Physical Sciences and Mathematics Commons^™

Protein Structure Data Management System, Yanchao Wang

Computer Science Dissertations

With advancement in the development of the new laboratory instruments and experimental techniques, the protein data has an explosive increasing rate. Therefore how to efficiently store, retrieve and modify protein data is becoming a challenging issue that most biological scientists have to face and solve. Traditional data models such as relational database lack of support for complex data types, which is a big issue for protein data application. Hence many scientists switch to the object-oriented databases since object-oriented nature of life science data perfectly matches the architecture of object-oriented databases, but there are still a lot of problems that need …

Critical Thinking Traits Of Top-Tier Experts And Implications For Computer Science Education, Dean Bushey

All Dissertations

A documented shortage of technical leadership and top-tier performers in
computer science jeopardizes the technological edge, security, and economic well-being of the nation. The 2005 President's Information and Technology Advisory Committee (PITAC) Report on competitiveness in computational sciences highlights the major impact of science, technology, and innovation in keeping America competitive in the global marketplace. It stresses the fact that the supply of science, technology, and engineering experts is at the core
of America's technological edge, national competitiveness and security. However, recent data shows that both undergraduate and postgraduate production of computer scientists is falling.

Past research on expert performance …

Upper Limits On Gravitational Wave Emission From 78 Radio Pulsars, B. Abbott, R. Abbott, R. Adhikari, J. Agresti, P. Ajith, B. Allen, R. Amin, S. B. Anderson, W. G. Anderson, M. Arain, M. Araya, H. Armandula, M. Ashley, S. Aston, P. Aufmuth, C. Aulbert, S. Babak, S. Ballmer, H. Bantilan, B. C. Barish, C. Barker, D. Barker, B. Barr, P. Barriga, M. A. Barton, K. Bayer, K. Belczynski, J. Betzwieser, P. T. Beyersdorf, B. Bhawal, I. A. Bilenko, Tiffany Z. Summerscales

Faculty Publications

We present upper limits on the gravitational wave emission from 78 radio pulsars based on data from the third and fourth science runs of the LIGO and GEO 600 gravitational wave detectors. The data from both runs have been combined coherently to maximize sensitivity. For the first time, pulsars within binary (or multiple) systems have been included in the search by taking into account the signal modulation due to their orbits. Our upper limits are therefore the first measured for 56 of these pulsars. For the remaining 22, our results improve on previous upper limits by up to a factor …

New Integrable Hierarchy, Its Parametric Solutions, Cuspons, One-Peak Solitons, And M/W-Shape Peak Solitons, Zhijun Qiao

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

In this paper, we propose a new completely integrable hierarchy. Particularly in the hierarchy we draw two new soliton equations: 1 mt= 1 2 1/m2xxx− 1 2 1/m2 x; 2 mt+mx u2−ux 2+2m2ux=0, m=u−uxx. The first one is the second positive member in the hierarchy while the second one is the second negative member in the hierarchy. Both equations can be derived from the two-dimensional Euler equation by using the approximation procedure. All equations in the hierarchy are proven to have bi-Hamiltonian operators and Lax pairs through solving a crucial matrix equation. Moreover, we develop parametric solutions of the entire …

Biomimetic Interactions Of Proteins With Functionalized Nanoparticies: A Thermodynamic Study, M De, Cc You, S Srivastava, Vm Rotello

Vincent Rotello

Gold nanoparticles (NPs) functionalized with L-amino acid-terminated monolayers provide an effective platform for the recognition of protein surfaces. Isothermal titration calorimetry (ITC) was used to quantify the binding thermodynamics of these functional NPs with alpha-chymotrypsin (ChT), histone, and cytochrome c (CytC). The enthalpy and entropy changes for the complex formation depend upon the nanoparticle structure and the surface characteristics of the proteins, e.g., distributions of charged and hydrophobic residues on the surface. Enthalpy-entropy compensation studies on these NP-protein systems indicate an excellent linear correlation between DeltaH and TDeltaS with a slope (alpha) of 1.07 and an intercept (TDeltaS0) of 35.2 …

Empirical Likelihood-Based Nonparametric Inference For The Difference Between Two Partial Aucs, Yan Yuan

Mathematics Theses

Compare the accuracy of two continuous-scale tests is increasing important when a new test is developed. The traditional approach that compares the entire areas under two Receiver Operating Characteristic (ROC) curves is not sensitive when two ROC curves cross each other. A better approach to compare the accuracy of two diagnostic tests is to compare the areas under two ROC curves (AUCs) in the interested specificity interval. In this thesis, we have proposed bootstrap and empirical likelihood (EL) approach for inference of the difference between two partial AUCs. The empirical likelihood ratio for the difference between two partial AUCs is …

