531 research outputs found
The three species monomer-monomer model: A mean-field analysis and Monte Carlo study
We study the phase diagram and critical behavior of a one dimensional three
species monomer-monomer surface reaction model. Static Monte Carlo simulations
show a phase diagram consisting of a reactive steady state bordered by three
equivalent unreactive phases where the surface is saturated with one monomer
species. The transitions from the reactive to saturated phases are all
continuous, while the transitions between poisoned phases are first-order, with
bicritical points where the reactive phase meets two poisoned phases. A
mean-field cluster analysis predicts all of the qualitative features of the
phase diagram only when correlations up to triplets of adjacent sites are
included. Dynamic Monte Carlo simulations show that the transition from the
reactive to a saturated phase show critical behavior in the directed
percolation universality class, while the bicritical point shows critical
behavior in the even branching annihilating random walk class. The crossover
from bicritical to critical behavior is also studied.Comment: 16 pages using RevTeX, plus 10 figures. Uses psfig.st
Simple deterministic dynamical systems with fractal diffusion coefficients
We analyze a simple model of deterministic diffusion. The model consists of a
one-dimensional periodic array of scatterers in which point particles move from
cell to cell as defined by a piecewise linear map. The microscopic chaotic
scattering process of the map can be changed by a control parameter. This
induces a parameter dependence for the macroscopic diffusion coefficient. We
calculate the diffusion coefficent and the largest eigenmodes of the system by
using Markov partitions and by solving the eigenvalue problems of respective
topological transition matrices. For different boundary conditions we find that
the largest eigenmodes of the map match to the ones of the simple
phenomenological diffusion equation. Our main result is that the difffusion
coefficient exhibits a fractal structure by varying the system parameter. To
understand the origin of this fractal structure, we give qualitative and
quantitative arguments. These arguments relate the sequence of oscillations in
the strength of the parameter-dependent diffusion coefficient to the
microscopic coupling of the single scatterers which changes by varying the
control parameter.Comment: 28 pages (revtex), 12 figures (postscript), submitted to Phys. Rev.
Color-to-Grayscale: Does the Method Matter in Image Recognition?
In image recognition it is often assumed the method used to convert color images to grayscale has little impact on recognition performance. We compare thirteen different grayscale algorithms with four types of image descriptors and demonstrate that this assumption is wrong: not all color-to-grayscale algorithms work equally well, even when using descriptors that are robust to changes in illumination. These methods are tested using a modern descriptor-based image recognition framework, on face, object, and texture datasets, with relatively few training instances. We identify a simple method that generally works best for face and object recognition, and two that work well for recognizing textures
Everyday characterizations of translational research:Researchers’ own use of terminology and models in medical research and practice
The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey
The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic
data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data
release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median
z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar
spectra, along with the data presented in previous data releases. These spectra
were obtained with the new BOSS spectrograph and were taken between 2009
December and 2011 July. In addition, the stellar parameters pipeline, which
determines radial velocities, surface temperatures, surface gravities, and
metallicities of stars, has been updated and refined with improvements in
temperature estimates for stars with T_eff<5000 K and in metallicity estimates
for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars
presented in DR8, including stars from SDSS-I and II, as well as those observed
as part of the SDSS-III Sloan Extension for Galactic Understanding and
Exploration-2 (SEGUE-2).
The astrometry error introduced in the DR8 imaging catalogs has been
corrected in the DR9 data products. The next data release for SDSS-III will be
in Summer 2013, which will present the first data from the Apache Point
Observatory Galactic Evolution Experiment (APOGEE) along with another year of
data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at
http://www.sdss3.org/dr
Integrative pathway genomics of lung function and airflow obstruction
Chronic respiratory disorders are important contributors to the global burden of disease. Genome-wide association studies (GWASs) of lung function measures have identified several trait-associated loci, but explain only a modest portion of the phenotypic variability. We postulated that integrating pathway-based methods with GWASs of pulmonary function and airflow obstruction would identify a broader repertoire of genes and processes influencing these traits. We performed two independent GWASs of lung function and applied gene set enrichment analysis to one of the studies and validated the results using the second GWAS. We identified 131 significantly enriched gene sets associated with lung function and clustered them into larger biological modules involved in diverse processes including development, immunity, cell signaling, proliferation and arachidonic acid. We found that enrichment of gene sets was not driven by GWAS-significant variants or loci, but instead by those with less stringent association P-values. Next, we applied pathway enrichment analysis to a meta-analyzed GWAS of airflow obstruction. We identified several biologic modules that functionally overlapped with those associated with pulmonary function. However, differences were also noted, including enrichment of extracellular matrix (ECM) processes specifically in the airflow obstruction study. Network analysis of the ECM module implicated a candidate gene, matrix metalloproteinase 10 (MMP10), as a putative disease target. We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema. By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung diseas
Interplay of Nkx3.2, Sox9 and Pax3 Regulates Chondrogenic Differentiation of Muscle Progenitor Cells
Muscle satellite cells make up a stem cell population that is capable of differentiating into myocytes and contributing to muscle regeneration upon injury. In this work we investigate the mechanism by which these muscle progenitor cells adopt an alternative cell fate, the cartilage fate. We show that chick muscle satellite cells that normally would undergo myogenesis can be converted to express cartilage matrix proteins in vitro when cultured in chondrogenic medium containing TGFß3 or BMP2. In the meantime, the myogenic program is repressed, suggesting that muscle satellite cells have undergone chondrogenic differentiation. Furthermore, ectopic expression of the myogenic factor Pax3 prevents chondrogenesis in these cells, while chondrogenic factors Nkx3.2 and Sox9 act downstream of TGFß or BMP2 to promote this cell fate transition. We found that Nkx3.2 and Sox9 repress the activity of the Pax3 promoter and that Nkx3.2 acts as a transcriptional repressor in this process. Importantly, a reverse function mutant of Nkx3.2 blocks the ability of Sox9 to both inhibit myogenesis and induce chondrogenesis, suggesting that Nkx3.2 is required for Sox9 to promote chondrogenic differentiation in satellite cells. Finally, we found that in an in vivo mouse model of fracture healing where muscle progenitor cells were lineage-traced, Nkx3.2 and Sox9 are significantly upregulated while Pax3 is significantly downregulated in the muscle progenitor cells that give rise to chondrocytes during fracture repair. Thus our in vitro and in vivo analyses suggest that the balance of Pax3, Nkx3.2 and Sox9 may act as a molecular switch during the chondrogenic differentiation of muscle progenitor cells, which may be important for fracture healing
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