Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa

HCV genotype 4 is prevalent in many African countries, yet little is known about the genotype׳s epidemic history on the continent. We present a comprehensive study of the molecular epidemiology of genotype 4. To address the deficit of data from the Democratic Republic of the Congo (DRC) we PCR amplified 60 new HCV isolates from the DRC, resulting in 33 core- and 48 NS5B-region sequences. Our data, together with genotype 4 database sequences, were analysed using Bayesian phylogenetic approaches. We find three well-supported intra-genotypic lineages and estimate that the genotype 4 common ancestor existed around 1733 (1650-1805). We show that genotype 4 originated in central Africa and that multiple lineages have been exported to north Africa since ~1850, including subtype 4a which dominates the epidemic in Egypt. We speculate on the causes of the historical intra-continental spread of genotype 4, including population movements during World War 2

Numerical studies on the approximation of horizontal diffusion using sigma coordinate system

The original publication can be found at www.springerlink.comIn this paper, horizontal diffusion using sigma coordinates was examined numerically. To transform the horizontal diffusion equation, the chain rule was applied twice resulting in extra terms that are cumbersome to treat computationally. Two publisheddirect modifications to the transformed equation were chosen, and numerical solutions using these modified equations are compared to those using the fully transformed equation. Our numerical studies have shown that only the fully transformed equation produces realistic solutions.Jong Wook Lee, Michael D. Teubner, John B. Nixon and Yong-Sik Ch

The parallelization of the Princeton Ocean Model

In this paper we present the parallel implementation of the Princeton Ocean Model (POM) using message passing. Domain decomposition techniques are used for the horizontal discretization whereas in the vertical direction each column per grid point is computed. The required interprocessor communication was implemented on the PVM message passing library. Three different data partitioning schemes are studied. It is found that the checkerboard partitioning produces the best results when the number of processors becomes larger than 15, otherwise row block striped partitioning is to be preferred. © Springer-Verlag Berlin Heidelberg 1999