Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

We will provide a review of some of the physics which can be addressed by studying fluctuations and correlations in heavy ion collisions. We will discuss Lattice QCD results on fluctuations and correlations and will put them into context with observables which have been measured in heavy-ion collisions. Special attention will be given to the QCD critical point and the first order co-existence region, and we will discuss how the measurement of fluctuations and correlations can help in an experimental search for non-trivial structures in the QCD phase diagram.

Evaporitic environments are found in a variety of depositional environments as early as the Archean. The depositional settings, microbial community and mineralogical composition vary significantly as no two settings are identical. The common thread linking all of the settings is that evaporation exceeds precipitation resulting in elevated concentrations of cations and anions that are higher than in oceanic systems. The Dead Sea and Storrs Lake are examples of two diverse modern evaporitic settings as the former is below sea level and the latter is a coastal lake on an island in the Caribbean. Each system varies in water chemistry as the Dead Sea dissolved ions originate from surface weathered materials, springs, and aquifers while Storrs Lake dissolved ion concentration is primarily derived from sea water. Consequently some of the ions, i.e., Sr, Ba are found at significantly lower concentrations in Storrs Lake than in the Dead Sea. The origin of the dissolved ions are ultimately responsible for the pH of each system, alkaline versus mildly acidic. Each system exhibits unique biogeochemical properties as the extreme environments select certain microorganisms. Storrs Lake possesses significant biofilms and stromatolitic deposits and the alkalinity varies depending on rainfall and storm activity. The microbial community …

Arguments pertaining to the mind-brain connection and to the physical effectiveness of our conscious choices have been presented in two recent books, one by John Searle, the other by Jaegwon Kim. These arguments are examined, and it is argued that the difficulties encountered arise from a defective understanding and application of a pertinent part of contemporary science, namely quantum mechanics.

The Defense Waste Processing Facility (DWPF) initiated processing of Sludge Batch 4 (SB4) in May 2007. SB4 was the first DWPF sludge batch to contain significant quantities of HM or high Al sludge. Initial testing with SB4 simulants showed potential negative impacts to DWPF processing; therefore, Savannah River National Laboratory (SRNL) performed extensive testing in an attempt to optimize processing. SRNL's testing has resulted in the highest DWPF production rates since start-up. During SB4 processing, DWPF also began incorporating waste streams from the interim salt processing facilities to initiate coupled operations. While DWPF has been processing SB4, the Liquid Waste Organization (LWO) and the SRNL have been preparing Sludge Batch 5 (SB5). SB5 has undergone low-temperature aluminum dissolution to reduce the mass of sludge for vitrification and will contain a small fraction of Purex sludge. A high-level review of SB4 processing and the SB5 preparation studies will be provided.

In widely distributed systems generally, and in science-oriented Grids in particular, software, CPU time, storage, etc., are treated as"services" -- they can be allocated and used with service guarantees that allows them to be integrated into systems that perform complex tasks. Network communication is currently not a service -- it is provided, in general, as a"best effort" capability with no guarantees and only statistical predictability. In order for Grids (and most types of systems with widely distributed components) to be successful in performing the sustained, complex tasks of large-scale science -- e.g., the multi-disciplinary simulation of next generation climate modeling and management and analysis of the petabytes of data that will come from the next generation of scientific instrument (which is very soon for the LHC at CERN) -- networks must provide communication capability that is service-oriented: That is it must be configurable, schedulable, predictable, and reliable. In order to accomplish this, the research and education network community is undertaking a strategy that involves changes in network architecture to support multiple classes of service; development and deployment of service-oriented communication services, and; monitoring and reporting in a form that is directly useful to the application-oriented system so that it may …

Releases of acutely toxic airborne contaminants in or near a building can lead to significant human exposures unless prompt response measures are identified and implemented. Commonly, possible responses include conflicting strategies, such as shutting the ventilation system off versus running it in a purge (100percent outside air) mode, or having occupants evacuate versus sheltering in place. The right choice depends in part on quickly identifying the source locations, the amounts released, and the likely future dispersion routes of the pollutants. This paper summarizes recent developments to provide such estimates in real time using an approach called Bayesian Monte Carlo updating. This approach rapidly interprets measurements of airborne pollutant concentrations from multiple sensors placed in the building and computes best estimates and uncertainties of the release conditions. The algorithm is fast, capable of continuously updating the estimates as measurements stream in from sensors. The approach is employed, as illustration, to conduct two specific investigations under different situations.

