A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the concept of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.

Pseudomonas putida strain AJ and Ochrobactrum strain TD were isolated from hazardous waste sites based on their ability to use vinyl chloride (VC) as a sole source of carbon and energy under aerobic conditions. Strains AJ and TD also use ethene and ethylene oxide as growth substrates. Strain AJ contained a linear megaplasmid (approximately 260 kb) when grown on VC or ethene, but no circular plasmids. While growing on ethylene oxide, the size of the linear plasmid in strain AJ decreased to approximately 100 kb, although its ability to use VC as a substrate was retained. The linear plasmids in strain AJ were cured and its ability to consume VC, ethene, and ethylene oxide was lost following growth on a rich substrate (Luria-Bertani broth) through at least three transfers. Strain TD contained three linear plasmids, ranging in size from approximately 100 kb to 320 kb, when growing on VC or ethene. As with strain AJ, the linear plasmids in strain TD were cured following growth on Luria -Bertani broth and its ability to consume VC and ethene was lost. Further analysis of these linear plasmids may help reveal the pathway for VC biodegradation in strains AJ and TD and explain …

One of the biggest challenges in cell biology is the imaging of living cells. For this purpose, the most commonly used visualization tool is fluorescent markers. However, conventional labels, such as organic fluorescent dyes or green fluorescent proteins (GFP), lack the photostability to allow the tracking of cellular events that happen over minutes to days. In addition, they are either toxic to cells (dyes), or difficult to construct and manipulate (GFP). We report here the use of a new class of fluorescent labels, silanized CdSe/ZnS nanocrystal-peptide conjugates, for imaging the nuclei of living cells. CdSe/ZnS nanocrystals, or so called quantum dots (qdots), are extremely photostable, and have been used extensively in cellular imaging of fixed cells. However, most of the studies about living cells so far have been concerned only with particle entry into the cytoplasm or the localization of receptors on the cell membrane. Specific targeting of qdots to the nucleus of living cells ha s not been reported in previous studies, due to the lack of a targeting mechanism and proper particle size. Here we demonstrate for the first time the construction of a CdSe/ZnS nanocrystal-peptide conjugate that carries the SV40 large T antigen nuclear localization signal (NLS), …

In heavy-ion inertial-confinement fusion systems, intense beams of ions must be transported from the exit of the final focus magnet system through the fusion chamber to hit millimeter-sized spots on the target. Effective plasma neutralization of intense ion beams in this final transport is essential for a heavy-ion fusion power plant to be economically competitive. The physics of neutralized drift has been studied extensively with particle-in-cell simulations. To provide quantitative comparisons of theoretical predictions with experiment, the Virtual National Laboratory for Heavy Ion Fusion has completed the construction and has begun experimentation with the Neutralized Transport Experiment (NTX). The experiment consists of three main sections, each with its own physics issues. The injector is designed to generate a very high-brightness, space-charge-dominated potassium beam while still allowing variable perveance by a beam aperturing technique. The magnetic-focusing section, consisting of four pulsed magnetic quadrupoles, permits the study of beam tuning, as well as the effects of phase space dilution due to higher-order nonlinear fields. In the final section, the converging ion beam exiting the magnetic section is transported through a drift region with plasma sources for beam neutralization, and the final spot size is measured under various conditions of neutralization. In this …

Although its value varies with the microstructure, hysteresis always accompanies hydride formation and decomposition in Pd(pure)-H, e.g., it is present even in nano-crystalline and thin films. Internal oxidation of Pd0.93Cr0.07 alloys leads to a pure Pd matrix containing nano-crystalline chromia precipitates. The characteristic hysteresis of Pd-H almost disappears in this form of Pd. The reasons for this are discussed. Hysteresis is an almost universal feature of first order solid state transitions. Its presence means that when such a transition is reversed, it follows a different path than that taken in the forward direction leading to a loss of useful work. Hysteresis is, of course, a reflection of the irreversibility of the transition.

