Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset

We present an approach in which the semantics of an XML language is defined by means of a transformation from an XML document model (an XML schema) to an application specific model. The application specific model implements the intended behavior of documents written in the language. A transformation is specified in a model transformation language used in the Model Driven Architecture (MDA) approach for software development. Our approach provides a better separation of three concerns found in XML applications: syntax, syntax processing logic and intended meaning of the syntax. It frees the developer of low-level syntactical details and improves the adaptability and reusability of XML applications. Declarative transformation rules and the explicit application model provide a finer control over the application parts affected by adaptations. Transformation rules and the application model for an XML language may be composed with the corresponding rules and application models defined for other XML languages. In that way we achieve reuse and composition of XML applications

Full Sequence and Comparative Analysis of the Plasmid pAPEC-1 of Avian Pathogenic E. coli χ7122 (O78∶K80∶H9)

(APEC), are very diverse. They cause a complex of diseases in Human, animals, and birds. Even though large plasmids are often associated with the virulence of ExPEC, their characterization is still in its infancy., are also present in the sequence of pAPEC-1. The comparison of the pAPEC-1 sequence with the two available plasmid sequences reveals more gene loss and reorganization than previously appreciated. The presence of pAPEC-1-associated genes is assessed in human ExPEC by PCR. Many patterns of association between genes are found.The pathotype typical of pAPEC-1 was present in some human strains, which indicates a horizontal transfer between strains and the zoonotic risk of APEC strains. ColV plasmids could have common virulence genes that could be acquired by transposition, without sharing genes of plasmid function

Horizontal Gene Transfer of a ColV Plasmid Has Resulted in a Dominant Avian Clonal Type of Salmonella enterica Serovar Kentucky

Salmonella enterica continues to be a significant cause of foodborne gastrointestinal illness in humans. A wide variety of Salmonella serovars have been isolated from production birds and from retail poultry meat. Recently, though, S. enterica subsp. enterica serovar Kentucky has emerged as one of the prominent Salmonella serovars isolated from broiler chickens. Recent work suggests that its emergence apparently coincides with its acquisition of a ColV virulence plasmid. In the present study, we examined 902 Salmonella isolates belonging to 59 different serovars for the presence of this plasmid. Of the serovars examined, the ColV plasmid was found only among isolates belonging to the serovars Kentucky (72.9%), Typhimurium (15.0%) and Heidelberg (1.7%). We demonstrated that a single PFGE clonal type of S. Kentucky harbors this plasmid, and acquisition of this plasmid by S. Kentucky significantly increased its ability to colonize the chicken cecum and cause extraintestinal disease. Comparison of the completed sequences of three ColV plasmids from S. Kentucky isolated from different geographical locales, timepoints and sources revealed a nearly identical genetic structure with few single nucleotide changes or insertions/deletions. Overall, it appears that the ColV plasmid was recently acquired by a single clonal type S. Kentucky and confers to its host enhanced colonization and fitness capabilities. Thus, the potential for horizontal gene transfer of virulence and fitness factors to Salmonella from other enteric bacteria exists in poultry, representing a potential human health hazard

Search for Standard Model Higgs Boson Production in Association with a W Boson using a Neural Network

