An integrated map of structural variation in 2,504 human genomes

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association. © 2015 Macmillan Publishers Limited. All rights reserved

Características físico-químicas e sensoriais da carne de cordeiros terminados com dietas contendo cana-de-açúcar ou silagem de milho e dois níveis de concentrado

Com o objetivo de avaliar as características físico-químicas e sensoriais da carne de cordeiros terminados em confinamento com dietas contendo cana-de-açúcar ou silagem de milho em duas relações volumoso:concentrado, 60:40 ou 40:60, utilizaram-se 32 cordeiros Ile de France, não-castrados, com 15 kg de peso corporal. Os animais foram confinados em baias individuais e abatidos aos 32 kg. As dietas e os músculos estudados não influenciaram o pH aos 45 minutos (6,56) e 24 horas (5,62) após o abate nem a capacidade de retenção de água (58,38%) e a perda de peso por cocção (34,04%). A cor da carne e da gordura subcutânea não diferiu entre as dietas, entretanto a cor da carne variou entre os músculos longissimus lumborum e triceps brachii. A força de cisalhamento (1,85 kgf/cm²) não foi afetada pelas dietas, porém diferiu entre os músculos, com valores de 1,41 e 2,28 kgf/cm² para o longissimus lumborum e triceps brachii, respectivamente. Nas análises sensoriais do lombo e da paleta, foram obtidas para os cordeiros alimentados com cana-de-açúcar e maior quantidade de concentrado as maiores notas para sabor (8,07 e 8,26), textura (8,53 e 8,53), preferência (8,20 e 8,46) e aceitação (8,33 e 8,26), respectivamente. A cana-de-açúcar na alimentação de cordeiros em confinamento manteve a qualidade físicoquímica da carne, podendo ser utilizada nesta fase de produção e, quando associada a maior quantidade de concentrado na dieta, melhora a qualidade sensorial da carne de cordeiros.With the objective of evaluating physic-chemical and sensorial characteristics of meat from lambs finished in feedlot with diets containing sugar cane or corn silage at two roughage:concentrate ratios, 60:40 or 40:60, 32 non-castrated Ile de France lambs, with 15 kg body weight were used. Animals were confined in individual stalls and were slaughtered at 32 kg body weight. Studied diets and muscles did not affect pH at 45 minutes (6.56) and 24 hours (5.62) after slaughter, water holding capacity (58.38%) or cooking losses (34.04%). Meat color and subcutaneous fat color did not differ between diets, but meat color varied for the muscles longissimus lumborum and triceps brachii. Shear force (1.85 kgf/cm²) was not affected by diets, but it was different between muscles, with values 1.41 and 2.28 kgf/cm² for the longissimus lumborum and triceps brachii, respectively. At sensorial analysis of ovine loin and shoulder, the lambs fed sugar cane and higher quantity of concentrate had higher scores for flavor (8.07 and 8.26), texture (8.53 and 8.53), preference (8.20 and 8.46) and acceptance (8.33 and 8.26), respectively. In the diet for feedlot lambs, sugar cane maintained the physic-chemical quality of the meat, so it can be used in this production phase. When associated to higher quantity of concentrate in the diet, sugar cane improves the sensorial quality of lamb meat

Search for intermediate mass black hole binaries in the first observing run of Advanced LIGO

During their first observational run, the two Advanced LIGO detectors attained an unprecedented sensitivity, resulting in the first direct detections of gravitational-wave signals produced by stellar-mass binary black hole systems. This paper reports on an all-sky search for gravitational waves (GWs) from merging intermediate mass black hole binaries (IMBHBs). The combined results from two independent search techniques were used in this study: the first employs a matched-filter algorithm that uses a bank of filters covering the GW signal parameter space, while the second is a generic search for GW transients (bursts). No GWs from IMBHBs were detected; therefore, we constrain the rate of several classes of IMBHB mergers. The most stringent limit is obtained for black holes of individual mass 100 M, with spins aligned with the binary orbital angular momentum. For such systems, the merger rate is constrained to be less than 0.93 Gpc-3 yr-1 in comoving units at the 90% confidence level, an improvement of nearly 2 orders of magnitude over previous upper limits. © 2017 American Physical Society

Neutrino interaction vertex reconstruction in DUNE with Pandora deep learning

The Pandora Software Development Kit and algorithm libraries perform reconstruction of neutrino interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at the Deep Underground Neutrino Experiment, which will operate four large-scale liquid argon time projection chambers at the far detector site in South Dakota, producing high-resolution images of charged particles emerging from neutrino interactions. While these high-resolution images provide excellent opportunities for physics, the complex topologies require sophisticated pattern recognition capabilities to interpret signals from the detectors as physically meaningful objects that form the inputs to physics analyses. A critical component is the identification of the neutrino interaction vertex. Subsequent reconstruction algorithms use this location to identify the individual primary particles and ensure they each result in a separate reconstructed particle. A new vertex-finding procedure described in this article integrates a U-ResNet neural network performing hit-level classification into the multi-algorithm approach used by Pandora to identify the neutrino interaction vertex. The machine learning solution is seamlessly integrated into a chain of pattern-recognition algorithms. The technique substantially outperforms the previous BDT-based solution, with a more than 20% increase in the efficiency of sub-1 cm vertex reconstruction across all neutrino flavours

DUNE Phase II: scientific opportunities, detector concepts, technological solutions

The international collaboration designing and constructing the Deep Underground Neutrino Experiment (DUNE) at the Long-Baseline Neutrino Facility (LBNF) has developed a two-phase strategy toward the implementation of this leading-edge, large-scale science project. The 2023 report of the US Particle Physics Project Prioritization Panel (P5) reaffirmed this vision and strongly endorsed DUNE Phase I and Phase II, as did the European Strategy for Particle Physics. While the construction of the DUNE Phase I is well underway, this White Paper focuses on DUNE Phase II planning. DUNE Phase-II consists of a third and fourth far detector (FD) module, an upgraded near detector complex, and an enhanced 2.1 MW beam. The fourth FD module is conceived as a "Module of Opportunity", aimed at expanding the physics opportunities, in addition to supporting the core DUNE science program, with more advanced technologies. This document highlights the increased science opportunities offered by the DUNE Phase II near and far detectors, including long-baseline neutrino oscillation physics, neutrino astrophysics, and physics beyond the standard model. It describes the DUNE Phase II near and far detector technologies and detector design concepts that are currently under consideration. A summary of key R&D goals and prototyping phases needed to realize the Phase II detector technical designs is also provided. DUNE's Phase II detectors, along with the increased beam power, will complete the full scope of DUNE, enabling a multi-decadal program of groundbreaking science with neutrinos