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Recent progress in genomics and experimental biology has brought exponential growth of the biological information available for computational analysis in public genomics databases. However, applying the potentially enormous scientific value of this information to the understanding of biological systems requires computing and data storage technology of an unprecedented scale. The Grid, with its aggregated and distributed computational and storage infrastructure, offers an ideal platform for high-throughput bioinformatics analysis. To leverage this we have developed the Genome Analysis Research Environment (GNARE)--a scalable computational system for the high-throughput analysis of genomes, which provides an integrated database and computational backend for data-driven bioinformatics applications. GNARE efficiently automates the major steps of genome analysis including acquisition of data from multiple genomic databases; data analysis by a diverse set of bioinformatics tools; and storage of results and annotations. High-throughput computations in GNARE are performed using distributed heterogeneous Grid computing resources such as Grid2003, TeraGrid, and the DOE Science Grid. Multi-step genome analysis workflows involving massive data processing, the use of application-specific tools and algorithms and updating of an integrated database to provide interactive web access to results are all expressed and controlled by a "virtual data" model which transparently maps computational workflows to distributed Grid resources. This paper describes how Grid technologies such as Globus, Condor, and the Gryphyn Virtual Data System were applied in the development of GNARE. It focuses on our approach to Grid resource allocation and to the use of GNARE as a computational framework for the development of bioinformatics applications.
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PMID:GNARE: automated system for high-throughput genome analysis with grid computational backend. 1632 50

The VBI Microbial Database (VMD) is a database system designed to host a range of microbial genome sequences. At present, the database contains genome sequence and annotation data of two plant pathogens Phytophthora sojae and Phytophthora ramorum. With the completion of the draft genome sequences of these pathogens in collaboration with the DOE Joint Genome Institute (JGI), we have created this resource to make the sequences publicly available. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. We used two different statistical methods to validate these gene models, Fickett's and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, we could assign putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum. We created an easy-to-use genome browser to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs. The database is publicly available at http://phytophthora.vbi.vt.edu/.
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PMID:VMD: a community annotation database for oomycetes and microbial genomes. 1638 91

The utilization of hydrogen in fuel-cell powered vehicles is limited by the lack of a safe and effective system for hydrogen storage. At the present time, there is no viable storage technology capable of meeting the DOE targets. Porous metal-organic frameworks (MOFs) are novel and potential candidates for hydrogen storage. Until now it is still not possible to achieve any significant hydrogen storage capacity in MOFs at ambient temperature. Here, we report, for the first time, significant amounts of hydrogen storage in MOF-5 and IRMOF-8 at ambient temperature by using a very simple technique via hydrogen dissociation and spillover. Thus, hydrogen uptakes for MOF-5 and IRMOF-8 can be enhanced by a factor of 3.3 and 3.1, respectively (to nearly 2 wt % at 10 MPa and 298 K). Furthermore, the isotherms are totally reversible. These findings suggest that our technique is suitable for hydrogen storage in a variety of MOF materials because of their similar structures as MOF-5 and IRMOF-8.
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PMID:Significantly enhanced hydrogen storage in metal-organic frameworks via spillover. 1641 55

Radioactive strontium (90Sr) is an important constituent of the complex wastes from past nuclear weapons production and has been stored in underground tanks at U.S. DOE sites (e.g., Hanford, WA). Using bulk and microfocused EXAFS spectroscopy, we examined temporal changes in solid-phase Sr speciation in kaolinite samples reacted for 1-369 d with high-pH, high ionic strength synthetic tank-waste leachate containing Sr(2+) and Cs(+) at 10(-3) mol kg(-1). Analyses of bulk EXAFS spectra showed that Sr initially forms a precipitate by 7 d with a local structure similar to SrCO(3-) (s). At 33 d, microfocused EXAFS of individual particles in one sample revealed a mixture of hydrated and dehydrated Sr associated with neoformed sodalite-type phases. At aging times of 93 d and longer, bulk EXAFS spectra and supporting characterizations indicated nonexchangeable Sr with a local structure consistent with incorporation into increasingly crystalline aluminosilicate particles, particularly sodalite. These experimental studies suggest that irreversible trapping of radionuclides occurs if they are present during the formation and aging of feldspathoid alteration products of local Si-bearing sediment minerals. This may serve as an effective contaminant sequestration mechanism at sites such as Hanford.
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PMID:Strontium speciation during reaction of kaolinite with simulated tank-waste leachate: bulk and microfocused EXAFS analysis. 1668 99

We report herein the fabrication of a simple and price-affordable portable reaction station for use in parallel solution-phase synthesis. This homemade device uses currently available laboratory components and equipment. Specifically designed to fit standard magnetic hotplates/stirrers, it can simultaneously hold up to 24 heated and magnetically stirred glass reactors of both 10 and 50 mL capacities. Glass reactors are connected by flexible 16-gauge metal needles to a central gas manifold equipped with an inlet/outlet for vacuum and inert gases. Reaction temperatures can be optimally varied from -78 ( composite function)C to 150 degrees C. Using a statistical screening DOE method, this parallel array reactor station has been successfully operated to optimize the one-step deprotective O-formylation of a sterically hindered bis-O-tert-butyldiphenylsilyl (O-TBDPS) aromatic diol. The latter transformation was mediated by the Vilsmeier-Haack reagent POCl3.DMF using a range of Lewis acid and metal salt promoters, including their binary combinations.
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PMID:A simple homemade reaction station for use in parallel solution-phase synthesis. Optimization of a regioselective one-step deprotective o-formylation reaction mediated by the Vilsmeier-Haack reagent POCl3.DMF. 1671 Aug 6

