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Design And Synthesis Of Boronic Acid-Modified Nucleotides For Fluorescent Sensing And Cell Imaging, Xiaochuan Yang

Chemistry Dissertations

With the rapidly increasing interest in the field of glycomics, which is the comprehensive study of the roles carbohydrates play in a living system, urgent need for developing quick and highly selective carbohydrate sensors is growing. The boronic acid group, with its electron-deficient structure (6 valence electrons with an open shell), acts as a Lewis acid with high intrinsic affinity towards Lewis bases such as fluoride, cyanide and hydroxyl groups. Specifically, formation of a 5- or 6- membered ring between the boronic acid moiety and a1,2- or 1,3-diol in aqueous solution has been fully explored as a strategy of carbohydrate …

Nanoscopic Investigation Of Surface Morphology Of Neural Growth Cones And Indium Containing Group-Iii Nitrides, Göksel Durkaya

Physics and Astronomy Dissertations

This research focuses on the nanoscopic investigation of the three-dimensional surface morphology of the neural growth cones from the snail Helisoma trivolvis, and InN and InGaN semiconductor material systems using Atomic Force Microscopy (AFM). In the analysis of the growth cones, the results obtained from AFM experiments have been used to construct a 3D architecture model for filopodia. The filopodia from B5 and B19 neurons have exhibited different tapering mechanisms. The volumetric analysis has been used to estimate free Ca2+ concentration in the filopodium. The Phase Contrast Microscopy (PCM) images of the growth cones have been corrected to thickness provided …

Integrating Information Theory Measures And A Novel Rule-Set-Reduction Tech-Nique To Improve Fuzzy Decision Tree Induction Algorithms, Nael Mohammed Abu-Halaweh

Computer Science Dissertations

Machine learning approaches have been successfully applied to many classification and prediction problems. One of the most popular machine learning approaches is decision trees. A main advantage of decision trees is the clarity of the decision model they produce. The ID3 algorithm proposed by Quinlan forms the basis for many of the decision trees’ application. Trees produced by ID3 are sensitive to small perturbations in training data. To overcome this problem and to handle data uncertainties and spurious precision in data, fuzzy ID3 integrated fuzzy set theory and ideas from fuzzy logic with ID3. Several fuzzy decision trees algorithms and …

Analysis Of Gan/Alxga1?Xn Heterojunction Dual-Band Photodetectors Using Capacitance Profiling Techniques, Laura E. Byrum

Physics and Astronomy Theses

Capacitance-voltage-frequency measurements on n+-GaN/AlxGa1−xN UV/IR dual-band detectors are reported. The presence of shallow Si-donor, deep Si-donor, and C-donor/N-vacancy defect states were found to significantly alter the electrical characteristics of the detectors. The barrier Al fraction was found to change the position of the interface defect states relative to the Fermi level. The sample with Al fraction of 0.1 shows a distinct capacitance-step and hysteresis, which is attributed to C-donor/N-vacancy electron trap states located above the Fermi level (200 meV) at the heterointerface; whereas, the sample with Al fraction of 0.026 shows negative capacitance and dispersion, indicating C-donor/N-vacancy and deep Si-donor …

Some Contributions In Statistical Discrimination Of Different Pathogens Using Observations Through Ftir, Dongmei Wang

Mathematics Theses

Fourier Transform Infrared (FTIR) has been use to discriminate different pathogens by signals from cells infected with these versus normal cells as references. To do the statistical analysis, Partial Least Square Regression (PLSR) was utilized to distinguish any two kinds of virus‐infected cells and normal cells. Validation using Bootstrap method and Cross‐validations were employed to calculate the shrinkages of Area Under the ROC Curve (AUC) and specificities corresponding to 80%, 90%, and 95% sensitivities. The result shows that our procedure can significantly discriminate these pathogens when we compare infected cells with the normal cells. On the height of this success, …

Theoretical And Numerical Study Of Tikhonov's Regularization And Morozov's Discrepancy Principle, Marygeorge L. Whitney

