Measuring helical FCG voltage with an electric field antenna

A method of measuring the voltage produced by a helical explosive flux compression generator using a remote electric field antenna is described in detail. The diagnostic has been successfully implemented on several experiments. Measured data from the diagnostic compare favorably with voltages predicted using the code CAGEN, validating our predictive modeling tools. The measured data is important to understanding generator performance, and is measured with a low-risk, minimally intrusive approach

OURCOAST, A European initiative to support exchange of experiences and best practices in coastal management

OURCOAST is a three-year initiative commissioned by the General Directorate (DG) Environment of the European Commission to support and ensure the exchange of experiences and best practices in coastal management. This initiative was made possible thanks to the European Parliament that voted a dedicated resource for this purpose into the EU budget in 2008. The European Commission has intensively worked on developing and promoting Integrated Coastal Zone Management (ICZM) principles. More recently, an evaluation on ICZM in Europe concluded that although there is still great willingness of Authorities at national, regional and locals levels to implement ICZM, there is still a number of fundamental obstacles that need to be overcome. Some of these constraints are reflected in the lack of proper means for exchange of experiences and access to outstanding studies and best practices being produced in Coastal Member States, at different authority levels. The overall goal of OURCOAST is to create an information base and groundwork that will further support and promote the implementation of ICZM in coastal areas by the establishment of long-lasting information mechanisms that will promote the sharing of experiences and practices and the accomplishments of the project. The project will produce numerous studies of public interest, such as, a comparative analysis of ICZM and marine planning experiences, a state-of-the-art report on EU policies and legislation for ICZM and marine planning. Guidance for future integrated and marine planning projects, and policy recommendations will be formulated for future development of ICZM in Europe. The final results will be presented at an international stakeholders conference in Autumn 2011. The OURCOAST initiative aims to establish a multi-lingual database of Europe-wide ICZM practices in the form of case studies that will be freely accessible through the EUROPA ­ European Commission official web-site to the broad coastal and marine communities and to provide practical guidance to all those who are seeking sustainable solutions to their coastal management practices. Following these challenges, this paper aims to provide more insight and details about the progress activities and various components of the OURCOAST initiative, which is being implemented by a consortium led by ARCADIS and it's subcontractor the Coastal & Marine Union (EUCC). The implementation has started in January 2009 and will end in December 2011. The data collection, website development as well as the analysis are currently being carried out

Radiatively inefficient MHD accretion-ejection structures

We present magnetohydrodynamic simulations of a resistive accretion disk continuously launching transmagnetosonic, collimated jets. We time-evolve the full set of magnetohydrodynamic equations, but neglect radiative losses in the energetics (radiatively inefficient). Our calculations demonstrate that a jet is self-consistently produced by the interaction of an accretion disk with an open, initially bent large-scale magnetic field. A constant fraction of heated disk material is launched in the inner equipartition disk regions, leading to the formation of a hot corona and a bright collimated, super-fastmagnetosonic jet. We illustrate the complete dynamics of the ``hot'' near steady-state outflow (where thermal pressure $\simeq$ magnetic pressure) by showing force balance, energy budget and current circuits. The evolution to this near stationary state is analyzed in terms of the temporal variation of energy fluxes controlling the energetics of the accretion disk. We find that unlike advection-dominated accretion flow, the energy released by accretion is mainly sent into the jet rather than transformed into disk enthalpy. These magnetized, radiatively inefficient accretion-ejection structures can account for under-luminous thin disks supporting bright fast collimated jets as seen in many systems displaying jets (for instance M87).Comment: Astrophysical Journal (in press). Figures are missing due to file size restrictions. To have the complete paper just click on http://www-laog.obs.ujf-grenoble.fr/~fcasse/MS56638.pd

Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e25386, doi:10.1371/journal.pone.0025386.Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.Funding has been provided by the NSF Microbial Observatories Program (KJE, DE), NSF’s Science and Technology Program, by the Gordon and Betty Moore Foundation (KJE), the College of Letters, Arts, and Sciences at the University of Southern California (KJE), and by the NASA Astrobiology Institute (KJE, DE). Advanced Light Source analyses at the Lawrence Berkeley National Lab are supported by the Office of Science, Basic Energy Sciences, Division of Materials Science of the United States Department of Energy (DE-AC02-05CH11231)

Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

<p>Abstract</p> <p>Background</p> <p>Polymerase chain reaction (PCR) is used in directed sequencing for the discovery of novel polymorphisms. As the first step in PCR directed sequencing, effective PCR primer design is crucial for obtaining high-quality sequence data for target regions. Since current computational primer design tools are not fully tuned with stable underlying laboratory protocols, researchers may still be forced to iteratively optimize protocols for failed amplifications after the primers have been ordered. Furthermore, potentially identifiable factors which contribute to PCR failures have yet to be elucidated. This inefficient approach to primer design is further intensified in a high-throughput laboratory, where hundreds of genes may be targeted in one experiment.</p> <p>Results</p> <p>We have developed a fully integrated computational PCR primer design pipeline that plays a key role in our high-throughput directed sequencing pipeline. Investigators may specify target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. In the process of improving our sequencing success rate, which currently exceeds 95% for exons, we have discovered novel and accurate computational methods capable of identifying primers that may lead to PCR failures. We reveal the laboratory protocols and their associated, empirically determined computational parameters, as well as describe the novel computational methods which may benefit others in future primer design research.</p> <p>Conclusion</p> <p>The high-throughput PCR primer design pipeline has been very successful in providing the basis for high-quality directed sequencing results and for minimizing costs associated with labor and reprocessing. The modular architecture of the primer design software has made it possible to readily integrate additional primer critique tests based on iterative feedback from the laboratory. As a result, the primer design software, coupled with the laboratory protocols, serves as a powerful tool for low and high-throughput primer design to enable successful directed sequencing.</p

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix

Explosive pulsed power experimental capability at LLNL

Abstract not provide

The effect of LRRK2 loss-of-function variants in humans

Analysis of large genomic datasets, including gnomAD, reveals that partial LRRK2 loss of function is not strongly associated with diseases, serving as an example of how human genetics can be leveraged for target validation in drug discovery. Human genetic variants predicted to cause loss-of-function of protein-coding genes (pLoF variants) provide natural in vivo models of human gene inactivation and can be valuable indicators of gene function and the potential toxicity of therapeutic inhibitors targeting these genes(1,2). Gain-of-kinase-function variants in LRRK2 are known to significantly increase the risk of Parkinson's disease(3,4), suggesting that inhibition of LRRK2 kinase activity is a promising therapeutic strategy. While preclinical studies in model organisms have raised some on-target toxicity concerns(5-8), the biological consequences of LRRK2 inhibition have not been well characterized in humans. Here, we systematically analyze pLoF variants in LRRK2 observed across 141,456 individuals sequenced in the Genome Aggregation Database (gnomAD)(9), 49,960 exome-sequenced individuals from the UK Biobank and over 4 million participants in the 23andMe genotyped dataset. After stringent variant curation, we identify 1,455 individuals with high-confidence pLoF variants in LRRK2. Experimental validation of three variants, combined with previous work(10), confirmed reduced protein levels in 82.5% of our cohort. We show that heterozygous pLoF variants in LRRK2 reduce LRRK2 protein levels but that these are not strongly associated with any specific phenotype or disease state. Our results demonstrate the value of large-scale genomic databases and phenotyping of human loss-of-function carriers for target validation in drug discovery.Peer reviewe

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead