970 research outputs found
Recon 2.2: from reconstruction to model of human metabolism.
IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001)
Correlating Remote Sensing Data with the Abundance of Pupae of the Dengue Virus Mosquito Vector, Aedes aegypti, in Central Mexico
Using a geographic transect in Central Mexico, with an elevation/climate gradient, but uniformity in socio-economic conditions among study sites, this study evaluates the applicability of three widely-used remote sensing (RS) products to link weather conditions with the local abundance of the dengue virus mosquito vector, Aedes aegypti (Ae. aegypti). Field-derived entomological measures included estimates for the percentage of premises with the presence of Ae. aegypti pupae and the abundance of Ae. aegypti pupae per premises. Data on mosquito abundance from field surveys were matched with RS data and analyzed for correlation. Daily daytime and nighttime land surface temperature (LST) values were obtained from Moderate Resolution Imaging Spectroradiometer (MODIS)/Aqua cloud-free images within the four weeks preceding the field survey. Tropical Rainfall Measuring Mission (TRMM)-estimated rainfall accumulation was calculated for the four weeks preceding the field survey. Elevation was estimated through a digital elevation model (DEM). Strong correlations were found between mosquito abundance and RS-derived night LST, elevation and rainfall along the elevation/climate gradient. These findings show that RS data can be used to predict Ae. aegypti abundance, but further studies are needed to define the climatic and socio-economic conditions under which the correlations observed herein can be assumed to apply
Search for Charged Higgs Bosons in Decays of Top Quark Pairs
We present a search for charged Higgs bosons in decays of pair-produced top
quarks using 109.2 +- 5.8 pb^-1 of data recorded from ppbar collisions at
sqrt{s} = 1.8 TeV by the D0 detector during 1992-96 at the Fermilab Tevatron.
No evidence is found for charged Higgs production, and most parts of the
[m(H+),tan(beta)] parameter space where the decay t -> bH+ has a branching
fraction close to or larger than that for t -> bW+ are excluded at 95%
confidence level. Assuming m(t) = 175 GeV and sigma(ppbar -> ttbar) = 5.5 pb,
for m(H+) = 60 GeV, we exclude tan(beta) 40.9.Comment: 11 pages, 3 figures, submitted to PR
Search for Electroweak Production of Single Top Quarks in ppbar Collisions
We present a search for electroweak production of single top quarks in the
electron+jets and muon+jets decay channels. The measurements use ~90 pb^-1 of
data from Run 1 of the Fermilab Tevatron collider, collected at 1.8 TeV with
the DZero detector between 1992 and 1995. We use events that include a tagging
muon, implying the presence of a b jet, to set an upper limit at the 95%
confidence level on the cross section for the s-channel process ppbar->tb+X of
39 pb. The upper limit for the t-channel process ppbar->tqb+X is 58 pb.Comment: 11 pages, 2 figures. This is the published versio
Probing BFKL Dynamics in the Dijet Cross Section at Large Rapidity Intervals in ppbar Collisions at sqrt{s}=1800 and 630 GeV
Inclusive dijet production at large pseudorapidity intervals (delta_eta)
between the two jets has been suggested as a regime for observing BFKL
dynamics. We have measured the dijet cross section for large delta_eta in ppbar
collisions at sqrt{s}=1800 and 630 GeV using the DO detector. The partonic
cross section increases strongly with the size of delta_eta. The observed
growth is even stronger than expected on the basis of BFKL resummation in the
leading logarithmic approximation. The growth of the partonic cross section can
be accommodated with an effective BFKL intercept of
a_{BFKL}(20GeV)=1.65+/-0.07.Comment: Published in Physical Review Letter
Search for Squarks and Gluinos in Events Containing Jets and a Large Imbalance in Transverse Energy
Using data corresponding to an integrated luminosity of 79 pb-1, D0 has
searched for events containing multiple jets and large missing transverse
energy in pbar-p collisions at sqrt(s)=1.8 TeV at the Fermilab Tevatron
collider. Observing no significant excess beyond what is expected from the
standard model, we set limits on the masses of squarks and gluinos and on the
model parameters m_0 and m_1/2, in the framework of the minimal low-energy
supergravity models of supersymmetry. For tan(beta) = 2 and A_0 = 0, with mu <
0, we exclude all models with m_squark < 250 GeV/c^2. For models with equal
squark and gluino masses, we exclude m < 260 GeV/c^2.Comment: 10 pages, 3 figures, Submitted to PRL, Fixed typo on page bottom of
p. 6 (QCD multijet background is 35.4 events
Direct Search for Charged Higgs Bosons in Decays of Top Quarks
We present a search for charged Higgs bosons in decays of pair-produced top
quarks in pbar p collisions at sqrt(s) = 1.8 TeV using 62.2 pb^-1 of data
recorded by the D0 detector at the Fermilab Tevatron collider. No evidence is
found for signal, and we exclude at 95% confidence most regions of the (M
higgs, tan beta) parameter space where the decay t->H b has a branching
fraction greater than 0.36 and B(H -> tau nu) is large.Comment: 11 pages, 4 figures, submitted to Phys. Rev. Let
A Quasi-Model-Independent Search for New Physics at Large Transverse Momentum
We apply a quasi-model-independent strategy ("Sleuth") to search for new high
p_T physics in approximately 100 pb^-1 of ppbar collisions at sqrt(s) = 1.8 TeV
collected by the DZero experiment during 1992-1996 at the Fermilab Tevatron.
Over thirty-two e mu X, W+jets-like, Z+jets-like, and 3(lepton/photon)X
exclusive final states are systematically analyzed for hints of physics beyond
the standard model. Simultaneous sensitivity to a variety of models predicting
new phenomena at the electroweak scale is demonstrated by testing the method on
a particular signature in each set of final states. No evidence of new high p_T
physics is observed in the course of this search, and we find that 89% of an
ensemble of hypothetical similar experimental runs would have produced a final
state with a candidate signal more interesting than the most interesting
observed in these data.Comment: 28 pages, 17 figures. Submitted to Physical Review
Search for R-parity Violating Supersymmetry in Dimuon and Four-Jets Channel
We present results of a search for R-parity-violating decay of the neutralino
chi_1^0, taken to be the Lightest Supersymmetric Particle. It is assumed that
this decay proceeds through one of the lepton-number violating couplings
lambda-prime_2jk (j=1,2; k=1,2,3). This search is based on 77.5 pb-1 of data,
collected by the D0 experiment at the Fermilab Tevatron in ppbar collisions at
a center of mass energy of 1.8 TeV in 1992-1995.Comment: 10 pages, 3 figure
Search for bottom squarks in pbarp collisions at sqrt(s)=1.8 TeV
We report on a search for bottom squarks produced in pbarp collisions at
sqrt(s) = 1.8 TeV using the D0 detector at Fermilab. Bottom squarks are assumed
to be produced in pairs and to decay to the lightest supersymmetric particle
(LSP) and a b quark with branching fraction of 100%. The LSP is assumed to be
the lightest neutralino and stable. We set limits on the production cross
section as a function of bottom squark mass and LSP mass.Comment: 5 pages, Latex. submitted 3-12-1999 to PRD - Rapid Communicatio
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