Increase In Near-Surface Atmospheric Moisture Content Due To Land Use Changes: Evidence From The Observed Dewpoint Temperature Data, Rezaul Mamood, Kenneth G. Hubbard, Ronnie D. Leeper, Stuart A. Foster

School of Natural Resources: Faculty Publications

Land use change can significantly affect root zone soil moisture, surface energy balance, and near-surface atmospheric temperature and moisture content. During the second half of the twentieth century, portions of the North American Great Plains have experienced extensive introduction of irrigated agriculture. It is expected that land use change from natural grass to irrigated land use would significantly increase nearsurface atmospheric moisture content. Modeling studies have already shown an enhanced rate of evapotranspiration from the irrigated areas. The present study analyzes observed dewpoint temperature (Td) to assess the affect of irrigated land use on near-surface atmospheric moisture content. This investigation …

A Domain-Specific Conceptual Query System, Xiuyun Shen

Computer Science Theses

This thesis presents the architecture and implementation of a query system resulted from a domain-specific conceptual data modeling and querying methodology. The query system is built for a high level conceptual query language that supports dynamically user-defined domain-specific functions and application-specific functions. It is DBMS-independent and can be translated to SQL and OQL through a normal form. Currently, it has been implemented in neuroscience domain and can be applied to any other domain.

Compartmentalization Of Hiv-1 In The Secondary Lymphoid Tissues, James Peter Gregson

Theses and Dissertations

Follicular dendritic cells (FDCs) reside in the lymphoid follicles of the secondary lymphoid tissues (sLTs). Following the infection of an individual with human immunodeficiency virus type 1 (HIV-1), viral particles are trapped in massive quantities on the surfaces of FDCs. HIV-1 viral compartments are cell types or tissues between which there is a restriction of virus flow. Compartmentalization of HIV-1 creates numerous sites within the body in which the virus can undergo independent evolution, giving rise to a more diverse total viral population. Given the sessile nature of the FDC, I hypothesized that contrary to common assumptions, FDC-trapped HIV-1 is …

Text Identification By Example, Daniel Joseph Preece

Theses and Dissertations

The World-Wide Web contains a lot of information and reading through the web pages to collect this information is tedious, time consuming and error prone. Users need an automated solution for extracting or highlighting the data that they are interested in. Building a regular expression to match the text they are interested in will automate the process, but regular expressions are hard to create and certainly are not feasible for non-programmers to construct. Text Identification by Example (TIBE) makes it easier for end-users to harvest information from the web and other text documents. With TIBE, training text classifiers from user-selected …

X-Ray Crystallographic Characterization Of The Co(Ii)-Substituted Tris-Bound Form Of The Aminopeptidase From Aeromonas Proteolytica, Petra Munih, Aaron Moulin, Carin Stamper, Brian Bennett, Dagmar Ringe, Gregory A. Petsko, Richard C. Holz

Physics Faculty Research and Publications

The X-ray crystal structure of the Co(II)-loaded form of the aminopeptidase from Aeromonas proteolytica ([CoCo(AAP)]) was solved to 2.2 Å resolution. [CoCo(AAP)] folds into an α/β globular domain with a twisted β-sheet hydrophobic core sandwiched between α-helices, identical to [ZnZn(AAP)]. Co(II) binding to AAP does not introduce any major conformational changes to the overall protein structure and the amino acid residues ligated to the dicobalt(II) cluster in [CoCo(AAP)] are the same as those in the native Zn(II)-loaded structure with only minor perturbations in bond lengths. The Co(II)–Co(II) distance is 3.3 Å. Tris(hydroxymethyl)aminomethane (Tris) coordinates to the dinuclear Co(II) active site …

The Influence Of Online Word Of Mouth On Product Sales In Retail E-Commerce: An Empirical Investigation, Alanah Davis, Deepak Khazanchi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

The ability to exchange opinions and experiences online is known as online word of mouth (WOM). Due to the high acceptance of consumers and their apparent reliance on online WOM it is important for organizations to understand how it works and what kind of impact it has on product sales. Using the well-established notions of volume and valence to describe online WOM, we empirically evaluate the hypothesized relationship between online WOM in a retail e-commerce site and actual product sales. Our analysis of the data shows that there is a significant change in the number of products sold following the …

An Information Technology Therapy Approach To Micro-Enterprise Adoption Of Icts, Peter Wolcott, Sajda Qureshi, Mehruz Kamal

