3,945 research outputs found
A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology
We present a mixture model-based analysis for identifying differences in the distribution of RNA polymerase II (Pol II) in transcribed regions, measured using ChIP-seq (chromatin immunoprecipitation following massively parallel sequencing technology). The statistical model assumes that the number of Pol II-targeted sequences contained within each genomic region follows a Poisson distribution. A Poisson mixture model was then developed to distinguish Pol II binding changes in transcribed region using an empirical approach and an expectation-maximization (EM) algorithm developed for estimation and inference. In order to achieve a global maximum in the M-step, a particle swarm optimization (PSO) was implemented. We applied this model to Pol II binding data generated from hormone-dependent MCF7 breast cancer cells and antiestrogen-resistant MCF7 breast cancer cells before and after treatment with 17β-estradiol (E2). We determined that in the hormone-dependent cells, ~9.9% (2527) genes showed significant changes in Pol II binding after E2 treatment. However, only ~0.7% (172) genes displayed significant Pol II binding changes in E2-treated antiestrogen-resistant cells. These results show that a Poisson mixture model can be used to analyze ChIP-seq data
Determining the Contribution of Epidermal Cell Shape to Petal Wettability Using Isogenic Antirrhinum Lines
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Graph Zeta Function and Gauge Theories
Along the recently trodden path of studying certain number theoretic
properties of gauge theories, especially supersymmetric theories whose vacuum
manifolds are non-trivial, we investigate Ihara's Graph Zeta Function for large
classes of quiver theories and periodic tilings by bi-partite graphs. In
particular, we examine issues such as the spectra of the adjacency and whether
the gauge theory satisfies the strong and weak versions of the graph
theoretical analogue of the Riemann Hypothesis.Comment: 35 pages, 7 Figure
Higgs friends and counterfeits at hadron colliders
We consider the possibility of "Higgs counterfeits" - scalars that can be
produced with cross sections comparable to the SM Higgs, and which decay with
identical relative observable branching ratios, but which are nonetheless not
responsible for electroweak symmetry breaking. We also consider a related
scenario involving "Higgs friends," fields similarly produced through gg fusion
processes, which would be discovered through diboson channels WW, ZZ, gamma
gamma, or even gamma Z, potentially with larger cross sections times branching
ratios than for the Higgs. The discovery of either a Higgs friend or a Higgs
counterfeit, rather than directly pointing towards the origin of the weak
scale, would indicate the presence of new colored fields necessary for the
sizable production cross section (and possibly new colorless but electroweakly
charged states as well, in the case of the diboson decays of a Higgs friend).
These particles could easily be confused for an ordinary Higgs, perhaps with an
additional generation to explain the different cross section, and we emphasize
the importance of vector boson fusion as a channel to distinguish a Higgs
counterfeit from a true Higgs. Such fields would naturally be expected in
scenarios with "effective Z's," where heavy states charged under the SM produce
effective charges for SM fields under a new gauge force. We discuss the
prospects for discovery of Higgs counterfeits, Higgs friends, and associated
charged fields at the LHC.Comment: 27 pages, 5 figures. References added and typos fixe
Quantifying the behavior of stock correlations under market stress
Understanding correlations in complex systems is crucial in the face of turbulence, such as the ongoing financial crisis. However, in complex systems, such as financial systems, correlations are not constant but instead vary in time. Here we address the question of quantifying state-dependent correlations in stock markets. Reliable estimates of correlations are absolutely necessary to protect a portfolio. We analyze 72 years of daily closing prices of the 30 stocks forming the Dow Jones Industrial Average (DJIA). We find the striking result that the average correlation among these stocks scales linearly with market stress reflected by normalized DJIA index returns on various time scales. Consequently, the diversification effect which should protect a portfolio melts away in times of market losses, just when it would most urgently be needed. Our empirical analysis is consistent with the interesting possibility that one could anticipate diversification breakdowns, guiding the design of protected portfolios
Psychometric precision in phenotype definition is a useful step in molecular genetic investigation of psychiatric disorders
