Fluorescence in situ hybridization (FISH) is a sensitive and rapid procedure to detect gene rearrangements in tumor cells using non-isotopically labeled DNA probes. Large insert recombinant DNA clones such as bacterial artificial chromosome (BAC) or P1/PAC clones have established themselves in recent years as preferred starting material for probe preparations due to their low rates of chimerism and ease of use. However, when developing probes for the quantitative analysis of rearrangements involving genomic intervals of less than 100kb, careful probe selection and characterization are of paramount importance. We describe a sensitive approach to quality control probe clones suspected of carrying deletions or for measuring clone overlap with near kilobase resolution. The method takes advantage of the fact that P1/PAC/BAC's can be isolated as circular DNA molecules, stretched out on glass slides and fine-mapped by multicolor hybridization with smaller probe molecules. Two examples demonstrate the application of this technique: mapping of a gene-specific {approx}6kb plasmid onto an unusually small, {approx}55kb circular P1 molecule and the determination of the extent of overlap between P1 molecules homologous to the human NF-{kappa}B2 locus. The relatively simple method presented here does not require specialized equipment and may thus find widespread applications in DNA probe preparation …

This report summarizes NOAA's budget request for the 2009 fiscal year.

Foot-and-mouth disease is a highly infectious vesicular disease of cloven-hoofed animals caused by foot-and-mouth disease virus. It spreads by direct contact between animals, by animal products (milk, meat and semen), by mechanical transfer on people or fomites and by the airborne route - with the relative importance of each mechanism depending on the particular outbreak characteristics. Over the years a number of workers have developed or adapted atmospheric dispersion models to assess the risk of foot-and-mouth disease virus spread through the air. Six of these models were compared at a workshop hosted by the Institute for Animal Health/Met Office during 2008. A number of key issues emerged from the workshop and subsequent modelling work: (1) in general all of the models predicted similar directions for 'at risk' livestock with much of the remaining differences strongly related to differences in the meteorological data used; (2) determination of an accurate sequence of events is highly important, especially if the meteorological conditions vary substantially during the virus emission period; and (3) differences in assumptions made about virus release, environmental fate, and subsequent infection can substantially modify the size and location of the downwind risk area. Close relationships have now been established between participants, …

We describe an algorithm for the numerical solution of a phase-field model (PFM) of microstructure evolution in polycrystalline materials. The PFM system of equations includes a local order parameter, a quaternion representation of local orientation and a species composition parameter. The algorithm is based on the implicit integration of a semidiscretization of the PFM system using a backward difference formula (BDF) temporal discretization combined with a Newton-Krylov algorithm to solve the nonlinear system at each time step. The BDF algorithm is combined with a coordinate projection method to maintain quaternion unit length, which is related to an important solution invariant. A key element of the Newton-Krylov algorithm is the selection of a preconditioner to accelerate the convergence of the Generalized Minimum Residual algorithm used to solve the Jacobian linear system in each Newton step. Results are presented for the application of the algorithm to 2D and 3D examples.

Screening studies and a Design of Experiment were performed to evaluate measurement variation of a new, non-destructive NMR test system designed to assess age induced degradation of Outer Pressure Pads. The test method and results from 76,746 measurements are described indicating that a metal support strut adjacent to the front position of the test chamber interferes with the measurements and that there is a measurement property gradient from the front to the back of the chamber. Also, obvious compression set areas on a surveillance OPP were not detected, but hidden, internal voids within a newly molded OPP were detected.

Abstract The history of IEC development will be briefly described, and some speculation about future directions will be offered. The origin of IEC is due to the brilliance of Phil Farnsworth, inventor of electronic TV in the US. Early experiments were pioneered in the late 1960s by Robert Hirsch who later became head of the DOE fusion program. At that time studies of IEC physics quickly followed at the University of Illinois and at Penn State University. However, despite many successes in this early work, IEC research died as DOE funding stopped in the mid 1980s. In the early 90’s, R. W. Bussard of EMC revived work with a new major project based on a magnetic assisted IEC. While doing supportive studies for that project, G. Miley proposed a grided “STAR mode” IEC as a neutron source for NAA. This concept was later used commercially by Daimler- Benz in Germany to analysis impurities in incoming ores. This represented a first practical application of the IEC. During this period other research groups at LANL, U of Wisconsin and Kyoto University entered IEC research with innovative new concepts and approaches to IEC physics and applications. Much of this work is documented in …

The BRAHMS collaboration ended its data collection program in 2006. We are now well advanced in the analysis of a comprehensive set of data that spans systems ranging in mass from p+p to Au+Au and in energy from {radical}{ovr {sup S}N N} = 62.4 to 200 GeV. Our analysis has taken two distinct paths: we explore the rapidity dependence of intermediate and high-transverse-momentum, identified-particle production, thus helping to characterize the strongly-interacting quark-gluon plasma (sQGP) formed at RHIC; we also explore particle yields at lower transverse momentum to develop a systematic understanding of bulk particle production at RHIC energies.

During the contract year beginning July 1, 2007 and ending June 30, 2008, the CREP technician contacted 15 new landowners regarding an interest in either the CREP or the Continuous CRP programs. Most landowners requested a second meeting and most sites were visited to discuss possibilities of enrolling in a USDA riparian program. This year, a considerable amount of time was spent providing technical assistance to prior contracts as the practices are implemented. More time is being spent in planning site preparation so that NRCS and FSAs increasing concerns over plant survival are satisfied. A continued concern that the rate paid to the landowner for maintenance is not enough. Controlling competing vegetation is a major factor in increasing plant survival. Increasing costs in the methods used to control unwanted plants has made it difficult for contract holders to perform these methods as effectively as they would like. The projects that have continued maintenance are considerably more successful.

This report summarizes work completed by U.S. Geological Survey's Columbia River Research Laboratory (USGS-CRRL) in the Wind River subbasin during the period April 2006 through March 2007 under Bonneville Power Administration (BPA) contract 26922. During this period, we collected temperature, flow, and habitat data to characterize physical habitat condition and variation within and among tributaries and mainstem sections in the Wind River subbasin. We also conducted electrofishing and snorkeling surveys to determine juvenile salmonid populations within select study areas throughout the subbasin. Portions of this work were completed with additional funding from U.S. Fish and Wildlife Service (USFWS) and the Lower Columbia Fish Enhancement Group (LCFEG). Funding from USFWS was for work to contribute to a study of potential interactions between introduced Chinook salmon Oncorhynchus tshawytscha and wild steelhead O. mykiss. Funding from LCFEG was for work to evaluate the effects of nutrient enrichment in small streams. A statement of work (SOW) was submitted to BPA in March 2006 that outlined work to be performed by USGS-CRRL. The SOW was organized by work elements, with each describing a research task. This report summarizes the progress completed under each work element.

This paper introduces this special issue on plasma diagnostics for magnetic fusion devices. Its primary purpose is to relate the measurements of plasma parameters to the physics challenges to be faced on operating and planned devices, and also to identify the diagnostic techniques that are used to make these measurements. The specific physics involved in the application of the techniques will be addressed in subsequent chapters. This chapter is biased toward measurements for tokamaks because of their proximity to the burning plasma frontier, and to set the scene for the development work associated with ITER. Hence, there is some emphasis on measurements for alpha-physics studies and the needs for plasma measurements as input to actuators to control the plasma, both for optimizing the device performance and for protection of the surrounding material. The very different approach to the engineering of diagnostics for a burning plasma is considered, emphasizing the needs for new calibration ideas, reliability and hardness against, and compatibility with, radiation. New ideas take a long time to be converted into "work-horse" sophisticated diagnostics so that investment in new developments is essential for ITER, particularly for the measurement of alpha-particles.

The author reviews the history of the efforts using heavy ion collisions to make new forms of matter. Both the development of the theoretical ideas about such new forms of matter, and as well the past, present and planned experimental efforts are discussed. The development of this activity in both India and China are highlighted.

Over the past four years, the Electrical Safety Program at PPPL has evolved in addressing changing regulatory requirements and lessons learned from accident events, particularly in regards to arc flash hazards and implementing NFPA 70E requirements. This presentation will discuss PPPL's approaches to the areas of electrical hazards evaluation, both shock and arc flash; engineered solutions for hazards mitigation such as remote racking of medium voltage breakers, operational changes for hazards avoidance, targeted personnel training and hazard appropriate personal protective equipment. Practical solutions for nominal voltage identification and zero voltage checks for lockout/tagout will also be covered. Finally, we will review the value of a comprehensive electrical drawing program, employee attitudes expressed as a personal safety work ethic, integrated safety management, and sustained management support for continuous safety improvement.

A substantial narrowmg of the plume of the cylindrical RaIl thruster (CRT) was observed upon the enhancement of the electron emission from the hollow cathode discharge, which implies the possibility for the thruster efficiency increase due to the ion beam focusing. It is demonstrated that the miniaturized CRT can be operated in the non-self-sustained regime, with the discharge current limited by the cathode electron emission. The thruster operation in this mode greatly expands the range of the plasma and discharge parameters normally accessible for the CRT.

New chemistries based upon liquid cyclohexasilane (Si{sub 6}H{sub 12} or CHS) have been used as precursors to silicon-containing electronic materials. Spin-coating of CHS-based inks with subsequent UV light and/or thermal treatment yielded amorphous silicon (a-Si:H) films. While initial ink chemistries gave a-Si:H with high resistivity (i.e., > 10{sup 6} {Omega}.cm), several doping strategies are under development to address this limitation. In this contribution, the current status of solution processed rectifying diodes and field effect transistors fabricated from CHS-based inks will be presented. Additionally, a new printing approach termed collimated aerosol beam direct write (CAB-DW{sup TM}) was developed that allows the deposition of printed Ag lines 5 {mu}m in width. A status update will be given where CHS-based inks have been used to CAB-DW silicon-based features with linewidths <10 {mu}m. Assuming silicon thin film materials with good electrical properties will be developed, there may be significant cost advantages associated with the ability to controllably deposit the semiconductor in a metered fashion.

The Grays River Watershed and Biological Assessment was funded to address degradation and loss of spawning habitat for chum salmon (Onchorhynchus keta) and fall Chinook salmon (Onchoryhnchus tshawytscha). In 1999, the National Marine Fisheries Service listed lower Columbia River chum salmon as a threatened Evolutionarily Significant Unit (ESU) under the Endangered Species Act of 1973 (ESA). The Grays River watershed is one of two remaining significant chum salmon spawning locations in this ESU. Runs of Grays River chum and Chinook salmon have declined significantly during the past century, largely because of damage to spawning habitat associated with timber harvest and agriculture in the watershed. In addition, approximately 20-25% of the then-remaining chum salmon spawning habitat was lost during a 1999 channel avulsion that destroyed an important artificial spawning channel operated by the Washington Department of Fish and Wildlife (WDFW). Although the lack of stable, high-quality spawning habitat is considered the primary physical limitation on Grays River chum salmon production today, few data are available to guide watershed management and channel restoration activities. The objectives of the Grays River Watershed and Biological Assessment project were to (1) perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessments; (2) …

The goal of this project is to enhance and restore the ecological integrity and ecosystem function of the Grays River watershed. The recommended restoration and enhancement efforts developed in this project should incorporate local community stakeholder interests and needs. The objectives of this project are (1) to perform a comprehensive watershed and biological analysis, including hydrologic, geomorphic, and ecological assessment; (2) to develop a prioritized list of actions that protect and restore critical chum and Chinook salmon spawning habitat in the Grays River based on comprehensive geomorphic, hydrologic, and stream channel assessments; and (3) to gain a better understanding of chum and Chinook salmon habitat requirements and survival within the lower Columbia River and the Grays River sub-basin.

Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog(TM) system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.

There is a multiplicity of development pathways in which low energy sector emissions are not necessarily associated with low economic growth. However, changes in development pathways can rarely be imposed from the top. On this basis, examples of energy efficiency opportunities to change development pathways toward lower emissions are presented in this paper. We review opportunities at the sectoral and macro level. The potential for action on nonclimate policies that influence energy use and emissions are presented. Examples are drawn from policies already adopted and implemented in the energy sector. The paper discusses relationships between energy efficiency policies and their synergies and tradeoffs with sustainable development and greenhouse gas emissions. It points to ways that energy efficiency could be mainstreamed into devel?opment choices.