Population distribution during the day can be defined as distribution of population in an area during the daytime hours. However, a precise definition of daytime hours is challenging given the geographic variability in the length of a day or daylight hours. The US Census Bureau used "normal business hours" as the span of time to describe daytime population. Given that Censuses typically estimates residential population, it represents a nighttime population distribution. In that respect, daytime population in an area may be broadly defined as distribution of population at times other than when they are expected to be at their residences at night which extends the duration from business hours to include the evening hours as well.

Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

EUV lithography (EUVL) employs illumination wavelengths around 13.5 nm, and in many aspects it is considered an extension of optical lithography, which is used for the high-volume manufacturing (HVM) of today's microprocessors. The EUV wavelength of illumination dictates the use of reflective optical elements (mirrors) as opposed to the refractive lenses used in conventional lithographic systems. Thus, EUVL tools are based on all-reflective concepts: they use multilayer (ML) coated optics for their illumination and projection systems, and they have a ML-coated reflective mask.

Over the course of the nineteenth and twentieth centuries, the United States developed a wealthy society on the basis of cheap and abundant fossil fuel energy. As fossil fuels have become ecologically and economically expensive in the twenty-first century, America has shown mixed progress in transitioning to a more sustainable energy system. From 2000 to 2006, energy and carbon intensity of GDP continued favorable long-term trends of decline. Energy end-use efficiency also continued to improve; for example, per-capita electricity use was 12.76 MWh per person per year in 2000 and again in 2006, despite 16 percent GDP growth over that period. Environmental costs of U.S. energy production and consumption have also been reduced, as illustrated in air quality improvements. However, increased fossil fuel consumption, stagnant efficiency standards, and expanding corn-based ethanol production have moved the energy system in the opposite direction, toward a less sustainable energy system. This chapter reviews energy system developments between 2000 and 2006 and presents policy recommendations to move the United States toward a more sustainable energy system.

The interaction of metal ions and oxyanions with nanoscale mineral phases has not yet been extensively studied despite the increased recognition of their prevalence in natural systems as a significant component of geomedia. A combination of macroscopic uptake studies to investigate the adsorption behavior of As(V), Cu(II), Hg(II), and Zn(II) onto nanoparticulate goethite ({alpha}-FeOOH) as a function of aging time at elevated temperature (75 C) and synchrotron-based X-ray studies to track changes in both the sorption mode and the rate of nanoparticle growth reveal the effects that uptake has on particle growth. Metal(loid) species which sorb quickly to the iron oxyhydroxide particles (As(V), Cu(II)) appear to passivate the particle surface, impeding the growth of the nanoparticles with progressive aging; in contrast, species that sorb more slowly (Hg(II), Zn(II)) have considerably less impact on particle growth. Progressive changes in the speciation of these particular metals with time suggest shifts in the mode of metal uptake with time, possibly indicating structural incorporation of the metal(loid) into the nanoparticle; this is supported by the continued increase in uptake concomitant with particle growth, implying that metal species may transform from surface-sorbed species to more structurally incorporated forms. This type of incorporation would have implications …

As our dependence on the cyber infrastructure grows ever larger, more complex and more distributed, the systems that compose it become more prone to failures and/or exploitation. Intelligence is information valued for its currency and relevance rather than its detail or accuracy. Information explosion describes the pervasive abundance of (public/private) information and the effects of such. Gathering, analyzing, and making use of information constitutes a business- / sociopolitical- / military-intelligence gathering activity and ultimately poses significant advantages and liabilities to the survivability of "our" society. The combination of increased vulnerability, increased stakes and increased threats make cyber security and information intelligence (CSII) one of the most important emerging challenges in the evolution of modern cyberspace "mechanization." The goal of the workshop was to challenge, establish and debate a far-reaching agenda that broadly and comprehensively outlined a strategy for cyber security and information intelligence that is founded on sound principles and technologies. We aimed to discuss novel theoretical and applied research focused on different aspects of software security/dependability, as software is at the heart of the cyber infrastructure.

Historically, attention on soil organic matter (SOM) has focused on the central role that it plays in ecosystem fertility and soil properties, but in the past two decades the role of soil organic carbon in moderating atmospheric CO{sub 2} concentrations has emerged as a critical research area. This chapter will focus on the storage and turnover of natural organic matter in soil (SOM), in the context of the global carbon cycle. Organic matter in soils is the largest carbon reservoir in rapid exchange with atmospheric CO{sub 2}, and is thus important as a potential source and sink of greenhouse gases over time scales of human concern (Fischlin and Gyalistras 1997). SOM is also an important human resource under active management in agricultural and range lands worldwide. Questions driving present research on the soil C cycle include: Are soils now acting as a net source or sink of carbon to the atmosphere? What role will soils play as a natural modulator or amplifier of climatic warming? How is C stabilized and sequestered, and what are effective management techniques to foster these processes? Answering these questions will require a mechanistic understanding of how and where C is stored in soils. The quantity …

Significant numbers of viable ancient microorganisms are known to be present within the permafrost. They have been isolated in both polar regions from the cores up to 400 m deep and ground temperatures of -27 C. The age of the cells corresponds to the longevity of the permanently frozen state of the soils, with the oldest cells dating back to {approx}3 million years in the Arctic, and {approx}5 million years in the Antarctic. They are the only life forms known to have retained viability over geological time. Thawing of the permafrost renews their physiological activity and exposes ancient life to modern ecosystems. Thus, the permafrost represents a stable and unique physicochemical complex, which maintains life incomparably longer than any other known habitats. If we take into account the depth of the permafrost layers, it is easy to conclude that they contain a total microbial biomass many times higher than that of the soil cover. This great mass of viable matter is peculiar to permafrost only.

Abstract. Interest in complex integrated digital or virtual human modeling has seen a significant increase over the last decade. Coincident with that increased interest, Oak Ridge National Laboratory (ORNL) initiated the development of a human simulation tool, the Virtual Human. The Virtual Human includes a problem-solving environment (PSE) for implementing the integration of physiological models in different programming languages and connecting physiological function to anatomy. The Virtual Human PSE (VHPSE) provides the computational framework with which to develop the concept of a "Virtual Human." Supporting the framework is a data definition for modeling parameters, PhysioML, a Virtual Human Database (VHDB), and a Web-based graphical user interface (GUI) developed using Java. Following description of the VHPSE, we discuss four example implementations of models within the framework. Further expansion of a human modeling environment was carried out in the Defense Advanced Research Projects Agency Virtual Soldier Project. SCIRun served as the Virtual Soldier problem solving environment (VSPSE). We review and compare specific developments in these projects that have significant potential for the future of Virtual Human modeling and simulation. We conclude with an evaluation of areas of future work that will provide important extensions to the VHPSE and VSPSE and make possible …

An antibody that recognizes a chelated form of hexavalent uranium was used in the development of two different immunosensors for uranium detection. Specifically, these sensors were utilized for the analysis of groundwater samples collected during a 2007 field study of in situ bioremediation in a aquifer located at Rifle, CO. The antibody-based sensors provided data comparable to that obtained using Kinetic Phosphorescence Analysis (KPA). Thus, these novel instruments and associated reagents should provide field researchers and resource managers with valuable new tools for on-site data acquisition.

