Development of code evaluation criteria for assessing predictive capability and performance

Computational Fluid Dynamics (CFD), because of its unique ability to predict complex three-dimensional flows, is being applied with increasing frequency in the aerospace industry. Currently, no consistent code validation procedure is applied within the industry. Such a procedure is needed to increase confidence in CFD and reduce risk in the use of these codes as a design and analysis tool. This final contract report defines classifications for three levels of code validation, directly relating the use of CFD codes to the engineering design cycle. Evaluation criteria by which codes are measured and classified are recommended and discussed. Criteria for selecting experimental data against which CFD results can be compared are outlined. A four phase CFD code validation procedure is described in detail. Finally, the code validation procedure is demonstrated through application of the REACT CFD code to a series of cases culminating in a code to data comparison on the Space Shuttle Main Engine High Pressure Fuel Turbopump Impeller

Cryptic MHC Polymorphism Revealed but Not Explained by Selection on the Class IIB Peptide-Binding Region

The immune genes of the major histocompatibility complex (MHC) are characterized by extraordinarily high levels of nucleotide and haplotype diversity. This variation is maintained by pathogen-mediated balancing selection that is operating on the peptide-binding region (PBR). Several recent studies have found, however, that some populations possess large clusters of alleles that are translated into virtually identical proteins. Here, we address the question of how this nucleotide polymorphism is maintained with little or no functional variation for selection to operate on. We investigate circa 750–850 bp of MHC class II DAB genes in four wild populations of the guppy Poecilia reticulata. By sequencing an extended region, we uncovered 40.9% more sequences (alleles), which would have been missed if we had amplified the exon 2 alone. We found evidence of several gene conversion events that may have homogenized sequence variation. This reduces the visible copy number variation (CNV) and can result in a systematic underestimation of the CNV in studies of the MHC and perhaps other multigene families. We then focus on a single cluster, which comprises 27 (of a total of 66) sequences. These sequences are virtually identical and show no signal of selection. We use microsatellites to reconstruct the populations' demography and employ simulations to examine whether so many similar nucleotide sequences can be maintained in the populations. Simulations show that this variation does not behave neutrally. We propose that selection operates outside the PBR, for example, on linked immune genes or on the “sheltered load” that is thought to be associated to the MHC. Future studies on the MHC would benefit from extending the amplicon size to include polymorphisms outside the exon with the PBR. This may capture otherwise cryptic haplotype variation and CNV, and it may help detect other regions in the MHC that are under selection

Material-Specific Investigations of Correlated Electron Systems

We present the results of numerical studies for selected materials with strongly correlated electrons using a combination of the local-density approximation and dynamical mean-field theory (DMFT). For the solution of the DMFT equations a continuous-time quantum Monte-Carlo algorithm was employed. All simulations were performed on the supercomputer HLRB II at the Leibniz Rechenzentrum in Munich. Specifically we have analyzed the pressure induced metal-insulator transitions in Fe2O3 and NiS2, the charge susceptibility of the fluctuating-valence elemental metal Yb, and the spectral properties of a covalent band-insulator model which includes local electronic correlations.Comment: 14 pages, 7 figures, to appear in "High Performance Computing in Science and Engineering, Garching 2009" (Springer

Playing in the dark with online games for girls

Pregnant Rapunzel Emergency is part of a series of online free games aimed at young girls (forhergames.com or babygirlgames.com), where dozens of characters from fairy tales, children’s toys and media feature in recovery settings, such as ‘Barbie flu’. The range of games available to choose from includes not only dressing, varnishing nails or tidying messy rooms, but also rather more troubling options such as extreme makeovers, losing weight, or a plethora of baby showers, cravings, hospital pregnancy checks, births (including caesarean), postnatal ironing, washing and baby care. Taking the online game Pregnant Rapunzel Emergency as an exemplar of a current digital trend, the authors explore the workings of ‘dark digital play’ from a number of perspectives – one by each named author. The game selected has (what may appear to adults) several disturbing features in that the player is invited to treat wounds of the kind of harm that might usually be associated with domestic violence towards women

On snail-borne hippo parasites: do artificial lakes and biological invasions pose a burden on Hippopotamus amphibius?

Background Humans impose a significant pressure on large herbivore populations in Africa through hunting, poaching and habitat destruction. Indirect anthropogenic disturbances such as artificial lake creation and the subsequent introduction of invasive species that alter the ecosystem have been less studied. Still, these events can lead to drastic changes in parasite diversity and transmission. Results In order to document and identify trematode parasites of hippopotami in artificial water systems of Zimbabwe, we applied an integrative taxonomic approach, combining molecular diagnostics and morphometrics on archived and new samples. In doing so, we provide DNA reference sequences of the hippo liver fluke Fasciola nyanzae, enabling us to construct the first complete Fasciola phylogeny. We describe parasite spillback of F. nyanzae by the invasive freshwater snail Pseudosuccinea columella, as a consequence of a cascade of biological invasions in Lake Kariba, one of the biggest artificial lakes in the world. Additionally, we report an unknown stomach fluke of the hippopotamus transmitted by the non-endemic snail Radix aff. plicatula, an Asian snail species that has not been found in Africa before, and the stomach fluke Carmyerius cruciformis transmitted by the native snail Bulinus truncatus. Finally, Biomphalaria pfeifferi and two Bulinus species were found as new snail host records for the poorly documented hippo blood fluke Schistosoma edwardiense. Conclusions Our findings indicate that artificial lakes are breeding grounds for endemic and non-endemic snails that transmit trematode parasites of the common hippopotamus. This has important implications, as existing research links trematode parasite infections combined with other stressors to declining wild herbivore populations. Therefore, we argue that monitoring the anthropogenic impact on parasite transmission should become an integral part of wildlife conservation efforts

A cascade of biological invasions and parasite spillback in man-made Lake Kariba

Parasite spillback, the infection of a non-indigenous organism by a native parasite, is a highly important although understudied component of ecological invasion dynamics. Here, through the first analysis of the parasite fauna of lymnaeid gastropods of Lake Kariba (Zimbabwe). We illustrate how the creation of an artificial lake may lead to a cascade of biological invasions in which an invasive aquatic plant promotes the proliferation of invasive gastropods, which in turn alters the epidemiology of trematodiases of potential medical and veterinary importance. Using a new multiplex Rapid Diagnostic PCR assay, we assessed the prevalence of Fasciola sp. infections in the gastropod populations. Both gastropod hosts and trematode parasites were identified using DNA barcoding. We provide the first record of the invasive North-American gastropod Pseudosuccinea columella in Lake Kariba. This species was found at 14 out of 16 sampled sites and its abundance was strongly positively correlated with the abundance of the invasive South-American water hyacinth (Eichhornia crassipes). About 65% of the P. columella specimens analysed were infected with a hitherto unknown Fasciola species. Phylogenetic analyses indicate close affinity to Fasciola hepatica and F. gigantica, which cause fasciolosis, an important liver disease affecting both ruminants and humans. In addition, another non-native Lymnaeid species was found: a Radix sp. that clustered closely with a Vietnamese Radix species. Radix sp. hosted both amphistome and Fasciola trematodes. By linking an invasion cascade and parasite spillback, this study shows how both processes can act in combination to lead to potentially important epidemiological changes