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Thermal neutron imaging in an active interrogation environment
Gain an in-depth understanding of the role of quark flavor.
Date:
July 3, 2009
Creator:
Jaffe, D. E.; Marciano, W.; Soni, A.; Parsa, Z. & Van de Water,R.
System:
The UNT Digital Library
Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments
Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmark the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.
Date:
May 20, 2009
Creator:
Seshagiri, Lakshminarasimhan; Sosonkina, Masha & Zhang, Zhao
System:
The UNT Digital Library
Experimental Mathematics and Computational Statistics
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.
Date:
April 30, 2009
Creator:
Bailey, David H. & Borwein, Jonathan M.
System:
The UNT Digital Library
Genomics of Secondary Metabolism in Populus: Interactions With Biotic and Abiotic Environments
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 …
Date:
January 1, 2009
Creator:
Chen, Feng; Liu, Chang-Jun; Tschaplinski, Timothy J & Zhao, Nan
System:
The UNT Digital Library
Fluid effects on seismic waves in hard rocks with fractures and in soft granular media
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.
Date:
March 1, 2009
Creator:
Berryman, James G.
System:
The UNT Digital Library
Mathematical models as tools for probing long-term safety of CO2 storage
Subsurface reservoirs being considered for storing CO{sub 2} include saline aquifers, oil and gas reservoirs, and unmineable coal seams (Baines and Worden, 2004; IPCC, 2005). By far the greatest storage capacity is in saline aquifers (Dooley et al., 2004), and our discussion will focus primarily on CO{sub 2} storage in saline formations. Most issues for safety and security of CO{sub 2} storage arise from the fact that, at typical temperature and pressure conditions encountered in terrestrial crust, CO{sub 2} is less dense than aqueous fluids. Accordingly, CO{sub 2} will experience an upward buoyancy force in most subsurface environments, and will tend to migrate upwards whenever (sub-)vertical permeable pathways are available, such as fracture zones, faults, or improperly abandoned wells (Bachu, 2008; Pruess, 2008a, b; Tsang et al., 2008). CO{sub 2} injection will increase fluid pressures in the target formation, thereby altering effective stress distributions, and potentially triggering movement along fractures and faults that could increase their permeability and reduce the effectiveness of a caprock in containing CO{sub 2} (Rutqvist et al., 2008; Chiaramonte et al., 2008). Induced seismicity as a consequence of fluid injection is also a concern (Healy et al., 1968; Raleigh et al., 1976; Majer et al., 2007). …
Date:
February 1, 2009
Creator:
Pruess, Karsten; Birkholzer, Jens & Zhou, Quanlin
System:
The UNT Digital Library
Cometabolic bioremediation
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.
Date:
February 15, 2009
Creator:
Hazen, Terry C.
System:
The UNT Digital Library
Exceptional groups, symmetric spaces and applications
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.
Date:
March 31, 2009
Creator:
Cerchiai, Bianca L. & Cacciatori, Sergio L.
System:
The UNT Digital Library
OVERVIEW OF BERYLLIUM SAMPLING AND ANALYSIS
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 …
Date:
April 1, 2009
Creator:
Brisson, M
System:
The UNT Digital Library
Quantitative Assessment of Robot-generated Maps
Mobile robotic mapping is now considered to be a sufficiently mature field with demonstrated successes in various domains. While much progress has been made in the development of computationally efficient and consistent mapping schemes, it is still murky, at best, on how these maps can be evaluated. We are motivated by the absence of an accepted standard for quantitatively measuring the performance of robotic mapping systems against user-defined requirements. It is our belief that the development of standardized methods for quantitatively evaluating existing robotic technologies will improve the utility of mobile robots in already established application areas, such as vacuum cleaning, robot surveillance, and bomb disposal. This approach will also enable the proliferation and acceptance of such technologies in emerging markets. This chapter summarizes our preliminary efforts by bringing together the research community towards addressing this important problem which has ramifications not only from researchers perspective but also from consumers, robot manufacturers, and developers viewpoints.