Functional gene arrays (FGA) are microarrays that contain probes for genes encoding proteins or enzymes involved in functions of interest and allow for the study of thousands of genes at one time. The most comprehensive FGA to date is the GeoChip, which contains ~;;24,000 probes for ~;;10,000 genes involved in the geochemical cycling of C, N, P, and S, as well as genes involved in metal resistance and reduction and contaminant degradation. This chapter details the methods necessary for GeoChip analysis. Methods covered include preparation of DNA (whole community genome amplification and labeling), array setup (prehybridization steps), hybridization (sample and hybridization buffers), and post hybridization steps (slide washing and array scanning).

Crosswell seismic acquisition provides an ideal geometry for monitoring travel time changes in the subsurface. Analysis of delay time in terms of a characteristic frequency allows us to estimate optimal acquisition parameters (frequency and distance). We have deployed standard data acquisition equipment for continuous monitoring of crosswell travel time in two separate field experiments, with well spacing of 3 and 30 m. The acquisition hardware used for the field experiments is described, along with environmental effects (such as temperature) that influence the measurements. Two field experiments are described that correlate changes in travel time (and therefore velocity) with changes in barometric pressure. The results from the two field sites show a pressure sensitivity for velocity of 10{sup -6}/Pa to 10{sup -8}/Pa.

For better or worse, natural gas has become the fuel of choice for new power plants being built across the United States. According to the Energy Information Administration (EIA), natural gas-fired units account for nearly 90% of the total generating capacity added in the U.S. between 1999 and 2005 (EIA 2006b), bringing the nationwide market share of gas-fired generation to 19%. Looking ahead over the next decade, the EIA expects this trend to continue, increasing the market share of gas-fired generation to 22% by 2015 (EIA 2007a). Though these numbers are specific to the US, natural gas-fired generation is making similar advances in many other countries as well. A large percentage of the total cost of gas-fired generation is attributable to fuel costs--i.e., natural gas prices. For example, at current spot prices of around $7/MMBtu, fuel costs account for more than 75% of the levelized cost of energy from a new combined cycle gas turbine, and more than 90% of its operating costs (EIA 2007a). Furthermore, given that gas-fired plants are often the marginal supply units that set the market-clearing price for all generators in a competitive wholesale market, there is a direct link between natural gas prices and wholesale …

This standard specifies the set of tribal names and codes necessary to constitute consistent and unambiguous identification of federally-recognized American Indian and Alaska Native entities.

The identification of crystalline phases in solids requires knowledge of two microstructural properties: crystallographic structure and chemical composition. Traditionally, this has been accomplished using X-ray diffraction techniques where the measured crystallographic information, in combination with separate chemical composition measurements for specimens of unknown pedigrees, is used to deduce the unknown phases. With the latest microstructural analysis tools for scanning electron microscopes, both the crystallography and composition can be determined in a single analysis utilizing electron backscatter diffraction and energy dispersive spectroscopy, respectively. In this chapter, we discuss the approach required to perform these experiments, elucidate the benefits and limitations of this technique, and detail via case studies how composition, crystallography, and diffraction contrast can be used as phase discriminators.

Most current scanning electron microscopes (SEMs) have the ability to analyze samples in a low vacuum mode, whereby a partial pressure of water vapor is introduced into the SEM chamber, allowing the characterization of nonconductive samples without any special preparation. Although the presence of water vapor in the chamber degrades electron backscatter diffraction (EBSD) patterns, the potential of this setup for EBSD characterization of nonconductive samples is immense. In this chapter we discuss the requirements, advantages and limitations of low vacuum EBSD (LV-EBSD), and present how this technique can be applied to a two-phase ceramic composite as well as hydrated biominerals as specific examples of when LV-EBSD can be invaluable.

Agency strategic plan for the Texas Department of Criminal Justice describing the organization's planned services, activities, and other goals during fiscal years 2009 through 2013.