Submitted to Phys. Rev. DWe present a search for standard model Higgs boson production in association with a W boson in proton-antiproton collisions at a center of mass energy of 1.96 TeV. The search employs data collected with the CDF II detector that correspond to an integrated luminosity of approximately 1.9 inverse fb. We select events consistent with a signature of a single charged lepton, missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with a secondary vertex tagging method, a jet probability tagging method, and a neural network filter. We use kinematic information in an artificial neural network to improve discrimination between signal and background compared to previous analyses. The observed number of events and the neural network output distributions are consistent with the standard model background expectations, and we set 95% confidence level upper limits on the production cross section times branching fraction ranging from 1.2 to 1.1 pb or 7.5 to 102 times the standard model expectation for Higgs boson masses from 110 to $150 GeV/c^2, respectively.We present a search for standard model Higgs boson production in association with a W boson in proton-antiproton collisions (pp̅ →W±H→ℓνbb̅ ) at a center of mass energy of 1.96 TeV. The search employs data collected with the CDF II detector that correspond to an integrated luminosity of approximately 1.9  fb-1. We select events consistent with a signature of a single charged lepton (e±/μ±), missing transverse energy, and two jets. Jets corresponding to bottom quarks are identified with a secondary vertex tagging method, a jet probability tagging method, and a neural network filter. We use kinematic information in an artificial neural network to improve discrimination between signal and background compared to previous analyses. The observed number of events and the neural network output distributions are consistent with the standard model background expectations, and we set 95% confidence level upper limits on the production cross section times branching fraction ranging from 1.2 to 1.1 pb or 7.5 to 102 times the standard model expectation for Higgs boson masses from 110 to 150  GeV/c2, respectively.Peer reviewe

Observation of exclusive charmonium production and gamma+gamma to mu+mu- in p+pbar collisions at sqrt{s} = 1.96 TeV

7 pages, 3 figures, 1 table. Version accepted for Phys.Rev.Lett. Phys.Rev.Lett. (to be published)We have observed the reactions p+pbar --> p+X+pbar, with X being a centrally produced J/psi, psi(2S) or chi_c0, and gamma+gamma --> mu+mu-, in proton- antiproton collisions at sqrt{s} = 1.96 TeV using the Run II Collider Detector at Fermilab. The event signature requires two oppositely charged muons, each with pseudorapidity |eta| mu+mu-. Events with a J/psi and an associated photon candidate are consistent with exclusive chi_c0 production through double pomeron exchange. The exclusive vector meson production is as expected for elastic photo- production, gamma+p --> J/psi(psi(2S)) + p, which is observed here for the first time in hadron-hadron collisions. The cross sections ds/dy(y=0) for p + pbar --> p + X + pbar with X = J/psi, psi(2S) orchi_c0 are 3.92+/-0.62 nb, 0.53+/-0.14 nb, and 75+/-14 nb respectively. The cross section for the continuum, with |eta(mu+/-)|In CDF we have observed the reactions p+p̅ →p+X+p̅ , with X being a centrally produced J/ψ, ψ(2S), or χc0, and γγ→μ+μ- in pp̅ collisions at √s=1.96  TeV. The event signature requires two oppositely charged central muons, and either no other particles or one additional photon detected. Exclusive vector meson production is as expected for elastic photoproduction, γ+p→J/ψ(ψ(2S))+p, observed here for the first time in hadron-hadron collisions. We also observe exclusive χc0→J/ψ+γ. The cross sections dσ/dy|y=0 for J/ψ, ψ(2S), and χc0 are 3.92±0.25(stat)±0.52(syst)  nb, 0.53±0.09(stat)±0.10(syst)  nb, and 76±10(stat)±10(syst)  nb, respectively, and the continuum is consistent with QED. We put an upper limit on the cross section for Odderon exchange in exclusive J/ψ production.Peer reviewe

Search for the Production of Narrow tb Resonances in 1.9 fb-1 of ppbar Collisions at sqrt(s) = 1.96 TeV

We present new limits on resonant tb production in proton-antiproton collisions at 1.96 TeV, using 1.9 fb^-1 of data recorded with the CDF II detector at the Fermilab Tevatron. We reconstruct a candidate mass in events with a lepton, neutrino candidate, and two or three jets, and search for anomalous tb production as modeled by W'->tb. We set a new limit on a right-handed W' with standard model-like coupling, excluding any mass below 800 GeV at 95% C.L. The cross-section for any narrow, resonant tb production between 750 and 950 GeV is found to be less than 0.28 pb at 95% C.L. We also present an exclusion of the W' coupling strength versus W' mass over the range 300 to 950 GeV.We present new limits on resonant tb̅ production in pp̅ collisions at √s=1.96  TeV, using 1.9  fb-1 of data recorded with the CDF II detector at the Fermilab Tevatron. We reconstruct a candidate tb̅ mass in events with a lepton, neutrino candidate, and two or three jets, and search for anomalous tb̅ production as modeled by W′→tb̅ . We set a new limit on a right-handed W′ with standard model-like coupling, excluding any mass below 800  GeV/c2 at 95% C.L. The cross section for any narrow, resonant tb̅ production between 750 and 950  GeV/c2 is found to be less than 0.28 pb at 95% C.L. We also present an exclusion of the W′ coupling strength versus W′ mass over the range 300–950  GeV/c2.Peer reviewe

Measurement of b hadron lifetimes in exclusive decays containing a J/psi in p-pbar collisions at sqrt(s)=1.96TeV

We report on a measurement of $b$-hadron lifetimes in the fully reconstructed decay modes B^+ -->J/Psi K+, B^0 --> J/Psi K*, B^0 --> J/Psi Ks, and Lambda_b --> J/Psi Lambda using data corresponding to an integrated luminosity of 4.3 ${\rm fb}^{-1}$, collected by the CDF II detector at the Fermilab Tevatron. The measured lifetimes are $\tau$B^+ = $1.639 \pm 0.009 ({\rm stat}) \pm 0.009 {\rm (syst) ~ ps}$, $\tau$B^0 = $1.507 \pm 0.010 ({\rm stat}) \pm 0.008 {\rm (syst) ~ ps}$ and $\tau$Lambda_b = $1.537 \pm 0.045 ({\rm stat}) \pm 0.014 {\rm (syst) ~ ps}$. The lifetime ratios are $\tau$B^+/$\tau$B^0 = $1.088 \pm 0.009 ({\rm stat})\pm 0.004 ({\rm syst})$ and $\tau$Lambda_b/$\tau$B^0 = $1.020 \pm 0.030 ({\rm stat})\pm 0.008 ({\rm syst})$. These are the most precise determinations of these quantities from a single experiment.Comment: revised version. accepted for PRL publicatio

Measurement of b Hadron Lifetimes in Exclusive Decays Containing a J/Psi in p(p)over-bar Collisions at root s=1.96 TeV

We report on a measurement of b-hadron lifetimes in the fully reconstructed decay modes B+-> J/psi K+, B-0 -> J/psi K*(892)(0), B-0 -> J/psi K-s(0), and Lambda(0)(b)-> J/psi Lambda(0) using data corresponding to an integrated luminosity of 4.3 fb(-1), collected by the CDF II detector at the Fermilab Tevatron. The measured lifetimes are tau(B+)=[1.639 +/- 0.009(stat)+/- 0.009(syst)]ps, tau(B-0)=[1.507 +/- 0.010(stat)+/- 0.008(syst)]ps, and tau(Lambda(0)(b))=[1.537 +/- 0.045(stat)+/- 0.014(syst)]ps. The lifetime ratios are tau(B+)/tau(B-0)=[1.088 +/- 0.009(stat)+/- 0.004(syst)] and tau(Lambda(0)(b))/tau(B-0)=[1.020 +/- 0.030(stat)+/- 0.008(syst)]. These are the most precise determinations of these quantities from a single experiment

Search for High Mass Resonances Decaying to Muon Pairs in root s=1.96 TeV p(p)over-bar Collisions

We present a search for a new narrow, spin-1, high mass resonance decaying to mu(+)mu(-) + X, using a matrix-element-based likelihood and a simultaneous measurement of the resonance mass and production rate. In data with 4.6 fb(-1) of integrated luminosity collected by the CDF detector in p (p) over bar collisions at root s = 1960 GeV, the most likely signal cross section is consistent with zero at 16% confidence level. We therefore do not observe evidence for a high mass resonance and place limits on models predicting spin-1 resonances, including M > 1071 GeV/c(2) at 95% confidence level for a Z' boson with the same couplings to fermions as the Z boson