Date:
January 1, 2009
Creator:
Scrapper, Chris; Madhavan, Raj & Lakaemper, Rolf
System:
The UNT Digital Library
Hadron Production in Heavy Ion Collisions
Heavy ion collisions are an ideal tool to explore the QCD phase diagram. The goal is to study the equation of state (EOS) and to search for possible in-medium modifications of hadrons. By varying the collision energy a variety of regimes with their specific physics interest can be studied. At energies of a few GeV per nucleon, the regime where experiments were performed first at the Berkeley Bevalac and later at the Schwer-Ionen-Synchrotron (SIS) at GSI in Darmstadt, we study the equation of state of dense nuclear matter and try to identify in-medium modifications of hadrons. Towards higher energies, the regime of the Alternating Gradient Synchrotron (AGS) at the Brookhaven National Laboratory (BNL), the Super-Proton Synchrotron (SPS) at CERN, and the Relativistic Heavy Ion Collider (RHIC) at BNL, we expect to produce a new state of matter, the Quark-Gluon Plasma (QGP). The physics goal is to identify the QGP and to study its properties. By varying the energy, different forms of matter are produced. At low energies we study dense nuclear matter, similar to the type of matter neutron stars are made of. As the energy is increased the main constituents of the matter will change. Baryon excitations will become …
Date:
May 19, 2009
Creator:
Ritter, Hans Georg & Xu, Nu
System:
The UNT Digital Library
Proteomic Insights: Cryoadaption of Permafrost Bacteria
The permafrost microbial community has been described as 'a community of survivors' (Friedman 1994). Because of the permanently cold condition and the long term isolation of the permafrost sediments, the permafrost microorganisms have acquired various adaptive features in the membrane, enzymes, and macromolecular synthesis. This chapter reviews the different adaptive mechanisms used by permafrost microorganisms with a focus on the proteomic level of cryoadaptation that have recently been identified during the low temperature growth in permafrost bacteria.
Date:
January 1, 2009
Creator:
Qiu, Yinghua; Vishnivetskaya, Tatiana A. & Lubman, David M.
System:
The UNT Digital Library
CHAPTER 7. BERYLLIUM ANALYSIS BY NON-PLASMA BASED METHODS
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.
Date:
April 20, 2009
Creator:
Ekechukwu, A
System:
The UNT Digital Library
Mass Transport within Soils
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 …
Date:
March 1, 2009
Creator:
McKone, Thomas E.
System:
The UNT Digital Library
Viable Cyanobacteria and Green Algae from the Permafrost Darkness
This review represents an overview of the existence, distribution and abundance of the photoautotrophic microorganisms in the deep subsurface permafrost of the Northeast Russia and McMurdo Dry Valleys, Antarctica. The morphology, growth rate, spectral properties, phylogenetic position of the viable permafrost green algae and cyanobacteria have been studied. Viable photoautotrophs were represented by unicellular green algae and filamentous cyanobacteria with low growth rate. Spectral studies of ancient cyanobacteria and green algae did not reveal any significant differences between them and their contemporary relatives. Phylogenetic analyses have shown that permafrost photoautotrophs were closely related to strains and more often to uncultured environmental clones from cold regions.
Date:
January 1, 2009
Creator:
Vishnivetskaya, Tatiana A.
System:
The UNT Digital Library
Chapter 27 -- Breast Cancer Genomics, Section VI, Pathology and Biological Markers of Invasive Breast Cancer
Breast cancer is predominantly a disease of the genome with cancers arising and progressing through accumulation of aberrations that alter the genome - by changing DNA sequence, copy number, and structure in ways that that contribute to diverse aspects of cancer pathophysiology. Classic examples of genomic events that contribute to breast cancer pathophysiology include inherited mutations in BRCA1, BRCA2, TP53, and CHK2 that contribute to the initiation of breast cancer, amplification of ERBB2 (formerly HER2) and mutations of elements of the PI3-kinase pathway that activate aspects of epidermal growth factor receptor (EGFR) signaling and deletion of CDKN2A/B that contributes to cell cycle deregulation and genome instability. It is now apparent that accumulation of these aberrations is a time-dependent process that accelerates with age. Although American women living to an age of 85 have a 1 in 8 chance of developing breast cancer, the incidence of cancer in women younger than 30 years is uncommon. This is consistent with a multistep cancer progression model whereby mutation and selection drive the tumor's development, analogous to traditional Darwinian evolution. In the case of cancer, the driving events are changes in sequence, copy number, and structure of DNA and alterations in chromatin structure or …
Date:
June 18, 2009
Creator:
Spellman, Paul T.; Heiser, Laura & Gray, Joe W.