Urban population density can influence transportation demand, as expressed through average daily vehicle-kilometers traveled per capita (VKT). In turn, changes in transportation demand influence total passenger vehicle emissions. Population density can also influence the fraction of total emissions that are inhaled by the exposed urban population. Equations are presented that describe these relationships for an idealized representation of an urban area. Using analytic solutions to these equations, we investigate the effect of three changes in urban population and urban land area (infill, sprawl, and constant-density growth) on per capita inhalation intake of primary pollutants from passenger vehicles. The magnitude of these effects depends on density-emissions elasticity ({var_epsilon}{sub e}), a normalized derivative relating change in population density to change in vehicle emissions. For example, if urban population increases, per capita intake is less with infill development than with constant-density growth if {var_epsilon}{sub e} is less than -0.5, while for {var_epsilon}{sub e} greater than -0.5 the reverse is true.

Production of 18 superconducting low-beta quadrupoles (MQXB) for the LHC is well advanced. These 5.5 m long magnets are designed to operate at 1.9 K with a peak field gradient of 215 T/m in 70 mm aperture. Two MQXB cold masses with a dipole orbit corrector between them form a single cryogenic unit (LQXB) which is the Q2 optical element of the final focus triplets in the LHC interaction regions. A program of magnetic field quality and alignment measurements of the cold masses is performed at room temperature during magnet fabrication and of the LQXB assembly as well as at superfluid helium temperature. Results of these measurements are summarized in this paper.

This paper informally speculates on the challenges of determining the atomic-scale surface and interface structure of nanomaterials. The relative capabilities of different techniques are compared. This includes discussion of theoretical methods needed to interpret experimental techniques.

Department of Energy (DOE) facilities within the weapons complex face a daunting challenge of remediating huge below inventories of legacy radioactive and toxic metal waste. More often than not, the scope of the problem is massive, particularly in the high recharge, humid regions east of the Mississippi river, where the off-site migration of contaminants continues to plague soil water, groundwater, and surface water sources. As of 2002, contaminated sites are closing rapidly and many remediation strategies have chosen to leave contaminants in-place. In situ barriers, surface caps, and bioremediation are often the remedial strategies of chose. By choosing to leave contaminants in-place, we must accept the fact that the contaminants will continue to interact with subsurface and surface media. Contaminant interactions with the geosphere are complex and investigating long term changes and interactive processes is imperative to verifying risks. We must be able to understand the consequences of our action or inaction. The focus of this manuscript is to describe recent technical developments for assessing the performance of in situ bioremediation and immobilization of subsurface metals and radionuclides. Research within DOE's NABIR and EMSP programs has been investigating the possibility of using subsurface microorganisms to convert redox sensitive toxic metals …

Although it is well known that the rate of sintering is governed by deceleratory kinetics, it is often difficult to fit power-law and nth-order reaction models over broad time-temperature ranges. This work shows that a phenomenological model combining a reaction order with an activation energy distribution can correlate surface area as a function of sintering time and temperature over a greater range of those variables. Qualitatively, the activation energy distribution accounts the dependence of free energy on particle size and material defects, while the reaction order accounts for geometric factors such as a distribution of diffusion lengths. The model is demonstrated for sintering of hydroxyapatite using data of Bailliez and Nzihou (Chem. Eng. J. 98 (2004), 141-152).

Although materials that exhibit nearest-neighbor-only antiferromagnetic interactions and geometrical frustration theoretically should not magnetically order in the absence of disorder, few such systems have been observed experimentally. One such system appears to be the pyrochlore Tb{sub 2}Ti{sub 2}O{sub 7}. However, previous structural studies indicated that Tb{sub 2}Ti{sub 2}O{sub 7} is an imperfect pyrochlore. To clarify the situation, we performed neutron powder diffraction (NPD) and x-ray absorption fine structure (XAFS) measurements on samples that were prepared identically to those that show no magnetic order. The NPD measurements show that the long-range structure of Tb{sub 2}Ti{sub 2}O{sub 7} is well ordered with no structural transitions between 4.5 and 600 K. In particular, mean-squared displacements (u{sup 2}'s) for each site follow a Debye model with no offsets. No evidence for Tb/Ti site interchange was observed within an upper limit of 2%. Likewise, no excess or deficiency in the oxygen stoichiometry was observed, within an upper limit of 2% of the nominal pyrochlore value. Tb L{sub III} and Ti K-edge XAFS measurements from 20-300 K similarly indicate a well-ordered local structure. Other aspects of the structure are considered. We conclude that Tb{sub 2}Ti{sub 2}O{sub 7} has, within experimental error, an ideal, disorder-free pyrochlore lattice, …

Algebraic sub-structuring refers to the process of applying matrix reordering and partitioning algorithms to divide a large sparse matrix into smaller submatrices from which a subset of spectral components are extracted and combined to form approximate solutions to the original problem. In this paper, we show that algebraic sub-structuring can be effectively used to solve generalized eigenvalue problems arising from the finite element analysis of an accelerator structure.

Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access …

The knowledge of how to ventilate buildings, and how much ventilation is necessary for human health and comfort, has evolved over centuries of trial and error. Humans and animals have developed successful solutions to the problems of regulating temperature and removing air pollutants through the use of ventilation. These solutions include ingenious construction methods, such as engineered passive ventilation (termite mounds and passive stacks), mechanical means (wing-powered, fans), and an evolving effort to identify problems and develop solutions. Ventilation can do more than help prevent building occupants from getting sick; it can provide an improved indoor environment. Codes and standards provide minimum legal requirements for ventilation, but the need for ventilation goes beyond code minima. In this paper we will look at indoor air pollutant sources over time, the evolution of ventilation strategies, current residential ventilation codes and standards (e.g., recently approved ASHRAE Standard 62.2), and briefly discuss ways in which we can go beyond the standards to optimize residential ventilation, reduce indoor air quality problems, and provide corresponding social and economic benefit.

This paper presents the basics of this model, including what physical conditions could produce a calibration constant shift and what might cause those conditions to arise. The new evidences are discussed and it is shown that the possibility of at-the-electrode recombination cannot be eliminated, in fact prior photographic evidence is shown to be reasonable evidence of this phenomenon. Thus in the absence of definitive data, the conclusion that apparent excess heat arises from a nuclear cause is premature. If the apparent excess heat signal is not representative of a true heat source, but is instead an equipment/method malfunction, integrating the signal is of no value. This paper proposes that is the situation, and will therefore focus on examining the phenomenon of apparent excess enthalpy (sometimes called excess heat). Not addressed will be the myriad of other purported evidences of nuclear reactions. The apparent excess heat claims form the largest block of claims for a nuclear FPHE cause, and the correlation of apparent excess heat with apparent nuclear ash detection is often cited as evidence of the nuclear nature of the FPHE. But confidence in the validity of the apparent excess heat signal is of critical importance in validating a nuclear …

The 9975 shipping package incorporates a cane fiberboard overpack for thermal insulation and impact resistance. Mechanical properties (tensile and compressive behavior) have been measured on cane fiberboard and a similar wood-based product following short-term conditioning in several temperature/humidity environments. Both products show similar trends, and vary in behavior with material orientation, temperature and humidity. A memory effect is also seen in that original strength values are only partially recovered following exposure to a degrading environment and return to ambient conditions.

The mechanisms responsible for noble gas concentrations, abundance patterns, and strong retentivity in sedimentary lithologies remain poorly explained. Diffusion-controlled fractionation of noble gases is modeled and examined as an explanation for the absolute and relative abundances of noble gases observed in sediments. Since the physical properties of the noble gases are strong functions of atomic mass, the individual diffusion coefficients, adsorption coefficients and atomic radii combine to impede heavy noble gas (Xe) diffusion relative to light noble gas (Ne) diffusion. Filling of lithic grains/half-spaces by diffusive processes thus produces Ne enrichments in the early and middle stages of the filling process with F(Ne) values similar to that observed in volcanic glasses. Emptying lithic grains/half-spaces produces a Xe-enriched residual in the late (but not final) stages of the process producing F(Xe) values similar to that observed in shales. 'Exotic but unexceptional' shales that exhibit both F(Ne) and F(Xe) enrichments can be produced by incomplete emptying followed by incomplete filling. This mechanism is consistent with literature reported noble gas abundance patterns but may still require a separate mechanism for strong retention. A system of labyrinths-with-constrictions and/or C-, Si-nanotubes when combined with simple adsorption can result in stronger diffusive separation and non-steady-state enrichments …

