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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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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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de Souza, P. M., Muller, A., Beniaich, A., Mayer-Miebach, E., Oehlke, K., Stahl, M., et al. (2015). Functional properties and nutritional composition of liquid egg products treated in a coiled tube UV-C reactor. Innov. Food Sci. Emerg. Technol., 32, 156–164.
Abstract: Pasteurization of eggs has adverse effects on nutrient composition and functionality of egg proteins. UV processing is an alternative technology with potentially fewer adverse effects as it is less intrusive. Egg white, whole egg and egg yolk vitamins (A, B-2, B-5, C and E), minerals (P, Cl, K, Na, Ca, Mg, Fe and Zn) and main secondary metabolites (lutein and zeaxanthin) were examined after exposure to UV in a coiled tube UV-C reactor at doses known to achieve microbiologically stable egg fractions. The studied nutrients were fairly stable to a treatment with UVC light with the exception of retinal, vitamin C and carotenoids, which showed loses up to 80%, 66% and 61%, respectively. Moreover, the functional properties of ultraviolet-treated eggs were investigated. Results showed a positive impact on the foam ability and foam stability, and an increase on the emulsifying activity index above 20% versus pasteurized samples. Processing with UV can maintain most of the egg nutritive properties, and retain or even improve the technological properties of foaming and emulsification in eggs. Industrial relevance:: This novel UV-C system can be applied successfully to the Food Industry. UV-C does not impair nutritional damage to egg-treated products, and even improve egg functional properties.
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Tain, J. L., Agramunt, J., Algora, A., Aprahamian, A., Cano-Ott, D., Fraile, L. M., et al. (2015). The sensitivity of LaBr3:Ce scintillation detectors to low energy neutrons: Measurement and Monte Carlo simulation. Nucl. Instrum. Methods Phys. Res. A, 774, 17–24.
Abstract: The neutron sensitivity of a cylindrical circle minus 1.5 in x 1.5 in LaBr3:Ce scintillation detector was measured using quasi-monoenergetic neutron beams in the energy range from 40 keV to 2.5 MeV. In this energy range the detector is sensitive to gamma-rays generated in neutron inelastic and capture processes. The experimental energy response was compared with Monte Carlo simulations performed with the Geant4 simulation toolkit using the so-called High Precision Neutron Models. These models rely on relevant information stored in evaluated nuclear data libraries. The performance of the Geant4 Neutron Data Library as well as several standard nuclear data libraries was investigated. In the latter case this was made possible by the use of a conversion tool that allowed the direct use of the data from other libraries in Geant4. Overall it was found that there was good agreement with experiment for some of the neutron data bases like ENDF/B-VII.0 or JENDL-3.3 but not with the others such as ENDF/B-VI.8 or JEFF-3.1.
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Modamio, V., Valiente-Dobon, J. J., Jaworski, G., Huyuk, T., Triossi, A., Egea, J., et al. (2015). Digital pulse-timing technique for the neutron detector array NEDA. Nucl. Instrum. Methods Phys. Res. A, 775, 71–76.
Abstract: A new digital pulse-timing algorithm, to be used with the future neutron detector array NEDA, has been developed and tested. The time resolution of four 5 in diameter photomultiplier tubes (XP4512, R4144, R11833-100, and ET9390-kb), coupled to a cylindrical 5 in by 5 in BC501A liquict scintillator detector was measured by employing digital sampling electronics and a constant fraction discriminator (CFD) algorithm. The zero crossing of the CM algorithm was obtained with a cubic spline interpolation, which was continuous up to the second derivative. The performance of the algorithm was studied at sampling rates of 500 MS/s and 200 MS/s. The time resolution obtained with the digital electronics was compared to the values acquired with a standard analog CFD. The result of this comparison shows that the time resolution from the analog and the digital measurements at 500 MS/s and at 200 MS/s are within 15% for all the tested photomultiplier tubes.
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