Mathematics Theses

A concept of a well-posed problem was initially introduced by J. Hadamard in 1923, who expressed the idea that every mathematical model should have a unique solution, stable with respect to noise in the input data. If at least one of those properties is violated, the problem is ill-posed (and unstable). There are numerous examples of ill- posed problems in computational mathematics and applications. Classical numerical algorithms, when used for an ill-posed model, turn out to be divergent. Hence one has to develop special regularization techniques, which take advantage of an a priori information (normally available), in order to solve …

Analyzing Gene Expression Data In Terms Of Gene Sets: Gene Set Enrichment Analysis, Wei Li

Mathematics Theses

The DNA microarray biotechnology simultaneously monitors the expression of thousands of genes and aims to identify genes that are differently expressed under different conditions. From the statistical point of view, it can be restated as identify genes strongly associated with the response or covariant of interest. The Gene Set Enrichment Analysis (GSEA) method is one method which focuses the analysis at the functional related gene sets level instead of single genes. It helps biologists to interpret the DNA microarray data by their previous biological knowledge of the genes in a gene set. GSEA has been shown to efficiently identify gene …

Analysis Of The Total Food Folate Intake Data From The National Health And Nutrition Exa-Amination Survey (Nhanes) Using Generalized Linear Model, Kyung Ah Lee

Mathematics Theses

The National health and nutrition examination survey (NHANES) is a respected nation-wide program in charge of assessing the health and nutritional status of adults and children in United States. Recent cal research found that folic acid play an important role in preventing baby birth defects. In this paper, we use the generalized estimating equation (GEE) method to study the generalized linear model (GLM) with compound symmetric correlation matrix for the NHANES data and investigate significant factors to ence the intake of food folic acid.

Comparative Studies Between Robotic Laparoscopic Myomectomy And Abdominal Myomectomy With Factors Affecting Short-Term Surgical Outcomes, Amy N. Fomo

Mathematics Theses

The purpose of this study is to compare short-term surgical outcomes of robotic and abdominal myomectomy and to analyze the factors affecting the total operative time, estimated blood loss and length of hospital stay from a retrospective study of a consecutive case series of 122 pa-tients with symptomatic leiomyomata. Wilcoxon, t tests, multiple linear and logistic regressions analyses were performed. Patients in abdominal group had larger number of leiomyomata, larger tumor size and BMI. The operative time was longer in robotic group and was affected by the size and number of tumors, parity and interaction between parity and BMI. Estimated …

Metabolic Network Alignments And Their Applications, Qiong Cheng

Computer Science Dissertations

The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have …

Evaluating The Effects Of Green Roofs As Tools For Stormwater Management In An Urban Metropolis, Robyn R. Polinsky

Geosciences Theses

Stormwater management is an essential aspect of urban hydrology. Urbanized areas have large amounts of impervious surface cover (ISC) and well developed sewer and drainage networks which rapidly channel water and pollutants off of streets and into local streams. This research evaluates the use of vegetated roofs as mechanisms to reduce ISC and stormwater runoff in downtown Atlanta. A 3-D model of the study site was created so that runoff rates could be measured for various rooftop scenarios under different size storm events. The results revealed a reduction in peak runoff and an increase in both the lag time and …

Comparing Cognitive Decision Models Of Iowa Gambling Task In Indivituals Following Temporal Lobectomy, Jenny Vennukkah Jeyarajah

Mathematics Theses

This study examined the theoretical basis for decision making behavior of patients with right or left temporal lobectomy and a control group when they participated in the Iowa Gambling Task. Two cognitive decision models, Expectancy Valence Model and Strategy Switching Heuristic Choice Model, were compared for best fit. The best fitting model was then chosen to provide the basis for parameter estimation (sources of decision making, i.e. cognitive, motivational, and response processes) and interpretation. Both models outperformed the baseline model. However comparison of G2 means between the two cognitive decision models showed the expectancy valence model having a higher mean …

Optical And Terahertz Energy Concentration On The Nanoscale In Plasmonics, Anastasia Rusina

Physics and Astronomy Dissertations

We introduce an approach to implement full coherent control on nanometer length scales. It is based on spatiotemporal modulation of the surface plasmon polariton (SPP) fields at the thick edge of a nanowedge. The SPP wavepackets propagating toward the sharp edge of this nanowedge are compressed and adiabatically concentrated at a nanofocus, forming an ultrashort pulse of local fields. The profile of the focused waveform as a function of time and one spatial dimension is completely coherently controlled. We establish the principal limits for the nanoconcentration of the terahertz (THz) radiation in metal/dielectric waveguides and determine their optimum shapes required …

Giant Plasmonic Energy And Momentum Transfer On The Nanoscale, Maxim Durach

Physics and Astronomy Dissertations

We have developed a general theory of the plasmonic enhancement of many-body phenomena resulting in a closed expression for the surface plasmon-dressed Coulomb interaction. It is shown that this interaction has a resonant nature. We have also demonstrated that renormalized interaction is a long-ranged interaction whose intensity is considerably increased compared to bare Coulomb interaction over the entire region near the plasmonic nanostructure. We illustrate this theory by re-deriving the mirror charge potential near a metal sphere as well as the quasistatic potential behind the so-called perfect lens at the surface plasmon (SP) frequency. The dressed interaction for an important …

Duty Cycle Maintenance In An Artificial Neuron, William Halbert Barnett

Physics and Astronomy Theses

Neuroprosthetics is at the intersection of neuroscience, biomedical engineering, and physics. A biocompatible neuroprosthesis contains artificial neurons exhibiting biophysically plausible dynamics. Hybrid systems analysis could be used to prototype such artificial neurons. Biohybrid systems are composed of artificial and living neurons coupled via real-time computing and dynamic clamp. Model neurons must be thoroughly tested before coupled with a living cell. We use bifurcation theory to identify hazardous regimes of activity that may compromise biocompatibility and to identify control strategies for regimes of activity desirable for functional behavior. We construct real-time artificial neurons for the analysis of hybrid systems and demonstrate …

Photoionization Of The Be Isoelectronic Sequence: Relativistic And Nonrelativistic R-Matrix Calculations, Wei-Chun Chu

Physics and Astronomy Dissertations

The photoionization of the beryllium-like isoelectronic series has been studied. The bound state wave functions of the target ions were built with CIV3 program. The relativistic Breit-Pauli R-matrix method was used to calculate the cross sections in the photon energy range between the ionization threshold and 1s24f7/2 threshold for each ion. For the total cross sections of Be, B+, C+2, N+3, and O+4, our results match experiment well. The comparison between the present work and other theoretical works are also discussed. We show the comparison with our LS results as it indicates the importance of relativistic effects on different ions. …

Distributed Algorithms For Maximizing The Lifetime Of Wireless Sensor Networks, Akshaye Dhawan

Computer Science Dissertations

Wireless sensor networks (WSNs) are emerging as a key enabling technology for applications domains such as military, homeland security, and environment. However, a major constraint of these sensors is their limited battery. In this dissertation we examine the problem of maximizing the duration of time for which the network meets its coverage objective. Since these networks are very dense, only a subset of sensors need to be in "sense" or "on" mode at any given time to meet the coverage objective, while others can go into a power conserving "sleep" mode. This active set of sensors is known as a …

A Task-Centered Visualization Design Environment And A Method For Measuring The Complexity Of Visualization Designs, Xiaoyuan Suo

Computer Science Dissertations

Recent years have seen a growing interest in the emerging area of computer security visualization which is about developing visualization methods to help solve computer security problems. In this thesis, we will first present a method for measuring the complexity of information visualization designs. The complexity is measured in terms of visual integration, number of separable dimensions for each visual unit, the complexity of interpreting the visual attributes, number of visual units, and the efficiency of visual search. This method is designed to better assist fellow developers to quickly evaluate multiple design choices, potentially enables computer to automatically measure the …

Discovery And Extraction Of Protein Sequence Motif Information That Transcends Protein Family Boundaries, Bernard Chen

