Efficient error correction and haplotypes reconstruction for deep sequencing of hepatitis c amplicons

Секция 1. Защита информации и компьютерный анализ данныхWe present two new highly efficient pyrosequencing error correction algorithms: (i) k-mer – based error correction (KEC); and (ii) empirical frequency threshold (ET). Both were compared to the recently published clustering algorithm SHORAH to evaluate the relative performance using 24 experimental datasets obtained by 454-sequencing of amplicons with known sequences. We found that all three algorithms showed similar performance in terms of finding true haplotypes, but KEC and ET methods significantly outperformed SHORAH both in terms of their ability to remove false haplotypes and to estimate the frequency of true ones

Study of Non-Standard Neutrino Interactions with Atmospheric Neutrino Data in Super-Kamiokande I and II

In this paper we study non-standard neutrino interactions as an example of physics beyond the standard model using atmospheric neutrino data collected during the Super-Kamiokande I(1996-2001) and II(2003-2005) periods. We focus on flavor-changing-neutral-currents (FCNC), which allow neutrino flavor transitions via neutral current interactions, and effects which violate lepton non-universality (NU) and give rise to different neutral-current interaction-amplitudes for different neutrino flavors. We obtain a limit on the FCNC coupling parameter, varepsilon_{mu tau}, |varepsilon_{mu tau}|<1.1 x 10^{-2} at 90%C.L. and various constraints on other FCNC parameters as a function of the NU coupling, varepsilon_{e e}. We find no evidence of non-standard neutrino interactions in the Super-Kamiokande atmospheric data.Comment: 12 Pages, 14 figures. To be submitted to Phys. Rev.

Search for Nucleon Decay into Charged Anti-lepton plus Meson in Super-Kamiokande I and II

Searches for a nucleon decay into a charged anti-lepton (e^+ or {\mu}^+) plus a light meson ({\pi}^0, {\pi}^-, {\eta}, {\rho}^0, {\rho}^-, {\omega}) were performed using the Super-Kamiokande I and II data. Twelve nucleon decay modes were searched for. The total exposure is 140.9 kiloton \cdot years, which includes a 91.7 kiloton \cdot year exposure (1489.2 live days) of Super-Kamiokande-I and a 49.2 kiloton \cdot year exposure (798.6 live days) of Super-Kamiokande-II. The number of candidate events in the data was consistent with the atmospheric neutrino background expectation. No significant evidence for a nucleon decay was observed in the data. Thus, lower limits on the nucleon partial lifetime at 90% confidence level were obtained. The limits range from 3.6 \times 10^31 to 8.2 \times 10^33 years, depending on the decay modes.Comment: 25 pages, 18 figure

An Indirect Search for WIMPs in the Sun using 3109.6 days of upward-going muons in Super-Kamiokande

We present the result of an indirect search for high energy neutrinos from WIMP annihilation in the Sun using upward-going muon (upmu) events at Super-Kamiokande. Datasets from SKI-SKIII (3109.6 days) were used for the analysis. We looked for an excess of neutrino signal from the Sun as compared with the expected atmospheric neutrino background in three upmu categories: stopping, non-showering, and showering. No significant excess was observed. The 90% C.L. upper limits of upward-going muon flux induced by WIMPs of 100 GeV/c$^2$ were 6.4$\times10^{-15}$ cm$^{-2}$ sec$^{-1}$ and 4.0$\times10^{-15}$ cm$^{-2}$ sec$^{-1}$ for the soft and hard annihilation channels, respectively. These limits correspond to upper limits of 4.5$\times10^{-39}$ cm$^{-2}$ and 2.7$\times10^{-40}$ cm$^{-2}$ for spin-dependent WIMP-nucleon scattering cross sections in the soft and hard annihilation channels, respectively.Comment: Add journal reference. Also fixed typo and cosmetic things in the old draf

Atmospheric neutrino oscillation analysis with sub-leading effects in Super-Kamiokande I, II, and III

We present a search for non-zero theta_{13} and deviations of sin^2 theta_{23} from 0.5 in the oscillations of atmospheric neutrino data from Super-Kamiokande -I, -II, and -III. No distortions of the neutrino flux consistent with non-zero theta_{13} are found and both neutrino mass hierarchy hypotheses are in agreement with the data. The data are best fit at Delta m^2 = 2.1 x 10^-3 eV^2, sin^2 theta_{13} = 0.0, and sin^2 theta_{23} =0.5. In the normal (inverted) hierarchy theta_{13} and Delta m^2 are constrained at the one-dimensional 90% C.L. to sin^2 theta_{13} < 0.04 (0.09) and 1.9 (1.7) x 10^-3 < Delta m^2 < 2.6 (2.7) x 10^-3 eV^2. The atmospheric mixing angle is within 0.407 <= sin^2 theta_{23} <= 0.583 at 90% C.L.Comment: 17 Pages, 14 figures. To be submitted to Phys. Rev. D Minor update to text after referee comments. Figures modified for better grayscale printing

