638 research outputs found
Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants
Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brad
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Challenges of ultra large scale integration of biomedical computing systems
The NCRI Informatics Initiative is overseeing the implementation of an informatics
framework for the UK cancer research community. The framework advocates an integrated
multidisciplinary method of working between scientific and medical communities. Key to this
process is community adoption of high quality acquisition, storage, sharing and integration of
diverse data elements to improve knowledge of the causes, prevention and treatment of
cancer. The integration of the complex data and meta-data used by these multiple
communities is a significant challenge and there are technical, resource-based and
sociological issues to be addressed. In this paper we review progress aimed at establishing
the framework and outline key challenges in ultra large scale integration of biomedical
computing systems
Metric Perturbation Approach to Gravitational Waves in Isotropic Cosmologies
Gravitational waves in isotropic cosmologies were recently studied using the
gauge-invariant approach of Ellis-Bruni. We now construct the linearised metric
perturbations of the background Robertson-Walker space-time which reproduce the
results obtained in that study. The analysis carried out here also facilitates
an easy comparison with Bardeen.Comment: 29 pages, Latex file, accepted for publication in Physical Review
Multiple GF-1 binding sites flank the erythroid specific transcription unit of the human carbonic anhydrase I gene
AbstractSix potential GF-1 sites which bind an erythroid factor are present in the 5' and 3' regions flanking the erythroid-speciflc transcription unit of the human carbonic anhydrase 1 (HCAI) gene. When two of these sites are placed upstream of a minimal eukaryotic promoter they confer upregulated expression in erythroid over non-erythroid cells. The presence of the erythroid factor in TPA-treated HEL cells in which the level of HCAI transcript has greatly decreased and in non-HCAI-expressing K562 cells suggests that in these cases the presence of the factor is not sufficient for HCAI expression
Numerical simulation of the massive scalar field evolution in the Reissner-Nordstr\"{o}m black hole background
We studied the massive scalar wave propagation in the background of
Reissner-Nordstr\"{o}m black hole by using numerical simulations. We learned
that the value plays an important role in determining the properties of
the relaxation of the perturbation. For the relaxation process
depends only on the field parameter and does not depend on the spacetime
parameters. For , the dependence of the relaxation on the black hole
parameters appears. The bigger mass of the black hole, the faster the
perturbation decays. The difference of the relaxation process caused by the
black hole charge has also been exhibited.Comment: Accepted for publication in Phys. Rev.
Scalar wave propagation in topological black hole backgrounds
We consider the evolution of a scalar field coupled to curvature in
topological black hole spacetimes. We solve numerically the scalar wave
equation with different curvature-coupling constant and show that a rich
spectrum of wave propagation is revealed when is introduced. Relations
between quasinormal modes and the size of different topological black holes
have also been investigated.Comment: 26 pages, 18 figure
Strong Phase Separation in a Model of Sedimenting Lattices
We study the steady state resulting from instabilities in crystals driven
through a dissipative medium, for instance, a colloidal crystal which is
steadily sedimenting through a viscous fluid. The problem involves two coupled
fields, the density and the tilt; the latter describes the orientation of the
mass tensor with respect to the driving field. We map the problem to a 1-d
lattice model with two coupled species of spins evolving through conserved
dynamics. In the steady state of this model each of the two species shows
macroscopic phase separation. This phase separation is robust and survives at
all temperatures or noise levels--- hence the term Strong Phase Separation.
This sort of phase separation can be understood in terms of barriers to
remixing which grow with system size and result in a logarithmically slow
approach to the steady state. In a particular symmetric limit, it is shown that
the condition of detailed balance holds with a Hamiltonian which has
infinite-ranged interactions, even though the initial model has only local
dynamics. The long-ranged character of the interactions is responsible for
phase separation, and for the fact that it persists at all temperatures.
Possible experimental tests of the phenomenon are discussed.Comment: To appear in Phys Rev E (1 January 2000), 16 pages, RevTex, uses
epsf, three ps figure
Stochastic model for the dynamics of interacting Brownian particles
Using the scheme of mesoscopic nonequilibrium thermodynamics, we construct
the one- and two- particle Fokker-Planck equations for a system of interacting
Brownian particles. By means of these equations we derive the corresponding
balance equations. We obtain expressions for the heat flux and the pressure
tensor which enable one to describe the kinetic and potential energy
interchange of the particles with the heat bath. Through the momentum balance
we analyze in particular the diffusion regime to obtain the collective
diffusion coefficient in terms of the hydrodynamic and the effective forces
acting on the Brownian particles.Comment: latex fil
Field propagation in de Sitter black holes
We present an exhaustive analysis of scalar, electromagnetic and
gravitational perturbations in the background of Schwarzchild-de Sitter and
Reissner-Nordstrom-de Sitter spacetimes. The field propagation is considered by
means of a semi-analytical (WKB) approach and two numerical schemes: the
characteristic and general initial value integrations. The results are compared
near the extreme cosmological constant regime, where analytical results are
presented. A unifying picture is established for the dynamics of different spin
fields.Comment: 15 pages, 16 figures, published versio
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