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

History state formalism for Dirac's theory

We propose a history state formalism for a Dirac particle. By introducing a reference quantum clock system it is first shown that Dirac's equation can be derived by enforcing a timeless Wheeler-DeWitt-like equation for a global state. The Hilbert space of the whole system constitutes a unitary representation of the Lorentz group with respect to a properly defined invariant product, and the proper normalization of global states directly ensures standard Dirac's norm. Moreover, by introducing a second quantum clock, the previous invariant product emerges naturally from a generalized continuity equation. The invariant parameter $\tau$ associated with this second clock labels history states for different particles, yielding an observable evolution in the case of an hypothetical superposition of different masses. Analytical expressions for both space-time density and electron-time entanglement are provided for two particular families of electron's states, the former including Pryce localized particles.Comment: 9 pages, 2 figures, final versio

The rotation rates of massive stars: How slow are the slow ones?

Context: Rotation plays a key role in the life cycles of stars with masses above 8 Msun. Hence, accurate knowledge of the rotation rates of such massive stars is critical for understanding their properties and for constraining models of their evolution. Aims: This paper investigates the reliability of current methods used to derive projected rotation speeds v sin i from line-broadening signatures in the photospheric spectra of massive stars, focusing on stars that are not rapidly rotating. Methods: We use slowly rotating magnetic O-stars with well-determined rotation periods to test the Fourier transform (FT) and goodness-of-fit (GOF) methods typically used to infer projected rotation rates of massive stars. Results: For our two magnetic test stars with measured rotation periods longer than one year, i.e., with v sin i < 1 km/s, we derive v sin i ~ 40-50 km/s from both the FT and GOF methods. These severe overestimates are most likely caused by an insufficient treatment of the competing broadening mechanisms referred to as microturbulence and macroturbulence. Conclusions: These findings warn us not to rely uncritically on results from current standard techniques to derive projected rotation speeds of massive stars in the presence of significant additional line broadening, at least when v sin i <~ 50 km/s. This may, for example, be crucial for i) determining the statistical distribution of observed rotation rates of massive stars, ii) interpreting the evolutionary status and spin-down histories of rotationally braked B-supergiants, and iii) explaining the deficiency of observed O-stars with spectroscopically inferred v sin i ~ 0 km/s. Further investigations of potential shortcomings of the above techniques are presently under way.Comment: 4 pages, 4 figures, accepted for publication in A&A Letter

Internal kinematic and physical properties in a BCD galaxy: Haro 15 in detail

We present a detailed study of the kinematic and physical properties of the ionized gas in multiple knots of the blue compact dwarf galaxy Haro 15. Using echelle and long slit spectroscopy data, obtained with different instruments at Las Campanas Observatory, we study the internal kinematic and physical conditions (electron density and temperature), ionic and total chemical abundances of several atoms, reddening and ionization structure. Applying direct and empirical methods for abundance determination, we perform a comparative analysis between these regions and in their different components. On the other hand, our echelle spectra show complex kinematics in several conspicuous knots within the galaxy. To perform an in-depth 2D spectroscopic study we complete this work with high spatial and spectral resolution spectroscopy using the Integral Field Unit mode on the Gemini Multi-Object Spectrograph instrument at the Gemini South telescope. With these data we are able to resolve the complex kinematical structure within star forming knots in Haro 15 galaxy.Comment: 6 pages, 2 figures, IX Scientific Meeting of the Spanish Astronomical Society held on September 13-17, 2010, in Madrid, Spai

XMM-Newton EPIC and OM observation of Nova Centauri 1986 (V842 Cen)

We report the results from the temporal and spectral analysis of an XMM-Newton observation of Nova Centauri 1986 (V842 Cen). We detect a period at 3.51$\pm$0.4 h in the EPIC data and at 4.0$\pm$0.8 h in the OM data. The X-ray spectrum is consistent with the emission from an absorbed thin thermal plasma with a temperature distribution given by an isobaric cooling flow. The maximum temperature of the cooling flow model is $kT_{max}=43_{-12}^{+23}$ keV. Such a high temperature can be reached in a shocked region and, given the periodicity detected, most likely arises in a magnetically-channelled accretion flow characteristic of intermediate polars. The pulsed fraction of the 3.51 h modulation decreases with energy as observed in the X-ray light curves of magnetic CVs, possibly due either to occultation of the accretion column by the white dwarf body or phase-dependent to absorption. We do not find the 57 s white dwarf spin period, with a pulse amplitude of 4 mmag, reported by Woudt et al. (2009) either in the Optical Monitor (OM) data, which are sensitive to pulse amplitudes $\gtrsim$ 0.03 magnitudes, or the EPIC data, sensitive to pulse fractions $p \gtrsim$ 14 $\pm$2%.Comment: 5 pages, 3 figures; MNRAS, accepte