We use Time-of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS) to image and classify individual cells based on their characteristic mass spectra. Using statistical data reduction on the large data sets generated during TOF-SIMS analysis, similar biological materials can be differentiated based on a combination of small changes in protein expression, metabolic activity and cell structure. We apply this powerful technique to image and differentiate three carcinoma-derived human breast cancer cell lines (MCF-7, T47D and MDA-MB-231). In homogenized cells, we show the ability to differentiate the cell types as well as cellular compartments (cytosol, nuclear and membrane). These studies illustrate the capacity of TOF-SIMS to characterize individual cells by chemical composition, which could ultimately be applied to detect and identify single aberrant cells within a normal cell population. Ultimately, we anticipate characterizing rare chemical changes that may provide clues to single cell progression within carcinogenic and metastatic pathways.

Using a large sample of D{sup +} {yields} K{sup -}K{sup +}{pi}{sup +} decays collected by the FOCUS photoproduction experiment at Fermilab, we present the first non-parametric analysis of the K{sup -} {pi}{sup +} amplitudes in D{sup +} {yields} K{sup -}K{sup +}{pi}{sup +} decay. The technique is similar to the technique used for our non-parametric measurements of the D{sup +} {yields} {bar K}*{sup 0} e{sup +}{nu} form factors. Although these results are in rough agreement with those of E687, we observe a wider S-wave contribution for the {bar K}*{sub 0}{sup 0}(1430) contribution than the standard, PDG [1] Breit-Wigner parameterization. We have some weaker evidence for the existence of a new, D-wave component at low values of the K{sup -} {pi}{sup +} mass.

Several different spare modules of the D0 experiment Silicon Microstrip Tracker (SMT) have been irradiated at the Fermilab Booster Radiation Damage Facility (RDF). The total dose received was 2.1 MRads with a proton flux of {approx} 3 {center_dot} 10{sup 11} p/cm{sup 2} sec. The irradiation was carried out in steps of 0.3 or 0.6 MRad, with several days between the steps to allow for annealing and measurements. The leakage currents and depletion voltages of the devices increased with dose, as expected from bulk radiation damage. The double sided, double metal devices showed worse degradation than the less complex detectors.

Sum frequency generation (SFG) surface vibrational spectroscopy was used to characterize interfaces pertinent to current surface engineering applications, such as thin film polymers and novel catalysts. An array of advanced surface science techniques like scanning probe microscopy (SPM), x-ray photoelectron spectroscopy (XPS), gas chromatography (GC) and electron microscopy were used to obtain experimental measurements complementary to SFG data elucidating polymer and catalyst surface composition, surface structure, and surface mechanical behavior. Experiments reported in this dissertation concentrate on three fundamental questions: (1) How does the interfacial molecular structure differ from that of the bulk in real world applications? (2) How do differences in chemical environment affect interface composition or conformation? (3) How do these changes correlate to properties such as mechanical or catalytic performance? The density, surface energy and bonding at a solid interface dramatically alter the polymer configuration, physics and mechanical properties such as surface glass transition, adhesion and hardness. The enhanced sensitivity of SFG at the buried interface is applied to three systems: a series of acrylates under compression, the compositions and segregation behavior of binary polymer polyolefin blends, and the changes in surface structure of a hydrogel as a function of hydration. In addition, a catalytically active thin …

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Computational chemists are using Common Component Architecture (CCA) technology to increase the parallel scalability of their application ten-fold. Combustion researchers are publishing science faster because the CCA manages software complexity for them. Both the solver and meshing communities in SciDAC are converging on community interface standards as a direct response to the novel level of interoperability that CCA presents. Yet, there is much more to do before component technology becomes mainstream computational science. This paper highlights the impact that the CCA has made on scientific applications, conveys some lessons learned from five years of the SciDAC program, and previews where applications could go with the additional capabilities that the CCA has planned for SciDAC 2.

Independent review report on the available information concerning the technologies needed for forecourts producing 150 kg/day of hydrogen from natural gas.

The Bio-Aerosol Mass Spectrometry (BAMS) system is an instrument used for the real time detection and identification of biological aerosols. Particles are drawn from the atmosphere directly into vacuum and tracked as they scatter light from several continuous wave lasers. After tracking, the fluorescence of individual particles is excited by a pulsed 266nm or 355nm laser. Molecules from those particles with appropriate fluorescence properties are subsequently desorbed and ionized using a pulsed 266nm laser. Resulting ions are analyzed in a dual polarity mass spectrometer. During two field deployments at the San Francisco International Airport, millions of ambient particles were analyzed and a small but significant fraction were found to have fluorescent properties similar to Bacillus spores and vegetative cells. Further separation of non-biological background particles from potential biological particles was accomplished using laser desorption/ionization mass spectrometry. This has been shown to enable some level of species differentiation in specific cases, but the creation and observation of higher mass ions is needed to enable a higher level of specificity across more species. A soft ionization technique, matrix-assisted laser desorption/ionization (MALDI) is being investigated for this purpose. MALDI is particularly well suited for mass analysis of biomolecules since it allows for the …

Large-scale scientific computation and all of the disciplines that support and help validate it have been placed at the focus of Lawrence Livermore National Laboratory (LLNL) by the Advanced Simulation and Computing (ASC) program of the National Nuclear Security Administration (NNSA) and the Scientific Discovery through Advanced Computing (SciDAC) initiative of the Office of Science of the Department of Energy (DOE). The maturation of simulation as a fundamental tool of scientific and engineering research is underscored in the President's Information Technology Advisory Committee (PITAC) June 2005 finding that ''computational science has become critical to scientific leadership, economic competitiveness, and national security''. LLNL operates several of the world's most powerful computers--including today's single most powerful--and has undertaken some of the largest and most compute-intensive simulations ever performed, most notably the molecular dynamics simulation that sustained more than 100 Teraflop/s and won the 2005 Gordon Bell Prize. Ultrascale simulation has been identified as one of the highest priorities in DOE's facilities planning for the next two decades. However, computers at architectural extremes are notoriously difficult to use in an efficient manner. Furthermore, each successful terascale simulation only points out the need for much better ways of interacting with the resulting avalanche of …

This paper investigates ballasting and remineralization controls of carbon sedimentation in the twilight zone (100-1000 m) of the Southern Ocean. Size-fractionated (<1 {micro}m, 1-51 {micro}m, >51 {micro}m) suspended particulate matter was collected by large volume in-situ filtration from the upper 1000 m in the Subantarctic (55 S, 172 W) and Antarctic (66 S, 172 W) zones of the Southern Ocean during the Southern Ocean Iron Experiment (SOFeX) in January-February 2002. Particles were analyzed for major chemical constituents (POC, P, biogenic Si, CaCO3), and digital and SEM image analyses of particles were used to aid in the interpretation of the chemical profiles. Twilight zone waters at 66 S in the Antarctic had a steeper decrease in POC with depth than at 55 S in the Subantarctic, with lower POC concentrations in all size fractions at 66 S than at 55 S, despite up to an order of magnitude higher POC in surface waters at 66 S. The decay length scale of >51 {micro}m POC was significantly shorter in the upper twilight zone at 66 S ({delta}{sub e}=26 m) compared to 55 S ({delta}{sub e}=81 m). Particles in the carbonate-producing 55 S did not have higher excess densities than particles from the …

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Sensitivity analysis is a study of how changes in the inputs to a model influence the results of the model. Many techniques have recently been proposed for use when the model is probabilistic. This report considers the related problem of sensitivity analysis when the model includes uncertain numbers that can involve both aleatory and epistemic uncertainty and the method of calculation is Dempster-Shafer evidence theory or probability bounds analysis. Some traditional methods for sensitivity analysis generalize directly for use with uncertain numbers, but, in some respects, sensitivity analysis for these analyses differs from traditional deterministic or probabilistic sensitivity analyses. A case study of a dike reliability assessment illustrates several methods of sensitivity analysis, including traditional probabilistic assessment, local derivatives, and a ''pinching'' strategy that hypothetically reduces the epistemic uncertainty or aleatory uncertainty, or both, in an input variable to estimate the reduction of uncertainty in the outputs. The prospects for applying the methods to black box models are also considered.

The large-x behavior of the transverse-momentum dependent quark distributions is analyzed in the factorization-inspired perturbative QCD framework, particularly for the naive time-reversal-odd quark Sivers function which is responsible for the single transverse-spin asymmetries in various semi-inclusive hard processes. By examining the dominant hard gluon exchange Feynman diagrams, and using the resulting power counting rule, we find that the Sivers function has power behavior (1-x){sup 4} at x {yields} 1, which is one power of (1-x) suppressed relative to the unpolarized quark distribution. These power-counting results provide important guidelines for the parameterization of quark distributions and quark-gluon correlations.

The CH2M HILL Hanford Group, Inc. (CH2M HILL) is producing risk/performance assessments to support the closure of single-shell tanks at the U.S. Department of Energy's Hanford Site. As part of this effort, staff at Pacific Northwest National Laboratory were asked to develop release models for contaminants of concern that are present in residual sludge remaining in tank 241-C-106 (C-106) after final retrieval of waste from the tank. Initial work to produce release models was conducted on residual tank sludge using pure water as the leaching agent. The results were reported in an earlier report. The decision has now been made to close the tanks after waste retrieval with a cementitious grout to minimize infiltration and maintain the physical integrity of the tanks. This report describes testing of the residual waste with a leaching solution that simulates the composition of water passing through the grout and contacting the residual waste at the bottom of the tank.