Solar neutrino results in Super-Kamiokande-III

The results of the third phase of the Super-Kamiokande solar neutrino measurement are presented and compared to the first and second phase results. With improved detector calibrations, a full detector simulation, and improved analysis methods, the systematic uncertainty on the total neutrino flux is estimated to be ?2.1%, which is about two thirds of the systematic uncertainty for the first phase of Super-Kamiokande. The observed 8B solar flux in the 5.0 to 20 MeV total electron energy region is 2.32+/-0.04 (stat.)+/-0.05 (sys.) *10^6 cm^-2sec^-1, in agreement with previous measurements. A combined oscillation analysis is carried out using SK-I, II, and III data, and the results are also combined with the results of other solar neutrino experiments. The best-fit oscillation parameters are obtained to be sin^2 {\theta}12 = 0.30+0.02-0.01(tan^2 {\theta}12 = 0.42+0.04 -0.02) and {\Delta}m2_21 = 6.2+1.1-1.9 *10^-5eV^2. Combined with KamLAND results, the best-fit oscillation parameters are found to be sin^2 {\theta}12 = 0.31+/-0.01(tan^2 {\theta}12 = 0.44+/-0.03) and {\Delta}m2_21 = 7.6?0.2*10^-5eV^2 . The 8B neutrino flux obtained from global solar neutrino experiments is 5.3+/-0.2(stat.+sys.)*10^6cm^-2s^-1, while the 8B flux becomes 5.1+/-0.1(stat.+sys.)*10^6cm^-2s^-1 by adding KamLAND result. In a three-flavor analysis combining all solar neutrino experiments, the upper limit of sin^2 {\theta}13 is 0.060 at 95% C.L.. After combination with KamLAND results, the upper limit of sin^2 {\theta}13 is found to be 0.059 at 95% C.L..Comment: 19 pages, 33 figures in the main text. The appendix section on errata is added in v

Search for Astrophysical Neutrino Point Sources at Super-Kamiokande

It has been hypothesized that large fluxes of neutrinos may be created in astrophysical "cosmic accelerators." The primary background for a search for astrophysical neutrinos comes from atmospheric neutrinos, which do not exhibit the pointlike directional clustering that characterizes a distant astrophysical signal. We perform a search for neutrino point sources using the upward-going muon data from three phases of operation (SK-I, SK-II, and SK-III) spanning 2623 days of live time taken from April 1, 1996 to August 11, 2007. The search looks for signals from suspected galactic and extragalactic sources, transient sources, and unexpected sources. We find interesting signatures from two objects--RX J1713.7-3946 (97.5% CL) and GRB 991004D (95.3% CL)--but the signatures lack compelling statistical significance given trial factors. We set limits on the flux and fluence of neutrino point sources above energies of 1.6 GeV

Three-dimensional magnetic resonance imaging of the anterolateral ligament of the knee: an evaluation of intact and anterior cruciate ligament–deficient knees from the scientific anterior cruciate ligament network international (SANTI) Study Group

Purpose: The aim of this study was to determine the visualisation rate of the ALL in uninjured and ACL deficient knees when using 3D-MRI. In addition, it was sought to characterize the spectrum of ALL injury in acute and chronically ACL deficient knees, and also to determine the inter and intra-observer reliability of a 3D-MRI classification of ALL injury. Methods: 100 knees underwent 3D-MRI (60 with ACL rupture and 40 non-injured knees). The ALL was evaluated by two blinded orthopaedic surgeons. The ALL was classified as Type A: continuous, clearly defined low-signal band, Type B: with warping, thinning, or iso-signal changes, Type C: without clear continuity. Comparison between acute (<1 month) and chronically ACL injured knees was evaluated as well as intra and inter-observer reliability. Results: Complete visualisation of the full path of the ALL was achieved in all non-injured knees. In the ACL injured group, 24 acutely injured knees were imaged: 87.5% showed evidence of injury (3 knees were normal/Type A (12.5%), 18 Type B (75.0%), and 3 Type C (12.5%)). 36 knees chronically ACL injured knees were imaged: 55.6% showed evidence of injury (16 Type A (44.4%), 18 Type B (50.0%), and 2 Type C (5.6%)). The difference in the rate of injury between the two groups was significant (p = 0.03). Multivariate analysis demonstrated that the delay from ACL injury to MRI was the only factor (negatively) associated with the rate of injury to the ALL. Inter- and intra-observer reliability of the classification of ALL type were good (kappa 0.86 and 0.93 respectively). Conclusion: 3D-MRI allows full visualisation of the ALL in all knees. The rate of injury to the ALL in acutely ACL injured knees identified on 3D-MRI is higher than previous reports using standard MRI techniques. This rate is significantly higher than the rate of injury to the ALL identified in chronically ACL injured knees. Level of Evidence: IV, Diagnostic, case control study