The focus of this study was to define the shape and extent of tritium groundwater contamination emanating from a legacy burial ground and to identify vadose zone sources of tritium using helium isotopes (3He and 4He) in soil gas. Helium isotopes were measured in soil-gas samples collected from 70 sampling points around the perimeter and downgradient of a burial ground that contains buried radioactive solid waste. The soil-gas samples were analyzed for helium isotopes using rare gas mass spectrometry. 3He/4He ratios, reported as normalized to the air ratio (RA), were used to locate the tritium groundwater plume emanating from the burial ground. The 3He (excess) suggested that the general location of the tritium source is within the burial ground. This study clearly demonstrated the efficacy of the 3He method for application to similar sites elsewhere within the DOE weapons complex.
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PMID:Measurement of helium isotopes in soil gas as an indicator of tritium groundwater contamination. 1671 88

Research for materials offering efficient hydrogen storage and transport has recently received increased attention. Metal organic frameworks (MOFs) provide one promising group of materials where several recent advances were reported in this direction. In this computational study ab initio methods are employed to study the physisorption of hydrogen on conjugated systems. These systems are used as models for the organic linker within MOFs. Here, we focus on the adsorption sites related to the organic linker with special attention to the edge site, which was only recently reported to exist as the weakest adsorbing site in MOFs. We also investigate chemically modified models of the organic connector that result in enforcing this adsorption site. This may be crucial for improving the uptake properties of these materials to the goal defined by DOE for efficient hydrogen transport materials.
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PMID:Hydrogen physisorption on the organic linker in metal organic frameworks: ab initio computational study. 1672 57

The primary goal of this study is to compare wet versus dry sampling methods for three different media, (Whatman 41 filter papers, GhostWipes, and SKC Smear Tabs), These media were selected because they are the most commonly used means for the collection of beryllium from contaminated surfaces within the DOE Complex. A range of known concentrations of beryllium was introduced onto a smooth nonporous surface. All three types of media were tested for collection efficiency in both the wet and dry mode and analyzed by inductively-coupled plasma atomic emission spectrometry (ICP-AES).
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PMID:Comparison of collection efficiencies of sampling methods for removable beryllium surface contamination. 1676 30

The poor flowability and bad compressibility characteristics of paracetamol are well known. As a result, the production of paracetamol tablets is almost exclusively by wet granulation, a disadvantageous method when compared to direct compression. The development of a new tablet formulation is still based on a large number of experiments and often relies merely on the experience of the analyst. The purpose of this study was to apply experimental design methodology (DOE) to the development and optimization of tablet formulations containing high amounts of paracetamol (more than 70%) and manufactured by direct compression. Nineteen formulations, screened by DOE methodology, were produced with different proportions of Microcel 102, Kollydon VA 64, Flowlac, Kollydon CL 30, PEG 4000, Aerosil, and magnesium stearate. Tablet properties, except friability, were in accordance with the USP 28th ed. requirements. These results were used to generate plots for optimization, mainly for friability. The physical-chemical data found from the optimized formulation were very close to those from the regression analysis, demonstrating that the mixture project is a great tool for the research and development of new formulations.
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PMID:Optimization of poorly compactable drug tablets manufactured by direct compression using the mixture experimental design. 1680 56

Bulk X-ray diffraction (XRD), synchrotron X-ray microdiffraction (microXRD), and scanning electron microscopy/ energy-dispersive X-ray spectroscopy (SEM/EDS) were used to characterize solids in residual sludge from single-shell underground waste tanks C-203 and C-204 at the U.S. Department of Energy's Hanford Site in southeastern Washington state. Cejkaite [Na4(UO2)(CO3)3] was the dominant crystalline phase in the C-203 and C-204 sludges. This is one of the few occurrences of cejkaite reported in the literature and may be the first documented occurrence of this phase in radioactive wastes from DOE sites. Characterization of residual solids from water leach and selective extraction tests indicates that cejkaite has a high solubility and a rapid rate of dissolution in water at ambient temperature and that these sludges may also contain poorly crystalline Na2U207 [or clarkeite Na[(UO2)O(OH)](H2O)0-1] as well as nitratine (soda niter, NaNO3), goethite [alpha-FeO(OH)], and maghemite (gamma-Fe2O3). Results of the SEM/EDS analyses indicate that the C-204 sludge also contains a solid that lacks crystalline form and is composed of Na, Al, P, O, and possibly C. Other identified solids include Fe oxides that often also contain Cr and Ni and occur as individual particles, coatings on particles, and botryoidal aggregates; a porous-looking material (or an aggregate of submicrometer particles) that typically contain Al, Cr, Fe, Na, Ni, Si, U, P, O, and C; Si oxide (probably quartz); and Na-Al silicate(s). The latter two solids probably represent minerals from the Hanford sediment, which were introduced into the tank during prior sampling campaigns or other tank operation activities. The surfaces of some Fe-oxide particles in residual solids from the water leach and selective extraction tests appear to have preferential dissolution cavities. If these Fe oxides contain contaminants of concern, then the release of these contaminants into infiltrating water would be limited by the dissolution rates of these Fe oxides, which in general have lowto very low solubilities and slow dissolution rates at near neutral to basic pH values under oxic conditions.
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PMID:Residual waste from Hanford tanks 241-C-203 and 241-C-204. 1. Solids characterization. 1683 May 37


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