488 research outputs found
Bayesian correlated clustering to integrate multiple datasets
Motivation: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct â but often complementary â information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured via parameters that describe the agreement among the datasets.
Results: Using a set of 6 artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real S. cerevisiae datasets. In the 2-dataset case, we show that MDIâs performance is comparable to the present state of the art. We then move beyond the capabilities of current approaches and integrate gene expression, ChIP-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques â as well as to non-integrative approaches â demonstrate that MDI is very competitive, while also providing information that would be difficult or impossible to extract using other methods
Targeting Antibiotics to Households for Trachoma Control
Repeated ocular infection with the bacterium Chlamydia trachomatis leads to the development of trachoma, a major cause of infectious blindness worldwide. Mass distribution of antibiotics, a component of the current trachoma control strategy, has had success in reducing infection in some areas, but results in a large number of uninfected people receiving antibiotics. We have previously shown that transmission of the bacteria between people in the same household is very efficient. Here, we investigated the effectiveness and cost-effectiveness of targeting antibiotics to households with active trachoma (inflammatory disease) compared to mass distribution, using data from four trachoma-endemic populations and a mathematical model of transmission. We found a high correspondence between households with active trachoma and infected households. In all populations the household targeted approach was predicted to be as effective as mass distribution, but it reduced the number of uninfected individuals receiving antibiotics, making the targeted strategy more cost-effective when antibiotics are not donated. Assuming antibiotics are donated, we predicted the targeted strategy to be more cost effective if it increases the proportion of infected individuals receiving treatment. Further work to address the feasibility and the cost variability in implementing the targeted approach in different settings is now required
Professionalism, Golf Coaching and a Master of Science Degree: A commentary
As a point of reference I congratulate Simon Jenkins on tackling the issue of professionalism in coaching. As he points out coaching is not a profession, but this does not mean that coaching would not benefit from going through a professionalization process. As things stand I find that the stimulus article unpacks some critically important issues of professionalism, broadly within the context of golf coaching. However, I am not sure enough is made of understanding what professional (golf) coaching actually is nor how the development of a professional golf coach can be facilitated by a Master of Science Degree (M.Sc.). I will focus my commentary on these two issues
Direct Measurement of the Top Quark Mass at D0
We determine the top quark mass m_t using t-tbar pairs produced in the D0
detector by \sqrt{s} = 1.8 TeV p-pbar collisions in a 125 pb^-1 exposure at the
Fermilab Tevatron. We make a two constraint fit to m_t in t-tbar -> b W^+bbar
W^- final states with one W boson decaying to q-qbar and the other to e-nu or
mu-nu. Likelihood fits to the data yield m_t(l+jets) = 173.3 +- 5.6 (stat) +-
5.5 (syst) GeV/c^2. When this result is combined with an analysis of events in
which both W bosons decay into leptons, we obtain m_t = 172.1 +- 5.2 (stat) +-
4.9 (syst) GeV/c^2. An alternate analysis, using three constraint fits to fixed
top quark masses, gives m_t(l+jets) = 176.0 +- 7.9 (stat) +- 4.8 (syst)
GeV/C^2, consistent with the above result. Studies of kinematic distributions
of the top quark candidates are also presented.Comment: 43 pages, 53 figures, 33 tables. RevTeX. Submitted to Phys. Rev.
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
Profound and Sustained Reduction in Chlamydia trachomatis in The Gambia: A Five-Year Longitudinal Study of Trachoma Endemic Communities
Trachoma is the most common infectious cause of blindness worldwide. Mass antibiotic treatment with azithromycin is used to control ocular Chlamydia trachomatis infection. There is uncertainty over how frequently and for how long treatment is needed, particularly in low prevalence settings. This study examines the effect of a single round of treatment on clinical disease and infection in a cluster of trachoma endemic Gambian villages over a five-year period. These villages had good water supplies and sanitation improved part way through the study. We found treatment was followed by a marked decline in infection prevalence (by PCR) to less than 1%. The decline in prevalence of active disease in children was less marked. Several villages had a prevalence of active trachoma in 1 to 9 year old children of greater than 10% during the follow-up period, mostly in the absence of detectable infection. The implication of this study is that a single, high coverage mass treatment may be sufficient to control C. trachomatis infection in a low prevalence setting, particularly when combined with environmental measures to limit transmission. However, relying on clinical signs to guide treatment decisions is likely to lead to significant amounts of over treatment where current guidelines are implemented
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
Measurement of the Boson Mass
A measurement of the mass of the boson is presented based on a sample of
5982 decays observed in collisions at
= 1.8~TeV with the D\O\ detector during the 1992--1993 run. From a
fit to the transverse mass spectrum, combined with measurements of the
boson mass, the boson mass is measured to be .Comment: 12 pages, LaTex, style Revtex, including 3 postscript figures
(submitted to PRL
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