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

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 $Mm$ plays an important role in determining the properties of the relaxation of the perturbation. For $Mm << 1$ the relaxation process depends only on the field parameter and does not depend on the spacetime parameters. For $Mm >> 1$, 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 $Q$ 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 $\xi$ and show that a rich spectrum of wave propagation is revealed when $\xi$ 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