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

The advent of Information and Communication Technologies (ICTs) has opened up new opportunities for micro-enterprises to improve their businesses. However the challenges to using ICTs are impeding these businesses from growing into the drivers for development that they can be. This suggests that a potentially important driver of development needs to be supported. This paper investigates the adoption of ICTs in eight micro-enterprises in an underserved community of Omaha, Nebraska. Following an action research study, this research provides insight into the key challenges and opportunities facing micro-enterprises in their use of ICTs to create value for their businesses. Its contribution …

Boron And Metal Halides In Organic Synthesis, Scott T. Borella

Doctoral Dissertations

This dissertation summarizes the recent use of organoboron and metal halides to form new carbon-carbon bonds. Several novel reactions have been discovered. These include the halovinyl alkenylation of alkoxides with alkenylboron dihalides; alkynylation of alkoxides with alkynylboron dihalides; boron trichloride and ferric chloride-mediated allylation of alkoxides. The results of these studies strongly imply a cationic mechanism, and prompted a reinvestigation of the boron trihalide mediated alkyne-aldehyde coupling reaction. The olefin stereochemistry of the resultant 1,5-dihalo-1,4-pentadienes can be influenced by controlling the reaction temperature and the sequence of reagent addition. The reaction methodology of the research described herein can be characterized …

Synthesis And Reactivity Of Titanium Amido Complexes With Relevance To Olefin Polymerization, Michael A. Blanchard

Doctoral Dissertations

Ziegler-Natta catalysts are well known in the chemical industry. They are responsible for the production of more than half of the HDPE and HDPP worldwide annually. Ziegler-Natta catalysts exist in many forms, both in homogeneous and heterogeneous types as well as both with early and late transition metal basis. While Ziegler-Natta catalysts can exist in various forms, all polymerize via the same general mechanism. Dissecting the known mechanism(s) results in three items that must be in place for polymerization to occur. First, the active metal center must be highly Lewis acidic, enough to allow coordination of approaching olefins. Second, a …

Past Fire Regimes Of Table Mountain Pine (Pinus Pungens L.) Stands In The Central Appalachian Mountains, Virginia, U.S.A., Georgina Deweese

Doctoral Dissertations

Table Mountain pine is an Appalachian endemic that occurs in a patchy distribution from Georgia to Pennsylvania and is prolific at sites with a history of fire disturbance. The purpose of this dissertation was to reconstruct the fire regimes of Table Mountain pine stands in the Jefferson National Forest, Virginia. Sections from firescarred Table Mountain pines were collected at four sites to analyze fire history, while increment cores and stand composition information were collected from macroplots within each fire history site to investigate the possible influence of fires that were more ecologically severe. Results show that fire was frequent before …

A Team-Based Approach To Social Learning Research In Natural Resource Management, Jonah Malachai Fogel

Doctoral Dissertations

This thesis responds to the need to quantify social learning and its outcomes as it relates to natural resource management. Social learning enables individuals engaging in collective action to understand each other’s perspectives, encourages integration of diverse knowledge bases, and the creation of new knowledge (Keen, Brown, & Dyball, 2005). However, the concept currently lacks a clear operational definition in natural resource management. The lack of an operational definition for social learning has stymied attempts to validate its espoused ability to improve civic discourse and, ultimately, resource governance (Pahl-Wostl & Hare, 2004). This report is composed of three papers that …

Novel Approaches To Metal Ion Sensing, Nathan Allen Carrington

Doctoral Dissertations

The primary focus of this dissertation is the development of new chemical analyses for metal ions. Approaches combining electrochemical, spectroscopic, analytical, inorganic, and materials chemistry have been used to investigate novel methods for metal ion sensing. Topics discussed in this dissertation include pyridinium-functionalized sol-gel films for the enhanced electrochemical analysis of Cr(VI), pyridinium-functionalized sol-gel monoliths for the optical determination of Cr(VI), the use of the electrochemical quartz crystal microbalance for the determination of Pd(II), novel electrochemical and spectroscopic approaches to Fe(III) sensing, and the electrochemical quartz crystal microbalance investigation of the Cr(III)-DTPA complex.