Computer Science Dissertations

Protein sequence motifs are gathering more and more attention in the field of sequence analysis. The recurring patterns have the potential to determine the conformation, function and activities of the proteins. In our work, we obtained protein sequence motifs which are universally conserved across protein family boundaries. Therefore, unlike most popular motif discovering algorithms, our input dataset is extremely large. As a result, an efficient technique is essential. We use two granular computing models, Fuzzy Improved K-means (FIK) and Fuzzy Greedy K-means (FGK), in order to efficiently generate protein motif information. After that, we develop an efficient Super Granular SVM …

An Application Of Armitage Trend Test To Genome-Wide Association Studies, Nigel A. Scott

Mathematics Theses

Genome-wide Association (GWA) studies have become a widely used method for analyzing genetic data. It is useful in detecting associations that may exist between particular alleles and diseases of interest. This thesis investigates the dataset provided from problem 1 of the Genetic Analysis Workshop 16 (GAW 16). The dataset consists of GWA data from the North American Rheumatoid Arthritis Consortium (NARAC). The thesis attempts to determine a set of single nucleotide polymorphisms (SNP) that are associated significantly with rheumatoid arthritis. Moreover, this thesis also attempts to address the question of whether the one-sided alternative hypothesis that the minor allele is …

Sizing Up The Stars, Tabetha Suzanne Boyajian

Physics and Astronomy Dissertations

For the main part of this dissertation, I have executed a survey of nearby, main sequence A, F, and G-type stars with the CHARA Array, successfully measuring the angular diameters of forty-four stars to better than 4% accuracy. The results of these observations also yield empirical determinations of stellar linear radii and effective temperatures for the stars observed. In addition, these CHARA-determined temperatures, radii, and luminosities are fit to Yonsei-Yale isochrones to constrain the masses and ages of the stars. These quantities are compared to the results found in Allende Prieto & Lambert (1999), Holmberg et al. (2007), and Takeda …

A Multi-Wavelength Investigation Of Seyfert 1.8 And 1.9 Galaxies, Margaret Trippe

Physics and Astronomy Dissertations

We focus on determining the underlying physical cause of a Seyfert galaxy's appearance as type a 1.8 or 1.9. Are these "intermediate" Seyfert types typical Seyfert 1 nuclei reddened by central dusty tori or by nuclear dust lanes/spirals in the narrow-line region? Or, are they similar to NGC 2992, objects that have intrinsically weak continua and weak broad emission lines? Our study compares measurements of the reddenings of the narrow and broad-line regions with each other and with the X-ray column derived from XMM Newton 0.5-10 keV spectra to determine the presence and location of dust in the line of …

Analysis Of Channel Networks And The Potential For Sediment Transport In The Vicinity Of The North Polar Seas Of Titan, Richard Cartwright

Geosciences Theses

This study analyzes the available radar evidence in order to describe the morphology of channel networks around the north polar seas of Titan. Critical flow depths necessary to entrain water-ice grains, and denudation rates for a north polar channel network are discussed. The results indicate that channel networks on Titan have similar morphologies to channel networks cut by water on Earth. We also find that water-ice sediment should be readily entrained in the headwaters and downstream sections of the analyzed Titanian basin, given sufficient flow depths of liquid hydrocarbons. Also, the importance of slope and the elevated topography of the …

Epr, Endor And Dft Studies On X-Irradiated Single Crystals Of L-Lysine Monohydrochloride Monohydrate And L-Arginine Monohydrocloride Monohydrate, Yiying Zhou

Physics and Astronomy Dissertations

When proteins and DNA interact, arginine and lysine are the two amino acids most often in close contact with the DNA. In order to understand the radiation damage to DNA in vivo, which is always associated with protein, it is important to learn the radiation chemistry of arginine and lysine independently, and when complexed to DNA. This work studied X-irradiated single crystals of L-lysine monohydrochloride dihydrate (L-lysine·HCl·2H2O) and L-arginine monohydrochloride monohydrate (L-arginine·HCl·H2O) with EPR, ENDOR, EIE techniques and DFT calculations. In both crystal types irradiated at 66K, the carboxyl anion radical and the decarboxylation radical were detected. DFT calculations supported …

Multistability In Bursting Patterns In A Model Of A Multifunctional Central Pattern Generator., Matthew Bryan Brooks

