Clustering and Alignment of Polymorphic Sequences for HLA-DRB1 Genotyping

Located on Chromosome 6p21, classical human leukocyte antigen genes are highly polymorphic. HLA alleles associate with a variety of phenotypes, such as narcolepsy, autoimmunity, as well as immunologic response to infectious disease. Moreover, high resolution genotyping of these loci is critical to achieving long-term survival of allogeneic transplants. Development of methods to obtain high resolution analysis of HLA genotypes will lead to improved understanding of how select alleles contribute to human health and disease risk. Genomic DNAs were obtained from a cohort of n = 383 subjects recruited as part of an Ulcerative Colitis study and analyzed for HLA-DRB1. HLA genotypes were determined using sequence specific oligonucleotide probes and by next-generation sequencing using the Roche/454 GSFLX instrument. The Clustering and Alignment of Polymorphic Sequences (CAPSeq) software application was developed to analyze next-generation sequencing data. The application generates HLA sequence specific 6-digit genotype information from next-generation sequencing data using MUMmer to align sequences and the R package diffusionMap to classify sequences into their respective allelic groups. The incorporation of Bootstrap Aggregating, Bagging to aid in sorting of sequences into allele classes resulted in improved genotyping accuracy. Using Bagging iterations equal to 60, the genotyping results obtained using CAPSeq when compared with sequence specific oligonucleotide probe characterized 4-digit genotypes exhibited high rates of concordance, matching at 759 out of 766 (99.1%) alleles. © 2013 Ringquist et al

Giant phonon anomalies and central peak due to charge density wave formation in YBa2_2Cu3_3O6.6_{6.6}

The electron-phonon interaction is a major factor influencing the competition between collective instabilities in correlated-electron materials, but its role in driving high-temperature superconductivity in the cuprates remains poorly understood. We have used high-resolution inelastic x-ray scattering to monitor low-energy phonons in YBa$_2$Cu$_3$O$_{6.6}$ (superconducting $\bf T_c = 61$ K), which is close to a charge density wave (CDW) instability. Phonons in a narrow range of momentum space around the CDW ordering vector exhibit extremely large superconductivity-induced lineshape renormalizations. These results imply that the electron-phonon interaction has sufficient strength to generate various anomalies in electronic spectra, but does not contribute significantly to Cooper pairing. In addition, a quasi-elastic "central peak" due to CDW nanodomains is observed in a wide temperature range above and below $\bf T_c$, suggesting that the gradual onset of a spatially inhomogeneous CDW domain state with decreasing temperature is a generic feature of the underdoped cuprates

Z boson production in Pb+Pb collisions at √Snn = 5.02 TeV measured by the ATLAS experiment

The production yield of Z bosons is measured in the electron and muon decay channels in Pb+Pb collisions at √S = 5.02 TeV with the ATLAS detector. Data from the 2015 LHC run corresponding to an integrated luminosity of 0.49 nb are used for the analysis. The Z boson yield, normalised by the total number of minimum-bias events and the mean nuclear thickness function, is measured as a function of dilepton rapidity and event centrality. The measurements in Pb+Pb collisions are compared with similar measurements made in proton-proton collisions at the same centre-of-mass energy. The nuclear modification factor is found to be consistent with unity for all centrality intervals. The results are compared with theoretical predictions obtained at next-to-leading order using nucleon and nuclear parton distribution functions. The normalised Z boson yields in Pb+Pb collisions lie 1-3σ above the predictions. The nuclear modification factor measured as a function of rapidity agrees with unity and is consistent with a next-to-leading-order QCD calculation including the isospin effect. nn -

Combination of searches for Higgs boson pairs in pp collisions at s=13TeV with the ATLAS detector

This letter presents a combination of searches for Higgs boson pair production using up to 36.1 fb−1 of proton–proton collision data at a centre-of-mass energy s=13 TeV recorded with the ATLAS detector at the LHC. The combination is performed using six analyses searching for Higgs boson pairs decaying into the bb¯bb¯, bb¯W+W−, bb¯τ+τ−, W+W−W+W−, bb¯γγ and W+W−γγ final states. Results are presented for non-resonant and resonant Higgs boson pair production modes. No statistically significant excess in data above the Standard Model predictions is found. The combined observed (expected) limit at 95% confidence level on the non-resonant Higgs boson pair production cross-section is 6.9 (10) times the predicted Standard Model cross-section. Limits are also set on the ratio (κλ) of the Higgs boson self-coupling to its Standard Model value. This ratio is constrained at 95% confidence level in observation (expectation) to −5.0<κλ<12.0 (−5.8<κλ<12.0). In addition, limits are set on the production of narrow scalar resonances and spin-2 Kaluza–Klein Randall–Sundrum gravitons. Exclusion regions are also provided in the parameter space of the habemus Minimal Supersymmetric Standard Model and the Electroweak Singlet Model

Measurement of Azimuthal Anisotropy of Muons from Charm and Bottom Hadrons in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector.

