576 research outputs found
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli
Coexpression of genes or, more generally, similarity in the expression
profiles poses an unsurmountable obstacle to inferring the gene regulatory
network (GRN) based solely on data from DNA microarray time series. Clustering
of genes with similar expression profiles allows for a course-grained view of
the GRN and a probabilistic determination of the connectivity among the
clusters. We present a model for the temporal evolution of a gene cluster
network which takes into account interactions of gene products with genes and,
through a non-constant degradation rate, with other gene products. The number
of model parameters is reduced by using polynomial functions to interpolate
temporal data points. In this manner, the task of parameter estimation is
reduced to a system of linear algebraic equations, thus making the computation
time shorter by orders of magnitude. To eliminate irrelevant networks, we test
each GRN for stability with respect to parameter variations, and impose
restrictions on its behavior near the steady state. We apply our model and
methods to DNA microarray time series' data collected on Escherichia coli
during glucose-lactose diauxie and infer the most probable cluster network for
different phases of the experiment.Comment: 20 pages, 4 figures; Systems and Synthetic Biology 5 (2011
Determining Risk of Falls in Community-Dwelling Older Adults: A Systematic Review and Meta-analysis Using Posttest Probability
BACKGROUND:
Falls and their consequences are significant concerns for older adults, caregivers, and health care providers. Identification of fall risk is crucial for appropriate referral to preventive interventions. Falls are multifactorial; no single measure is an accurate diagnostic tool. There is limited information on which history question, self-report measure, or performance-based measure, or combination of measures, best predicts future falls.
PURPOSE:
First, to evaluate the predictive ability of history questions, self-report measures, and performance-based measures for assessing fall risk of community-dwelling older adults by calculating and comparing posttest probability (PoTP) values for individual test/measures. Second, to evaluate usefulness of cumulative PoTP for measures in combination.
DATA SOURCES:
To be included, a study must have used fall status as an outcome or classification variable, have a sample size of at least 30 ambulatory community-living older adults (≥65 years), and track falls occurrence for a minimum of 6 months. Studies in acute or long-term care settings, as well as those including participants with significant cognitive or neuromuscular conditions related to increased fall risk, were excluded. Searches of Medline/PubMED and Cumulative Index of Nursing and Allied Health (CINAHL) from January 1990 through September 2013 identified 2294 abstracts concerned with fall risk assessment in community-dwelling older adults.
STUDY SELECTION:
Because the number of prospective studies of fall risk assessment was limited, retrospective studies that classified participants (faller/nonfallers) were also included. Ninety-five full-text articles met inclusion criteria; 59 contained necessary data for calculation of PoTP. The Quality Assessment Tool for Diagnostic Accuracy Studies (QUADAS) was used to assess each study\u27s methodological quality.
DATA EXTRACTION:
Study design and QUADAS score determined the level of evidence. Data for calculation of sensitivity (Sn), specificity (Sp), likelihood ratios (LR), and PoTP values were available for 21 of 46 measures used as search terms. An additional 73 history questions, self-report measures, and performance-based measures were used in included articles; PoTP values could be calculated for 35.
DATA SYNTHESIS:
Evidence tables including PoTP values were constructed for 15 history questions, 15 self-report measures, and 26 performance-based measures. Recommendations for clinical practice were based on consensus.
LIMITATIONS:
Variations in study quality, procedures, and statistical analyses challenged data extraction, interpretation, and synthesis. There was insufficient data for calculation of PoTP values for 63 of 119 tests.
