MUC1 polymorphism in relation to susceptibility to Helicobacter pylori gastritis.

The gene MUC1 encodes a transmembrane mucin glycoprotein that is expressed on the apical surface of most epithelia and is aberrantly expressed in cancer. MUC1 contains an extended domain of tandemly repeated (TR) amino-acid sequence, which acts as the backbone for a large amount of O-linked glycosylation, and which varies in length and sequence in different alleles. Previous studies on MUC1 tandem repeat variation in patients with gastritis (Vinall et al, 2002) and gastric cancer (Carvalho et al, 1997) showed an overrepresentation of short TR alleles in the patient groups when compared with normal controls. The major aim of this thesis is to pursue this observation further. MUC1 allele and three locus haplotype frequencies were compared in 3 populations of different ancestry, from UK, Nigeria and Portugal, which show dramatic differences in gastric disease incidence in patients with gastric disease, patients with other gastrointestinal disease as well as associated controls. There were differences between the Nigerians and unselected European control groups, but there was no significant difference between the groups collected in London and Porto. Analysis of the gastric disease groups showed an over-representation of a particular MUC1 haplotype. A search was made, by sequencing and using a bioinformatics approach, for additional polymorphic markers within and surrounding the MUC1 gene, that might act as convenient markers for future disease association studies. Patterns of Linkage Disequilibrium were established across a 600Kb genomic region containing MUC1 using information in the HapMap resource and this information was used to assist in the selection of the single nucleotide polymorphisms (SNPs) within a 70Kb region to test on disease groups. During the course of this thesis work, a second UK cohort of patients and controls was collected and characterised and a replication study attempted. DNA samples from a total of 154 Northern Europeans classified as H. pylori gastritis (n=33), former H. pylori gastritis (n=44), No H. pylori gastritis (n=18) and normal (n=59). Examination of the MUC1 polymorphisms failed to show over-representation, in the H. pylori gastritis group, of the same haplotype found in the first gastritis cohort. The extended 70Kb haplotypes showed the expected association in the first cohort but no significant differences in the second cohort. However, in the population overall, it was noteworthy that there is a very high frequency haplogroup containing long tandem repeat arrays and this was somewhat lower in frequency in both H. pylori gastritis groups

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter