Geochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes. These sulfate reducers were sustained by geologically produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically derived substrates.

For over 25 years, the U.S. DOE's Industrial Technologies Program (ITP) has championed the application of emerging technologies in industrial plants and monitored these technologies impacts on industrial energy consumption. The cumulative energy savings of more than 160 completed and tracked projects is estimated at approximately 3.99 quadrillion Btu (quad), representing a production cost savings of $20.4 billion. Properly documenting the impacts of such technologies is essential for assessing their effectiveness and for delivering insights about the optimal direction of future technology research. This paper analyzes the impacts that several emerging technologies have had in the food processing industry. The analysis documents energy savings, carbon emissions reductions and production improvements and assesses the market penetration and sector-wide savings potential. Case study data is presented demonstrating the successful implementation of these technologies. The paper's conclusion discusses the effects of these technologies and offers some projections of sector-wide impacts.

Thermal imaging is an important, though challenging, diagnostic for shockwave experiments. Shock-compressed materials undergo transient temperature changes that cannot be recorded with standard (greater than ms response time) infrared detectors. A further complication arises when optical elements near the experiment are destroyed. We have designed a thermal-imaging system for studying shock temperatures produced inside a gas gun at Sandia National Laboratories. Inexpensive, diamond-turned, parabolic mirrors relay an image of the shocked target to the exterior of the gas gun chamber through a sapphire vacuum port. The 3000–5000-nm portion of this image is directed to an infrared camera which acquires a snapshot of the target with a minimum exposure time of 150 ns. A special mask is inserted at the last intermediate image plane, to provide dynamic thermal background recording during the event. Other wavelength bands of this image are split into high-speed detectors operating at 900–1700 nm, and at 1700–3000 nm for timeresolved pyrometry measurements. This system incorporates 90-degree, off-axis parabolic mirrors, which can collect low f/# light over a broad spectral range, for high-speed imaging. Matched mirror pairs must be used so that aberrations cancel. To eliminate image plane tilt, proper tip-to-tip orientation of the parabolic mirrors is required. …

Experiments at the LOASIS laboratory of LBNL havedemonstrated production of 100 MeV to 1 GeV electron bunches with lowenergy spread and low divergence from laser wakefield acceleration. Theradiation pressure of a 10 TW laser pulse, guided over 10 diffractionranges by a few-mm long plasma density channel, was used to drive anintense plasma wave (wakefield), producing electron bunches with energieson the order of 100 MeV and acceleration gradients on the order of 100GV/m. Beam energy was increased from 100 MeV to 1 GeV by using a few-cmlong guiding channel at lower density, driven by a 40 TW laser,demonstrating the anticipated scaling to higher beam energies. Particlesimulations indicate that the low energy spread beams were produced fromself-trapped electrons through the interplay of trapping, loading, anddephasing. Other experiments and simulations are also underway to controlinjection of particles into the wake, and hence improve beam quality andstability further.

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In this commentary, we advocate building a richer set of descriptions about our invaluable and exponentially growing collection of genomes and metagenomic datasets through the construction of consensus-driven data capture and exchange mechanisms. Standardization activities must proceed within the auspices of open-access and international working bodies, and to tackle the issues surrounding the development of better descriptions of genomic investigations we have formed the Genomic Standards Consortium (GSC). Here, we introduce the 'Minimum Information about a Genome Sequence' specification in the hopes of gaining wider participation in its development and discuss the resources that will be required to support it (standardization of annotations through the use of ontologies and mechanisms of metadata capture, exchange). As part of its wider goals, the GSC also strongly supports improving the 'transparency' of the information contained in existing genomic databases that contain calculated analyses and genomic annotations.

The exponential increase of genomic and metagenomic data,fueled in part by recent advancements in sequencing technology, aregreatly expanding our understanding of the phylogenetic diversity andmetabolic capacity present in the environment. Two of the centralchallenges that bioinformaticians and ecologists alike must face are thedesign of bioinformatic resources that facilitate the analysis of genomicand metagenomic data in a comparative context and the efficient captureand organization of the plethora of descriptive information required tousefully describe these data sets. In this commentary, we review threeinitiatives presented in the "new frontiers" session of the second SCOPEmeeting on Microbial Environmental Genomics (MicroEnGen-II, Shanghai,June 12-15, 2006). These are (1) the Integrated Microbial GenomesResources (IMG), (2) the Genomic Standards Consortium (GSC), and (3) theNatural Environment Research Council (NERC) Environmental BioinformaticsCentre (NEBC). These integrative bioinformatics and data managementinitiatives underscore the increasingly important role ecologists have toplay in the genomic (metagenomic) revolution.

In the event of a short-term, large-scale toxic chemical release to the atmosphere, shelter-in-place (SIP) may be used as an emergency response to protect public health. We modeled hypothetical releases using realistic, empirical parameters to explore how key factors influence SIP effectiveness for single-family dwellings in a residential district. Four classes of factors were evaluated in this case-study: (a) time scales associated with release duration, SIP implementation delay, and SIP termination; (b) building air-exchange rates, including air infiltration and ventilation; (c) the degree of sorption of toxic chemicals to indoor surfaces; and (d) the shape of the dose-response relationship for acute adverse health effects. Houses with lower air leakage are more effective shelters, and thus variability in the air leakage of dwellings is associated with varying degrees of SIP protection in a community. Sorption on indoor surfaces improves SIP effectiveness by lowering the peak indoor concentrations and reducing the amount of contamination in the indoor air. Nonlinear dose-response relationships imply substantial reduction in adverse health effects from lowering the peak exposure concentration. However, if the scenario is unfavorable for sheltering (e.g. sheltering in leaky houses for protection against a nonsorbing chemical with a linear dose-response), the community must implement SIP …

Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms …

A general geometry gyro-kinetic model for particle simulation of plasma turbulence in tokamak experiments is described. It incorporates the comprehensive influence of noncircular cross section, realistic plasma profiles, plasma rotation, neoclassical (equilibrium) electric fields, and Coulomb collisions. An interesting result of global turbulence development in a shaped tokamak plasma is presented with regard to nonlinear turbulence spreading into the linearly stable region. The mutual interaction between turbulence and zonal flows in collisionless plasmas is studied with a focus on identifying possible nonlinear saturation mechanisms for zonal flows. A bursting temporal behavior with a period longer than the geodesic acoustic oscillation period is observed even in a collisionless system. Our simulation results suggest that the zonal flows can drive turbulence. However, this process is too weak to be an effective zonal flow saturation mechanism.

Inorganic scintillator/photomultiplier-based spectrometers are the systems of choice for a multitude of X-ray and gamma radiation measurement applications. Despite widespread use, they have numerous shortcomings. The most serious shortcoming is the relatively poor energy resolution that makes isotope identification problematic, particularly in the case of trace quantities. Energy resolution in scintillator/photomultiplier tube (PMT) spectrometers is governed by a combination of the crystal intrinsic resolution that includes non-linearity effects, photomultiplier statistics, and the variability in the probability of a scintillation photon generating a photoelectron at the photocathode. It is evident that energy resolution in these systems is linked to both the physics of light generation in the scintillator and the characteristics of the PMT. PMTs also present design problems, especially in the case of handheld and portable instruments, due to their considerable weight and volume. Additionally, PMTs require well-regulated high voltage, and are vulnerable to magnetic fields. The objective of this work is to provide instrument designers of scintillation-based gamma-ray spectrometers with superior energy resolution and greatly reduced weight and volume. It is planned to achieve this advancement by optimizing the performance of a new class of inorganic scintillators by matching their emission spectra with the enhanced quantum efficiency of certain …

Healthy dentin, the mineralized tissue that makes up the bulk of the tooth, is naturally hydrated in vivo; however, it is known that various chemical reagents including acetone and ethanol can induce dehydration and thereby affect its properties. Here, we seek to investigate this in light of the effect alcohol can have on the mechanical properties of dentin, specifically by measuring the stiffness, strength and toughness of dentin in simulated body fluid and scotch whisky. Results indicate that chemical dehydration induced by the whisky has a significant beneficial effect on the elastic modulus, strength and fracture toughness of dentin. Although this makes teeth more resistant to fracture, the change in properties is fully reversible upon rehydration. This effect is considered to be associated with increased cross-linking of the collagen molecules from intermolecular hydrogen-bonding where water is replaced with weaker hydrogen-bond forming solvents such as alcohol.

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

The widespread commercial adaptation of slagging gasifier technology to produce power, fuel, and/or chemicals from coal will depend in large measure on the technology’s ability to prove itself both economic and reliable. Improvements in gasifier reliability, availability, and maintainability will in part depend on the development of improved performance structural materials with longer service life in this application. Current generation refractory materials used to line the air-cooled, slagging gasifier vessel, and contain the gasification reaction, often last no more than three to 18 months in commercial applications. The downtime required for tear-out and replacement of these critical materials contributes to gasifier on-line availabilities that fall short of targeted goals. In this talk we will discuss the development of an improved refractory material engineered by the NETL for longer service life in this application, and provide an update on recent field test results.

Enhanced Biological Phosphorus Removal (EBPR) is not wellunderstood at the metabolic level despite being one of the best-studiedmicrobially-mediated industrial processes due to its ecological andeconomic relevance. Here we present a metagenomic analysis of twolab-scale EBPR sludges dominated by the uncultured bacterium, "CandidatusAccumulibacter phosphatis." This analysis resolves several controversiesin EBPR metabolic models and provides hypotheses explaining the dominanceof A. phosphatis in this habitat, its lifestyle outside EBPR and probablecultivation requirements. Comparison of the same species from differentEBPR sludges highlights recent evolutionary dynamics in the A. phosphatisgenome that could be linked to mechanisms for environmental adaptation.In spite of an apparent lack of phylogenetic overlap in the flankingcommunities of the two sludges studied, common functional themes werefound, at least one of them complementary to the inferred metabolism ofthe dominant organism. The present study provides a much-needed blueprintfor a systems-level understanding of EBPR and illustrates thatmetagenomics enables detailed, often novel, insights into evenwell-studied biological systems.

