spectroscopic investigation of a sample of 20 of the brightest type 2 Seyfert nuclei. Our goal is to search for the direct spectroscopic signature of massive stars, and thereby probe the role of circumnuclear starbursts in the Seyfert phenomenon. The method used is based on the detection of the higher order Balmer lines and HeI lines in absorption and the Wolf-Rayet feature at $\sim$4680 \AA in emission. These lines are strong indicators of the presence of young (a few Myrs) and intermediate-age (a few 100 Myrs) stellar populations. In over half the sample, we have detected HeI and/or strong stellar absorption features in the high-order (near-UV) Balmer series together with relatively weak lines from an old stellar population. In three others we detect a broad emission feature near 4680 \AA that is most plausibly ascribed to a population of Wolf-Rayet stars (the evolved descendants of the most massive stars). We therefore conclude that the blue and near-UV light of over half of the sample is dominated by young and/or intermediate age stars. The ``young'' Seyfert 2's have have larger far-IR luminosities, cooler mid/far-IR colors, and smaller [OIII]/H$\beta$ flux ratios than the ``old'' ones. These differences are consistent with a starburst playing a significant energetic role in the former class. We consider the possibility that there may be two distinct sub-classes of Seyfert 2 nuclei (``starbursts'' and ``hidden BLR''). However, the fact that hidden BLRs have been found in three of the ``young'' nuclei argues against this, and suggests that nuclear starbursts may be a more general part of the Seyfert phenomenon.Comment: To be published in ApJ, 546, Jan 10, 200

A Burst Mode, Ultrahigh Temperature UF4 Vapor Core Reactor Rankine Cycle Space Power System Concept

Static and dynamic neutronic analyses have been performed on an innovative burst mode (100's of MW output for a few thousand seconds) Ulvahigh Temperature Vapor Core Reactor (UTVR) space nuclear power system. The NVTR employs multiple, neutronically-coupled fissioning cores and operates on a direct, closed Rankine cycle using a disk Magnetohydrodynamic (MHD) generater for energy conversion. The UTVR includes two types of fissioning core regions: (1) the central Ultrahigh Temperature Vapor Core (UTVC) which contains a vapor mixture of highly enriched UF4 fuel and a metal fluoride working fluid and (2) the UF4 boiler column cores located in the BeO moderator/reflector region. The gaseous nature of the fuel the fact that the fuel is circulating, the multiple coupled fissioning cores, and the use of a two phase fissioning fuel lead to unique static and dynamic neutronic characteristics. Static neutronic analysis was conducted using two-dimensional S sub n, transport theory calculations and three-dimensional Monte Carlo transport theory calculations. Circulating-fuel, coupled-core point reactor kinetics equations were used for analyzing the dynamic behavior of the UTVR. In addition to including reactivity feedback phenomena associated with the individual fissioning cores, the effects of core-to-core neutronic and mass flow coupling between the UTVC and the surrounding boiler cores were also included in the dynamic model The dynamic analysis of the UTVR reveals the existence of some very effectlve inherent reactivity feedback effects that are capable of quickly stabilizing this system, within a few seconds, even when large positive reactivity insertions are imposed. If the UTVC vapor fuel density feedback is suppressed, the UTVR is still inherently stable because of the boiler core liquid-fuel volume feedback; in contrast, suppression of the vapor fuel density feedback in 'conventional" gas core cavity reactors causes them to become inherently unstable. Due to the strength of the negative reactivity feedback in the UTVR, it is found that external reactivity insertions alone are inadequate for bringing about significant power level changes during normal reactor operations. Additional methods of reactivity control such as variations in the gaseous fuel mass flow rate, are needed to achieve the desired power level oontrol

The X-ray Properties of the Nearby Star-Forming Galaxy IC 342: The XMM-Newton View

We present the X-ray properties of IC342 using XMM-Newton. Thirty-five sources are detected coincident with the disk of IC342 (more than tripling the number known), of which ~31 are likely to be intrinsic to IC342. This population shows a range of spectral properties and has an X-ray luminosity function slope and infrared luminosity comparable to that of starburst galaxies such as M82 and the Antennae, while its relative lack of extended X-ray emission is similar to the properties of quiescent spirals. We do detect long-term variability between this observation and the 1991 ROSAT and 1993/2000 ASCA observations for five sources. Notably, the second most luminous source IC342 X-2 is is found to be in its the lowest luminosity state observed for X-2 to date, although the slope of the spectrum is intermediate between the previously observed low/hard and high/soft states. IC342 X-1, on the other hand, is found to be in an identical state to that observed in 2000 with ASCA. Assuming X-1 is in an anomalous very high (VH) state, then either (1) X-1 has remained in this state between 2000 and 2002, and is therefore the longest duration VH-state binary ever observed, or (2) it was simply caught in a VH state by chance in both the 2000 ASCA and 2002 XMM-Newton observations. We have also confirmed the ROSAT HRI result that the nucleus of IC342 is made up of both point-like and extended emission. The relative fluxes of the two spectral components suggest that the nucleus is complex, with a soft extended component contributing approximately half of the total luminosity. (Abridged)Comment: AJ in press (December 2003), 9 pages, 7 figures, 2 tables, emulateapj.cls use

Angular momentum effects in Michelson-Morley type experiments

The effect of the angular momentum density of a gravitational source on the times of flight of light rays in an interferometer is analyzed. The calculation is made imagining that the interferometer is at the equator of the gravity source and, as long as possible, the metric, provided it is stationary and axisymmetric, is not approximated. Finally, in order to evaluate the size of the effect in the case of the Earth a weak field approximation is introduced. For laboratory scales and non-geodesic paths the correction turns out to be comparable with the sensitivity expected in gravitational waves interferometric detectors, whereas it drops under the threshold of detectability when using free (geodesic) light rays.Comment: 12 pages, LaTeX; more about the detection technique, references added; accepted for publication in GR