Validating the FLASH Code: Vortex-Dominated Flows

As a component of the Flash Center's validation program, we compare FLASH simulation results with experimental results from Los Alamos National Laboratory. The flow of interest involves the lateral interaction between a planar Ma=1.2 shock wave with a cylinder of gaseous sulfur hexafluoride (SF_6) in air, and in particular the development of primary and secondary instabilities after the passage of the shock. While the overall evolution of the flow is comparable in the simulations and experiments, small-scale features are difficult to match. We focus on the sensitivity of numerical results to simulation parameters.Comment: 10 pages, 5 figures, presented at the 5th International Conference on High Energy Laboratory Astrophysics, Tucson, AZ, March 10-13, 200

Preferential magma extraction from K-and metal-enriched source regions in the crust

Abstract We compare melting of potassic alteration zones in metamorphosed gold deposits with that of unaltered rocks of the same protolith to examine their relative contributions to crust-derived magmas and to investigate the implications for ore genesis. Potassic hydrothermal alteration, at the crustal levels where orogenic gold deposits form, stabilizes a higher proportion of muscovite and biotite than is possible in unaltered rocks at high metamorphic grades. Because these micas contain water, they control the melt fraction generated through dehydration melting in that a greater proportion of micas permits more extensive melting. Orogenic gold deposits, in which mineralization is typically encapsulated by potassic alteration, form at deep-enough crustal levels to survive repeated tectonic activity, which can lead to their being metamorphosed. In the vicinity of this metamorphosed gold mineralization, the greatest proportion of felsic melt is generated in the more metal-and sulfur-rich rocks because of the associated potassic alteration. Ore minerals dissolve and are physically incorporated into the resulting felsic melt, which thereby becomes metal-and sulfur-enriched. Since melt fraction is the dominant control on strain partitioning and melt mobilization, increased melting in K-altered mineralized rocks implies that these sites will be the first to experience melt escape and will continue to be the focus of melt escape during ongoing metamorphism. This strain partitioning promotes shear zone development, and once shearing is localized to K-altered mineralized domains, it may attract external magma, allowing extension and linking with nearby active shear zones. In this way, mineralized zones may connect to a regional network of magma transfer, allowing metal enrichment of migrating magmas. Terrains that underwent widespread K alteration associated with mid-crustal gold enrichment are likely, when metamorphosed, to produce significant volumes of reduced, relatively metal-and sulfur-enriched felsic magma. The ages and relative tectonic preservation potential of different K alteration-associated ore types implies that Au, Ag, As, Sb, Bi, Te, and W may be recycled within the crust through this mechanism, whereas Cu and Mo are unlikely to be recycled and require mantle sourcing to form new intrusion-related ores. Silicate melt derived from preexisting zones of gold enrichment in the lower crust may contribute significantly to the metal budget of intrusion-related gold systems, and possibly some gold-rich porphyry deposits

Effects of numerical methods on comparisons between experiments and simulations of shock-accelerated mixing.

We consider the detailed structures of mixing flows for Richtmyer-Meshkov experiments of Prestridge et al. [PRE 00] and Tomkins et al. [TOM 01] and examine the most recent measurements from the experimental apparatus. Numerical simulations of these experiments are performed with three different versions of high resolution finite volume Godunov methods. We compare experimental data with simulations for configurations of one and two diffuse cylinders of SF{sub 6} in air using integral measures as well as fractal analysis and continuous wavelet transforms. The details of the initial conditions have a significant effect on the computed results, especially in the case of the double cylinder. Additionally, these comparisons reveal sensitive dependence of the computed solution on the numerical method

A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure

Background: Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome.Results: Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella.Conclusions: When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution

A Single Molecule Scaffold for the Maize Genome

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars

Psychosocial impact of undergoing prostate cancer screening for men with BRCA1 or BRCA2 mutations.

OBJECTIVES: To report the baseline results of a longitudinal psychosocial study that forms part of the IMPACT study, a multi-national investigation of targeted prostate cancer (PCa) screening among men with a known pathogenic germline mutation in the BRCA1 or BRCA2 genes. PARTICPANTS AND METHODS: Men enrolled in the IMPACT study were invited to complete a questionnaire at collaborating sites prior to each annual screening visit. The questionnaire included sociodemographic characteristics and the following measures: the Hospital Anxiety and Depression Scale (HADS), Impact of Event Scale (IES), 36-item short-form health survey (SF-36), Memorial Anxiety Scale for Prostate Cancer, Cancer Worry Scale-Revised, risk perception and knowledge. The results of the baseline questionnaire are presented. RESULTS: A total of 432 men completed questionnaires: 98 and 160 had mutations in BRCA1 and BRCA2 genes, respectively, and 174 were controls (familial mutation negative). Participants' perception of PCa risk was influenced by genetic status. Knowledge levels were high and unrelated to genetic status. Mean scores for the HADS and SF-36 were within reported general population norms and mean IES scores were within normal range. IES mean intrusion and avoidance scores were significantly higher in BRCA1/BRCA2 carriers than in controls and were higher in men with increased PCa risk perception. At the multivariate level, risk perception contributed more significantly to variance in IES scores than genetic status. CONCLUSION: This is the first study to report the psychosocial profile of men with BRCA1/BRCA2 mutations undergoing PCa screening. No clinically concerning levels of general or cancer-specific distress or poor quality of life were detected in the cohort as a whole. A small subset of participants reported higher levels of distress, suggesting the need for healthcare professionals offering PCa screening to identify these risk factors and offer additional information and support to men seeking PCa screening

Prevalence and architecture of de novo mutations in developmental disorders.

The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year