A versatile computational pipeline for bacterial genome annotation improvement and comparative analysis, with Brucella as a use case

We present a bacterial genome computational analysis pipeline, called GenVar. The pipeline, based on the program GeneWise, is designed to analyze an annotated genome and automatically identify missed gene calls and sequence variants such as genes with disrupted reading frames (split genes) and those with insertions and deletions (indels). For a given genome to be analyzed, GenVar relies on a database containing closely related genomes (such as other species or strains) as well as a few additional reference genomes. GenVar also helps identify gene disruptions probably caused by sequencing errors. We exemplify GenVar's capabilities by presenting results from the analysis of four Brucella genomes. Brucella is an important human pathogen and zoonotic agent. The analysis revealed hundreds of missed gene calls, new split genes and indels, several of which are species specific and hence provide valuable clues to the understanding of the genome basis of Brucella pathogenicity and host specificity

Ecological Invasion, Roughened Fronts, and a Competitor's Extreme Advance: Integrating Stochastic Spatial-Growth Models

Both community ecology and conservation biology seek further understanding of factors governing the advance of an invasive species. We model biological invasion as an individual-based, stochastic process on a two-dimensional landscape. An ecologically superior invader and a resident species compete for space preemptively. Our general model includes the basic contact process and a variant of the Eden model as special cases. We employ the concept of a "roughened" front to quantify effects of discreteness and stochasticity on invasion; we emphasize the probability distribution of the front-runner's relative position. That is, we analyze the location of the most advanced invader as the extreme deviation about the front's mean position. We find that a class of models with different assumptions about neighborhood interactions exhibit universal characteristics. That is, key features of the invasion dynamics span a class of models, independently of locally detailed demographic rules. Our results integrate theories of invasive spatial growth and generate novel hypotheses linking habitat or landscape size (length of the invading front) to invasion velocity, and to the relative position of the most advanced invader.Comment: The original publication is available at www.springerlink.com/content/8528v8563r7u2742

Search for Higgs bosons decaying to tautau pairs in ppbar collisions at sqrt(s) = 1.96 TeV

We present a search for the production of neutral Higgs bosons decaying into tautau pairs in ppbar collisions at a center-of-mass energy of 1.96 TeV. The data, corresponding to an integrated luminosity of 5.4 fb-1, were collected by the D0 experiment at the Fermilab Tevatron Collider. We set upper limits at the 95% C.L. on the product of production cross section and branching ratio for a scalar resonance decaying into tautau pairs, and we then interpret these limits as limits on the production of Higgs bosons in the minimal supersymmetric standard model (MSSM) and as constraints in the MSSM parameter space.Comment: 7 pages, 5 figures, submitted to PL

Measurement of the photon+b+b-jet production differential cross section in ppˉp\bar{p} collisions at \sqrt{s}=1.96~\TeV

We present measurements of the differential cross section dsigma/dpT_gamma for the inclusive production of a photon in association with a b-quark jet for photons with rapidities |y_gamma|< 1.0 and 30<pT_gamma <300 GeV, as well as for photons with 1.5<|y_gamma|< 2.5 and 30< pT_gamma <200 GeV, where pT_gamma is the photon transverse momentum. The b-quark jets are required to have pT>15 GeV and rapidity |y_jet| < 1.5. The results are based on data corresponding to an integrated luminosity of 8.7 fb^-1, recorded with the D0 detector at the Fermilab Tevatron $p\bar{p}$ Collider at sqrt(s)=1.96 TeV. The measured cross sections are compared with next-to-leading order perturbative QCD calculations using different sets of parton distribution functions as well as to predictions based on the kT-factorization QCD approach, and those from the Sherpa and Pythia Monte Carlo event generators.Comment: 10 pages, 9 figures, submitted to Phys. Lett.

Limits on anomalous trilinear gauge boson couplings from WW, WZ and Wgamma production in pp-bar collisions at sqrt{s}=1.96 TeV

We present final searches of the anomalous gammaWW and ZWW trilinear gauge boson couplings from WW and WZ production using lepton plus dijet final states and a combination with results from Wgamma, WW, and WZ production with leptonic final states. The analyzed data correspond to up to 8.6/fb of integrated luminosity collected by the D0 detector in pp-bar collisions at sqrt{s}=1.96 TeV. We set the most stringent limits at a hadron collider to date assuming two different relations between the anomalous coupling parameters Delta\kappa_\gamma, lambda, and Delta g_1^Z for a cutoff energy scale Lambda=2 TeV. The combined 68% C.L. limits are -0.057<Delta\kappa_\gamma<0.154, -0.015<lambda<0.028, and -0.008<Delta g_1^Z<0.054 for the LEP parameterization, and -0.007<Delta\kappa<0.081 and -0.017<lambda<0.028 for the equal couplings parameterization. We also present the most stringent limits of the W boson magnetic dipole and electric quadrupole moments.Comment: 10 pages, 5 figures, submitted to PL

