The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Is The amphibian tree of life really fatally flawed?

Wiens (2007, Q. Rev. Biol. 82, 55-56) recently published a severe critique of Frost et al.'s (2006, Bull. Am. Mus. Nat. Hist. 297, 1-370) monographic study of amphibian systematics, concluding that it is a disaster and recommending that readers simply ignore this study. Beyond the hyperbole, Wiens raised four general objections that he regarded as fatal flaws: (1) the sampling design was insufficient for the generic changes made and taxonomic changes were made without including all type species; (2) the nuclear gene most commonly used in amphibian phylogenetics, RAG-1, was not included, nor were the morphological characters that had justified the older taxonomy; (3) the analytical method employed is questionable because equally weighted parsimony assumes that all characters are evolving at equal rates; and (4) the results were at times clearly erroneous, as evidenced by the inferred non-monophyly of marsupial frogs. In this paper we respond to these criticisms. In brief: (1) the study of Frost et al. did not exist in a vacuum and we discussed our evidence and evidence previously obtained by others that documented the non-monophyletic taxa that we corrected. Beyond that, we agree that all type species should ideally be included, but inclusion of all potentially relevant type species is not feasible in a study of the magnitude of Frost et al. and we contend that this should not prevent progress in the formulation of phylogenetic hypotheses or their application outside of systematics. (2) Rhodopsin, a gene included by Frost et al. is the nuclear gene that is most commonly used in amphibian systematics, not RAG-1. Regardless, ignoring a study because of the absence of a single locus strikes us as unsound practice. With respect to previously hypothesized morphological synapomorphies, Frost et al. provided a lengthy review of the published evidence for all groups, and this was used to inform taxonomic decisions. We noted that confirming and reconciling all morphological transformation series published among previous studies needed to be done, and we included evidence from the only published data set at that time to explicitly code morphological characters (including a number of traditionally applied synapomorphies from adult morphology) across the bulk of the diversity of amphibians (Haas, 2003, Cladistics 19, 23-90). Moreover, the phylogenetic results of the Frost et al. study were largely consistent with previous morphological and molecular studies and where they differed, this was discussed with reference to the weight of evidence. (3) The claim that equally weighted parsimony assumes that all characters are evolving at equal rates has been shown to be false in both analytical and simulation studies. (4) The claimed strong support for marsupial frog monophyly is questionable. Several studies have also found marsupial frogs to be non-monophyletic. Wiens et al. (2005, Syst. Biol. 54, 719-748) recovered marsupial frogs as monophyletic, but that result was strongly supported only by Bayesian clade confidence values (which are known to overestimate support) and bootstrap support in his parsimony analysis was < 50%. Further, in a more recent parsimony analysis of an expanded data set that included RAG-1 and the three traditional morphological synapomorphies of marsupial frogs, Wiens et al. (2006, Am. Nat. 168, 579-596) also found them to be non-monophyletic.Although we attempted to apply the rule of monophyly to the naming of taxonomic groups, our phylogenetic results are largely consistent with conventional views even if not wth the taxonomy current at the time of our writing. Most of our taxonomic changes addressed examples of non-monophyly that had previously been known or suspected (e.g., the non-monophyly of traditional Hyperoliidae, Microhylidae, Hemiphractinae, Leptodactylidae, Phrynobatrachus, Ranidae, Rana, Bufo; and the placement of Brachycephalus within Eleutherodactylus, and Lineatriton within Pseudoeurycea), and it is troubling that Wiens and others, as evidenced by recent publications, continue to perpetuate recognition of non-monophyletic taxonomic groups that so profoundly misrepresent what is known about amphibian phylogeny. (C) The Willi Hennig Society 2007.