CONCLUSIONS:
No single test/measure demonstrated strong PoTP values. Five history questions, 2 self-report measures, and 5 performance-based measures may have clinical usefulness in assessing risk of falling on the basis of cumulative PoTP. Berg Balance Scale score (≤50 points), Timed Up and Go times (≥12 seconds), and 5 times sit-to-stand times (≥12) seconds are currently the most evidence-supported functional measures to determine individual risk of future falls. Shortfalls identified during review will direct researchers to address knowledge gaps
Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)
This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4 fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation
Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events
The - oscillation frequency has been measured with a sample of
23 million \B\bar B pairs collected with the BABAR detector at the PEP-II
asymmetric B Factory at SLAC. In this sample, we select events in which both B
mesons decay semileptonically and use the charge of the leptons to identify the
flavor of each B meson. A simultaneous fit to the decay time difference
distributions for opposite- and same-sign dilepton events gives ps.Comment: 7 pages, 1 figure, submitted to Physical Review Letter
Measurement of D-s(+) and D-s(*+) production in B meson decays and from continuum e(+)e(-) annihilation at √s=10.6 GeV
This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APSNew measurements of Ds+ and Ds*+ meson production rates from B decays and from qq̅ continuum events near the Υ(4S) resonance are presented. Using 20.8 fb-1 of data on the Υ(4S) resonance and 2.6 fb-1 off-resonance, we find the inclusive branching fractions B(B⃗Ds+X)=(10.93±0.19±0.58±2.73)% and B(B⃗Ds*+X)=(7.9±0.8±0.7±2.0)%, where the first error is statistical, the second is systematic, and the third is due to the Ds+→φπ+ branching fraction uncertainty. The production cross sections σ(e+e-→Ds+X)×B(Ds+→φπ+)=7.55±0.20±0.34pb and σ(e+e-→Ds*±X)×B(Ds+→φπ+)=5.8±0.7±0.5pb are measured at center-of-mass energies about 40 MeV below the Υ(4S) mass. The branching fractions ΣB(B⃗Ds(*)+D(*))=(5.07±0.14±0.30±1.27)% and ΣB(B⃗Ds*+D(*))=(4.1±0.2±0.4±1.0)% are determined from the Ds(*)+ momentum spectra. The mass difference m(Ds+)-m(D+)=98.4±0.1±0.3MeV/c2 is also measured.This work was supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the Swiss NSF, A. P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation
A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)
We present a measurement of time-dependent CP-violating asymmetries in
neutral B meson decays collected with the BABAR detector at the PEP-II
asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data
sample consists of 29.7 recorded at the
resonance and 3.9 off-resonance. One of the neutral B mesons,
which are produced in pairs at the , is fully reconstructed in
the CP decay modes , , , () and , or in flavor-eigenstate
modes involving and (). The flavor of the other neutral B meson is tagged at the time of
its decay, mainly with the charge of identified leptons and kaons. The proper
time elapsed between the decays is determined by measuring the distance between
the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample
finds . The value of the asymmetry amplitude is determined from
a simultaneous maximum-likelihood fit to the time-difference distribution of
the flavor-eigenstate sample and about 642 tagged decays in the
CP-eigenstate modes. We find , demonstrating that CP violation exists in the neutral B meson
system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review
Measurement of the Branching Fraction for B- --> D0 K*-
We present a measurement of the branching fraction for the decay B- --> D0
K*- using a sample of approximately 86 million BBbar pairs collected by the
BaBar detector from e+e- collisions near the Y(4S) resonance. The D0 is
detected through its decays to K- pi+, K- pi+ pi0 and K- pi+ pi- pi+, and the
K*- through its decay to K0S pi-. We measure the branching fraction to be
B.F.(B- --> D0 K*-)= (6.3 +/- 0.7(stat.) +/- 0.5(syst.)) x 10^{-4}.Comment: 7 pages, 1 postscript figure, submitted to Phys. Rev. D (Rapid
Communications
Evidence for the Rare Decay B -> K*ll and Measurement of the B -> Kll Branching Fraction
We present evidence for the flavor-changing neutral current decay and a measurement of the branching fraction for the related
process , where is either an or
pair. These decays are highly suppressed in the Standard Model,
and they are sensitive to contributions from new particles in the intermediate
state. The data sample comprises
decays collected with the Babar detector at the PEP-II storage ring.
Averaging over isospin and lepton flavor, we obtain the branching
fractions and , where the
uncertainties are statistical and systematic, respectively. The significance of
the signal is over , while for it is .Comment: 7 pages, 2 postscript figues, submitted to Phys. Rev. Let
Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses
SummarySystems approaches for the study of immune signaling pathways have been traditionally based on purified cells or cultured lines. However, in vivo responses involve the coordinated action of multiple cell types, which interact to establish an inflammatory microenvironment. We employed standardized whole-blood stimulation systems to test the hypothesis that responses to Toll-like receptor ligands or whole microbes can be defined by the transcriptional signatures of key cytokines. We found 44 genes, identified using Support Vector Machine learning, that captured the diversity of complex innate immune responses with improved segregation between distinct stimuli. Furthermore, we used donor variability to identify shared inter-cellular pathways and trace cytokine loops involved in gene expression. This provides strategies for dimension reduction of large datasets and deconvolution of innate immune responses applicable for characterizing immunomodulatory molecules. Moreover, we provide an interactive R-Shiny application with healthy donor reference values for induced inflammatory genes
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