Measurement of three-jet differential cross sections d sigma-3jet / d M-3jet in p anti-p collisions at sqrt(s)=1.96 TeV

We present the first measurement of the inclusive three-jet differential cross section as a function of the invariant mass of the three jets with the largest transverse momenta in an event in p anti-p collisions at sqrt(s) = 1.96 TeV. The measurement is made in different rapidity regions and for different jet transverse momentum requirements and is based on a data set corresponding to an integrated luminosity of 0.7 fb^{-1} collected with the D0 detector at the Fermilab Tevatron Collider. The results are used to test the three-jet matrix elements in perturbative QCD calculations at next-to-leading order in the strong coupling constant. The data allow discrimination between parametrizations of the parton distribution functions of the proton.Comment: 10 pages, 4 figures, 2 tables, submitted to Phys. Lett. B, corrected chi2 values for NNPD

Search for pair production of the scalar top quark in muon+tau final states

We present a search for the pair production of scalar top quarks ($\tilde{t}_{1}$), the lightest supersymmetric partners of the top quarks, in $p\bar{p}$ collisions at a center-of-mass energy of 1.96 TeV, using data corresponding to an integrated luminosity of {7.3 $fb^{-1}$} collected with the \dzero experiment at the Fermilab Tevatron Collider. Each scalar top quark is assumed to decay into a $b$ quark, a charged lepton, and a scalar neutrino ($\tilde{\nu}$). We investigate final states arising from $\tilde{t}_{1} \bar{\tilde{t}_{1}} \rightarrow b\bar{b}\mu\tau \tilde{\nu} \tilde{\nu}$ and $\tilde{t}_{1} \bar{\tilde{t}_{1}} \rightarrow b\bar{b}\tau\tau \tilde{\nu} \tilde{\nu}$. With no significant excess of events observed above the background expected from the standard model, we set exclusion limits on this production process in the ($m_{\tilde{t}_{1}}$,$m_{\tilde{\nu}}$) plane.Comment: Submitted to Phys. Lett.

Measurements of inclusive W+jets production rates as a function of jet transverse momentum in ppbar collisions at sqrt{s}=1.96 TeV

This Letter describes measurements of inclusive W (--> e nu) + n jet cross sections (n = 1-4), presented as total inclusive cross sections and differentially in the nth jet transverse momentum. The measurements are made using data corresponding to an integrated luminosity of 4.2 fb-1 collected by the D0 detector at the Fermilab Tevatron Collider, and achieve considerably smaller uncertainties on W +jets production cross sections than previous measurements. The measurements are compared to next-to-leading order perturbative QCD (pQCD) calculations in the n =1-3 jet multiplicity bins and to leading order pQCD calculations in the 4-jet bin. The measurements are generally in agreement with pQCD predictions, although certain regions of phase space are identified where the calculations could be improved

Measurement of spin correlation in ttbar production using dilepton final states

We measure the correlation between the spin of the top quark and the spin of the anti-top quark in (ttbar -> W+ W- b bbar -> l+ nu b l- nubar bbar) final states produced in ppbar collisions at a center of mass energy sqrt(s)=1.96 TeV, where l is an electron or muon. The data correspond to an integrated luminosity of 5.4 fb-1 and were collected with the D0 detector at the Fermilab Tevatron collider. The correlation is extracted from the angles of the two leptons in the t and tbar rest frames, yielding a correlation strength C= 0.10^{+0.45}_{-0.45}, in agreement with the NLO QCD prediction within two standard deviations, but also in agreement with the no correlation hypothesis.Comment: 10 pages, 3 figures, submitted to PL

Measurement of the ttbar production cross section using dilepton events in ppbar collisions

We present a measurement of the ttbar production cross section sigma(ttbar) in ppbar collisions at sqrt{s} = 1.96 TeV using 5.4 fb-1 of integrated luminosity collected with the D0 detector. We consider final states with at least two jets and two leptons (ee, emu, mumu), and events with one jet for the the emu final state as well. The measured cross section is sigma(ttbar)= 7.36 +0.90-0.79 (stat + syst) pb. This result combined with the cross section measurement in the lepton + jets final state yields sigma(ttbar)=7.56 +0.63-0.56 (stat + syst) pb, which agrees with the standard model expectation. The relative precision of 8% of this measurement is comparable to the latest theoretical calculations.Comment: 9 pages, published in Phys. Lett.