Measurements of differential and double-differential Drell-Yan cross sections in proton-proton collisions at [Formula: see text][Formula: see text]

Measurements of the differential and double-differential Drell-Yan cross sections in the dielectron and dimuon channels are presented. They are based on proton-proton collision data at [Formula: see text] recorded with the CMS detector at the LHC and corresponding to an integrated luminosity of 19.7[Formula: see text]. The measured inclusive cross section in the [Formula: see text] peak region (60-120[Formula: see text]), obtained from the combination of the dielectron and dimuon channels, is [Formula: see text], where the statistical uncertainty is negligible. The differential cross section [Formula: see text] in the dilepton mass range 15-2000[Formula: see text] is measured and corrected to the full phase space. The double-differential cross section [Formula: see text] is also measured over the mass range 20 to 1500[Formula: see text] and absolute dilepton rapidity from 0 to 2.4. In addition, the ratios of the normalized differential cross sections measured at [Formula: see text] and 8[Formula: see text] are presented. These measurements are compared to the predictions of perturbative QCD at next-to-leading and next-to-next-to-leading (NNLO) orders using various sets of parton distribution functions (PDFs). The results agree with the NNLO theoretical predictions computed with fewz 3.1 using the CT10 NNLO and NNPDF2.1 NNLO PDFs. The measured double-differential cross section and ratio of normalized differential cross sections are sufficiently precise to constrain the proton PDFs.

Search for monotop signatures in proton-proton collisions at √s=8 TeV

Results are presented from a search for new decaying massive particles whose presence is inferred from an imbalance in transverse momentum and which are produced in association with a single top quark that decays into a bottom quark and two light quarks. The measurement is performed using 19.7  fb^{-1} of data from proton-proton collisions at a center-of-mass energy of 8 TeV, collected with the CMS detector at the CERN LHC. No deviations from the standard model predictions are observed and lower limits are set on the masses of new invisible bosons. In particular, scalar and vector particles, with masses below 330 and 650 GeV, respectively, are excluded at 95% confidence level, thereby substantially extending a previous limit published by the CDF Collaboration.

Risk factors of hyperthyroidism with hepatic function injury: a 4-year retrospective study

Hepatic function injury is one of the common complications of hyperthyroidism (mainly Graves' disease), which affects the choice of treatment and the curative rate. Our goal was to describe clinical and biochemical patterns in patients suffering from Graves' disease (GD) and hepatic function injury and to determine the influential factors. A cohort of 1 070 patients who received (131)I treatment were studied. Many examinations were performed before (131)I therapy, such as: the 24-h radioactive iodine uptake of thyroid (RAIU(24 h)) and serum-free triiodothyronine (FT(3)), free thyroxine (FT(4)), sensitive thyroid-stimulating hormone (sTSH), antithyrotrophin receptor antibody (TRAb), thyroglobulin antibody (TgAb), and antithyroid peroxidase antibody (TPOAb), serum hepatic function tests, etc. Data were analyzed by the unpaired t-test, the independent samples t-test, the χ(2) test, logistic regression, and Pearson bivariate correlation. Age, course of GD, thyroid's weight, FT(4), TPOAb, and TRAb in GD patients with hepatic function injury were higher than those with normal hepatic function patients. The influential factors were age, hyperthyroidism duration, heart rate, thyroid's weight, FT(4), RAIU(24 h), TgAb, TPOAb, and TRAb. RAIU(24 h) was the protecting factor. Age, course of GD, heart rate, thyroid's weight, FT(4), TRAb, and TPOAb were the risk factors. Patients whose age was higher than 45 years old, heart rate above 90 bpm, thyroid weight more than 35 g, the hyperthyroidism duration more than 3 years, FT(4) higher than 70.5 pmol/l, the level of TPOAb above 360 IU/ml, and the level of TRAb above 15 IU/l have increased risk of hepatic function injury. As treatment (131)I therapy was found to be the best choice.

Search for displaced supersymmetry in events with an electron and a muon with large impact parameters

A search for new long-lived particles decaying to leptons is presented using proton-proton collisions produced by the LHC at √[s]=8  TeV. Data used for the analysis were collected by the CMS detector and correspond to an integrated luminosity of 19.7  fb(-1). Events are selected with an electron and muon with opposite charges that both have transverse impact parameter values between 0.02 and 2 cm. The search has been designed to be sensitive to a wide range of models with nonprompt e-μ final states. Limits are set on the "displaced supersymmetry" model, with pair production of top squarks decaying into an e-μ final state via R-parity-violating interactions. The results are the most restrictive to date on this model, with the most stringent limit being obtained for a top squark lifetime corresponding to cτ=2  cm, excluding masses below 790 GeV at 95% confidence level.

Measurement of electroweak production of two jets in association with a Z boson in proton-proton collisions at [Formula: see text]

The purely electroweak (EW) cross section for the production of two jets in association with a Z boson, in proton-proton collisions at [Formula: see text], is measured using data recorded by the CMS experiment at the CERN LHC, corresponding to an integrated luminosity of 19.7[Formula: see text]. The electroweak cross section for the [Formula: see text] final state (with [Formula: see text] or [Formula: see text] and j representing the quarks produced in the hard interaction) in the kinematic region defined by [Formula: see text][Formula: see text], [Formula: see text][Formula: see text], transverse momentum [Formula: see text][Formula: see text], and pseudorapidity [Formula: see text], is found to be [Formula: see text], in agreement with the standard model prediction. The associated jet activity of the selected events is studied, in particular in a signal-enriched region of phase space, and the measurements are found to be in agreement with QCD predictions.

Study of vector boson scattering and search for new physics in events with two same-sign leptons and two jets

A study of vector boson scattering in pp collisions at a center-of-mass energy of 8 TeV is presented. The data sample corresponds to an integrated luminosity of 19.4  fb(-1) collected with the CMS detector. Candidate events are selected with exactly two leptons of the same charge, two jets with large rapidity separation and high dijet mass, and moderate missing transverse energy. The signal region is expected to be dominated by electroweak same-sign W-boson pair production. The observation agrees with the standard model prediction. The observed significance is 2.0 standard deviations, where a significance of 3.1 standard deviations is expected based on the standard model. Cross section measurements for W(±)W(±) and WZ processes in the fiducial region are reported. Bounds on the structure of quartic vector-boson interactions are given in the framework of dimension-eight effective field theory operators, as well as limits on the production of doubly charged Higgs bosons.

Measurement of prompt ψ(2S) to J/ψ yield ratios in Pb-Pb and p-p collisions at sqrt[sNN]=2.76 TeV

The ratio between the prompt ψ(2S) and J/ψ yields, reconstructed via their decays into μ+ μ-, is measured in Pb-Pb and p-p collisions at sqrt[sNN]=2.76  TeV. The analysis is based on Pb-Pb and p-p data samples collected by CMS at the Large Hadron Collider, corresponding to integrated luminosities of 150  μb(-1) and 5.4  pb(-1), respectively. The double ratio of measured yields (Nψ(2S)/N(J/ψ))(Pb-Pb)/(Nψ(2S)/N(J/ψ))(p-p) is computed in three Pb-Pb collision centrality bins and two kinematic ranges: one at midrapidity, |y|<1.6, covering the transverse momentum range 6.5<pT<30  GeV/c, and the other at forward rapidity, 1.6<|y|<2.4, extending to lower pT values, 3<pT<30  GeV/c. The centrality-integrated double ratio changes from 0.45±0.13(stat)±0.07(syst) in the first range to 1.67±0.34(stat)±0.27(syst) in the second. This difference is most pronounced in the most central collisions.

Search for heavy neutrinos and [Formula: see text] bosons with right-handed couplings in proton-proton collisions at [Formula: see text]

A search for heavy, right-handed neutrinos, [Formula: see text] ([Formula: see text]), and right-handed [Formula: see text] bosons, which arise in the left-right symmetric extensions of the standard model, has been performed by the CMS experiment. The search was based on a sample of two lepton plus two jet events collected in proton-proton collisions at a center-of-mass energy of 8[Formula: see text] corresponding to an integrated luminosity of 19.7 [Formula: see text]. For models with strict left-right symmetry, and assuming only one [Formula: see text] flavor contributes significantly to the [Formula: see text] decay width, the region in the two-dimensional [Formula: see text] mass plane excluded at a 95 % confidence level extends to approximately [Formula: see text] and covers a large range of neutrino masses below the [Formula: see text] boson mass, depending on the value of [Formula: see text]. This search significantly extends the [Formula: see text] exclusion region beyond previous results.

Measurement of differential cross sections for the production of a pair of isolated photons in pp collisions at [Formula: see text]

A measurement of differential cross sections for the production of a pair of isolated photons in proton-proton collisions at [Formula: see text] is presented. The data sample corresponds to an integrated luminosity of 5.0[Formula: see text] collected with the CMS detector. A data-driven isolation template method is used to extract the prompt diphoton yield. The measured cross section for two isolated photons, with transverse energy above 40 and 25[Formula: see text] respectively, in the pseudorapidity range [Formula: see text], [Formula: see text] and with an angular separation [Formula: see text], is [Formula: see text][Formula: see text]. Differential cross sections are measured as a function of the diphoton invariant mass, the diphoton transverse momentum, the azimuthal angle difference between the two photons, and the cosine of the polar angle in the Collins-Soper reference frame of the diphoton system. The results are compared to theoretical predictions at leading, next-to-leading, and next-to-next-to-leading order in quantum chromodynamics.

Observation of the diphoton decay of the Higgs boson and measurement of its properties

Observation of the diphoton decay mode of the recently discovered Higgs boson and measurement of some of its properties are reported. The analysis uses the entire dataset collected by the CMS experiment in proton-proton collisions during the 2011 and 2012 LHC running periods. The data samples correspond to integrated luminosities of 5.1[Formula: see text]at [Formula: see text] and 19.7[Formula: see text]at 8[Formula: see text] . A clear signal is observed in the diphoton channel at a mass close to 125[Formula: see text] with a local significance of [Formula: see text], where a significance of [Formula: see text] is expected for the standard model Higgs boson. The mass is measured to be [Formula: see text] , and the best-fit signal strength relative to the standard model prediction is [Formula: see text][Formula: see text][Formula: see text]. Additional measurements include the signal strength modifiers associated with different production mechanisms, and hypothesis tests between spin-0 and spin-2 models.

Searches for electroweak production of charginos, neutralinos, and sleptons decaying to leptons and W, Z, and Higgs bosons in pp collisions at 8 TeV

Searches for the direct electroweak production of supersymmetric charginos, neutralinos, and sleptons in a variety of signatures with leptons and [Formula: see text], [Formula: see text], and Higgs bosons are presented. Results are based on a sample of proton-proton collision data collected at center-of-mass energy [Formula: see text] with the CMS detector in 2012, corresponding to an integrated luminosity of 19.5 [Formula: see text]. The observed event rates are in agreement with expectations from the standard model. These results probe charginos and neutralinos with masses up to 720 [Formula: see text], and sleptons up to 260 [Formula: see text], depending on the model details.

Evidence of b-jet quenching in PbPb collisions at √(s(NN))=2.76 TeV

The production of jets associated to bottom quarks is measured for the first time in PbPb collisions at a center-of-mass energy of 2.76 TeV per nucleon pair. Jet spectra are reported in the transverse momentum (p(T)) range of 80-250  GeV/c, and within pseudorapidity |η|<2. The nuclear modification factor (R(AA)) calculated from these spectra shows a strong suppression in the b-jet yield in PbPb collisions relative to the yield observed in pp collisions at the same energy. The suppression persists to the largest values of p(T) studied, and is centrality dependent. The R(AA) is about 0.4 in the most central events, similar to previous observations for inclusive jets. This implies that jet quenching does not have a strong dependence on parton mass and flavor in the jet p(T) range studied.

Measurement of top quark-antiquark pair production in association with a W or Z boson in pp collisions at [Formula: see text][Formula: see text]

A measurement of the cross section for the production of top quark-antiquark pairs ([Formula: see text]) in association with a vector boson V (W or Z) in proton-proton collisions at [Formula: see text][Formula: see text] is presented. The results are based on a dataset corresponding to an integrated luminosity of 19.5 fb[Formula: see text] recorded with the CMS detector at the LHC. The measurement is performed in three leptonic (e and [Formula: see text]) channels: a same-sign dilepton analysis targeting [Formula: see text] events, and trilepton and four-lepton analyses designed for [Formula: see text] events. In the same-sign dilepton channel, the [Formula: see text] cross section is measured as [Formula: see text], corresponding to a significance of 1.6 standard deviations over the background-only hypothesis. Combining the trilepton and four-lepton channels, a direct measurement of the [Formula: see text] cross section, [Formula: see text], is obtained with a significance of 3.1 standard deviations. The measured cross sections are compatible with standard model predictions within their experimental uncertainties. The inclusive [Formula: see text] process is observed with a significance of 3.7 standard deviations from the combination of all three leptonic channels.

Kaposi sarcoma-associated herpesvirus promotes tumorigenesis by modulating the Hippo pathway

Kaposi sarcoma-associated herpesvirus (KSHV) is an oncogenic virus and the culprit behind the human disease Kaposi sarcoma (KS), an AIDS-defining malignancy. KSHV encodes a viral G-protein-coupled receptor (vGPCR) critical for the initiation and progression of KS. In this study, we identified that YAP/TAZ, two homologous oncoproteins inhibited by the Hippo tumor suppressor pathway, are activated in KSHV-infected cells in vitro, KS-like mouse tumors and clinical human KS specimens. The KSHV-encoded vGPCR acts through Gq/11 and G12/13 to inhibit the Hippo pathway kinases Lats1/2, promoting the activation of YAP/TAZ. Furthermore, depletion of YAP/TAZ blocks vGPCR-induced cell proliferation and tumorigenesis in a xenograft mouse model. The vGPCR-transformed cells are sensitive to pharmacologic inhibition of YAP. Our study establishes a pivotal role of the Hippo pathway in mediating the oncogenic activity of KSHV and development of KS, and also suggests a potential of using YAP inhibitors for KS intervention.

Measurement of jet multiplicity distributions in [Formula: see text] production in pp collisions at [Formula: see text]

The normalised differential top quark-antiquark production cross section is measured as a function of the jet multiplicity in proton-proton collisions at a centre-of-mass energy of 7[Formula: see text] at the LHC with the CMS detector. The measurement is performed in both the dilepton and lepton+jets decay channels using data corresponding to an integrated luminosity of 5.0[Formula: see text]. Using a procedure to associate jets to decay products of the top quarks, the differential cross section of the [Formula: see text] production is determined as a function of the additional jet multiplicity in the lepton+jets channel. Furthermore, the fraction of events with no additional jets is measured in the dilepton channel, as a function of the threshold on the jet transverse momentum. The measurements are compared with predictions from perturbative quantum chromodynamics and no significant deviations are observed.

Search for invisible decays of Higgs bosons in the vector boson fusion and associated ZH production modes

A search for invisible decays of Higgs bosons is performed using the vector boson fusion and associated ZH production modes. In the ZH mode, the Z boson is required to decay to a pair of charged leptons or a [Formula: see text] quark pair. The searches use the 8 [Formula: see text] pp collision dataset collected by the CMS detector at the LHC, corresponding to an integrated luminosity of up to 19.7 [Formula: see text]. Certain channels include data from 7 [Formula: see text] collisions corresponding to an integrated luminosity of 4.9 [Formula: see text]. The searches are sensitive to non-standard-model invisible decays of the recently observed Higgs boson, as well as additional Higgs bosons with similar production modes and large invisible branching fractions. In all channels, the observed data are consistent with the expected standard model backgrounds. Limits are set on the production cross section times invisible branching fraction, as a function of the Higgs boson mass, for the vector boson fusion and ZH production modes. By combining all channels, and assuming standard model Higgs boson cross sections and acceptances, the observed (expected) upper limit on the invisible branching fraction at [Formula: see text] [Formula: see text] is found to be 0.58 (0.44) at 95 % confidence level. We interpret this limit in terms of a Higgs-portal model of dark matter interactions.

Measurement of WZ and ZZ production in pp collisions at [Formula: see text] in final states with b-tagged jets

Measurements are reported of the WZ and ZZ production cross sections in proton-proton collisions at [Formula: see text][Formula: see text] in final states where one Z boson decays to b-tagged jets. The other gauge boson, either W or Z, is detected through its leptonic decay (either [Formula: see text], [Formula: see text] or [Formula: see text], [Formula: see text], or [Formula: see text]). The results are based on data corresponding to an integrated luminosity of 18.9 fb[Formula: see text] collected with the CMS detector at the Large Hadron Collider. The measured cross sections, [Formula: see text] and [Formula: see text], are consistent with next-to-leading order quantum chromodynamics calculations.

The differential production cross section of the [Formula: see text](1020) meson in [Formula: see text] = 7 TeV [Formula: see text] collisions measured with the ATLAS detector

A measurement is presented of the [Formula: see text] production cross section at [Formula: see text] = 7 TeV using [Formula: see text] collision data corresponding to an integrated luminosity of 383 [Formula: see text], collected with the ATLAS experiment at the LHC. Selection of [Formula: see text](1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section is measured as a function of the transverse momentum, [Formula: see text], and rapidity, [Formula: see text], of the [Formula: see text](1020) meson in the fiducial region 500 [Formula: see text] 1200 MeV, [Formula: see text] 0.8, kaon [Formula: see text] 230 MeV and kaon momentum [Formula: see text] 800 MeV. The integrated [Formula: see text]-meson production cross section in this fiducial range is measured to be [Formula: see text] = 570 [Formula: see text] 8 (stat) [Formula: see text] 66 (syst) [Formula: see text] 20 (lumi) [Formula: see text].

Observation of the associated production of a single top quark and a W boson in pp collisions at sqrt[s] = 8 TeV

The first observation of the associated production of a single top quark and a W boson is presented. The analysis is based on a data set corresponding to an integrated luminosity of 12.2 fb(-1) of proton-proton collisions at sqrt[s] = 8 TeV recorded by the CMS experiment at the LHC. Events with two leptons and a jet originating from a b quark are selected. A multivariate analysis based on kinematic and topological properties is used to separate the signal from the dominant tt background. An excess consistent with the signal hypothesis is observed, with a significance which corresponds to 6.1 standard deviations above a background-only hypothesis. The measured production cross section is 23.4 ± 5.4 pb, in agreement with the standard model prediction.

Probing color coherence effects in pp collisions at [Formula: see text]

A study of color coherence effects in pp collisions at a center-of-mass energy of 7[Formula: see text] is presented. The data used in the analysis were collected in 2010 with the CMS detector at the LHC and correspond to an integrated luminosity of 36 pb[Formula: see text]. Events are selected that contain at least three jets and where the two jets with the largest transverse momentum exhibit a back-to-back topology. The measured angular correlation between the second- and third-leading jet is shown to be sensitive to color coherence effects, and is compared to the predictions of Monte Carlo models with various implementations of color coherence. None of the models describe the data satisfactorily.