A calibrated groundwater flow model for a contaminated site can provide substantial information for assessing and improving hydraulic measures implemented for remediation. A three-dimensional transient groundwater flow model was developed for a contaminated mountainous site, at which interim corrective measures were initiated to limit further spreading of contaminants. This flow model accounts for complex geologic units that vary considerably in thickness, slope, and hydrogeologic properties, as well as large seasonal fluctuations of the groundwater table and flow rates. Other significant factors are local recharge from leaking underground storm drains and recharge from steep uphill areas. The zonation method was employed to account for the clustering of high and low hydraulic conductivities measured in a geologic unit. A composite model was used to represent the bulk effect of thin layers of relatively high hydraulic conductivity found within bedrock of otherwise low conductivity. The inverse simulator ITOUGH2 was used to calibrate the model for the distribution of rock properties. The model was initially calibrated using data collected between 1994 and 1996. To check the validity of the model, it was subsequently applied to predicting groundwater level fluctuation and groundwater flux between 1996 and 1998. Comparison of simulated and measured data demonstrated that …

Energy conversion efficiencies of better than 23% have been demonstrated for small scale tests of a few thermophotovoltaic (TPV) cells using front surface, tandem filters [1, 2]. The engineering challenge is to build this level of efficiency into arrays of cells that provide useful levels of energy. Variations in cell and filter performance will degrade TPV array performance. Repeated fabrication runs of several filters each provide an initial quantification of the fabrication variation for front surface, tandem filters for TPV spectral control. For three performance statistics, within-run variation was measured to be 0.7-1.4 percent, and run-to-run variation was measured to be 0.5-3.2 percent. Fabrication runs using a mask have been shown to reduce variation across interference filters from as high as 8-10 percent to less than 1.5 percent. Finally, several system design and assembly approaches are described to further reduce variation.

Cellular senescence suppresses cancer by arresting cells at risk for malignant tumorigenesis. However, senescent cells also secrete molecules that can stimulate premalignant cells to proliferate and form tumors, suggesting the senescence response is antagonistically pleiotropic. We show that premalignant mammary epithelial cells exposed to senescent human fibroblasts in mice irreversibly lose differentiated properties, become invasive and undergo full malignant transformation. Moreover, using cultured mouse or human fibroblasts and non-malignant breast epithelial cells, we show that senescent fibroblasts disrupt epithelial alveolar morphogenesis, functional differentiation, and branching morphogenesis. Further, we identify MMP-3 as the major factor responsible for the effects of senescent fibroblasts on branching morphogenesis. Our findings support the idea that senescent cells contribute to age-related pathology, including cancer, and describe a new property of senescent fibroblasts--the ability to alter epithelial differentiation--that might also explain the loss of tissue function and organization that is a hallmark of aging.

The use of enriched stable isotopes combined with modern epitaxial deposition and depth profiling techniques enables the preparation of material heterostructures, highly appropriate for self- and foreign-atom diffusion experiments. Over the past decade we have performed diffusion studies with isotopically enriched elemental and compound semiconductors. In the present paper we highlight our recent results and demonstrate that the use of isotopically enriched materials ushered in a new era in the study of diffusion in solids which yields greater insight into the properties of native defects and their roles in diffusion. Our approach of studying atomic diffusion is not limited to semiconductors and can be applied also to other material systems. Current areas of our research concern the diffusion in the silicon-germanium alloys and glassy materials such as silicon dioxide and ion conducting silicate glasses.

The status of CP violation and the CKM matrix is reviewed. Direct CP violation in B decay has been established and the measurement of sin 2{beta} in {psi}K modes reached 5% accuracy. I discuss the implications of these, and of the possible deviations of the CP asymmetries in b {yields} s modes from that in {psi}K. The first meaningful measurements of {alpha} and {gamma} are explained, together with their significance for constraining both the SM and new physics in B-{bar B} mixing. I also discuss implications of recent developments in the theory of nonleptonic decays for B {yields} {pi}K rates and CP asymmetries, and for the polarization in charmless B decays to two vector mesons.

The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These include including complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at EBI. Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68 percent of all prokaryotic proteins (covering 59 percent of residues) and 61 percent of eukaryotic proteins (40 percent of residues). More fine-grained coverage which would allow accurate modeling of …

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