Search for pair produced fourth-generation up-type quarks in pp collisions at root s=7 TeV with a lepton in the final state

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Search for Heavy Neutrinos and W-R Bosons with Right-Handed Couplings in a Left-Right Symmetric Model in pp Collisions at root s=7 TeV

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Measurement of the single-top-quark t-channel cross section in pp collisions at √s=7 TeV

A measurement of the single-top-quark t-channel production cross section in pp collisions at √s=7 TeV with the CMS detector at the LHC is presented. Two different and complementary approaches have been followed. The first approach exploits the distributions of the pseudorapidity of the recoil jet and reconstructed top-quark mass using background estimates determined from control samples in data. The second approach is based on multivariate analysis techniques that probe the compatibility of the candidate events with the signal. Data have been collected for the muon and electron final states, corresponding to integrated luminosities of 1.17 and 1.56 fb-1, respectively. The single-top-quark production cross section in the t-channel is measured to be 67.2±6.1 pb, in agreement with the approximate next-to-next-to-leading- order standard model prediction. Using the standard model electroweak couplings, the CKM matrix element |V tb| is measured to be 1.020 ± 0.046 (meas.) ± 0.017 (theor.). © 2012 CERN for the benefit of the CMS collaboration.

Search for third-generation leptoquarks and scalar bottom quarks in pp collisions at √s=7Tev

Results are presented from a search for third-generation leptoquarks and scalar bottom quarks in a sample of proton-proton collisions at √s=7Tev collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 4.7 fb-1. A scenario where the new particles are pair produced and each decays to a b quark plus a tau neutrino or neutralino is considered. The number of observed events is found to be in agreement with the standard model prediction. Upper limits are set at 95% confidence level on the production cross sections. Leptoquarks with masses below ~450 GeV are excluded. Upper limits in the mass plane of the scalar quark and neutralino are set such that scalar bottom quark masses up to 410 GeV are excluded for neutralino masses of 50 GeV. © 2012 CERN for the benefit of CMS collaboration.

Observation of long-range, near-side angular correlations in pPb collisions at the LHC

Results on two-particle angular correlations for charged particles emitted in pPb collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV are presented. The analysis uses two million collisions collected with the CMS detector at the LHC. The correlations are studied over a broad range of pseudorapidity, η, and full azimuth, φ, as a function of charged particle multiplicity and particle transverse momentum, pT. In high-multiplicity events, a long-range (2<|δη|<4), near-side (δφ≈0) structure emerges in the two-particle δη-δφ correlation functions. This is the first observation of such correlations in proton-nucleus collisions, resembling the ridge-like correlations seen in high-multiplicity pp collisions at s=7 TeV and in AA collisions over a broad range of center-of-mass energies. The correlation strength exhibits a pronounced maximum in the range of pT=1-1.5 GeV/c and an approximately linear increase with charged particle multiplicity for high-multiplicity events. These observations are qualitatively similar to those in pp collisions when selecting the same observed particle multiplicity, while the overall strength of the correlations is significantly larger in pPb collisions. © 2012 CERN.

Measurement of the sum of WW and WZ production with W+dijet events in pp collisions at √s = 7 TeV

A measurement of the inclusive WW+WZ diboson production cross section in proton-proton collisions is reported, based on events containing a leptonically decaying W boson and exactly two jets. The data sample, collected at √s = 7 TeV with the CMS detector at the LHC, corresponds to an integrated luminosity of 5. 0 fb-1. The measured value of the sum of the inclusive WW and WZ cross sections is σ(pp→WW+WZ)=68. 9±8. 7 (stat.)±9. 7 (syst.)±1. 5 (lum.) pb, consistent with the standard model prediction of 65. 6±2. 2 pb. This is the first measurement of WW+WZ production in pp collisions using this signature. No evidence for anomalous triple gauge couplings is found and upper limits are set on their magnitudes. © 2013 CERN for the benefit of the CMS collaboration.