Measurements of tt spin correlations and top-quark polarization using dilepton final states in pp collisions at sqrt[s]=7 TeV

Spin correlations and polarization in the top quark-antiquark system are measured using dilepton final states produced in pp collisions at the LHC at sqrt[s]=7  TeV. The data correspond to an integrated luminosity of 5.0  fb(-1) collected with the CMS detector. The measurements are performed using events with two oppositely charged leptons (electrons or muons), a significant imbalance in transverse momentum, and two or more jets, where at least one of the jets is identified as originating from a b quark. The spin correlations and polarization are measured through asymmetries in angular distributions of the two selected leptons, unfolded to the parton level. All measurements are found to be in agreement with predictions of the standard model.

Search for top-quark partners with charge 5/3 in the same-sign dilepton final state

A search for the production of heavy partners of the top quark with charge 5/3 is performed in events with a pair of same-sign leptons. The data sample corresponds to an integrated luminosity of 19.5 fb(-1) and was collected at sqrt[s] = 8 TeV by the CMS experiment. No significant excess is observed in the data above the expected background, and the existence of top-quark partners with masses below 800 GeV is excluded at a 95% confidence level, assuming they decay exclusively to tW. This is the first limit on these particles from the LHC, and it is significantly more restrictive than previous limits.

Search for flavor-changing neutral currents in top-quark decays t → Zq in pp collisions at sqrt[s] = 8 TeV

A search for flavor-changing neutral currents in top-quark decays t → Zq is performed in events produced from the decay chain tt → Zq+Wb, where both vector bosons decay leptonically, producing a final state with three leptons (electrons or muons). A data set collected with the CMS detector at the LHC is used, corresponding to an integrated luminosity of 19.7 fb(-1) of proton-proton collisions at a center-of-mass energy of 8 TeV. No excess is seen in the observed number of events relative to the standard model prediction; thus, no evidence for flavor-changing neutral currents in top-quark decays is found. A combination with a previous search at 7 TeV excludes a t → Zq branching fraction greater than 0.05% at the 95% confidence level.

Search for top squark and Higgsino production using diphoton Higgs boson decays

Results are presented of a search for a "natural" supersymmetry scenario with gauge mediated symmetry breaking. It is assumed that only the supersymmetric partners of the top quark (the top squark) and the Higgs boson (Higgsino) are accessible. Events are examined in which there are two photons forming a Higgs boson candidate, and at least two b-quark jets. In 19.7  fb-1 of proton-proton collision data at s=8  TeV, recorded in the CMS experiment, no evidence of a signal is found and lower limits at the 95% confidence level are set, excluding the top squark mass below 360 to 410 GeV, depending on the Higgsino mass.

Possible pandemic threat from new reassortment of influenza A(H7N9) virus in China

Avian influenza A(H7N9) virus re-emerged in China in December 2013, after a decrease in the number of new cases during the preceding six months. Reassortment between influenza A(H7N9) and local H9N2 strains has spread from China's south-east coast to other regions. Three new reassortments of A(H7N9) virus were identified by phylogenetic analysis: between A(H7N9) and Zhejiang-derived strains, Guangdong/Hong Kong-derived strains or Hunan-derived A(H9N2) strains. Our findings suggest there is a possible risk that a pandemic could develop.

PD-L1 signal on liver dendritic cells is critical for Foxp3(+)CD4(+)CD25(+) Treg and liver tolerance induction in mice

Allogeneic liver transplantation induces spontaneous tolerance in mice without a requirement for immunosuppression. The underling mechanisms remain unclear. Our recent studies indicated that Foxp3(+)CD25(+)CD4(+) regulatory T (Treg) cells play an important role in the induction of spontaneous transplant tolerance. How Treg cells are induced and their functional mechanisms to regulate the response remain undefined. In this study, we employed a mouse liver transplant model using PD-L1-/-, and Flt3L-/- mice to critically examine the role of liver dendritic cells (DCs) and the PD-L1 signal in Treg induction. Our results showed that liver DCs, which expressed a great number of PD-L1 molecules, induced more Foxp3(+)CD25(+)CD4(+) Treg in vitro upon coculture with allogeneic CD4 T cells compared with spleen DCs. The DCs from PD-L1-deficient mice failed to expand Foxp3(+)CD25(+)CD4(+) Treg in vitro. Adoptive transfer of Foxp3(+)CD25(+)CD4(+)Treg expanded from liver DCs prolonged heart allograft survival significantly greater than spleen cell controls. Moreover, liver grafts from Flt3L-/- and PD-L1-/- mice were rejected acutely in C3H recipients. Immunohistochemistry revealed reduced Foxp3(+) cells and significantly increased IL-2, IL-10, and IFN-γ producing elements in the liver grafts and recipient spleens of Flt3L-/- and PD-L1-/- donors. In conclusion, liver DCs play a critical role in the induction of Foxp3(+)CD25(+)CD4(+) Treg, which may mediate spontaneous acceptance of MHC-mismatched liver allografts in mice. The effects of DCs on Foxp3(+)CD25(+)CD4(+) Treg induction and expansion appear to depend on the PD-L1 signal.

Jet and underlying event properties as a function of charged-particle multiplicity in proton-proton collisions at [Formula: see text]

Characteristics of multi-particle production in proton-proton collisions at [Formula: see text] are studied as a function of the charged-particle multiplicity, Nch. The produced particles are separated into two classes: those belonging to jets and those belonging to the underlying event. Charged particles are measured with pseudorapidity |η|<2.4 and transverse momentum pT>0.25 GeV/c. Jets are reconstructed from charged-particles only and required to have pT>5 GeV/c. The distributions of jet pT, average pT of charged particles belonging to the underlying event or to jets, jet rates, and jet shapes are presented as functions of Nch and compared to the predictions of the pythia and herwig event generators. Predictions without multi-parton interactions fail completely to describe the Nch-dependence observed in the data. For increasing Nch, pythia systematically predicts higher jet rates and harder pT spectra than seen in the data, whereas herwig shows the opposite trends. At the highest multiplicity, the data-model agreement is worse for most observables, indicating the need for further tuning and/or new model ingredients.

ReSeqTools: an integrated toolkit for large-scale next-generation sequencing based resequencing analysis

Large-scale next-generation sequencing (NGS)-based resequencing detects sequence variations, constructs evolutionary histories, and identifies phenotype-related genotypes. However, NGS-based resequencing studies generate extraordinarily large amounts of data, making computations difficult. Effective use and analysis of these data for NGS-based resequencing studies remains a difficult task for individual researchers. Here, we introduce ReSeqTools, a full-featured toolkit for NGS (Illumina sequencing)-based resequencing analysis, which processes raw data, interprets mapping results, and identifies and annotates sequence variations. ReSeqTools provides abundant scalable functions for routine resequencing analysis in different modules to facilitate customization of the analysis pipeline. ReSeqTools is designed to use compressed data files as input or output to save storage space and facilitates faster and more computationally efficient large-scale resequencing studies in a user-friendly manner. It offers abundant practical functions and generates useful statistics during the analysis pipeline, which significantly simplifies resequencing analysis. Its integrated algorithms and abundant sub-functions provide a solid foundation for special demands in resequencing projects. Users can combine these functions to construct their own pipelines for other purposes.

The association of anti-annexin1 antibodies with the occurrence of skin lesions in systemic lupus erythematosus

Anti-annexin1 antibodies are associated with the subtypes of cutaneous lupus and are elevated in systemic lupus erythematosus (SLE) patients. In this study, we investigated the correlation of this antibody with the incidence of SLE skin lesions. The presence of anti-annexin1-IgG and-IgM determined by Western blot was no different among healthy controls and SLE patients with and without skin lesions. Serum levels of anti-annexin1-IgG and -IgM measured by enzyme-linked immunosorbent assay were comparable between patients with and without skin lesions, whereas anti-annexin1-IgM was lower in SLE patients than in healthy controls. Annexin1 was abundantly detected in each epidermal layer in lupus lesional skin. Additionally, anti-annexin1-IgG was higher in SLE patients with arthritis and negatively correlated with white blood cells (WBC). Anti-annexin1-IgM was higher in patients with antinuclear antibody (ANA)-positive sera, and was positively related to hemoglobin and total serum IgM. Collectively, anti-annexin1 antibodies are not related to the incidence of skin lesions in SLE, and annexin1 abundantly distributes in epidermis in lesional skin.

Searches for new physics using the tt¯ invariant mass distribution in pp collisions at √s=8 TeV

Searches for anomalous top quark-antiquark production are presented, based on pp collisions at √s=8 TeV. The data, corresponding to an integrated luminosity of 19.7 fb(-1), were collected with the CMS detector at the LHC. The observed tt¯ invariant mass spectrum is found to be compatible with the standard model prediction. Limits on the production cross section times branching fraction probe, for the first time, a region of parameter space for certain models of new physics not yet constrained by precision measurements.

Microbial screening of unrelated cord blood units in a Chinese cord blood bank

BACKGROUND

Given limited sample volume available for sterility testing, optimal testing methods and algorithms of cord blood (CB) have not been established according to standards.

STUDY DESIGN AND METHODS

The volume of CB unit was reduced to 20 mL in a closed system. Hetastarch and cryopreservation solution was added to the processed CB unit in Class 100 environment. In the routine sterility testing, 20 mL of red blood cells (RBC) sample was cultured in aerobic and anaerobic culture bottles. In verification post-thaw culture of the final product, some of the discarded final product units were also sampled and cultured after thaw. All the culture bottles were incubated in the BacT/ALERT 3D system.

