Accelerated Event-by-Event Neutrino Oscillation Reweighting with Matter Effects on a GPU

Oscillation probability calculations are becoming increasingly CPU intensive in modern neutrino oscillation analyses. The independency of reweighting individual events in a Monte Carlo sample lends itself to parallel implementation on a Graphics Processing Unit. The library "Prob3++" was ported to the GPU using the CUDA C API, allowing for large scale parallelized calculations of neutrino oscillation probabilities through matter of constant density, decreasing the execution time by a factor of 75, when compared to performance on a single CPU.Comment: Final Update: Post submission update Updated version: quantified the difference in event rates for binned and event-by-event reweighting with a typical binning scheme. Improved formatting of reference

Quantifying bacterial evolution in the wild : A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the 'birthday problem'. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter colt (2.4 x 10(-6) s/s/y) and Campylobacter jejuni (3.4 x 10(-6) s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame-analogous to a shared birthday-and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.Peer reviewe

Argon Purification Studies and a Novel Liquid Argon Re-circulation System

Future giant liquid argon (LAr) time projection chambers (TPCs) require a purity of better than 0.1 parts per billion (ppb) to allow the ionised electrons to drift without significant capture by any electronegative impurities. We present a comprehensive study of the effects of electronegative impurity on gaseous and liquid argon scintillation light, an analysis of the efficacy of various purification chemicals, as well as the Liverpool LAr setup, which utilises a novel re-circulation purification system. Of the impurities tested - Air, O_2, H_2O, N_2 and CO_2 in the range of between 0.01 ppm to 1000 ppm - H_2O was found to have the most profound effect on gaseous argon scintillation light, and N_2 was found to have the least. Additionally, a correlation between the slow component decay time and the total energy deposited with 0.01 ppm - 100 ppm O_2 contamination levels in liquid argon has been established. The superiority of molecular sieves over anhydrous complexes at absorbing Ar gas, N_2 gas and H_2O vapour has been quantified using BET isotherm analysis. The efficiency of Cu and P_2O5 at removing O_2 and H_2O impurities from 1 bar N6 argon gas at both room temperature and -130 ^oC was investigated and found to be high. A novel, highly scalable LAr re-circulation system has been developed. The complete system, consisting of a motorised bellows pump operating in liquid and a purification cartridge, were designed and built in-house. The system was operated successfully over many days and achieved a re-circulation rate of 27 litres/hour and high purity

Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease

The use of antimicrobials in human and veterinary medicine has coincided with a rise in antimicrobial resistance (AMR) in the food-borne pathogens Campylobacter jejuni and Campylobacter coli. Faecal contamination from the main reservoir hosts (livestock, especially poultry) is the principal route of human infection but little is known about the spread of AMR among source and sink populations. In particular, questions remain about how Campylobacter resistomes interact between species and hosts, and the potential role of sewage as a conduit for the spread of AMR. Here, we investigate the genomic variation associated with AMR in 168 C. jejuni and 92 C. coli strains isolated from humans, livestock and urban effluents in Spain. AMR was tested in vitro and isolate genomes were sequenced and screened for putative AMR genes and alleles. Genes associated with resistance to multiple drug classes were observed in both species and were commonly present in multidrug-resistant genomic islands (GIs), often located on plasmids or mobile elements. In many cases, these loci had alleles that were shared among C. jejuni and C. coli consistent with horizontal transfer. Our results suggest that specific antibiotic resistance genes have spread among Campylobacter isolated from humans, animals and the environment.S.K.S., B.P. and S.C.B. were supported by grants from the Medical Research Council (MR/L015080/1), the Wellcome Trust (088786/C/09/Z), the Food Standards Agency (FS246004) and the Biotechnology and Biological Sciences Research Council (BB/I02464X/1). E.M. received a University of Bath Faculty of Science URSA studentship. D.F.C. is supported by the FPI program (BES-2013-065003) from the Spanish Ministry of Economy and Competitiveness. J.K.C. is supported by a BBSRC KTN PhD studentship (BB/P504750/1)

First measurement of the νμ charged-current cross section on a water target without pions in the final state

This paper reports the first differential measurement of the charged-current interaction cross section of νμ on water with no pions in the final state. This flux-averaged measurement has been made using the T2K experiment\u27s off-axis near detector, and is reported in doubly differential bins of muon momentum and angle. The flux-averaged total cross section in a restricted region of phase space was found to be σ=(0.95±0.08(stat)±0.06(det syst)±0.04(model syst)±0.08(flux))×10-38 cm2/n

Updated T2K measurements of muon neutrino and antineutrino disappearance using 1.5×1021 protons on target