System:
The UNT Digital Library
Density Functional Theory/A Practical Introduction
None
Date:
January 1, 2009
Creator:
Sholl, D. S. & Steckel, J. A.
System:
The UNT Digital Library
Genome Sequence Databases (Overview): Sequencing and Assembly
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. …
Date:
January 1, 2009
Creator:
Lapidus, Alla L.
System:
The UNT Digital Library
Proceedings of the 5th Annual Workshop on Cyber Security and Information Intelligence Research: Cyber Security and Information Intelligence Challenges and Strategies
Our reliance on the cyber infrastructure has further grown and the dependencies have become more complex. The infrastructure and applications running on it are not generally governed by the rules of bounded systems and inherit the properties of unbounded systems, such as the absence of global control, borders and barriers. Furthermore, the quest for increasing functionality and ease of operation is often at the cost of controllability, potentially opening up avenues for exploitation and failures. Intelligence is information valued for its currency and relevance rather than its detail or accuracy. In the presence of information explosion, i.e., the pervasive abundance of (public/private) information and the effects of such, intelligence has the potential to shift the advantages in the dynamic game of defense and attacks in cyber space. 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. The goal of the workshop is to establish, debate and challenge the far-reaching agenda that broadly and comprehensively …
Date:
January 1, 2009
Creator:
Sheldon, Frederick T; Peterson, Greg D; Krings, Axel; Abercrombie, Robert K & Mili, Ali
System:
The UNT Digital Library
Cometabolic bioremediation
This is a report on the comebiotic bioremediation which is the most under-appreciated strategy currently available.
Date:
February 15, 2009
Creator:
Hazen, Terry C.
System:
The UNT Digital Library
Congressional Record: Proceedings and Debates of the 111th Congress, First Session
The Congressional Record contains the records for sessions of the U.S. Congress including summaries of proceedings, letters, and speeches for the Senate and House of Representatives. There is a red tab sticking out of page E2255, highlight the speech Hon. Alcee L. Hastings gave about Helen Snapp.
Date:
September 14, 2009
Creator:
United States. Congress.
System:
The Portal to Texas History
Monodisperse metal nanoparticle catalysts on silica mesoporous supports: synthesis, characterizations, and catalytic reactions
The design of high performance catalyst achieving near 100% product selectivity at maximum activity is one of the most important goals in the modern catalytic science research. To this end, the preparation of model catalysts whose catalytic performances can be predicted in a systematic and rational manner is of significant importance, which thereby allows understanding of the molecular ingredients affecting the catalytic performances. We have designed novel 3-dimensional (3D) high surface area model catalysts by the integration of colloidal metal nanoparticles and mesoporous silica supports. Monodisperse colloidal metal NPs with controllable size and shape were synthesized using dendrimers, polymers, or surfactants as the surface stabilizers. The size of Pt, and Rh nanoparticles can be varied from sub 1 nm to 15 nm, while the shape of Pt can be controlled to cube, cuboctahedron, and octahedron. The 3D model catalysts were generated by the incorporation of metal nanoparticles into the pores of mesoporous silica supports via two methods: capillary inclusion (CI) and nanoparticle encapsulation (NE). The former method relies on the sonication-induced inclusion of metal nanoparticles into the pores of mesoporous silica, whereas the latter is performed by the encapsulation of metal nanoparticles during the hydrothermal synthesis of mesoporous silica. The …
Date:
September 14, 2009
Creator:
Somorjai, G.A.
System:
The UNT Digital Library
The use of microarrays in microbial ecology
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 …
Date:
September 15, 2009
Creator:
Andersen, G. L.; He, Z.; DeSantis, T. Z.; Brodie, E. L. & Zhou, J.
System:
The UNT Digital Library
Arsenic chemistry in soils and sediments
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 …
Date:
October 15, 2009
Creator:
Fendorf, S.; Nico, P.; Kocar, B.D.; Masue, Y. & Tufano, K.J.
System:
The UNT Digital Library