RESULTS

In the routine sterility testing, 139 of 7032 CB units (1·98%) were contaminated with microorganism. In 84 of these 139 units (60·4%) only the anaerobic bottle was positive. Lactobacillus spp. were the most prevalent contaminant. Sixty-two discarded CB stem cell units were recultured after thaw. Of these, 10 of 48 units with a positive culturing of RBC sample were negative in the post-thaw reculture. One of 14 units with negative culturing of RBC sample was contaminated with Bifidobacterium breve in special verification test.

CONCLUSION

Our study demonstrates the predominant organisms implicated in CB microbial contamination were part of the human intestinal and vaginal flora. The larger sample volume and anaerobic culture would significantly increase the detection rate of microbial contaminated CB. We also found that potential transfusion-transmitted bacterial infection risk still existed in final product although microbial screening was performed.

Search for supersymmetry in hadronic final states with missing transverse energy using the variables αT and b-quark multiplicity in pp collisions at [Formula: see text]

An inclusive search for supersymmetric processes that produce final states with jets and missing transverse energy is performed in pp collisions at a centre-of-mass energy of 8 TeV. The data sample corresponds to an integrated luminosity of 11.7 fb-1 collected by the CMS experiment at the LHC. In this search, a dimensionless kinematic variable, αT, is used to discriminate between events with genuine and misreconstructed missing transverse energy. The search is based on an examination of the number of reconstructed jets per event, the scalar sum of transverse energies of these jets, and the number of these jets identified as originating from bottom quarks. No significant excess of events over the standard model expectation is found. Exclusion limits are set in the parameter space of simplified models, with a special emphasis on both compressed-spectrum scenarios and direct or gluino-induced production of third-generation squarks. For the case of gluino-mediated squark production, gluino masses up to 950-1125 GeV are excluded depending on the assumed model. For the direct pair-production of squarks, masses up to 450 GeV are excluded for a single light first- or second-generation squark, increasing to 600 GeV for bottom squarks.

Measurement of the Bs(0)→μ+ μ- branching fraction and search for B(0)→μ+ μ- with the CMS experiment

Results are presented from a search for the rare decays Bs(0)→μ+ μ- and B(0)→μ+ μ- in pp collisions at sqrt[s]=7 and 8 TeV, with data samples corresponding to integrated luminosities of 5 and 20  fb(-1), respectively, collected by the CMS experiment at the LHC. An unbinned maximum-likelihood fit to the dimuon invariant mass distribution gives a branching fraction B(Bs(0)→μ+ μ-)=(3.0(-0.9)(+1.0))×10(-9), where the uncertainty includes both statistical and systematic contributions. An excess of Bs(0)→μ+ μ- events with respect to background is observed with a significance of 4.3 standard deviations. For the decay B(0)→μ+ μ- an upper limit of B(B(0)→μ+ μ-)<1.1×10(-9) at the 95% confidence level is determined. Both results are in agreement with the expectations from the standard model.

Improved luminosity determination in pp collisions at [Formula: see text] using the ATLAS detector at the LHC

The luminosity calibration for the ATLAS detector at the LHC during pp collisions at [Formula: see text] in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at [Formula: see text]. A luminosity uncertainty of [Formula: see text] is obtained for the 47 pb-1 of data delivered to ATLAS in 2010, and an uncertainty of [Formula: see text] is obtained for the 5.5 fb-1 delivered in 2011.

Estrogen aggravates iodoacetate-induced temporomandibular joint osteoarthritis

Temporomandibular joint osteoarthritis (TMJOA) is clinically characterized by female preponderance, with a female-to-male ratio of more than 2:1; however, the underlying mechanism remains obscure. We examined the effects of estrogen on TMJOA induced by monosodium iodoacetate. Female rats were randomly and equally divided into 5 groups: control, sham-ovariectomized, and ovariectomized rats treated, respectively, with 17β-estradiol (E2) at doses of 0 µg, 20 µg, and 80 µg/day until the end of the experiment. After induction of TMJOA, TMJs were evaluated by histopathology and microCT, and the expression of Fas, FasL, caspase 3, and caspase 8 was evaluated by real-time polymerase chain-reaction or immunohistochemistry. Another 5 groups of female rats were used to evaluate the effect of estrogen receptor antagonist ICI 182780 on E2 effects on TMJOA, when injected intraperitoneally into the control, sham-ovariectomized, and 80-µg-E2-treated groups. We found that E2 potentiated cartilage degradation and subchondral bone erosion in iodoacetate-induced TMJOA. E2 also potentiated mRNA expression of Fas, FasL, caspase 3, and caspase 8 in the condylar cartilage. Moreover, the estrogen receptor antagonist partially blocked E2 effects on TMJOA. These findings suggest that E2 could aggravate TMJOA, which may be an important mechanism underlying the sexual dimorphism of TMJOA.

