Status of ParaDyn: DYNA3D for parallel computing

The evolution of DYNA3D from a vector supercomputer code into a parallel code is reviewed. Current status and target applications, especially those of interest to the Department of Defense

Hybrid Inflatable Pressure Vessel

Figure 1 shows a prototype of a large pressure vessel under development for eventual use as a habitable module for long spaceflight (e.g., for transporting humans to Mars). The vessel is a hybrid that comprises an inflatable shell attached to a rigid central structural core. The inflatable shell is, itself, a hybrid that comprises (1) a pressure bladder restrained against expansion by (2) a web of straps made from high-strength polymeric fabrics. On Earth, pressure vessels like this could be used, for example, as portable habitats that could be set up quickly in remote locations, portable hyperbaric chambers for treatment of decompression sickness, or flotation devices for offshore platforms. In addition, some aspects of the design of the fabric straps could be adapted to such other items as lifting straps, parachute straps, and automotive safety belts. Figure 2 depicts selected aspects of the design of a vessel of this type with a toroidal configuration. The bladder serves as an impermeable layer to keep air within the pressure vessel and, for this purpose, is sealed to the central structural core. The web includes longitudinal and circumferential straps. To help maintain the proper shape upon inflation after storage, longitudinal and circumferential straps are indexed together at several of their intersections. Because the web is not required to provide a pressure seal and the bladder is not required to sustain structural loads, the bladder and the web can be optimized for their respective functions. Thus, the bladder can be sealed directly to the rigid core without having to include the web in the seal substructure, and the web can be designed for strength. The ends of the longitudinal straps are attached to the ends of the rigid structural core by means of clevises. Each clevis pin is surrounded by a roller, around which a longitudinal strap is wrapped to form a lap seam with itself. The roller is of a large diameter chosen to reduce bending of the fibers in the strap. The roller also serves to equalize the load in the portions of the strap on both sides of the clevis pin. The lap seam is formed near the clevis by use of a tapered diamond stitch: This stitch is designed specifically to allow fibers in the stitch and strap to relax under load in such a manner that the load becomes more nearly evenly distributed among all fibers in the stitch region. Thus, the tapered diamond stitch prevents load concentrations that could cause premature failure of the strap and thereby increases the strength of the strap/structural-core joint. The lap seam can be rated at >90 percent of the strength of the strap material

The principles of tomorrow's university

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility. In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled "Imagining Tomorrow's University." Workshop attendees were charged with launching a new dialog around open research – the current status, opportunities for advancement, and challenges that limit sharing. The workshop examined how the internet-enabled research world has changed, and how universities need to change to adapt commensurately, aiming to understand how universities can and should make themselves competitive and attract the best students, staff, and faculty in this new world. During the workshop, the participants re-imagined scholarship, education, and institutions for an open, networked era, to uncover new opportunities for universities to create value and serve society. They expressed the results of these deliberations as a set of 22 principles of tomorrow's university across six areas: credit and attribution, communities, outreach and engagement, education, preservation and reproducibility, and technologies. Activities that follow on from workshop results take one of three forms. First, since the workshop, a number of workshop authors have further developed and published their white papers to make their reflections and recommendations more concrete. These authors are also conducting efforts to implement these ideas, and to make changes in the university system. Second, we plan to organise a follow-up workshop that focuses on how these principles could be implemented. Third, we believe that the outcomes of this workshop support and are connected with recent theoretical work on the position and future of open knowledge institutions

Population structure and linkage disequilibrium unravelled in tetraploid potato

Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP® and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)—reported for the first time for tetraploid potato—was observed up to approximately 5 cM using r2 higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities

Insights into the Musa genome: Syntenic relationships to rice and between Musa species

<p>Abstract</p> <p>Background</p> <p><it>Musa </it>species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning <it>Musa </it>genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of <it>Musa </it>genomic sequence have been conducted. This study compares genomic sequence in two <it>Musa </it>species with orthologous regions in the rice genome.</p> <p>Results</p> <p>We produced 1.4 Mb of <it>Musa </it>sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for <it>Musa</it>-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the <it>Musa </it>lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from <it>M. acuminata </it>and <it>M. balbisiana </it>revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya.</p> <p>Conclusion</p> <p>These results point to the utility of comparative analyses between distantly-related monocot species such as rice and <it>Musa </it>for improving our understanding of monocot genome evolution. Sequencing the genome of <it>M. acuminata </it>would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated <it>Musa </it>polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.</p