Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to …

The field of statistics has long been noted for techniques to detect patterns and regularities in numerical data. In this article we explore connections between statistics and the emerging field of 'experimental mathematics'. These includes both applications of experimental mathematics in statistics, as well as statistical methods applied to computational mathematics.

When fractures in otherwise hard rocks are filled with fluids (oil, gas, water, CO{sub 2}), the type and physical state of the fluid (liquid or gas) can make a large difference in the wave speeds and attenuation properties of seismic waves. The present work summarizes methods of deconstructing theses effects of fractures, together with any fluids contained within them, on wave propagation as observed in reflection seismic data. Additional studies of waves in fluid-saturated granular media show that the behavior can be quite different from that for fractured media, since these materials are typically much softer mechanically than are the fractured rocks (i.e., having a very small drained moduli). Important fluid effects in such media are often governed as much by fluid viscosity as by fluid bulk modulus.

Because of its unique properties as a lightweight metal with high tensile strength, beryllium is widely used in applications including cell phones, golf clubs, aerospace, and nuclear weapons. Beryllium is also encountered in industries such as aluminium manufacturing, and in environmental remediation projects. Workplace exposure to beryllium particulates is a growing concern, as exposure to minute quantities of anthropogenic forms of beryllium may lead to sensitization and to chronic beryllium disease, which can be fatal and for which no cure is currently known. Furthermore, there is no known exposure-response relationship with which to establish a 'safe' maximum level of beryllium exposure. As a result, the current trend is toward ever lower occupational exposure limits, which in turn make exposure assessment, both in terms of sampling and analysis, more challenging. The problems are exacerbated by difficulties in sample preparation for refractory forms of beryllium, such as beryllium oxide, and by indications that some beryllium forms may be more toxic than others. This chapter provides an overview of sources and uses of beryllium, health risks, and occupational exposure limits. It also provides a general overview of sampling, analysis, and data evaluation issues that will be explored in greater depth in the remaining …

In this article we provide a detailed description of a technique to obtain a simple parameterization for different exceptional Lie groups, such as G{sub 2}, F{sub 4} and E{sub 6}, based on their fibration structure. For the compact case, we construct a realization which is a generalization of the Euler angles for SU(2), while for the non compact version of G{sub 2(2)}/SO(4) we compute the Iwasawa decomposition. This allows us to obtain not only an explicit expression for the Haar measure on the group manifold, but also for the cosets G{sub 2}/SO(4), G{sub 2}/SU(3), F{sub 4}/Spin(9), E{sub 6}/F{sub 4} and G{sub 2(2)}/SO(4) that we used to find the concrete realization of the general element of the group. Moreover, as a by-product, in the simplest case of G{sub 2}/SO(4), we have been able to compute an Einstein metric and the vielbein. The relevance of these results in physics is discussed.

Populus trees face constant challenges from the environment during their life cycle. To ensure their survival and reproduction, Populus trees deploy various types of defenses, one of which is the production of a myriad of secondary metabolites. Compounds derived from the shikimate-phenylpropanoid pathway are the most abundant class of secondary metabolites synthesized in Populus. Among other major classes of secondary metabolites in Populus are terpenoids and fatty acid-derivatives. Some of the secondary metabolites made by Populus trees have been functionally characterized. Some others have been associated with certain biological/ecological processes, such as defense against insects and microbial pathogens or acclimation or adaptation to abiotic stresses. Functions of many Populus secondary metabolites remain unclear. The advent of various novel genomic tools will enable us to explore in greater detail the complexity of secondary metabolism in Populus. Detailed data mining of the Populus genome sequence can unveil candidate genes of secondary metabolism. Metabolomic analysis will continue to identify new metabolites synthesized in Populus. Integrated genomics that combines various omics tools will prove to be the most powerful approach in revealing the molecular and biochemical basis underlying the biosynthesis of secondary metabolites in Populus. Characterization of the biological/ecological functions of secondary metabolites as …

In this paper, we present a Simple Distributed Particle Swarm Optimization (SDPSO) algorithm that can be used to track the optimal solution in a dynamic and noisy environment. The classic PSO algorithm lacks the ability to track changing optimum in a dynamic environment. Several approaches have been investigated to enhance the PSO algorithm s ability in dynamic environments. However, in dealing with dynamic environments, these approaches have lost PSO s original strengths of decentralized control and ease of implementation. The SDPSO algorithm proposed in this paper maintains these classic PSO features as well as provides the optimum result tracking capability in dynamic environments. In this research, the DF1 multimodal dynamic environment generator proposed by Morrison and De Jong is used to evaluate the classic PSO, SDPSO and other two adaptive PSOs.

