Showing papers by "Istanbul Technical University published in 2013"

Genomic Analysis of Non-NF2 Meningiomas Reveals Mutations in TRAF7, KLF4, AKT1, and SMO

Abstract: We report genomic analysis of 300 meningiomas, the most common primary brain tumors, leading to the discovery of mutations in TRAF7 , a proapoptotic E3 ubiquitin ligase, in nearly one-fourth of all meningiomas. Mutations in TRAF7 commonly occurred with a recurrent mutation (K409Q) in KLF4 , a transcription factor known for its role in inducing pluripotency, or with AKT1 E17K , a mutation known to activate the PI3K pathway. SMO mutations, which activate Hedgehog signaling, were identified in ~5% of non- NF2 mutant meningiomas. These non- NF2 meningiomas were clinically distinctive—nearly always benign, with chromosomal stability, and originating from the medial skull base. In contrast, meningiomas with mutant NF2 and/or chromosome 22 loss were more likely to be atypical, showing genomic instability, and localizing to the cerebral and cerebellar hemispheres. Collectively, these findings identify distinct meningioma subtypes, suggesting avenues for targeted therapeutics.

Observation of a new boson with mass near 125 GeV in pp collisions at $ \sqrt{s}=7 $ and 8 TeV

Abstract: A detailed description is reported of the analysis used by the CMS Collaboration in the search for the standard model Higgs boson in pp collisions at the LHC, which led to the observation of a new boson. The data sample corresponds to integrated luminosities up to 5.1 inverse femtobarns at sqrt(s) = 7 TeV, and up to 5.3 inverse femtobarns at sqrt(s) = 8 TeV. The results for five Higgs boson decay modes gamma gamma, ZZ, WW, tau tau, and bb, which show a combined local significance of 5 standard deviations near 125 GeV, are reviewed. A fit to the invariant mass of the two high resolution channels, gamma gamma and ZZ to 4 ell, gives a mass estimate of 125.3 +/- 0.4 (stat) +/- 0.5 (syst) GeV. The measurements are interpreted in the context of the standard model Lagrangian for the scalar Higgs field interacting with fermions and vector bosons. The measured values of the corresponding couplings are compared to the standard model predictions. The hypothesis of custodial symmetry is tested through the measurement of the ratio of the couplings to the W and Z bosons. All the results are consistent, within their uncertainties, with the expectations for a standard model Higgs boson.

Light‐Induced Click Reactions

Abstract: Spatial and temporal control over chemical and biological processes, both in terms of "tuning" products and providing site-specific control, is one of the most exciting and rapidly developing areas of modern science. For synthetic chemists, the challenge is to discover and develop selective and efficient reactions capable of generating useful molecules in a variety of matrices. In recent studies, light has been recognized as a valuable method for determining where, when, and to what extent a process is started or stopped. Accordingly, this Minireview will present the fundamental aspects of light-induced click reactions, highlight the applications of these reactions to diverse fields of study, and discuss the potential for this methodology to be applied to the study of biomolecular systems.

Study of the Mass and Spin-Parity of the Higgs Boson Candidate via Its Decays to Z Boson Pairs

Abstract: A study is presented of the mass and spin-parity of the new boson recently observed at the LHC at a mass near 125 GeV. An integrated luminosity of 17.3 fb^(-1), collected by the CMS experiment in proton-proton collisions at center-of-mass energies of 7 and 8 TeV, is used. The measured mass in the ZZ channel, where both Z bosons decay to e or μ pairs, is 126.2±0.6(stat)±0.2(syst) GeV. The angular distributions of the lepton pairs in this channel are sensitive to the spin-parity of the boson. Under the assumption of spin 0, the present data are consistent with the pure scalar hypothesis, while disfavoring the pure pseudoscalar hypothesis.

Measurement of the Bs0→μ+μ- branching fraction and search for B0→μ+μ- with the CMS experiment

Abstract: Results are presented from a search for the rare decays B0s→μ+μ− and B0→μ+μ− in pp collisions at 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(B0s→μ+μ−)=(3.0+1.0−0.9)×10−9, where the uncertainty includes both statistical and systematic contributions. An excess of B0s→μ+μ− events with respect to background is observed with a significance of 4.3 standard deviations. For the decay B0→μ+μ− an upper limit of B(B0→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.

Search for top-squark pair production in the single-lepton final state in pp collisions at √s=8 TeV

Abstract: This paper presents a search for the pair production of top squarks in events with a single isolated electron or muon, jets, large missing transverse momentum, and large transverse mass. The data sample corresponds to an integrated luminosity of 19.5 inverse femtobarns of pp collisions collected in 2012 by the CMS experiment at the LHC at a center-of-mass energy of sqrt(s) = 8 TeV. No significant excess in data is observed above the expectation from standard model processes. The results are interpreted in the context of supersymmetric models with pair production of top squarks that decay either to a top quark and a neutralino or to a bottom quark and a chargino. For small mass values of the lightest supersymmetric particle, top-squark mass values up to around 650 GeV are excluded.

Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis

Abstract: For an organism to survive, it must be able to sense its environment and regulate physiological processes accordingly. Understanding how bacteria integrate signals from various environmental factors and quorum sensing autoinducers to regulate the metabolism of various nucleotide second messengers c-di-GMP, c-di-AMP, cGMP, cAMP and ppGpp, which control several key processes required for adaptation is key for efforts to develop agents to curb bacterial infections. In this review, we provide an update of nucleotide signaling in bacteria and show how these signals intersect or integrate to regulate the bacterial phenotype. The intracellular concentrations of nucleotide second messengers in bacteria are regulated by synthases and phosphodiesterases and a significant number of these metabolism enzymes had been biochemically characterized but it is only in the last few years that the effector proteins and RNA riboswitches, which regulate bacterial physiology upon binding to nucleotides, have been identified and characterized by biochemical and structural methods. C-di-GMP, in particular, has attracted immense interest because it is found in many bacteria and regulate both biofilm formation and virulence factors production. In this review, we discuss how the activities of various c-di-GMP effector proteins and riboswitches are modulated upon c-di-GMP binding. Using V. cholerae, E. coli and B. subtilis as models, we discuss how both environmental factors and quorum sensing autoinducers regulate the metabolism and/or processing of nucleotide second messengers. The chemical syntheses of the various nucleotide second messengers and the use of analogs thereof as antibiofilm or immune modulators are also discussed.

Searches for long-lived charged particles in pp collisions at sqrt(s) = 7 and 8 TeV

Abstract: Results of searches for heavy stable charged particles produced in pp collisions at sqrt(s) = 7 and 8 TeV are presented corresponding to an integrated luminosity of 5.0 inverse femtobarns and 18.8 inverse femtobarns, respectively. Data collected with the CMS detector are used to study the momentum, energy deposition, and time-of-flight of signal candidates. Leptons with an electric charge between e/3 and 8e, as well as bound states that can undergo charge exchange with the detector material, are studied. Analysis results are presented for various combinations of signatures in the inner tracker only, inner tracker and muon detector, and muon detector only. Detector signatures utilized are long time-of-flight to the outer muon system and anomalously high (or low) energy deposition in the inner tracker. The data are consistent with the expected background, and upper limits are set on the production cross section of long-lived gluinos, scalar top quarks, and scalar tau leptons, as well as pair produced long-lived leptons. Corresponding lower mass limits, ranging up to 1322 GeV for gluinos, are the most stringent to date.

Search for dark matter candidates and large extra dimensions in events with a jet and missing transverse momentum with the ATLAS detector

Abstract: A search for new phenomena in events with a high-energy jet and large missing transverse momentum is performed using data from proton-proton collisions at root s = 7 TeV with the ATLAS experiment at the Large flatiron Collider. Four kinematic regions are explored using a dataset corresponding to an integrated luminosity of 4.7 fb(-1). No excess of events beyond expectations from Standard Model processes is observed, and limits are set on large extra dimensions and the pair production of dark matter particles.

Energy calibration and resolution of the CMS electromagnetic calorimeter in pp collisions at √s = 7 TeV

Abstract: The article is the pre-print version of the final publishing paper that is available from the link below.

Measurement of the elliptic anisotropy of charged particles produced in PbPb collisions at √sNN=2.76 TeV

Abstract: The anisotropy of the azimuthal distributions of charged particles produced in √s_(NN)=2.76 TeV PbPb collisions is studied with the CMS experiment at the LHC. The elliptic anisotropy parameter, v_2, defined as the second coefficient in a Fourier expansion of the particle invariant yields, is extracted using the event-plane method, two- and four-particle cumulants, and Lee-Yang zeros. The anisotropy is presented as a function of transverse momentum (p_T), pseudorapidity (η) over a broad kinematic range, 0.3

Search for supersymmetry in hadronic final states with missing transverse energy using the variables αT and b-quark multiplicity in pp collisions at √s = 8 TeV

Abstract: 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, α T, 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.

Measurements of differential jet cross sections in proton-proton collisions at √s=7 TeV with the CMS detector

Abstract: Measurements of inclusive jet and dijet production cross sections are presented. Data from LHC proton-proton collisions at √s=7 TeV, corresponding to 5.0 fb-1 of integrated luminosity, have been collected with the CMS detector. Jets are reconstructed up to rapidity 2.5, transverse momentum 2 TeV, and dijet invariant mass 5 TeV, using the anti-kT clustering algorithm with distance parameter R=0.7. The measured cross sections are corrected for detector effects and compared to perturbative QCD predictions at next-to-leading order, using five sets of parton distribution functions.

Search for squarks and gluinos with the ATLAS detector in final states with jets and missing transverse momentum using 4.7 fb − 1 of s = 7 TeV proton-proton collision data

Abstract: A search for squarks and gluinos in final states containing jets, missing transverse momentum and no high-p(T) electrons or muons is presented. The data represent the complete sample recorded in 2011 by the ATLAS experiment in 7 TeV proton-proton collisions at the Large Hadron Collider, with a total integrated luminosity of 4.7 fb(-1). No excess above the Standard Model background expectation is observed. Gluino masses below 860 GeV and squark masses below 1320 GeV are excluded at the 95% confidence level in simplified models containing only squarks of the first two generations, a gluino octet and a massless neutralino, for squark or gluino masses below 2 TeV, respectively. Squarks and gluinos with equal masses below 1410 GeV are excluded. In minimal supergravity/constrained minimal supersymmetric Standard Model models with tan beta = 10, A(0) = 0 and mu > 0, squarks and gluinos of equal mass are excluded for masses below 1360 GeV. Constraints are also placed on the parameter space of supersymmetric models with compressed spectra. These limits considerably extend the region of supersymmetric parameter space excluded by previous measurements with the ATLAS detector.

Recent analytical approaches to the analysis of biogenic amines in food samples

Abstract: Biogenic amines (BAs) are formed in certain food products during storage and processing, causing serious health problems, especially to sensitive persons. This review provides an overview on the studies published between 2011 and 2012, focusing on novelty, improvement, and optimization of analytical methods for the determination of BAs and on their applications to the important groups of food products.