MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants

The amount of genetic variation discovered in human populations is growing rapidly leading to challenging computational tasks, such as variant calling. Standard methods for addressing this problem include read mapping, a computationally expensive procedure; thus, mapping-free tools have been proposed in recent years. These tools focus on isolated, biallelic SNPs, providing limited support for multi-allelic SNPs and short insertions and deletions of nucleotides (indels). Here we introduce MALVA, a mapping-free method to genotype an individual from a sample of reads. MALVA is the first mapping-free tool able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variants. MALVA requires one order of magnitude less time to genotype a donor than alignment-based pipelines, providing similar accuracy. Remarkably, on indels, MALVA provides even better results than the most widely adopted variant discovery tools. Biological Sciences; Genetics; Genomics; Bioinformatic

Triplet-based similarity score for fully multilabeled trees with poly-occurring labels

Motivation: The latest advances in cancer sequencing, and the availability of a wide range of methods to infer the evolutionary history of tumors, have made it important to evaluate, reconcile and cluster different tumor phylogenies. Recently, several notions of distance or similarities have been proposed in the literature, but none of them has emerged as the golden standard. Moreover, none of the known similarity measures is able to manage mutations occurring multiple times in the tree, a circumstance often occurring in real cases. Results: To overcome these limitations, in this article, we propose MP3, the first similarity measure for tumor phylogenies able to effectively manage cases where multiple mutations can occur at the same time and mutations can occur multiple times. Moreover, a comparison of MP3 with other measures shows that it is able to classify correctly similar and dissimilar trees, both on simulated and on real data

Search for 14.4 keV solar axions from M1 transition of Fe-57 with CUORE crystals

We report the results of a search for axions from the 14.4 keV M1 transition from Fe-57 in the core of the sun using the axio-electric effect in TeO2 bolometers. The detectors are 5x5x5 cm3 crystals operated at about 10 mK in a facility used to test bolometers for the CUORE experiment at the Laboratori Nazionali del Gran Sasso in Italy. An analysis of 43.65 kg d of data was made using a newly developed low energy trigger which was optimized to reduce the detectors energy threshold. An upper limit of 0.63 c kg-1 d-1 was established at 95% C.L.. From this value, a lower bound at 95% C.L. was placed on the Peccei-Quinn energy scale of fa >= 0.76 10**6 GeV for a value of S=0.55 for the flavor-singlet axial vector matrix element. Bounds are given for the interval 0.15 < S < 0.55.Comment: 14 pages, 6 figures, submitted to JCA

Validation of techniques to mitigate copper surface contamination in CUORE

In this article we describe the background challenges for the CUORE experiment posed by surface contamination of inert detector materials such as copper, and present three techniques explored to mitigate these backgrounds. Using data from a dedicated test apparatus constructed to validate and compare these techniques we demonstrate that copper surface contamination levels better than 10E-07 - 10E-08 Bq/cm2 are achieved for 238U and 232Th. If these levels are reproduced in the final CUORE apparatus the projected 90% C.L. upper limit on the number of background counts in the region of interest is 0.02-0.03 counts/keV/kg/y depending on the adopted mitigation technique.Comment: 10 pages, 6 figures, 6 table

First results of the CUORICINO experiment

Preliminary results on double beta decay (DBD) of 130 Te, obtained in the first run of the CUORICINO experiment are presented. The set-up consists of an array of 62 crystals of TeO 2 operating as bolometers in a deep underground dilution unit at a temperature of about 10 mK. Due to a total mass of about 41 kg, CUORICINO represents by far the most massive running cryogenic mass to search for rare events. The achieved lower limit on the neutrinoless DBD is 5.5⋅10 23 years, that corresponds to a limit on the Majorana effective mass between 0.37 and 1.9 eV. Performances of the detectors together with the sensitivity estimation are discussed

Strong reduction of the off-momentum halo in crystal assisted collimation of the SPS beam