Measurement of the inclusive jet cross-section in pp collisions at [Formula: see text] and comparison to the inclusive jet cross-section at [Formula: see text] using the ATLAS detector

The inclusive jet cross-section has been measured in proton-proton collisions at [Formula: see text] in a dataset corresponding to an integrated luminosity of [Formula: see text] collected with the ATLAS detector at the Large Hadron Collider in 2011. Jets are identified using the anti-kt algorithm with two radius parameters of 0.4 and 0.6. The inclusive jet double-differential cross-section is presented as a function of the jet transverse momentum pT and jet rapidity y, covering a range of 20≤pT<430 GeV and |y|<4.4. The ratio of the cross-section to the inclusive jet cross-section measurement at [Formula: see text], published by the ATLAS Collaboration, is calculated as a function of both transverse momentum and the dimensionless quantity [Formula: see text], in bins of jet rapidity. The systematic uncertainties on the ratios are significantly reduced due to the cancellation of correlated uncertainties in the two measurements. Results are compared to the prediction from next-to-leading order perturbative QCD calculations corrected for non-perturbative effects, and next-to-leading order Monte Carlo simulation. Furthermore, the ATLAS jet cross-section measurements at [Formula: see text] and [Formula: see text] are analysed within a framework of next-to-leading order perturbative QCD calculations to determine parton distribution functions of the proton, taking into account the correlations between the measurements.

Search for a light charged Higgs boson in the decay channel [Formula: see text] in [Formula: see text] events using pp collisions at [Formula: see text] with the ATLAS detector

A search for a charged Higgs boson (H+) in [Formula: see text] decays is presented, where one of the top quarks decays via t→H+b, followed by H+→ two jets ([Formula: see text]). The other top quark decays to Wb, where the W boson then decays into a lepton (e/μ) and a neutrino. The data were recorded in pp collisions at [Formula: see text] by the ATLAS detector at the LHC in 2011, and correspond to an integrated luminosity of 4.7 fb-1. With no observation of a signal, 95 % confidence level (CL) upper limits are set on the decay branching ratio of top quarks to charged Higgs bosons varying between 5 % and 1 % for H+ masses between 90 GeV and 150 GeV, assuming [Formula: see text].

Measurement of kT splitting scales in W→ℓν events at [Formula: see text] with the ATLAS detector

A measurement of splitting scales, as defined by the kT clustering algorithm, is presented for final states containing a W boson produced in proton-proton collisions at a centre-of-mass energy of 7 TeV. The measurement is based on the full 2010 data sample corresponding to an integrated luminosity of 36 pb-1 which was collected using the ATLAS detector at the CERN Large Hadron Collider. Cluster splitting scales are measured in events containing W bosons decaying to electrons or muons. The measurement comprises the four hardest splitting scales in a kT cluster sequence of the hadronic activity accompanying the W boson, and ratios of these splitting scales. Backgrounds such as multi-jet and top-quark-pair production are subtracted and the results are corrected for detector effects. Predictions from various Monte Carlo event generators at particle level are compared to the data. Overall, reasonable agreement is found with all generators, but larger deviations between the predictions and the data are evident in the soft regions of the splitting scales.

Observation of associated near-side and away-side long-range correlations in sqrt[s(NN)]=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δø) and pseudorapidity (Δη) are measured in sqrt[s(NN)] = 5.02 TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 μb(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (ΣE(T)(Pb)) summed over 3.1 < η < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < |Δ η | < 5) "near-side" (Δø ~ 0) correlation that grows rapidly with increasing ΣE(T)(Pb). A long-range "away-side" (Δø ~ π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE(T)(Pb), is found to match the near-side correlation in magnitude, shape (in Δη and Δø) and ΣE(T)(Pb) dependence. The resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).

Multi-channel search for squarks and gluinos in [Formula: see text]pp collisions with the ATLAS detector at the LHC

A search for supersymmetric particles in final states with zero, one, and two leptons, with and without jets identified as originating from b-quarks, in 4.7 fb-1 of [Formula: see text]pp collisions produced by the Large Hadron Collider and recorded by the ATLAS detector is presented. The search uses a set of variables carrying information on the event kinematics transverse and parallel to the beam line that are sensitive to several topologies expected in supersymmetry. Mutually exclusive final states are defined, allowing a combination of all channels to increase the search sensitivity. No deviation from the Standard Model expectation is observed. Upper limits at 95 % confidence level on visible cross-sections for the production of new particles are extracted. Results are interpreted in the context of the constrained minimal supersymmetric extension to the Standard Model and in supersymmetry-inspired models with diverse, high-multiplicity final states.