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Ames, S. K., Gardner, S. N., Marti, J. M., Slezak, T. R., Gokhale, M. B., & Allen, J. E. (2015). Using populations of human and microbial genomes for organism detection in metagenomes. Genome Res., 25(7), 1056–1067.
Abstract: Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
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Amjad, M. S., Bilokin, S., Boronat, M., Doublet, P., Frisson, T., Garcia Garcia, I., et al. (2015). A precise characterisation of the top quark electro-weak vertices at the ILC. Eur. Phys. J. C, 75(10), 512–11pp.
Abstract: Top quark production in the process e(+)e(-) -> t t at a future linear electron positron collider with polarised beams is a powerful tool to determine indirectly the scale of new physics. The presented study, based on a detailed simulation of the ILD detector concept, assumes a centre-of-mass energy of root s = 500GeV and a luminosity of L = 500 fb(-1) equally shared between the incoming beam polarisations of Pe-, Pe+ = +/- 0.8, -/+ 0.3. Events are selected in which the top pair decays semi-leptonically and the cross sections and the forward-backward asymmetries are determined. Based on these results, the vector, axial vector and tensorial CP conserving couplings are extracted separately for the photon and the Z(0) component. With the expected precision, a large number of models in which the top quark acts as a messenger to new physics can be distinguished with many standard deviations. This will dramatically improve expectations from e.g. the LHC for electro-weak couplings of the top quark.
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Anderson, P. R., Fabbri, A., & Balbinot, R. (2015). Low frequency gray-body factors and infrared divergences: Rigorous results. Phys. Rev. D, 91(6), 064061–18pp.
Abstract: Formal solutions to the mode equations for both spherically symmetric black holes and Bose-Einstein condensate acoustic black holes are obtained by writing the spatial part of the mode equation as a linear Volterra integral equation of the second kind. The solutions work for a massless minimally coupled scalar field in the s-wave or zero angular momentum sector for a spherically symmetric black hole and in the longitudinal sector of a one-dimensional Bose-Einstein condensate acoustic black hole. These solutions are used to obtain in a rigorous way analytic expressions for the scattering coefficients and gray-body factors in the zero frequency limit. They are also used to study the infrared behaviors of the symmetric two-point function and two functions derived from it: the point-split stress-energy tensor for the massless minimally coupled scalar field in Schwarzschild-de Sitter spacetime and the density-density correlation function for a Bose-Einstein condensate acoustic black hole.
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ANTARES and TANAMI Collaborations(Adrian-Martinez, S. et al), Barrios-Marti, J., Gomez-Gonzalez, J. P., Hernandez-Rey, J. J., Lambard, G., Mangano, S., et al. (2015). ANTARES constrains a blazar origin of two IceCube PeV neutrino events. Astron. Astrophys., 576, L8–6pp.
Abstract: Context. The source(s) of the neutrino excess reported by the IceCube Collaboration is unknown. The TANAMI Collaboration recently reported on the multiwavelength emission of six bright, variable blazars which are positionally coincident with two of the most energetic IceCube events. Objects like these are prime candidates to be the source of the highest-energy cosmic rays, and thus of associated neutrino emission. Aims. We present an analysis of neutrino emission from the six blazars using observations with the ANTARES neutrino telescope. Methods. The standard methods of the ANTARES candidate list search are applied to six years of data to search for an excess of muons – and hence their neutrino progenitors – from the directions of the six blazars described by the TANAMI Collaboration, and which are possibly associated with two IceCube events. Monte Carlo simulations of the detector response to both signal and background particle fluxes are used to estimate the sensitivity of this analysis for different possible source neutrino spectra. A maximum-likelihood approach, using the reconstructed energies and arrival directions of through-going muons, is used to identify events with properties consistent with a blazar origin. Results. Both blazars predicted to be the most neutrino-bright in the TANAMI sample (1653-329 and 1714-336) have a signal flux fitted by the likelihood analysis corresponding to approximately one event. This observation is consistent with the blazar-origin hypothesis of the IceCube event IC 14 for a broad range of blazar spectra, although an atmospheric origin cannot be excluded. No ANTARES events are observed from any of the other four blazars, including the three associated with IceCube event IC20. This excludes at a 90% confidence level the possibility that this event was produced by these blazars unless the neutrino spectrum is flatter than -2.4.
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ANTARES Collaboration(Adrian-Martinez, S. et al), Barrios-Marti, J., Hernandez-Rey, J. J., Lambard, G., Mangano, S., Sanchez-Losa, A., et al. (2015). Search for muon-neutrino emission from GeV and TeV gamma-ray flaring blazars using five years of data of the ANTARES telescope. J. Cosmol. Astropart. Phys., 12(12), 014–27pp.
Abstract: The ANTARES telescope is well-suited for detecting astrophysical transient neutrino sources as it can observe a full hemisphere of the sky at all times with a high duty cycle. The background due to atmospheric particles can be drastically reduced, and the point-source sensitivity improved, by selecting a narrow time window around possible neutrino production periods. Blazars, being radio-loud active galactic nuclei with their jets pointing almost directly towards the observer, are particularly attractive potential neutrino point sources, since they are among the most likely sources of the very high-energy cosmic rays. Neutrinos and gamma rays may be produced in hadronic interactions with the surrounding medium. Moreover, blazars generally show high time variability in their light curves at different wavelengths and on various time scales. This paper presents a time-dependent analysis applied to a selection of flaring gamma-ray blazars observed by the FERMI/LAT experiment and by TeV Cherenkov telescopes using five years of ANTARES data taken from 2008 to 2012. The results are compatible with fluctuations of the background. Upper limits on the neutrino fluence have been produced and compared to the measured gamma-ray spectral energy distribution.
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