743 research outputs found
The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
Although recent advances in synthetic biology allow us to produce biological designs more efficiently than ever, our ability to predict the end result of these designs is still nascent. Predictive models require large amounts of high-quality data to be parametrized and tested, which are not generally available. Here, we present the Experiment Data Depot (EDD), an online tool designed as a repository of experimental data and metadata. EDD provides a convenient way to upload a variety of data types, visualize these data, and export them in a standardized fashion for use with predictive algorithms. In this paper, we describe EDD and showcase its utility for three different use cases: storage of characterized synthetic biology parts, leveraging proteomics data to improve biofuel yield, and the use of extracellular metabolite concentrations to predict intracellular metabolic fluxes
Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent
Sorghum is a multipurpose crop that is cultivated worldwide. Plant growth-promoting bacteria (PGPB) have important roles in enhancing sorghum biomass and nutrient uptake and suppressing plant pathogens. The aim of this research was to test the effects of the endophytic bacterial species Kosakonia radicincitans strain IAC/BECa 99, Enterobacter asburiae strain IAC/BECa 128, Pseudomonas fluorescens strain IAC/BECa 141, Burkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 on the growth and root architecture of four sorghum cultivars (SRN-39, Shanqui-Red, BRS330, BRS509), with different uses and strigolactone profiles. We hypothesized that the different bacterial species would trigger different growth plant responses in different sorghum cultivars. Burkholderia tropica and H. frisingense significantly increased the plant biomass of cultivars SRN-39 and BRS330. Moreover, cultivar BRS330 inoculated with either strain displayed isolates significant decrease in average root diameter. This study shows that Burkholderia tropica strain IAC/BECa 135 and H. frisingense strain IAC/BECa 152 are promising PGPB strains for use as inocula for sustainable sorghum cultivation
The Quest for Orthologs benchmark service and consensus calls in 2020.
The identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases
Evidence of Color Coherence Effects in W+jets Events from ppbar Collisions at sqrt(s) = 1.8 TeV
We report the results of a study of color coherence effects in ppbar
collisions based on data collected by the D0 detector during the 1994-1995 run
of the Fermilab Tevatron Collider, at a center of mass energy sqrt(s) = 1.8
TeV. Initial-to-final state color interference effects are studied by examining
particle distribution patterns in events with a W boson and at least one jet.
The data are compared to Monte Carlo simulations with different color coherence
implementations and to an analytic modified-leading-logarithm perturbative
calculation based on the local parton-hadron duality hypothesis.Comment: 13 pages, 6 figures. Submitted to Physics Letters
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-jet production differential cross section in 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 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
(), the lightest supersymmetric partners of the top quarks, in
collisions at a center-of-mass energy of 1.96 TeV, using data
corresponding to an integrated luminosity of {7.3 } collected with the
\dzero experiment at the Fermilab Tevatron Collider. Each scalar top quark is
assumed to decay into a quark, a charged lepton, and a scalar neutrino
(). We investigate final states arising from and
. 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 (,) 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
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