28,856 research outputs found
A Kolmogorov-Smirnov test for the molecular clock on Bayesian ensembles of phylogenies
Divergence date estimates are central to understand evolutionary processes
and depend, in the case of molecular phylogenies, on tests of molecular clocks.
Here we propose two non-parametric tests of strict and relaxed molecular clocks
built upon a framework that uses the empirical cumulative distribution (ECD) of
branch lengths obtained from an ensemble of Bayesian trees and well known
non-parametric (one-sample and two-sample) Kolmogorov-Smirnov (KS)
goodness-of-fit test. In the strict clock case, the method consists in using
the one-sample Kolmogorov-Smirnov (KS) test to directly test if the phylogeny
is clock-like, in other words, if it follows a Poisson law. The ECD is computed
from the discretized branch lengths and the parameter of the expected
Poisson distribution is calculated as the average branch length over the
ensemble of trees. To compensate for the auto-correlation in the ensemble of
trees and pseudo-replication we take advantage of thinning and effective sample
size, two features provided by Bayesian inference MCMC samplers. Finally, it is
observed that tree topologies with very long or very short branches lead to
Poisson mixtures and in this case we propose the use of the two-sample KS test
with samples from two continuous branch length distributions, one obtained from
an ensemble of clock-constrained trees and the other from an ensemble of
unconstrained trees. Moreover, in this second form the test can also be applied
to test for relaxed clock models. The use of a statistically equivalent
ensemble of phylogenies to obtain the branch lengths ECD, instead of one
consensus tree, yields considerable reduction of the effects of small sample
size and provides again of power.Comment: 14 pages, 9 figures, 8 tables. Minor revision, additin of a new
example and new title. Software:
https://github.com/FernandoMarcon/PKS_Test.gi
MCMC Bayesian Estimation in FIEGARCH Models
Bayesian inference for fractionally integrated exponential generalized
autoregressive conditional heteroskedastic (FIEGARCH) models using Markov Chain
Monte Carlo (MCMC) methods is described. A simulation study is presented to
access the performance of the procedure, under the presence of long-memory in
the volatility. Samples from FIEGARCH processes are obtained upon considering
the generalized error distribution (GED) for the innovation process. Different
values for the tail-thickness parameter \nu are considered covering both
scenarios, innovation processes with lighter (\nu2) tails
than the Gaussian distribution (\nu=2). A sensitivity analysis is performed by
considering different prior density functions and by integrating (or not) the
knowledge on the true parameter values to select the hyperparameter values
The Digitized Second Palomar Observatory Sky Survey (DPOSS) II: Photometric Calibration
We present the photometric calibration technique for the Digitized Second
Palomar Observatory Sky Survey (DPOSS), used to create seamless catalogs of
calibrated objects over large sky areas. After applying a correction for
telescope vignetting, the extensive plate overlap regions are used to transform
sets of plates onto a common instrumental photometric system. Photometric
transformations to the Gunn gri system for each plate, for stars and galaxies,
are derived using these contiguous stitched areas and an extensive CCD imaging
library obtained for this purpose. We discuss the resulting photometric
accuracy, survey depth, and possible systematic errors.Comment: 25 pages, 13 figures. Accepted to AJ. Some figures shrunk or missing
to limit file size; the full paper is available at
http://www.sdss.jhu.edu/~rrg/science/papers/photometrypaper.ps.g
Effective transport barriers in nontwist systems
In fluids and plasmas with zonal flow reversed shear, a peculiar kind of transport barrier appears in the shearless region, one that is associated with a proper route of transition to chaos. These barriers have been identified in symplectic nontwist maps that model such zonal flows. We use the so-called standard nontwist map, a paradigmatic example of nontwist systems, to analyze the parameter dependence of the transport through a broken shearless barrier. On varying a proper control parameter, we identify the onset of structures with high stickiness that give rise to an effective barrier near the broken shearless curve. Moreover, we show how these stickiness structures, and the concomitant transport reduction in the shearless region, are determined by a homoclinic tangle of the remaining dominant twin island chains. We use the finite-time rotation number, a recently proposed diagnostic, to identify transport barriers that separate different regions of stickiness. The identified barriers are comparable to those obtained by using finite-time Lyapunov exponents.FAPESPCNPqCAPESMCT/CNEN (Rede Nacional de Fusao)Fundacao AraucariaUS Department of Energy DE-FG05-80ET-53088Physic
Phase synchronization of coupled bursting neurons and the generalized Kuramoto model
Bursting neurons fire rapid sequences of action potential spikes followed by
a quiescent period. The basic dynamical mechanism of bursting is the slow
currents that modulate a fast spiking activity caused by rapid ionic currents.
Minimal models of bursting neurons must include both effects. We considered one
of these models and its relation with a generalized Kuramoto model, thanks to
the definition of a geometrical phase for bursting and a corresponding
frequency. We considered neuronal networks with different connection topologies
and investigated the transition from a non-synchronized to a partially
phase-synchronized state as the coupling strength is varied. The numerically
determined critical coupling strength value for this transition to occur is
compared with theoretical results valid for the generalized Kuramoto model.Comment: 31 pages, 5 figure
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