Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

Background: Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR).Methods/Principal Findings: The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm.Conclusions/Significance: Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.This work received financial support from the Ministry of Science and Technology of Argentina [PICT 2011-0207 to AGS] and the National Scientific and Technical Research Council in Argentina (CONICET) [PIP 112 2011-010-0974 to AGS]. Work related to evaluation of biological samples was partially sponsored by the Pan-American Health Organization (PAHO) [Small Grants Program PAHO-TDR]; the Drugs and Neglected Diseases Initiative (DNDi, Geneva, Switzerland), Wellcome Trust (London, United Kingdom), SANOFI-AVENTIS (Buenos Aires, Argentina) and the National Council for Science and Technology in Mexico (CONACYT) [FONSEC 161405 to JMR]

Search for resonances in the mass spectrum of muon pairs produced in association with b quark jets in proton-proton collisions at root 8 and 13 TeV

A search for resonances in the mass range 12-70 GeV produced in association with a b quark jet and a second jet, and decaying to a muon pair, is reported. The analysis is based on data from proton-proton collisions at center-of-mass energies of 8 and 13 TeV, collected with the CMS detector at the LHC and corresponding to integrated luminosities of 19.7 and 35.9 fb(-1), respectively. The search is carried out in two mutually exclusive event categories. Events in the first category are required to have a b quark jet in the central region (|| 2.4) and at least one jet in the forward region (|| > 2.4). Events in the second category are required to have two jets in the central region, at least one of which is identified as a b quark jet, no jets in the forward region, and low missing transverse momentum. An excess of events above the background near a dimuon mass of 28 GeV is observed in the 8 TeV data, corresponding to local significances of 4.2 and 2.9 standard deviations for the first and second event categories, respectively. A similar analysis conducted with the 13 TeV data results in a mild excess over the background in the first event category corresponding to a local significance of 2.0 standard deviations, while the second category results in a 1.4 standard deviation deficit. The fiducial cross section measurements and 95% confidence level upper limits on those for a resonance consistent with the 8 TeV excess are provided at both collision energies

Measurements of the differential jet cross section as a function of the jet mass in dijet events from proton-proton collisions at √s=13 TeV

Measurements of the differential jet cross section are presented as a function of the jet mass in dijet events, in bins of jet transverse momentum, with and without a jet grooming algorithm. The data have been recorded by the CMS Collaboration in proton-proton collisions at the LHC at a center-of-mass energy of 13 TeV and correspond to an integrated luminosity of 2.3 fb−1. The absolute cross sections show slightly different jet transverse momentum spectra in data and Monte Carlo event generators for the settings used. Removing this transverse momentum dependence, the normalized cross section for ungroomed jets is consistent with the prediction from Monte Carlo event generators for masses below 30% of the transverse momentum. The normalized cross section for groomed jets is measured with higher precision than the ungroomed cross section. Semi-analytical calculations of the jet mass beyond leading logarithmic accuracy are compared to data, as well as predictions at leading order and next-to-leading order, which include parton showering and hadronization. Overall, in the normalized cross section, the theoretical predictions agree with the measured cross sections within the uncertainties for masses from 10 to 30% of the jet transverse momentum

Charged-particle angular correlations in XeXe collisions at root s(NN)=5.44 TeV

Azimuthal correlations of charged particles in xenon-xenon collisions at a center-of-mass energy per nucleon pair of root s(NN) = 5.44 TeV are studied. The data were collected by the CMS experiment at the LHC with a total integrated luminosity of 3.42 mu b(-1). The collective motion of the system formed in the collision is parametrized by a Fourier expansion of the azimuthal particle density distribution. The azimuthal anisotropy coefficients v(2), v(3), and v(4) are obtained by the scalar-product, two-particle correlation, and multiparticle correlation methods. Within a hydrodynamic picture, these methods have different sensitivities to noncollective and fluctuation effects. The dependence of the Fourier coefficients on the size of the colliding system is explored by comparing the xenon-xenon results with equivalent lead-lead data. Model calculations that include initial-state fluctuation effects are also compared to the experimental results. The observed angular correlations provide new constraints on the hydrodynamic description of heavy ion collisions.Peer reviewe

Measurement of differential cross sections for inclusive isolated-photon and photon+jet production in proton-proton collisions at s=13 TeV\sqrt{s} = 13\,\text {TeV}

Measurements of inclusive isolated-photon and photon+jet production in proton–proton collisions at s √ =13TeV s=13TeV are presented. The analysis uses data collected by the CMS experiment in 2015, corresponding to an integrated luminosity of 2.26fb −1 fb−1 . The cross section for inclusive isolated photon production is measured as a function of the photon transverse energy in a fiducial region. The cross section for photon+jet production is measured as a function of the photon transverse energy in the same fiducial region with identical photon requirements and with the highest transverse momentum jet. All measurements are in agreement with predictions from next-to-leading-order perturbative QCD

Observation of ttˉ\bar{t}H Production

The observation of Higgs boson production in association with a top quark-antiquark pair is reported, based on a combined analysis of proton-proton collision data at center-of-mass energies of s√=7, 8, and 13 TeV, corresponding to integrated luminosities of up to 5.1, 19.7, and 35.9fb−1, respectively. The data were collected with the CMS detector at the CERN LHC. The results of statistically independent searches for Higgs bosons produced in conjunction with a top quark-antiquark pair and decaying to pairs of W bosons, Z bosons, photons, τ leptons, or bottom quark jets are combined to maximize sensitivity. An excess of events is observed, with a significance of 5.2 standard deviations, over the expectation from the background-only hypothesis. The corresponding expected significance from the standard model for a Higgs boson mass of 125.09 GeV is 4.2 standard deviations. The combined best fit signal strength normalized to the standard model prediction is 1.26+0.31−0.26

Study of the underlying event in top quark pair production in pp collisions at 13 TeV

Measurements of normalized differential cross sections as functions of the multiplicity and kinematic variables of charged-particle tracks from the underlying event in top quark and antiquark pair production are presented. The measurements are performed in proton-proton collisions at a center-of-mass energy of 13<, and are based on data collected by the CMS experiment at the LHC in 2016 corresponding to an integrated luminosity of 35.9fb(-1). Events containing one electron, one muon, and two jets from the hadronization and fragmentation of b quarks are used. These measurements characterize, for the first time, properties of the underlying event in top quark pair production and show no deviation from the universality hypothesis at energy scales typically above twice the top quark mass.Peer reviewe

Searches for pair production of charginos and top squarks in final states with two oppositely charged leptons in proton-proton collisions at √s=13 TeV

A search for pair production of supersymmetric particles in events with two oppositely charged leptons (electrons or muons) and missing transverse momentum is reported. The data sample corresponds to an integrated luminosity of 35.9 fb−1 of proton-proton collisions at s √ =13 s=13 TeV collected with the CMS detector during the 2016 data taking period at the LHC. No significant deviation is observed from the predicted standard model background. The results are interpreted in terms of several simplified models for chargino and top squark pair production, assuming R-parity conservation and with the neutralino as the lightest supersymmetric particle. When the chargino is assumed to undergo a cascade decay through sleptons, with a slepton mass equal to the average of the chargino and neutralino masses, exclusion limits at 95% confidence level are set on the masses of the chargino and neutralino up to 800 and 320 GeV, respectively. For top squark pair production, the search focuses on models with a small mass difference between the top squark and the lightest neutralino. When the top squark decays into an off-shell top quark and a neutralino, the limits extend up to 420 and 360 GeV for the top squark and neutralino masses, respectively