The workshop participants enthusiastically concluded that the time is ripe for new fundamental science to beget a revolution in lighting technology. SSL sources based on organic and inorganic materials have reached a level of efficiency where it is possible to envision their use for general illumination. The research areas articulated in this report are targeted to enable disruptive advances in SSL performance and realization of this dream. Broad penetration of SSL technology into the mass lighting market, accompanied by vast savings in energy usage, requires nothing less. These new ?good ideas? will be represented not by light bulbs, but by an entirely new lighting technology for the 21st century and a bright, energy-efficient future indeed.

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The Relativistic Heavy Ion Collider (RHIC) is designed to provide collisions of high energy polarized protons for the quest of understanding the proton spin structure. Polarized proton collisions at a beam energy of 100 GeV have been achieved in RHIC since 2001. Recently, polarized proton beam was accelerated to 250 GeV in RHIC for the first time. Unlike accelerating unpolarized protons, the challenge for achieving high energy polarized protons is to fight the various mechanisms in an accelerator that can lead to partial or total polarization loss due to the interaction of the spin vector with the magnetic fields. We report on the progress of the RHIC polarized proton program. We also present the strategies of how to preserve the polarization through the entire acceleration chain, i.e. a 200 MeV linear accelerator, the Booster, the AGS and RHIC.

Seismic borehole C4998 was cored through the upper portion of the Columbia River Basalt Group and Ellensburg Formation to provide detailed lithologic information and intact rock samples that represent the geology at the Waste Treatment Plant. This report describes the drilling of borehole C4998 and documents the geologic data collected during the drilling of the cored portion of the borehole.

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DOE is working on changing transportation fuel to hydrogen. To assist in that effort, we are developing a macro-system model that will link existing or developmental component models together.

We propose a novel mechanism for exclusive diffractive Higgs production pp {yields} pHp in which the Higgs boson carries a significant fraction of the projectile proton momentum. This mechanism will provide a clear experimental signal for Higgs production due to the small background in this kinematic region. The key assumption underlying our analysis is the presence of intrinsic heavy flavor components of the proton bound state, whose existence at high light-cone momentum fraction x has growing experimental and theoretical support. We also discuss the implications of this picture for exclusive diffractive quarkonium and other channels.

The MARO pilot project represents the first effort in the country to seek to obtain credit under a Clean Air Act (CAA) State Implementation Plan (SIP) for nitrogen oxide (NOx) emission reductions.

This report is one of the major products and deliverables of the Groundwater Remediation and Closure Assessment Projects detailed work plan for FY 2006, and reflects the requirements of The Groundwater Performance Assessment Project Quality Assurance Plan (PNNL-15014). This report presents the results of groundwater and vadose zone monitoring and remediation for fiscal year 2005 on the U.S. Department of Energy's Hanford Site, Washington. The most extensive contaminant plumes in groundwater are tritium, iodine-129, and nitrate, which all had multiple sources and are very mobile in groundwater. The largest portions of these plumes are migrating from the central Hanford Site to the southeast, toward the Columbia River. Carbon tetrachloride and associated organic constituents form a relatively large plume beneath the west-central part of the Hanford Site. Hexavalent chromium is present in plumes beneath the reactor areas along the river and beneath the central part of the site. Strontium-90 exceeds standards beneath all but one of the reactor areas. Technetium-99 and uranium plumes exceeding standards are present in the 200 Areas. A uranium plume underlies the 300 Area. Minor contaminant plumes with concentrations greater than standards include carbon-14, cesium-137, cis-1,2-dichloroethene, cyanide, fluoride, plutonium, and trichloroethene. Monitoring for the Comprehensive Environmental Response, …

Maintenance of apico-basal polarity in normal breast epithelial acini requires a balance between cell proliferation, cell death, and proper cell-cell and cell-extracellular matrix signaling. Aberrations in any of these processes can disrupt tissue architecture and initiate tumor formation. Here we show that the small GTPase Rap1 is a crucial element in organizing acinar structure and inducing lumen formation. Rap1 activity in malignant HMT-3522 T4-2 cells is appreciably higher than in S1 cells, their non-malignant counterparts. Expression of dominant-negative Rap1 resulted in phenotypic reversion of T4-2 cells, led to formation of acinar structures with correct apico-basal polarity, and dramatically reduced tumor incidence despite the persistence of genomic abnormalities. The resulting acini contained prominent central lumina not observed when other reverting agents were used. Conversely, expression of dominant-active Rap1 in T4-2 cells inhibited phenotypic reversion and led to increased invasiveness and tumorigenicity. Thus, Rap1 acts as a central regulator of breast architecture, with normal levels of activation instructing apical polarity during acinar morphogenesis, and increased activation inducing tumor formation and progression to malignancy.