Affective disorders are highly heritable, but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing the risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from the British 1946 birth cohort, we compared summary scores with psychometric modeling based on the General Health Questionnaire (GHQ-28) scale for affective symptoms in an association analysis of 27 candidate genes (249 single-nucleotide polymorphisms (SNPs)). The psychometric method utilized a bi-factor model that partitioned the phenotype variances into five orthogonal latent variable factors, in accordance with the multidimensional data structure of the GHQ-28 involving somatic, social, anxiety and depression domains. Results showed that, compared with the summation approach, the affective symptoms defined by the bi-factor psychometric model had a higher number of associated SNPs of larger effect sizes. These results suggest that psychometrically defined mental health phenotypes can reflect the dimensions of complex phenotypes better than summation scores, and therefore offer a useful approach in genetic association investigations
An interdisciplinary intervention for older Taiwanese patients after surgery for hip fracture improves health-related quality of life
Abstract Background The effects of intervention programs on health-related quality of life (HRQOL) of patients with hip fracture have not been well studied. We hypothesized that older patients with hip fracture who received our interdisciplinary intervention program would have better HRQOL than those who did not. Methods A randomized experimental design was used. Older patients with hip fracture (N = 162), 60 to 98 years old, from a medical center in northern Taiwan were randomly assigned to an experimental (n = 80) or control (n = 82) group. HRQOL was measured by the SF-36 Taiwan version at 1, 3, 6, and 12 months after discharge. Results The experimental group had significantly better overall outcomes in bodily pain (β = 9.38, p = 0.002), vitality (β = 9.40, p < 0.001), mental health (β = 8.16, p = 0.004), physical function (β = 16.01, p < 0.001), and role physical (β = 22.66, p < 0.001) than the control group at any time point during the first year after discharge. Physical-related health outcomes (physical functioning, role physical, and vitality) had larger treatment effects than emotional/mental- and social functioning-related health outcomes. Conclusions This interdisciplinary intervention program may improve health outcomes of elders with hip fracture. Our results may provide a reference for health care providers in countries using similar programs with Chinese/Taiwanese immigrant populations. Trial registration NCT01052636http://deepblue.lib.umich.edu/bitstream/2027.42/78259/1/1471-2474-11-225.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78259/2/1471-2474-11-225.pdfPeer Reviewe
c-axis preferential orientation of hydroxyapatite accounts for the high wear resistance of the teeth of black carp (Mylopharyngodon piceus)
Biological armors such as mollusk shells have long been recognized and studied for their values in inspiring novel designs of engineering materials with higher toughness and strength. However, no material is invincible and biological armors also have their rivals. In this paper, our attention is focused on the teeth of black carp (Mylopharyngodon piceus) which is a predator of shelled mollusks like snails and mussels. Nanoscratching test on the enameloid, the outermost layer of the teeth, indicates that the natural occlusal surface (OS) has much higher wear resistance compared to the other sections. Subsequent X-ray diffraction analysis reveals that the hydroxyapatite (HAp) crystallites in the vicinity of OS possess c-axis preferential orientation. The superior wear resistance of black carp teeth is attributed to the c-axis preferential orientation of HAp near the OS since the (001) surface of HAp crystal, which is perpendicular to the c-axis, exhibits much better wear resistance compared to the other surfaces as demonstrated by the molecular dynamics simulation. Our results not only shed light on the origin of the good wear resistance exhibited by the black carp teeth but are of great value to the design of engineering materials with better abrasion resistance
Procedure to determine the impact of the surface film resistance on the hygric properties of composite clay/fibre plasters
International audienc
Observation of CR Anisotropy with ARGO-YBJ
The measurement of the anisotropies of cosmic ray arrival direction provides
important informations on the propagation mechanisms and on the identification
of their sources. In this paper we report the observation of anisotropy regions
at different angular scales. In particular, the observation of a possible
anisotropy on scales between 10 and 30
suggests the presence of unknown features of the magnetic fields the charged
cosmic rays propagate through, as well as potential contributions of nearby
sources to the total flux of cosmic rays. Evidence of new weaker few-degree
excesses throughout the sky region R.A. is
reported for the first time.Comment: Talk given at 12th TAUP Conference 2011, 5-9 September 2011, Munich,
German
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