A Multi-Scale Analysis Of Disturbance Dynamics In Hardwood Forest Communities On The Cumberland Plateau, U.S.A., Justin L. Hart

Doctoral Dissertations

The purpose of this research was to quantify forest disturbance processes and evaluate the influence of these processes on secondary hardwood forest communities on a section of the Cumberland Plateau in Tennessee. The specific objectives of this study were to: (1) reconstruct the disturbance history of a secondary hardwood forest using species composition, stand structure, tree-ring data, and soil charcoal analyses, (2) quantify canopy gap formation mechanisms, (3) document canopy gap characteristics, and (4) determine the forest response to small-scale disturbance events. This information is useful to understand the importance of localized disturbances on stand development and forest successional patterns. …

Optimization Of Interfacial Interactions To Achieve The Nanoscale Dispersion Of Clay In Polymer/Clay Nanocomposites, Deepali Kumar

Doctoral Dissertations

Polymer clay nanocomposites are a promising class of multicomponent systems where incorporation of small amount of clay results in dramatic improvement of mechanical, thermal and barrier properties. However, accomplishment of these properties necessitates molecular level dispersion of the clay platelets in the polymer matrix. This thesis presents the guidelines for obtaining thermodynamically stable nanocomposites where strong specific interactions such as hydrogen bonding between the polymer and the clay can be utilized to achieve the desired goal of nanoscale dispersion of clay sheets.

In first part of the dissertation, optimization of intermolecular hydrogen bonding between the polymer and clay is carried …

Mapping The Martian Geologic Record: Studies Of The Gusev Crater Spirit Landing Site And Plagioclase Feldspar Compositions On Mars, Keith Alan Milam

Doctoral Dissertations

The flurry of activity involved in the scientific study of Mars has resulted in multiple new data sets from several missions (Mars Global Surveyor (MGS), Mars Odyssey (MO), Mars Exploration Rovers (MER), Mars Reconnaissance Orbiter (MRO), and Mars Express) that provide information for unlocking the planet’s geologic and climatic history.

This three part study utilized both orbital data and laboratory experiments to examine Mars for morphologic and mineralogic evidence of aqueous activity and magmatic evolution.

The first study examined Gusev Crater, landing site for the Spirit MER rover. This work began during final landing site selection and was published just …

Synthesis Of Novel Boronated Amino Acids For Bnct An Alternate Cancer Therapy And Use Of Microwaves In Organic Synthesis, Abhijit Achyut Naravane

Doctoral Dissertations

Boron neutron capture therapy (BNCT) is a binary form of cancer treatment wherein ¹⁰B nuclei, when irradiated with thermal neutrons, produce high energy transfer particles. These particles, due to their size and energy, are confined to a radius of 9-10μm, which is comparable to the size of single cell. Potential BNCT agents reported in the literature include boron-containing amino acids, nucleic acids, nucleosides, antibodies, and other biomolecules.

In recent years, microwaves have gained importance in organic chemistry. Microwave induced reactions are energy efficient, often enhance reaction rates, and generally lead to enhanced product yields. Recent studies have …

Newton's Method Obeys Benford's Law, Arno Berger, Theodore P. Hill

Research Scholars in Residence

No abstract provided.

Northern High-Latitude Ecosystems Respond To Climate Change, Andrew Godard Bunn, Scott J. Goetz, John S. Kimball, Ke Zhang

Environmental Sciences Faculty and Staff Publications

The northern high latitudes are an area of particular importance to global climate change. As a system dependent on freezing conditions, the top of the planet contains vast amounts of carbon in biomass, soils, and permafrost that have the potential to interact with the atmosphere through the biosphere, hydrosphere, lithosphere, and cryosphere. If released en masse, this carbon would greatly exacerbate the levels of greenhouse gases in the atmosphere.

Over the past 2 years, a growing body of research has provided evidence of substantial but idiosyncratic environmental changes, with some surprising aspects, across the region. This article reviews some recent …

Beam Criterion For Atmospheric Propagation, Olga Korotkova, Emil Wolf

Physics Articles and Papers

A criterion is introduced for testing whether a beam retains its beam-like form after it propagates any particular distance through the turbulent atmosphere. The criterion applies to monochromatic as well as to partially coherent beams and is illustrated by examples.

Parameter Estimation For Ornstein-Uhlenbeck Processes Driven By Α-Stable Lévy Motions, Yaozhong Hu, Hongwei Long

Communications on Stochastic Analysis

No abstract provided.

Generators Of Dynamical Systems On Hilbert Modules, Gholamreza Abbaspour Tabadkan, Michael Skeide

Communications on Stochastic Analysis

No abstract provided.

Space Regularity Of Stochastic Heat Equations Driven By Irregular Gaussian Processes, Oana Mocioalca, Frederi Viens

Communications on Stochastic Analysis

No abstract provided.

Quantum Stochastic Process Associated With Quantum Lévy Laplacian, Un Cig Ji, Habib Ouerdiane, Kimiaki Saitô

Communications on Stochastic Analysis

No abstract provided.

Markov Semigroups And Groups Of Operators, Jerome A Goldstein, Rosa Maria Mininni, Silvia Romanelli

Communications on Stochastic Analysis

No abstract provided.