Text describes the area, climate, agricultural history and statistics, soil-survey methods and definitions, soils and crops, land uses and agricultural methods, irrigation, and morphology and genesis of soils of Young County, Texas.

The most common method of analysis for beryllium is inductively coupled plasma atomic emission spectrometry (ICP-AES). This method, along with inductively coupled plasma mass spectrometry (ICP-MS), is discussed in Chapter 6. However, other methods exist and have been used for different applications. These methods include spectroscopic, chromatographic, colorimetric, and electrochemical. This chapter provides an overview of beryllium analysis methods other than plasma spectrometry (inductively coupled plasma atomic emission spectrometry or mass spectrometry). The basic methods, detection limits and interferences are described. Specific applications from the literature are also presented.

Arsenic is a naturally occurring trace element that poses a threat to human and ecosystem health, particularly when incorporated into food or water supplies. The greatest risk imposed by arsenic to human health results from contamination of drinking water, for which the World Health Organization recommends a maximum limit of 10 {micro}g L{sup -1}. Continued ingestion of drinking water having hazardous levels of arsenic can lead to arsenicosis and cancers of the bladder, skin, lungs and kidneys. Unfortunately, arsenic tainted drinking waters are a global threat and presently having a devastating impact on human health within Asia. Nearly 100 million people, for example, are presently consuming drinking water having arsenic concentrations exceeding the World Health Organization's recommended limit (Ahmed et al., 2006). Arsenic contamination of the environment often results from human activities such as mining or pesticide application, but recently natural sources of arsenic have demonstrated a devastating impact on water quality. Arsenic becomes problematic from a health perspective principally when it partitions into the aqueous rather than the solid phase. Dissolved concentrations, and the resulting mobility, of arsenic within soils and sediments are the combined result of biogeochemical processes linked to hydrologic factors. Processes favoring the partitioning of As …

Text describes the area, climate, agricultural history and statistics, soil-survey methods and definitions, soils and crops, land uses and agricultural methods, irrigation, and morphology and genesis of soils of Edwards and Real Counties, Texas.

Text describes the area, climate, agricultural history and statistics, soil-survey methods and definitions, soils and crops, land uses and agricultural methods, irrigation, and morphology and genesis of soils of Marion and Cass Counties, Texas.

Cometabolic bioremediation is probably the most under appreciated bioremediation strategy currently available. Cometabolism strategies stimulate only indigenous microbes with the ability to degrade the contaminant and cosubstrate e.g. methane, propane, toluene and others. This highly targeted stimulation insures that only those microbes that can degrade the contaminant are targeted, thus reducing amendment costs, well and formation plugging, etc. Cometabolic bioremediation has been used on some of the most recalcitrant contaminants, e.g. PCE, TCE, MTBE, TNT, dioxane, atrazine, etc. Methanotrophs have been demonstrated to produce methane monooxygense, an oxidase that can degrade over 300 compounds. Cometabolic bioremediation also has the advantage of being able to degrade contaminants to trace concentrations, since the biodegrader is not dependent on the contaminant for carbon or energy. Increasingly we are finding that in order to protect human health and the environment that we must remediate to lower and lower concentrations, especially for compounds like endocrine disrupters, thus cometabolism may be the best and maybe the only possibility that we have to bioremediate some contaminants.

This is a report on the comebiotic bioremediation which is the most under-appreciated strategy currently available.

In situ groundwater bioremediation of hydrocarbons has been used for more than 40 years. Most strategies involve biostimulation; however, recently bioaugmentation have been used for dehalorespiration. Aquifer and contaminant profiles are critical to determining the feasibility and strategy for in situ groundwater bioremediation. Hydraulic conductivity and redox conditions, including concentrations of terminal electron acceptors are critical to determine the feasibility and strategy for potential bioremediation applications. Conceptual models followed by characterization and subsequent numerical models are critical for efficient and cost effective bioremediation. Critical research needs in this area include better modeling and integration of remediation strategies with natural attenuation.