Measurement of the υ(1S), υ(2S), and υ(3S) polarizations in pp collisions at √s=7 TeV

The polarizations of the υ(1S), υ(2S), and υ(3S) mesons are measured in proton-proton collisions at √s=7 TeV, using a data sample of υ(nS)→μ+μ- decays collected by the CMS experiment, corresponding to an integrated luminosity of 4.9 fb-1. The dimuon decay angular distributions are analyzed in three different polarization frames. The polarization parameters λ™, λφ, and λ, as well as the frame-invariant quantity λ, are presented as a function of the υ(nS) transverse momentum between 10 and 50 GeV, in the rapidity ranges |y|<0.6 and 0.6<|y|<1.2. No evidence of large transverse or longitudinal polarizations is seen in the explored kinematic region. © 2013 CERN.

Study of the mass and spin-parity of the Higgs boson candidate via its decays to Z boson pairs

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. © 2013 CERN. Published by the American Physical Society under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

Search for contact interactions using the inclusive jet pT spectrum in pp collisions at √s=7 TeV

Results are reported of a search for a deviation in the jet production cross section from the prediction of perturbative quantum chromodynamics at next-to-leading order. The search is conducted using a 7 TeV proton-proton data sample corresponding to an integrated luminosity of 5.0 fb-1, collected with the Compact Muon Solenoid detector at the Large Hadron Collider. A deviation could arise from interactions characterized by a mass scale Λ too high to be probed directly at the LHC. Such phenomena can be modeled as contact interactions. No evidence of a deviation is found. Using the CL s criterion, lower limits are set on Λ of 9.9 TeV and 14.3 TeV at 95% confidence level for models with destructive and constructive interference, respectively. Limits obtained with a Bayesian method are also reported. © 2013 CERN.

Measurement of the tt̄ production cross section in the τ+jets channel in pp collisions at √s = 7 TeV

The top-quark pair production cross section in 7 TeV center-of-mass energy proton-proton collisions is measured using data collected by the CMS detector at the LHC. The measurement uses events with one jet identified as a hadronically decaying τ lepton and at least four additional energetic jets, at least one of which is identified as coming from a b quark. The analyzed data sample corresponds to an integrated luminosity of 3.9 fb-1 recorded by a dedicated multijet plus hadronically decaying τ trigger. A neural network has been developed to separate the top-quark pairs from the W+jets and multijet backgrounds. The measured value of σtt̄= 152 ± 12,(stat.) ± 32,(syst.) ±,(lum.) pb is consistent with the standard model predictions. © 2013 CERN for the benefit of the CMS collaboration.

Search for supersymmetry in events with opposite-sign dileptons and missing transverse energy using an artificial neural network

In this paper, a search for supersymmetry (SUSY) is presented in events with two opposite-sign isolated leptons in the final state, accompanied by hadronic jets and missing transverse energy. An artificial neural network is employed to discriminate possible SUSY signals from a standard model background. The analysis uses a data sample collected with the CMS detector during the 2011 LHC run, corresponding to an integrated luminosity of 4.98 fb-1 of proton-proton collisions at the center-of-mass energy of 7 TeV. Compared to other CMS analyses, this one uses relaxed criteria on missing transverse energy (EÌ̧T>40 GeV) and total hadronic transverse energy (HT>120 GeV), thus probing different regions of parameter space. Agreement is found between standard model expectation and observations, yielding limits in the context of the constrained minimal supersymmetric standard model and on a set of simplified models. © 2013 CERN.

Search for Z′ resonances decaying to tt̄ in dilepton+jets final states in pp collisions at √s=7 TeV

A search for resonances decaying to top quark-antiquark pairs is performed using a dilepton+jets data sample recorded by the CMS experiment at the LHC in pp collisions at √s=7 TeV corresponding to an integrated luminosity of 5.0 fb-1. No significant deviations from the standard model background are observed. Upper limits are presented for the production cross section times branching fraction of top quark-antiquark resonances for masses from 750 to 3000 GeV. In particular, the existence of a leptophobic topcolor particle Z′ is excluded at the 95% confidence level for resonance masses MZ ′<1.3 TeV for ΓZ′=0.012MZ ′, and M<1.9 TeV for ΓZ′=0.10MZ ′. © 2013 CERN.