We report measurements by the T2K experiment of the parameters θ23 and Δm322 governing the disappearance of muon neutrinos and antineutrinos in the three-flavor neutrino oscillation model. Utilizing the ability of the experiment to run with either a mainly neutrino or a mainly antineutrino beam, the parameters are measured separately for neutrinos and antineutrinos. Using 7.482×1020 POT in neutrino running mode and 7.471×1020 POT in antineutrino mode, T2K obtained sin2(θ23)=0.51-0.07+0.08 and Δm322=2.53-0.13+0.15×10-3 eV2/c4 for neutrinos, and sin2(θ-23)=0.42-0.07+0.25 and Δm-232=2.55-0.27+0.33×10-3 eV2/c4 for antineutrinos (assuming normal mass ordering). No significant differences between the values of the parameters describing the disappearance of muon neutrinos and antineutrinos were observed

Flavonoids from Pterogyne nitens Inhibit Hepatitis C Virus Entry

Hepatitis C virus (HCV) is one of the leading causes of liver diseases and transplantation worldwide. The current available therapy for HCV infection is based on interferon-α, ribavirin and the new direct-acting antivirals (DAAs), such as NS3 protease and NS5B polymerase inhibitors. However, the high costs of drug design, severe side effects and HCV resistance presented by the existing treatments demonstrate the need for developing more efficient anti-HCV agents. This study aimed to evaluate the antiviral effects of sorbifolin (1) and pedalitin (2), two flavonoids from Pterogyne nitens on the HCV replication cycle. These compounds were investigated for their anti-HCV activities using genotype 2a JFH-1 subgenomic replicons and infectious virus systems. Flavonoids 1 and 2 inhibited virus entry up to 45.0% and 78.7% respectively at non-cytotoxic concentrations. The mechanism of the flavonoid 2 block to virus entry was demonstrated to be by both the direct action on virus particles and the interference on the host cells. Alternatively, the flavonoid 1 activity was restricted to its virucidal effect. Additionally, no inhibitory effects on HCV replication and release were observed by treating cells with these flavonoids. These data are the first description of 1 and 2 possessing in vitro anti-HCV activity

Combined Analysis of Neutrino and Antineutrino Oscillations at T2K

T2K reports its first results in the search for CP violation in neutrino oscillations using appearance and disappearance channels for neutrino- and antineutrino-mode beams. The data include all runs from January 2010 to May 2016 and comprise 7.482×1020 protons on target in neutrino mode, which yielded in the far detector 32 e-like and 135 μ-like events, and 7.471×1020 protons on target in antineutrino mode, which yielded 4 e-like and 66 μ-like events. Reactor measurements of sin22θ13 have been used as an additional constraint. The one-dimensional confidence interval at 90% for the phase δCP spans the range (-3.13, -0.39) for normal mass ordering. The CP conservation hypothesis (δCP=0, π) is excluded at 90% C.L

Measurement of neutrino and antineutrino oscillations by the T2K experiment including a new additional sample of ve interactions at the far detector

The T2K experiment reports an updated analysis of neutrino and antineutrino oscillations in appearance and disappearance channels. Asample of electron neutrino candidates at Super-Kamiokande in which a pion decay has been tagged is added to the four single-ring samples used in previous T2K oscillation analyses. Through combined analyses of these five samples, simultaneous measurements of four oscillation parameters, j?m2 32j, sin2 ?23, sin2 ?13, and dCP and of the mass ordering are made. A set of studies of simulated data indicates that the sensitivity to the oscillation parameters is not limited by neutrino interaction model uncertainty. Multiple oscillation analyses are performed, and frequentist and Bayesian intervals are presented for combinations of the oscillation parameters with and without the inclusion of reactor constraints on sin2 ?13.When combined with reactor measurements, the hypothesis of CP conservation (dCP 0 or p) is excluded at 90% confidence level. The 90% confidence region for dCP is -2.95;-0.44(-1.47;-1.27) for normal (inverted) ordering. The central values and 68% confidence intervals for the other oscillation parameters for normal (inverted) ordering are ?m2 32 2.540.082.510.08 10-3 eV2=c4 and sin2?23 0.55+0.05 -0.09 (0.55+0.05 -0.08 ), compatible with maximal mixing. In the Bayesian analysis, the data weakly prefer normal ordering (Bayes factor 3.7) and the upper octant for sin2 ?23 (Bayes factor 2.4)

Campylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans

Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. jejuni isolates from patients who developed PI-IBS with those who did not. We show that variation in bacterial stress response (Cj0145_phoX), adhesion protein (Cj0628_CapA), and core biosynthetic pathway genes (biotin: Cj0308_bioD; purine: Cj0514_purQ; isoprenoid: Cj0894c_ispH) were associated with PI-IBS development. In vitro assays demonstrated greater adhesion, invasion, IL-8 and TNFα secretion on colonocytes with PI-IBS compared to PI-no-IBS strains. A risk-score for PI-IBS development was generated using 22 genomic markers, four of which were from Cj1631c, a putative heme oxidase gene linked to virulence. Our finding that specific Campylobacter genotypes confer greater in vitro virulence and increased risk of PI-IBS has potential to improve understanding of the complex host-pathogen interactions underlying this condition