In this chapter we review the spectroscopic data for actinide molecules and the reaction dynamics for atomic and molecular actinides that have been examined in the gas phase or in inert cryogenic matrices. The motivation for this type of investigation is that physical properties and reactions can be studied in the absence of external perturbations (gas phase) or under minimally perturbing conditions (cryogenic matrices). This information can be compared directly with the results from high-level theoretical models. The interplay between experiment and theory is critically important for advancing our understanding of actinide chemistry. For example, elucidation of the role of the 5f electrons in bonding and reactivity can only be achieved through the application of experimentally verified theoretical models. Theoretical calculations for the actinides are challenging due the large numbers of electrons that must be treated explicitly and the presence of strong relativistic effects. This topic has been reviewed in depth in Chapter 17 of this series. One of the goals of the experimental work described in this chapter has been to provide benchmark data that can be used to evaluate both empirical and ab initio theoretical models. While gas-phase data are the most suitable for comparison with theoretical calculations, …

Gain an in-depth understanding of the role of quark flavor.

A field guide to irrigation in the lower Rio Grande Valley containing information about all the districts in the lower Rio Grande Valley, as collected by Lila Knight and her associates from experts in the field and government documents.

A guide to freshwater ecosystems describing waters chemical properties, potential pollutants of surface waters, freshwater ecosystems and drainage basins, and common plants and animals of freshwater ecosystems in Texas.

Many modern scientific applications rely on highly parallel calculations, which scale to 10's of thousands processors. However, most applications do not concentrate on parallelizing input/output operations. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab initio nuclear structure calculations. In this paper, we develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient input/output of large datasets along with their portability and ease of use in the downstream processing.

From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. …

Non-destructive evaluation (NDE) is the science and technology of determining non-invasively the internal structure of manufactured parts, objects, and materials. NDE application areas include medicine, industrial manufacturing, military, homeland security, and airport luggage screening. X-ray measurement systems are most widely used because of their ability to image through a wide range of material densities (from human tissue in medical applications to the dense materials of weapon components). Traditional x-ray systems involve a single source and detector system that rotate and/or translate about the object under evaluation. At each angular location, the source projects x-rays through the object. The rays undergo attenuation proportional to the density of the object's constitutive material. The detector records a measure of the attenuation. Mathematical algorithms are used to invert the forward attenuated ray projection process to form images of the object. This is known as computed tomography (CT). In recent years, the single-source x-ray NDE systems have been generalized to arrays of x-ray sources. Array sources permit multiple views of the object with fewer rotations and translations of the source/detector system. The spatially diverse nature of x-ray array sources has the potential of reducing data collection time, reducing imaging artifacts, and increasing the resolution of …

The Hanford Site began as part of the United States Manhattan Project to research, test and build atomic weapons during World War II. The original 670-square mile Hanford Site, then known as the Hanford Engineer Works, was the last of three top-secret sites constructed in order to produce enriched uranium and plutonium for the world's first nuclear weapons. B Reactor, located about 45 miles northwest of Richland, Washington, is the world's first full-scale nuclear reactor. Not only was B Reactor a first-of-a-kind engineering structure, it was built and fully functional in just 11 months. Eventually, the shoreline of the Columbia River in southeastern Washington State held nine nuclear reactors at the height of Hanford's nuclear defense production during the Cold War era. The B Reactor was shut down in 1968. During the 1980's, the U.S. Department of Energy began removing B Reactor's support facilities. The reactor building, the river pumphouse and the reactor stack are the only facilities that remain. Today, the U.S. Department of Energy (DOE) Richland Operations Office offers escorted public access to B Reactor along a designated tour route. The National Park Service (NPS) is studying preservation and interpretation options for sites associated with the Manhattan Project. …

Contaminants in soil can impact human health and the environment through a complex web of interactions. Soils exist where the atmosphere, hydrosphere, geosphere, and biosphere converge. Soil is the thin outer zone of the earth's crust that supports rooted plants and is the product of climate and living organisms acting on rock. A true soil is a mixture of air, water, mineral, and organic components. The relative proportions of these components determine the value of the soil for agricultural and for other human uses. These proportions also determine, to a large extent, how a substance added to soil is transported and/or transformed within the soil (Spositio, 2004). In mass-balance models, soil compartments play a major role, functioning both as reservoirs and as the principal media for transport among air, vegetation, surface water, deeper soil, and ground water (Mackay, 2001). Quantifying the mass transport of chemicals within soil and between soil and atmosphere is important for understanding the role soil plays in controlling fate, transport, and exposure to multimedia pollutants. Soils are characteristically heterogeneous. A trench dug into soil typically reveals several horizontal layers having different colors and textures. As illustrated in Figure 1, these multiple layers are often divided into …