Ring polymer molecular dynamics (RPMD) is used to directly simulate the dynamics of an excess electron in a supercritical fluid over a broad range of densities. The accuracy of the RPMD model is tested against numerically exact path integral statistics through the use of analytical continuation techniques. At low fluid densities, the RPMD model substantially underestimates the contribution of delocalized states to the dynamics of the excess electron. However, with increasing solvent density, the RPMD model improves, nearly satisfying analytical continuation constraints at densities approaching those of typical liquids. In the high density regime, quantum dispersion substantially decreases the self-diffusion of the solvated electron. In this regime where the dynamics of the electron is strongly coupled to the dynamics of the atoms in the fluid, trajectories that can reveal diffusive motion of the electron are long in comparison to {beta}{h_bar}.

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We have developed complementary soft x-ray scattering and reflectometry techniques that allow for the morphological analysis of thin polymer films without resorting to chemical modification or isotopic 2 labeling. With these techniques, we achieve significant, x-ray energy-dependent contrast between carbon atoms in different chemical environments using soft x-ray resonance at the carbon edge. Because carbon-containing samples absorb strongly in this region, the scattering length density depends on both the real and imaginary parts of the atomic scattering factors. Using a model polymer film of poly(styrene-b-methyl methacrylate), we show that the soft x-ray reflectivity data is much more sensitive to these atomic scattering factors than the soft x-ray scattering data. Nevertheless, fits to both types of data yield useful morphological details on the polymer?slamellar structure that are consistent with each other and with literature values.

Bitmap indexes are known to be efficient for ad-hoc range queries that are common in data warehousing and scientific applications. However, they suffer from the curse of cardinality, that is, their efficiency deteriorates as attribute cardinalities increase. A number of strategies have been proposed, but none of them addresses the problem adequately. In this paper, we propose a novel binned bitmap index that greatly reduces the cost to answer queries, and therefore breaks the curse of cardinality. The key idea is to augment the binned index with an Order-preserving Bin-based Clustering (OrBiC) structure. This data structure significantly reduces the I/O operations needed to resolve records that cannot be resolved with the bitmaps. To further improve the proposed index structure, we also present a strategy to create single-valued bins for frequent values. This strategy reduces index sizes and improves query processing speed. Overall, the binned indexes with OrBiC great improves the query processing speed, and are 3 - 25 times faster than the best available indexes for high-cardinality data.

This memo summarizes simple calculations and results of the thermal analysis on the second stripper to be used in the driver linac of Rare Isotope Accelerator (RIA). Both liquid (Sodium) and solid (Titanium and Vanadium) stripper concepts were considered. These calculations were intended to provide basic information to evaluate the feasibility of liquid (thick film) and solid (rotating wheel) second strippers. Nuclear physics calculations to estimate the volumetric heat generation in the stripper material were performed by 'LISE for Excel'. In the thermal calculations, the strippers were modeled as a thin 2D plate with uniform heat generation within the beam spot. Then, temperature distributions were computed by assuming that the heat spreads conductively in the plate in radial direction without radiative heat losses to surroundings.

The authors present evidence of D{sup 0}-{bar D}{sup 0} mixing using a time-dependent amplitude analysis of the decay D{sup 0} {yields} K{sup +}{pi}{sup -}{pi}{sup 0} in a data sample of 384 fb{sup -1} collected with the BABAR detector at the PEP-II e{sup +}e{sup -} collider at SLAC. Assuming CP conservation, they measure the mixing parameters x{prime}{sub K{pi}{pi}{sup 0}} = [2.61{sub -0.68}{sup +0.57}(stat.) {+-} 0.39(syst.)]%, y{prime}{sub K{pi}{pi}{sup 0}} = [-0.06{sub -0.64}{sup +0.55}(stat.) {+-} 0.34(syst.)]%. The confidence level for the data to be consistent with the no-mixing hypothesis is 0.1%, including systematic uncertainties. This result is inconsistent with the no-mixing hypothesis with a significance of 3.2 standard deviations. They find no evidence of CP violation in mixing.