The elliptic flow of muons from the decay of charm and bottom hadrons is measured in pp collisions at sqrt[s]=13  TeV using a data sample with an integrated luminosity of 150  pb^{-1} recorded by the ATLAS detector at the LHC. The muons from heavy-flavor decay are separated from light-hadron decay muons using momentum imbalance between the tracking and muon spectrometers. The heavy-flavor decay muons are further separated into those from charm decay and those from bottom decay using the distance-of-closest-approach to the collision vertex. The measurement is performed for muons in the transverse momentum range 4-7 GeV and pseudorapidity range |η|<2.4. A significant nonzero elliptic anisotropy coefficient v_{2} is observed for muons from charm decays, while the v_{2} value for muons from bottom decays is consistent with zero within uncertainties

Measurement of W± boson production in Pb+Pb collisions at √sNN=5.02Te with the ATLAS detector

A measurement of W± boson production in Pb+Pb collisions at sNN=5.02Te is reported using data recorded by the ATLAS experiment at the LHC in 2015, corresponding to a total integrated luminosity of 0.49nb-1. The W± bosons are reconstructed in the electron or muon leptonic decay channels. Production yields of leptonically decaying W± bosons, normalised by the total number of minimum-bias events and the nuclear thickness function, are measured within a fiducial region defined by the detector acceptance and the main kinematic requirements. These normalised yields are measured separately for W+ and W- bosons, and are presented as a function of the absolute value of pseudorapidity of the charged lepton and of the collision centrality. The lepton charge asymmetry is also measured as a function of the absolute value of lepton pseudorapidity. In addition, nuclear modification factors are calculated using the W± boson production cross-sections measured in pp collisions. The results are compared with predictions based on next-to-leading-order calculations with CT14 parton distribution functions as well as with predictions obtained with the EPPS16 and nCTEQ15 nuclear parton distribution functions. No dependence of normalised production yields on centrality and a good agreement with predictions are observed for mid-central and central collisions. For peripheral collisions, the data agree with predictions within 1.7 (0.9) standard deviations for W- (W+) bosons

Search for flavour-changing neutral currents in processes with one top quark and a photon using 81 fb−1 of pp collisions at s=13TeV with the ATLAS experiment

A search for flavour-changing neutral current (FCNC) events via the coupling of a top quark, a photon, and an up or charm quark is presented using 81 fb−1 of proton–proton collision data taken at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC. Events with a photon, an electron or muon, a b-tagged jet, and missing transverse momentum are selected. A neural network based on kinematic variables differentiates between events from signal and background processes. The data are consistent with the background-only hypothesis, and limits are set on the strength of the tqγ coupling in an effective field theory. These are also interpreted as 95% CL upper limits on the cross section for FCNC tγ production via a left-handed (right-handed) tuγ coupling of 36 fb (78 fb) and on the branching ratio for t→γu of 2.8×10−5 (6.1×10−5). In addition, they are interpreted as 95% CL upper limits on the cross section for FCNC tγ production via a left-handed (right-handed) tcγ coupling of 40 fb (33 fb) and on the branching ratio for t→γc of 22×10−5 (18×10−5)

Search for Magnetic Monopoles and Stable High-Electric-Charge Objects in 13 Tev Proton-Proton Collisions with the ATLAS Detector.

A search for magnetic monopoles and high-electric-charge objects is presented using 34.4  fb^{-1} of 13 TeV pp collision data collected by the ATLAS detector at the LHC during 2015 and 2016. The considered signature is based upon high ionization in the transition radiation tracker of the inner detector associated with a pencil-shape energy deposit in the electromagnetic calorimeter. The data were collected by a dedicated trigger based on the tracker high-threshold hit capability. The results are interpreted in models of Drell-Yan pair production of stable particles with two spin hypotheses (0 and 1/2) and masses ranging from 200 to 4000 GeV. The search improves by approximately a factor of 5 the constraints on the direct production of magnetic monopoles carrying one or two Dirac magnetic charges and stable objects with electric charge in the range 20≤|z|≤60 and extends the charge range to 60<|z|≤100