A study of crystal assisted collimation has been continued at the CERN SPS for different energies of stored beams using 120 GeV/. c and 270 GeV/. c protons and Pb ions with 270 GeV/. c per charge. A bent silicon crystal used as a primary collimator deflected halo particles using channeling and directing them into the tungsten absorber. A strong correlation of the beam losses in the crystal and off-momentum halo intensity measured in the first high dispersion (HD) area downstream was observed. In channeling conditions, the beam loss rate induced by inelastic interactions of particles with nuclei is significantly reduced in comparison with the non-oriented crystal. A maximal reduction of beam losses in the crystal larger than 20 was observed with 270 GeV/. c protons. The off-momentum halo intensity measured in the HD area was also strongly reduced in channeling conditions. The reduction coefficient was larger than 7 for the case of Pb ions. A strong loss reduction was also detected in regions of the SPS ring far from the collimation area. It was shown by simulations that the miscut angle between the crystal surface and its crystallographic planes doubled the beam losses in the aligned crystal.peer-reviewe

Comparative results on collimation of the SPS beam of protons and Pb ions with bent crystals

New experiments on crystal assisted collimation have been carried out at the CERN SPS with stored beams of 120 GeV/. c protons and Pb ions. Bent silicon crystals of 2 mm long with about 170 μrad bend angle and a small residual torsion were used as primary collimators. In channeling conditions, the beam loss rate induced by inelastic interactions of particles with the crystal nuclei is minimal. The loss reduction was about 6 for protons and about 3 for Pb ions. Lower reduction value for Pb ions can be explained by their considerably larger ionization losses in the crystal. In one of the crystals, the measured fraction of the Pb ion beam halo deflected in channeling conditions was 74%, a value very close to that for protons. The intensity of the off-momentum halo leaking out from the collimation station was measured in the first high dispersion area downstream. The particle population in the shadow of the secondary collimator-absorber was considerably smaller in channeling conditions than for amorphous orientations of the crystal. The corresponding reduction was in the range of 2-5 for both protons and Pb ions.peer-reviewe

Observation of parametric X-rays produced by 400 GeV/c protons in bent crystals

Spectral maxima of parametric X-ray radiation (PXR) produced by 400 GeV/c protons in bent silicon crystals aligned with the beam have been observed in an experiment at the H8 external beam of the CERN SPS. The total yield of PXR photons was about 10-6 per proton. Agreement between calculations and the experimental data shows that the PXR kinematic theory is valid for bent crystals with sufficiently small curvature as used in the experiment. The intensity of PXR emitted from halo protons in a bent crystal used as a primary collimator in a circular accelerator may be considered as a possible tool to control its crystal structure, which is slowly damaged because of irradiation. The intensity distribution of PXR peaks depends on the crystal thickness intersected by the beam, which changes for different orientations of a crystal collimator. This dependence may be used to control crystal collimator alignment by analyzing PXR spectra produced by halo protons.peer-reviewe

Initial performance of the CUORE-0 experiment

CUORE-0 is a cryogenic detector that uses an array of tellurium dioxide bolometers to search for neutrinoless double-beta decay of ^{130}Te. We present the first data analysis with 7.1 kg y of total TeO_2 exposure focusing on background measurements and energy resolution. The background rates in the neutrinoless double-beta decay region of interest (2.47 to 2.57 MeV) and in the {\alpha} background-dominated region (2.70 to 3.90 MeV) have been measured to be 0.071 \pm 0.011 and 0.019 \pm 0.002 counts/keV/kg/y, respectively. The latter result represents a factor of 6 improvement from a predecessor experiment, Cuoricino. The results verify our understanding of the background sources in CUORE-0, which is the basis of extrapolations to the full CUORE detector. The obtained energy resolution (full width at half maximum) in the region of interest is 5.7 keV. Based on the measured background rate and energy resolution in the region of interest, CUORE-0 half-life sensitivity is expected to surpass the observed lower bound of Cuoricino with one year of live time.Comment: 8 pages, 5 figures, version 2 as published in Eur. Phys. J.

Neutrinoless double-beta decay search with CUORE and CUORE-0 experiments

The Cryogenic Underground Observatory for Rare Events (CUORE) is an upcoming experiment designed to search for the neutrinoless double-beta decays. Observation of the process would unambiguously establish that neutrinos are Majorana particles and provide information on their absolute mass scale hierarchy. CUORE is now under construction and will consist of an array of 988 TeO2 crystal bolometers operated at 10 mK, but the first tower (CUORE-0) is already taking data. The experimental techniques used will be presented as well as the preliminary CUORE-0 results. The current status of the full-mass experiment and its expected sensitivity will then be discussed