Mathematics Theses

A multifunctional central pattern generator (CPG) can produce bursting polyrhythms that determine locomotive activity in an animal: for example, swimming and crawling in a leech. Each rhythm corresponds to a specific attractor of the CPG. We employ a Hodgkin-Huxley type model of a bursting leech heart interneuron, and connect three such neurons by fast inhibitory synapses to form a ring. This network motif exhibits multistable co-existing bursting rhythms. The problem of determining rhythmic outcomes is reduced to an analysis of fixed points of Poincare mappings and their attractor basins, in a phase plane defined by the interneurons' phase differences along …

Solar Energy Conversion In Plants And Bacteria Studied Using Ftir Difference Spectroscopy And Quantum Chemical Computational Methodologies, Sreeja Parameswaran

Physics and Astronomy Dissertations

This dissertation presents a study of the molecular mechanism underlying the highly efficient solar energy conversion processes that occur in the Photosystem I (PS I) reaction centers in plants and bacteria. The primary electron donor P700 is at the heart of solar energy conversion process in PS I and the aim is to obtain a better understanding of the electronic and structural organization of P700 in the ground and excited states. Static Fourier Transform Infra-Red (FTIR) difference spectroscopy (DS) in combination with site directed mutagenesis and Density Functional Theory (DFT) based vibrational frequency simulations were used to investigate how protein …

Detection And Quantification Of Organophosphate Pesticides In Human Serum, Peter Kuklenyik

Chemistry Dissertations

The United States Environmental Agency permits the use of 39 organophosphate pesticides. Many of these pesticides are acutely toxic and have lasting effect on human health. Organophosphates quickly metabolize in the body, therefore currently human exposure is studied by measuring the metabolic products in urine. In this work a suite of analytical methods was developed to determine the presence of un-metabolized organophosphate pesticides in human serum. First mass spectroscopic detection methods were evaluated. Gas chromatograph coupled tandem mass spectrometer was used to compare the detection limits using chemical and electron impact ionization. Positive chemical ionization was selected, because it provided …

Magmatic Evolution Of The Eocene Volcanic Rocks Of The Bijgerd Kuh E Kharchin Area, Uromieh-Dokhtar Zone, Iran, Armita Davarpanah

Geosciences Theses

Composition and texture of the Middle and Late Eocene volcanic, volcaniclastic, and volcanic-sedimentary rocks in the Bijgerd-Kuh e Kharchin area, in the Uromieh-Dokhtar zone northwest of Saveh, Iran, suggest the complexity of the magmatic system that involved multiple eruptions from one or more sources. Hydrated volcanic fragments in hyaloclastic rocks, and the presence of a sequence of shallow and intermediate-depth marine microfossils, suggest that the Middle Eocene units were erupted in a marine basin. The bimodal volcanism of the Late Eocene is distinguished by the presence of four alternating sequences of hyaloclastite lava and ignimbrite. The REE patterns show spatial …

Two Problems On Bipartite Graphs, Albert Bush

Mathematics Theses

Erdos proved the well-known result that every graph has a spanning, bipartite subgraph such that every vertex has degree at least half of its original degree. Bollobas and Scott conjectured that one can get a slightly weaker result if we require the subgraph to be not only spanning and bipartite, but also balanced. We prove this conjecture for graphs of maximum degree 3.

The majority of the paper however, will focus on graph tiling. Graph tiling (or sometimes referred to as graph packing) is where, given a graph H, we find a spanning subgraph of some larger graph G that …

Advanced Statistical Methodologies In Determining The Observation Time To Discriminate Viruses Using Ftir, Shan Luo

Mathematics Theses

Fourier transform infrared (FTIR) spectroscopy, one method of electromagnetic radiation for detecting specific cellular molecular structure, can be used to discriminate different types of cells. The objective is to find the minimum time (choice among 2 hour, 4 hour and 6 hour) to record FTIR readings such that different viruses can be discriminated. A new method is adopted for the datasets. Briefly, inner differences are created as the control group, and Wilcoxon Signed Rank Test is used as the first selecting variable procedure in order to prepare the next stage of discrimination. In the second stage we propose either partial …