Bayesian latent class estimation of sensitivity and specificity parameters of diagnostic tests for bovine tuberculosis in chronically infected herds in Northern Ireland

Publication history: Accepted - 26 April 2018; Published online - 1 May 2018.In the European Union, the recommended ante-mortem diagnostic methods for bovine tuberculosis (bTB) include the single intradermal cervical comparative tuberculin (SICCT) test and the interferon-gamma (IFN- g) test as an ancillary test. The SICCT test has a moderate sensitivity (Se) and high specificity (Sp), while the IFN-g test has good Se, but a lower Sp than the SICCT test. A retrospective Bayesian latent class analysis was conducted on 71,185 cattle from 806 herds chronically infected with bTB distributed across Northern Ireland (NI) to estimate the Se and Sp of the common ante-mortem tests and meat inspection. Analyses were also performed on data stratified by farming type and herd location to explore possible differences in test performance given the heterogeneity in the population. The mean estimates in chronically infected herds were: (1) ‘standard’ SICCT: Se 40.5–57.7%, Sp 96.3–99.7%; (2) ‘severe’ SICCT: Se 49.0%–60.6%, Sp 94.4–99.4%; (3) IFN-g(bovine–avian) using a NI optical density (OD) cut-off difference of 0.05: IFN-g(B–A)NI: Se 85.8– 93.0%, Sp 75.6–96.2%; (4) IFN-g(bovine–avian) using a standard ‘commercial’ OD cut-off difference of 0.1: IFN-g(B–A)0.1: Se 83.1–92.1%, Sp 83.1–97.3%; and (5) meat inspection: Se 49.0–57.1% Se, Sp 99.1–100%. Se estimates were lower in cattle from dairy farms than from beef farms. There were no notable differences in estimates by location of herds. Certain population characteristics, such as production type, might influence the ability of bTB tests to disclose truly infected cases.This study is part of a larger project on the evaluation of the performance characteristics of the test in chronic bTB herds in NI from 2004 to 2010. It was financed by DAERA (E&I grant code 11/ 03/10)

Monitoring Mycobacterium bovis in Eurasian badgers ( Meles meles ) killed by vehicles in Northern Ireland between 1998 and 2011

Despite extensive long-term eradication programmes, bovine tuberculosis (bTB) remains endemic in much of the British Isles. The cost of the national eradication programme in Northern Ireland was estimated at £23 million in 2010/2011.1 There is evidence that badgers play a role in the maintenance and spread of Mycobacterium bovis to cattle (as reviewed by Allen and others2). Northern Ireland is a small country (13,843 km2) with an agricultural land that is dominated by grass production, which supports 1.6 million cattle among 20,000 farms.3 The estimated badger population of 34,100 (95 per cent confidence interval (CI) 26,200 to 42,000) is widespread and contained within 7600 social groups (95 per cent CI 6200 to 9000).4 A road traffic accident (RTA) survey began in 1998 in Northern Ireland with the aim of describing the occurrence of M bovis within the badger population

Search for the Rare Decay KL --> pi0 ee

The KTeV/E799 experiment at Fermilab has searched for the rare kaon decay KL--> pi0ee. This mode is expected to have a significant CP violating component. The measurement of its branching ratio could support the Standard Model or could indicate the existence of new physics. This letter reports new results from the 1999-2000 data set. One event is observed with an expected background at 0.99 +/- 0.35 events. We set a limit on the branching ratio of 3.5 x 10^(-10) at the 90% confidence level. Combining the results with the dataset taken in 1997 yields the final KTeV result: BR(KL --> pi0 ee) < 2.8 x 10^(-10) at 90% CL.Comment: 4 pages, three figure

Measurements of Direct CP Violation, CPT Symmetry, and Other Parameters in the Neutral Kaon System

We present a series of measurements based on K -> pi+pi- and K -> pi0pi0 decays collected in 1996-1997 by the KTeV experiment (E832) at Fermilab. We compare these four K -> pipi decay rates to measure the direct CP violation parameter Re(e'/e) = (20.7 +- 2.8) x 10^-4. We also test CPT symmetry by measuring the relative phase between the CP violating and CP conserving decay amplitudes for K->pi+pi- (phi+-) and for K -> pi0pi0 (phi00). We find the difference between the relative phases to be Delta-phi = phi00 - phi+- = (+0.39 +- 0.50) degrees and the deviation of phi+- from the superweak phase to be phi+- - phi_SW =(+0.61 +- 1.19) degrees; both results are consistent with CPT symmetry. In addition, we present new measurements of the KL-KS mass difference and KS lifetime: Delta-m = (5261 +- 15) x 10^6 hbar/s and tauS = (89.65 +- 0.07) x 10^-12 s.Comment: Submitted to Phys. Rev. D, August 6, 2002; 37 pages, 32 figure

Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV

Results are presented from a search for a W' boson using a dataset corresponding to 5.0 inverse femtobarns of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV. The W' boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both left-handed and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W' to t b, leading to a final state signature with a single lepton (e, mu), missing transverse energy, and jets, at least one of which is tagged as a b-jet. A W' boson that couples to fermions with the same coupling constant as the W, but to the right-handed rather than left-handed chiral projections, is excluded for masses below 1.85 TeV at the 95% confidence level. For the first time using LHC data, constraints on the W' gauge coupling for a set of left- and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe

Search for the standard model Higgs boson decaying into two photons in pp collisions at sqrt(s)=7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a centre-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 inverse femtobarns. Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1 sigma. The global significance of observing an excess with a local significance greater than 3.1 sigma anywhere in the search range 110-150 GeV is estimated to be 1.8 sigma. More data are required to ascertain the origin of this excess.Comment: Submitted to Physics Letters

Measurement of the Lambda(b) cross section and the anti-Lambda(b) to Lambda(b) ratio with Lambda(b) to J/Psi Lambda decays in pp collisions at sqrt(s) = 7 TeV

The Lambda(b) differential production cross section and the cross section ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7 TeV using data collected by the CMS experiment at the LHC. The measurements are based on Lambda(b) decays reconstructed in the exclusive final state J/Psi Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and Lambda to proton pion, using a data sample corresponding to an integrated luminosity of 1.9 inverse femtobarns. The product of the cross section times the branching ratio for Lambda(b) to J/Psi Lambda versus pt(Lambda(b)) falls faster than that of b mesons. The measured value of the cross section times the branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06 +/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are statistical and systematic, respectively.Comment: Submitted to Physics Letters

Search for new physics in events with opposite-sign leptons, jets, and missing transverse energy in pp collisions at sqrt(s) = 7 TeV

A search is presented for physics beyond the standard model (BSM) in final states with a pair of opposite-sign isolated leptons accompanied by jets and missing transverse energy. The search uses LHC data recorded at a center-of-mass energy sqrt(s) = 7 TeV with the CMS detector, corresponding to an integrated luminosity of approximately 5 inverse femtobarns. Two complementary search strategies are employed. The first probes models with a specific dilepton production mechanism that leads to a characteristic kinematic edge in the dilepton mass distribution. The second strategy probes models of dilepton production with heavy, colored objects that decay to final states including invisible particles, leading to very large hadronic activity and missing transverse energy. No evidence for an event yield in excess of the standard model expectations is found. Upper limits on the BSM contributions to the signal regions are deduced from the results, which are used to exclude a region of the parameter space of the constrained minimal supersymmetric extension of the standard model. Additional information related to detector efficiencies and response is provided to allow testing specific models of BSM physics not considered in this paper.Comment: Replaced with published version. Added journal reference and DO

Measurement of isolated photon production in pp and PbPb collisions at sqrt(sNN) = 2.76 TeV

Isolated photon production is measured in proton-proton and lead-lead collisions at nucleon-nucleon centre-of-mass energies of 2.76 TeV in the pseudorapidity range |eta|<1.44 and transverse energies ET between 20 and 80 GeV with the CMS detector at the LHC. The measured ET spectra are found to be in good agreement with next-to-leading-order perturbative QCD predictions. The ratio of PbPb to pp isolated photon ET-differential yields, scaled by the number of incoherent nucleon-nucleon collisions, is consistent with unity for all PbPb reaction centralities.Comment: Submitted to Physics Letters

Mutational processes molding the genomes of 21 breast cancers

All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we generated catalogs of somatic mutation from 21 breast cancers and applied mathematical methods to extract mutational signatures of the underlying processes. Multiple distinct single- and double-nucleotide substitution signatures were discernible. Cancers with BRCA1 or BRCA2 mutations exhibited a characteristic combination of substitution mutation signatures and a distinctive profile of deletions. Complex relationships between somatic mutation prevalence and transcription were detected. A remarkable phenomenon of localized hypermutation, termed "kataegis," was observed. Regions of kataegis differed between cancers but usually colocalized with somatic rearrangements. Base substitutions in these regions were almost exclusively of cytosine at TpC dinucleotides. The mechanisms underlying most of these mutational signatures are unknown. However, a role for the APOBEC family of cytidine deaminases is proposed