A high-resolution integrated map of copy number polymorphisms within and between breeds of the modern domesticated dog

<p>Abstract</p> <p>Background</p> <p>Structural variation contributes to the rich genetic and phenotypic diversity of the modern domestic dog, <it>Canis lupus familiaris</it>, although compared to other organisms, catalogs of canine copy number variants (CNVs) are poorly defined. To this end, we developed a customized high-density tiling array across the canine genome and used it to discover CNVs in nine genetically diverse dogs and a gray wolf.</p> <p>Results</p> <p>In total, we identified 403 CNVs that overlap 401 genes, which are enriched for defense/immunity, oxidoreductase, protease, receptor, signaling molecule and transporter genes. Furthermore, we performed detailed comparisons between CNVs located within versus outside of segmental duplications (SDs) and find that CNVs in SDs are enriched for gene content and complexity. Finally, we compiled all known dog CNV regions and genotyped them with a custom aCGH chip in 61 dogs from 12 diverse breeds. These data allowed us to perform the first population genetics analysis of canine structural variation and identify CNVs that potentially contribute to breed specific traits.</p> <p>Conclusions</p> <p>Our comprehensive analysis of canine CNVs will be an important resource in genetically dissecting canine phenotypic and behavioral variation.</p

Searching for low-mass dark matter via the Migdal effect in COSINE-100

We report on the search for weakly interacting massive particle (WIMP) dark matter candidates in the galactic halo that interact with sodium and iodine nuclei in the COSINE-100 experiment and produce energetic electrons that accompany recoil nuclei via the the Migdal effect. The WIMP mass sensitivity of previous COSINE-100 searches that relied on the detection of ionization signals produced by target nuclei recoiling from elastic WIMP-nucleus scattering was restricted to WIMP masses above ∼5 GeV/c2 by the detectors' 1 keVee energy-electron-equivalent threshold. The search reported here looks for recoil signals enhanced by the Migdal electrons that are ejected during the scattering process. This is particularly effective for the detection of low-mass WIMP scattering from the crystals' sodium nuclei in which a relatively larger fraction of the WIMP's energy is transferred to the nucleus recoil energy and the excitation of its orbital electrons. In this analysis, the low-mass WIMP search window of the COSINE-100 experiment is extended to WIMP mass down to 200 MeV/c2. The low-mass WIMP sensitivity will be further improved by lowering the analysis threshold based on a multivariable analysis technique. We consider the influence of these improvements and recent developments in detector performance to re-evaluate sensitivities for the future COSINE-200 experiment. With a 0.2 keVee analysis threshold and high light-yield NaI(Tl) detectors (22 photoelectrons/keVee), the COSINE-200 experiment can explore low-mass WIMPs down to 20 MeV/c2 and probe previously unexplored regions of parameter space

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties

Searching for low-mass dark matter via Migdal effect in COSINE-100 [preprint]

We report on the search for weakly interacting massive particle (WIMP) dark matter candidates in the galactic halo that interact with sodium and iodine nuclei in the COSINE-100 experiment and produce energetic electrons that accompany recoil nuclei via the the Migdal effect. The WIMP mass sensitivity of previous COSINE-100 searches that relied on the detection of ionization signals produced by target nuclei recoiling from elastic WIMP-nucleus scattering was restricted to WIMP masses above $\sim$5 GeV/$c^2$ by the detectors' 1 keVee energy-electron-equivalent threshold. The search reported here looks for recoil signals enhanced by the Migdal electrons that are ejected during the scattering process. This is particularly effective for the detection of low-mass WIMP scattering from the crystals' sodium nuclei in which a relatively larger fraction of the WIMP's energy is transferred to the nucleus recoil energy and the excitation of its orbital electrons. In this analysis, the low-mass WIMP search window of the COSINE-100 experiment is extended to WIMP mass down to 200 MeV/c. The low-mass WIMP sensitivity will be further improved by lowering the analysis threshold based on a multivariable analysis technique. We consider the influence of these improvements and recent developments in detector performance to re-evaluate sensitivities for the future COSINE-200 experiment. With a 0.2 keVee analysis threshold and high light-yield NaI(Tl) detectors (22photoelectrons/keVee), the COSINE-200 experiment can explore low-mass WIMPs down to 20 MeV/c2 and probe previously unexplored regions of parameter space

Separation of track- and shower-like energy deposits in ProtoDUNE-SP using a convolutional neural network

Liquid argon time projection chamber detector technology provides high spatial and calorimetric resolutions on the charged particles traversing liquid argon. As a result, the technology has been used in a number of recent neutrino experiments, and is the technology of choice for the Deep Underground Neutrino Experiment (DUNE). In order to perform high precision measurements of neutrinos in the detector, final state particles need to be effectively identified, and their energy accurately reconstructed. This article proposes an algorithm based on a convolutional neural network to perform the classification of energy deposits and reconstructed particles as track-like or arising from electromagnetic cascades. Results from testing the algorithm on experimental data from ProtoDUNE-SP, a prototype of the DUNE far detector, are presented. The network identifies track- and shower-like particles, as well as Michel electrons, with high efficiency. The performance of the algorithm is consistent between experimental data and simulation

Separation of track- and shower-like energy deposits in ProtoDUNE-SP using a convolutional neural network

Liquid argon time projection chamber detector technology provides high spatial and calorimetric resolutions on the charged particles traversing liquid argon. As a result, the technology has been used in a number of recent neutrino experiments, and is the technology of choice for the Deep Underground Neutrino Experiment (DUNE). In order to perform high precision measurements of neutrinos in the detector, final state particles need to be effectively identified, and their energy accurately reconstructed. This article proposes an algorithm based on a convolutional neural network to perform the classification of energy deposits and reconstructed particles as track-like or arising from electromagnetic cascades. Results from testing the algorithm on data from ProtoDUNE-SP, a prototype of the DUNE far detector, are presented. The network identifies track- and shower-like particles, as well as Michel electrons, with high efficiency. The performance of the algorithm is consistent between data and simulation

Low exposure long-baseline neutrino oscillation sensitivity of the DUNE experiment

The Deep Underground Neutrino Experiment (DUNE) will produce world-leading neutrino oscillation measurements over the lifetime of the experiment. In this work, we explore DUNE's sensitivity to observe charge-parity violation (CPV) in the neutrino sector, and to resolve the mass ordering, for exposures of up to 100 kiloton-megawatt-years (kt-MW-yr). The analysis includes detailed uncertainties on the flux prediction, the neutrino interaction model, and detector effects. We demonstrate that DUNE will be able to unambiguously resolve the neutrino mass ordering at a 3σ (5σ) level, with a 66 (100) kt-MW-yr far detector exposure, and has the ability to make strong statements at significantly shorter exposures depending on the true value of other oscillation parameters. We also show that DUNE has the potential to make a robust measurement of CPV at a 3σ level with a 100 kt-MW-yr exposure for the maximally CP-violating values \delta_{\rm CP}} = \pm\pi/2. Additionally, the dependence of DUNE's sensitivity on the exposure taken in neutrino-enhanced and antineutrino-enhanced running is discussed. An equal fraction of exposure taken in each beam mode is found to be close to optimal when considered over the entire space of interest