The BTeV Collaboration is starting to develop its C++ based offline software suite, an integral part of which is a series of tutorials. These tutorials are targeted at a diverse audience, including new graduate students, experienced physicists with little or no C++ experience, those with just enough C++ to be dangerous, and experts who need only an overview of the available tools. The tutorials must both teach C++ in general and the BTeV specific tools in particular. Finally, they must teach physicists how to find and use the detailed documentation. This report will review the status of the BTeV experiment, give an overview of the plans for and the state of the software and will then describe the plans for the tutorial suite.

A 2-inch schedule 40 steel core pipe in an evaporator overheads discharge line broke at several locations downstream from a section of the line where it bridges a road. Fish mouth openings that developed along the pipe seams were initiated at lack of fusion defects in the pipe welds. A vacuum created in the piping upstream of the breaks prevented full drainage of the water upon shut down of the pump. Freezing of water in the pipe (the line was not heat traced) and water hammer effects occurring with pump restart could each contribute to the extensive deformation and tearing observed at the breaks. Both the weld flaws and the over pressure contributed to the outcome. All pipe was replaced and a vacuum break was installed to eliminate the problem.

COUP-TFII is a central nuclear hormone receptor that tightly regulates the expression of numerous target lipid metabolism genes in vertebrates. However, it remains unclear how COUP-TFII itself is transcriptionally controlled since studies with its promoter and upstream region fail to recapitulate the genes liver expression. In an attempt to identify liver enhancers in the vicinity of COUP-TFII, we employed a comparative genomic approach. Initial comparisons between humans and mice of the 3,470kb gene poor region surrounding COUP-TFII revealed 2,023 conserved non-coding elements. To prioritize a subset of these elements for functional studies, we performed further genomic comparisons with the orthologous pufferfish (Fugu rubripes) locus and uncovered two anciently conserved non-coding sequences (CNS) upstream of COUP-TFII (CNS-62kb and CNS-66kb). Testing these two elements using reporter constructs in liver (HepG2) cells revealed that CNS-66kb, but not CNS-62kb, yielded robust in vitro enhancer activity. In addition, an in vivo reporter assay using naked DNA transfer with CNS-66kb linked to luciferase displayed strong reproducible liver expression in adult mice, further supporting its role as a liver enhancer. Together, these studies further support the utility of comparative genomics to uncover gene regulatory sequences based on evolutionary conservation and provide the substrates to better understand the …

It is well-known that the diversity of life appears to fluctuate during the course the Phanerozoic, the eon during which hard shells and skeletons left abundant fossils (0-542 Ma). Using Sepkoski's compendium of the first and last stratigraphic appearances of 36380 marine genera, we report a strong 62 {+-} 3 Myr cycle, which is particularly strong in the shorter-lived genera. The five great extinctions enumerated by Raup and Sepkoski may be an aspect of this cycle. Because of the high statistical significance, we also consider contributing environmental factors and possible causes.

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A modeling investigation was performed to choose moderator material and size for creating optimal epithermal neutron beams for BNCT based on a proton accelerator and the 7Li(p,n)7Be reaction as a neutrons source. An optimal configuration is suggested for the beam shaping assembly made from polytetrafluoroethylene and magnesium fluorine. Results of calculation were experimentally tested and are in good agreement with measurements.

Sea hare species within the Aplysia clade are distributed worldwide. Their phylogenetic and biogeographic relationships are, however, still poorly known. New molecular evidence is presented from a portion of the mitochondrial cytochrome oxidase c subunit 1 gene (cox1) that improves our understanding of the phylogeny of the group. Based on these data a preliminary discussion of the present distribution of sea hares in a biogeographic context is put forward. Our findings are consistent with only some aspects of the current taxonomy and nomenclatural changes are proposed. The first, is the use of a rank free classification for the different Aplysia clades and subclades as opposed to previously used genus and subgenus affiliations. The second, is the suggestion that Aplysia brasiliana (Rang, 1828) is a junior synonym of Aplysia fasciata (Poiret, 1789). The third, is the elimination of Neaplysia since its only member is confirmed to be part of the large Varria clade.

Yersinia pestis, the etiological agent of plague, is of concern to human health both from an infectious disease and a civilian biodefense perspective. While Y. pestis and Y. pseudotuberculosis share more than 90% DNA homology, they have significantly different clinical manifestations. Plague is often fatal if untreated, yet Y. pseudotuberculosis causes severe intestinal distress and is rarely fatal. A better understanding of host response to these closely related pathogens may help explain the different mechanisms of virulence and pathogenesis that result in such different clinical outcomes. The aim of this study was to characterize host protein expression changes in human monocyte-like U937 cells after exposure to Y. pestis and Y. pseudotuberculosis. In order to gain global proteomic coverage of host response, proteins from cytoplasmic, nuclear and membrane fractions of host cells were studied by 2-dimensional differential gel electrophoresis (2-D DIGE) and relative protein expression differences were quantitated. Differentially expressed proteins, with at least 1.5 fold expression changes and p values of 0.01 or less, were identified by MALDI-MS or LC/MS/MS. With these criteria, differential expression was detected in 16 human proteins after Y. pestis exposure and 13 human proteins after Y. pseudotuberculosis exposure, of which only two of the differentially …

The gap between peak and delivered performance for scientific applications running on microprocessor-based systems has grown considerably in recent years. The inability to achieve the desired performance even on a single processor is often attributed to an inadequate memory system, but without identification or quantification of a specific bottleneck. In this work, we use an adaptable synthetic benchmark to isolate application characteristics that cause a significant drop in performance, giving application programmers and architects information about possible optimizations. Our adaptable probe, called sqmat, uses only four parameters to capture key characteristics of scientific workloads: working-set size, computational intensity, indirection, and irregularity. This paper describes the implementation of sqmat and uses its tunable parameters to evaluate four leading 64-bit microprocessors that are popular building blocks for current high performance systems: Intel Itanium2, AMD Opteron, IBM Power3, and IBM Power4.

Relatively little is known about the genetic basis for the unique physiology of metal-reducing genera in the delta subgroup of the proteobacteria. The recent availability of complete finished or draft-quality genome sequences for seven representatives allowed us to investigate the genetic and regulatory factors in a number of key pathways involved in the biosynthesis of building blocks and cofactors, metal-ion homeostasis, stress response, and energy metabolism using a combination of regulatory sequence detection and analysis of genomic context. In the genomes of delta-proteobacteria, we identified candidate binding sites for four regulators of known specificity (BirA, CooA, HrcA,sigma-32), four types of metabolite-binding riboswitches (RFN-, THI-,B12-elements and S-box), and new binding sites for the FUR, ModE, NikR,PerR, and ZUR transcription factors, as well as for the previously uncharacterized factors HcpR and LysX. After reconstruction of the corresponding metabolic pathways and regulatory interactions, we identified possible functions for a large number of previously uncharacterized genes covering a wide range of cellular functions. Phylogenetically diverse delta-proteobacteria appear to have homologous regulatory components. This study for the first time demonstrates the adaptability of the comparative genomic approach to de novo reconstruction of a regulatory network in a poorly studied taxonomic group of bacteria. Recent efforts …

The outer can welder (OCW) in the FB-Line Facility at the Savannah River Site (SRS) is a Gas Tungsten Arc Weld (GTAW) system used to create outer canisters compliant with the Department of Energy 3013 Standard, DOE-STD-3013-2000, Stabilization, Packaging, and Storage of Plutonium-Bearing Materials. The key welding parameters controlled and monitored on the outer can welder Data Acquisition System (DAS) are weld amperage, weld voltage, and weld rotational speed. Inner 3013 canisters from the Bagless Transfer System that contain plutonium metal or plutonium oxide are placed inside an outer 3013 canister. The canister is back-filled with helium and welded using the outer can welder. The completed weld is screened to determine if it is satisfactory by reviewing the OCW DAS key welding parameters, performing a helium leak check, performing a visual examination by a qualified weld inspector, and performing digital radiography of the completed weld. Canisters with unsatisfactory welds are cut open and repackaged. Canisters with satisfactory welds are deemed compliant with the 3013 standard for long-term storage.

Over the past 2 years the Tevatron peak luminosity steadily progressed and reached the level of 92e30 cm-2s-1 which exceeds the original Run IIa goal. Over 0.57fb-1 have being delivered to each CDF and D0 experiments since the beginning of the Run II. In parallel to the Collider operation, we have started a project of the luminosity upgrade which should lead to peak luminosities of about 270e30 and total integrated luminosity of 4.4-8.5 fb-1 through FY2009. In this paper we describe the status of the Tevatron Collider complex, essence of the upgrades and novel accelerator technologies to be employed.

Saltwater, or brine, underlies fresh water in many aquifers, with a transition zone separating them. Pumping fresh water by wells located above the transition zone produces upconing of the latter, eventually salinizing the pumped water, forcing shut-off. The salinity of the pumped water depends on the pumping rate, on the location of the well's screen, on the fresh water flow regime, and on the difference in density between fresh and salt water, expressed as a dimensionless factor called density difference factor (DDF). Following the well's shut-off, the upconed saltwater mound undergoes decay, tending to return to the pre-pumping regime. In this paper, the upconing-decay processes in an axially symmetrical system are investigated to discover how they are affected by the DDF and by the dispersivities. The code FEAS-Brine, developed for the simulation of coupled density-dependent flow and salt transport, is used. In this code, the flow equation is solved by the Galer:wqkin finite element method (FEM), while the advective-dispersive salt transport equation is solved in the Eulerian-Lagrangian framework. This code does not suffer from the instability constraint on the Peclet number in the vicinity of the pumping well, where advection dominates the salt transport. Simulation results show that upconing is …

We review the physics of nuclear matter at high energy density and the experimental search for the Quark-Gluon Plasma at the Relativistic Heavy Ion Collider (RHIC). The data obtained in the first three years of the RHIC physics program provide several lines of evidence that a novel state of matter has been created in the most violent, head-on collisions of Au nuclei at {radical}s = 200 GeV. Jet quenching and global measurements show that the initial energy density of the strongly interacting medium generated in the collision is about two orders of magnitude larger than that of cold nuclear matter, well above the critical density for the deconfinement phase transition predicted by lattice QCD. The observed collective flow patterns imply that the system thermalizes early in its evolution, with the dynamics of its expansion consistent with ideal hydrodynamic flow based on a Quark-Gluon Plasma equation of state.

The acceleration of the expansion of the universe arises from unknown physical processes involving either new fields in high energy physics or modifications of gravitation theory. It is crucial for our understanding to characterize the properties of the dark energy or gravity through cosmological observations and compare and distinguish between them. In fact, close consistencies exist between a dark energy equation of state function w(z) and changes to the framework of the Friedmann cosmological equations as well as direct spacetime geometry quantities involving the acceleration, such as ''geometric dark energy'' from the Ricci scalar. We investigate these interrelationships, including for the case of super acceleration or phantom energy where the fate of the universe may be more gentle than the Big Rip.

The creation of an excavation disturbed zone or excavation damaged zone is expected around all man-made openings in geologic formations. Macro- and micro-fracturing, and in general a redistribution of in situ stresses and rearrangement of rock structures, will occur in this zone, resulting in drastic changes of permeability to flow, mainly through the fractures and cracks induced by excavation. Such an EDZ may have significant implications for the operation and long-term performance of an underground nuclear waste repository. Various issues of concern need to be evaluated, such as processes creating fractures in the excavation damaged zone, the degree of permeability increase, and the potential for sealing or healing (with permeability reduction) in the zone. In recent years, efforts along these lines have been made for a potential repository in four rock types-crystalline rock, salt, indurated clay, and plastic clay-and these efforts have involved field, laboratory, and theoretical studies. The present work involves a synthesis of the ideas and issues that emerged from presentations and discussions on EDZ in these four rock types at a CLUSTER Conference and Workshop held in Luxembourg in November, 2003. First, definitions of excavation disturbed and excavation damaged zones are proposed. Then, an approach is suggested …

It is a well-established fact that cardiovascular health requires periodic exercise during which the human body often experiences significant physical discomfort. It is not obvious to the exerciser that the short-term pain and discomfort has a long-term positive health impact. Many cultures have well-established practices that involve exposing the body to periodic thermal discomfort. Scandinavian saunas and American Indian sweat lodges are two examples. Both are believed to promote health and well-being. Vacations often intentionally include significant thermal discomfort as part of the experience (e.g., sunbathing, and downhill skiing). So people often intentionally make themselves thermally uncomfortable yet the entire foundation of providing the thermal environment in our buildings is done to minimize the percentage of people thermally dissatisfied. We must provide an environment that does not negatively impact short-term health and we need to consider productivity but are our current thermal comfort standards too narrowly defined and do these standards actually contribute to longer-term negative health impacts? This paper examines the possibility that the human body thermoregulatory system has a corollary relationship to the cardiovascular system. It explores the possibility that we have an inherent need to exercise our thermoregulatory system. Potential, physiological, sociological and energy ramifications of these …

The Risk Based End State Vision Report for the Savannah River Site includes a variance that proposes on-site near surface disposal of waste from the program to produce Pu-238 heat sources for deep space probes. On-site disposal would greatly reduce the risk to workers by eliminating the need to repackage the waste in order to characterize it and ship it to the Waste Isolation Pilot Plant. Significant cost savings can also be realized. A legacy inventory of 6145 m3 containing 590,000 curies of Heat Source plutonium exists at the Savannah River Site. Our plan is to ship as much of this material as possible to the Waste Isolation Pilot Plant using currently available facilities and equipment. We estimate that most of the volume can be safely packaged and transported to WIPP. The remainder, 1813 m3 containing 280,000 curies, is proposed to be disposed of at the SRS after demonstrating that all applicable environmental protection regulations can be met. A technical analysis has been done u sing the overall methodology developed for low-level waste disposal performance assessments. The results to date show that groundwater protection will be maintained, but that enhanced engineering measures are needed to meet the performance measures for …

Operation of the Tevatron at lower temperatures, for the purpose of allowing higher energies, has resulted in a renewed interest in thermal modeling of the magnet strings. Static heat load and AC loses in the superconducting coils are initially transported through subcooled liquid helium. Heat exchange between the subcooled liquid and a counter flowing two-phase stream transfers the load to the latent heat. Stratification of the two-phase helium stream has resulted in considerably less heat exchange compared to the original design. Spool pieces have virtually no heat transfer to the two-phase resulting in a ''warm'' dipole just downstream. A model of the magnet string thermal behavior has been developed. The model has been used to identify temperature profiles within magnet strings. The temperature profiles are being used in conjunction with initial magnet quench performance data to predict the location of quench limiting magnets within the Tevatron. During thermal cycles of magnet strings, the model is being used to ''shuffle'' magnets within the magnet string in order to better match the magnets quench performance with its actual predicted temperature. The motivation for this analysis is to raise the operating energy of the Tevatron using a minimal number of magnets from the …

The Yucca Mountain site has a dry climate and deep water table, with the repository located in the middle of an unsaturated zone approximately 600 m thick. Radionuclide transport processes from the repository to the water table are sensitive to the unsaturated zone flow field, as well as to sorption, matrix diffusion, radioactive decay, and colloid transport mechanisms. The unsaturated zone flow and transport models are calibrated against both physical and chemical data, including pneumatic pressure, liquid saturation, water potential, temperature, chloride, and calcite. The transport model predictions are further compared with testing specific to unsaturated zone transport: at Alcove 1 in the Exploratory Studies Facility (ESF), at Alcove 8 and Niche 3 of the ESF, and at the Busted Butte site. The models are applied to predict the breakthroughs at the water table for nonsorbing and sorbing radionuclides, with faults shown as the important paths for radionuclide transport. Daughter products of some important radionuclides, such as {sup 239}Pu and {sup 241}Am, have faster transport than the parents and must be considered in the unsaturated zone transport model. Colloid transport is significantly affected by colloid size, but only negligibly affected by lunetic declogging (reverse filtering) mechanisms. Unsaturated zone model uncertainties …

Chromium is used as an alloy addition in stainless steels and nickel-chromium alloys to form protective chromium oxide scales. Chromium oxide undergoes reactive evaporation in high temperature exposures in the presence of oxygen and/or water vapor. The deposition of gaseous chromium species onto solid oxide fuel cell electrodes can reduce the efficiency of the fuel cell. Manganese additions to the alloy can reduce the activity of chromium in the oxide, either from solid solution replacement of chromium with manganese (at low levels of manganese) or from the formation of manganese-chromium spinels (at high levels of manganese). This reduction in chromium activity leads to a predicted reduction in chromium evaporation by as much as a factor of 35 at 800 C and 55 at 700 C. The results of evaporation loss measurements on nickel-chromium-manganese alloys are compared with the predicted reduction. Quantifying the effects of manganese additions on chromium evaporation should aid alloy development of metallic interconnects and balance-of-plant alloys.

We have synthesized ternary and quaternary diluted II-VI oxides using the combination of O ion implantation and pulsed laser melting. CdO{sub x}Te{sub 1-x} thin films with x up to 0.015, and the energy gap reduced by 150 meV were formed by O{sup +}-implantation in CdTe followed by pulsed laser melting. Quaternary Cd{sub 0.6}Mn{sub 0.4}O{sub x}Te{sub 1-x} and Zn{sub 0.88}Mn{sub 0.12}O{sub x}Te{sub 1-x} with mole fraction of incorporated O as high as 0.03 were also formed. The enhanced O incorporation in Mn-containing alloys is believed to be due to the formation of relatively strong Mn-O bonds. Optical transitions associated with the lower (E{sub -}) and upper (E{sub +}) conduction subbands resulting from the anticrossing interaction between the localized O states and the extended conduction states of the host are clearly observed in these quaternary diluted II-VI oxides. These alloys fulfill the criteria for a multiband semiconductor that has been proposed as a material for making high efficiency, single-junction solar cells.

Increased deployment of renewable energy (RE) and energy efficiency (EE) is expected to reduce natural gas demand and in turn place downward pressure on gas prices. A number of recent modeling studies include an evaluation of this effect. Based on data compiled from those studies summarized in this paper, each 1% reduction in national natural gas demand appears likely to lead to a long-term average wellhead gas price reduction of 0.75% to 2.5%, with some studies predicting even more sizable reductions. Reductions in wellhead prices will reduce wholesale and retail electricity rates, and will also reduce residential, commercial, and industrial gas bills. We further find that many of these studies appear to represent the potential impact of RE and EE on natural gas prices within the bounds of current knowledge, but that current knowledge of how to estimate this effect is extremely limited. While more research is therefore needed, existing studies suggest that it is not unreasonable to expect that any increase in consumer electricity costs attributable to RE and/or EE deployment may be substantially offset by the corresponding reduction in delivered natural gas prices. This effect represents a wealth transfer (from natural gas producers to consumers) rather than a …

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