The paper describes the development of a model specification for performance monitoring systems for commercial buildings. The specification focuses on four key aspects of performance monitoring: (1) performance metrics; (2) measurement system requirements; (3) data acquisition and archiving; and (4) data visualization and reporting. The aim is to assist building owners in specifying the extensions to their control systems that are required to provide building operators with the information needed to operate their buildings more efficiently and to provide automated diagnostic tools with the information required to detect and diagnose faults and problems that degrade energy performance. The paper reviews the potential benefits of performance monitoring, describes the specification guide and discusses briefly the ways in which it could be implemented. A prototype advanced visualization tool is also described, along with its application to performance monitoring. The paper concludes with a description of the ways in which the specification and the visualization tool are being disseminated and deployed.

The passive film that forms on aluminum in 1:1 ethylene carbonate + ethylmethyl carbonate with 1.2M LiPF{sub 6} and 1:1 ethylene carbonate + dimethyl carbonate with 1.0M LiPF{sub 6} was investigated by a combination of electrochemical quartz crystal microbalance measurements (EQCM), electrochemical impedance spectroscopy (EIS), and x-ray photoelectron spectroscopy. During anodic polarization of aluminum a film of AlF{sub 3} forms on top of the air-formed oxide, creating a duplex, or two-layered film. The thickness of the AlF{sub 3} increases with the applied potential. Independent measurements of film thickness by EQCM and EIS indicate that at a potential of 5.5V vs. Li/Li{sup +}, the thickness of the AlF{sub 3} is approximately 1 nm.

Biclustering has many applications in text mining, web clickstream mining, and bioinformatics. When data entries are binary, the tightest biclusters become bicliques. We propose a flexible and highly efficient algorithm to compute bicliques. We first generalize the Motzkin-Straus formalism for computing the maximal clique from L{sub 1} constraint to L{sub p} constraint, which enables us to provide a generalized Motzkin-Straus formalism for computing maximal-edge bicliques. By adjusting parameters, the algorithm can favor biclusters with more rows less columns, or vice verse, thus increasing the flexibility of the targeted biclusters. We then propose an algorithm to solve the generalized Motzkin-Straus optimization problem. The algorithm is provably convergent and has a computational complexity of O(|E|) where |E| is the number of edges. It relies on a matrix vector multiplication and runs efficiently on most current computer architectures. Using this algorithm, we bicluster the yeast protein complex interaction network. We find that biclustering protein complexes at the protein level does not clearly reflect the functional linkage among protein complexes in many cases, while biclustering at protein domain level can reveal many underlying linkages. We show several new biologically significant results.

In theories with multiple vacua, reheating to a temperature greater than the height of a barrier can stimulate transitions from a desirable metastable vacuum to a lower energy state. We discuss the constraints this places on various theories and demonstrate that in a class of supersymmetric models this transition does not occur even for arbitrarily high reheating temperature.

The US LHC Accelerator Research Program (LARP) consists of four US laboratories (BNL, FNAL, LBNL, and SLAC) collaborating with CERN to achieve a successful commissioning of the LHC and to develop the next generation of Interaction Region magnets. In 2004, a large aperture Nb{sub 3}Sn racetrack quadrupole magnet (SQ01) has been fabricated and tested at LBNL. The magnet utilized four subscale racetrack coils and was instrumented with strain gauges on the support structure and directly over the coil's turns. SQ01 exhibited training quenches in two of the four coils and reached a peak field in the conductor of 10.4 T at a current of 10.6 kA. After the test, the magnet was disassembled, inspected with pressure indicating films, and reassembled with minor modifications. A second test (SQ01b) was performed at FNAL and included training studies, strain gauge measurements and magnetic measurements. Magnet inspection, test results, and magnetic measurements are reported and discussed, and a comparison between strain gauge measurements and 3D finite element computations is presented

The development of test plans to validate the CERTSMicrogrid concept is discussed, including the status of a testbed.Increased application of Distributed Energy Resources on the Distributionsystem has the potential to improve performance, lower operational costsand create value. Microgrids have the potential to deliver these highvalue benefits. This presentation will focus on operationalcharacteristics of the CERTS microgrid, the partners in the project andthe status of the CEC/CERTS microgrid testbed. Index Terms DistributedGeneration, Distributed Resource, Islanding, Microgrid,Microturbine

The US LHC Accelerator Research Program (LARP) is developing Nb{sub 3}Sn accelerator magnet technology for the LHC luminosity upgrade. Two 90 mm 'Technology Quadrupole' models (TQS01, TQC01) are being developed in close collaboration between LBNL and FNAL, using identical coil design, but two different support structures. The TQS01 structure was developed and tested at LBNL. With this approach coils are supported by an outer aluminum shell and assembled using keys and bladders. In contrast, the second model TQC01, utilize stainless steel collars and a thick stainless steel skin. This paper describes the TQS01 model magnet, its 3D ANSYS stress analysis, and anticipated instrumentation and assembly procedure.

Standard jet finding techniques used in elementary particle collisions have not been successful in the high track density of heavy-ion collisions. This paper describes a modified cone-type jet finding algorithm developed for the complex environment of heavy-ion collisions.