Physical Sciences and Mathematics Commons^™

Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, And Evaluations, Ken D. Nguyen

Computer Science Dissertations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences' structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes.

In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method …

Novel Near-Infrared Cyanine Dyes For Fluorescence Imaging In Biological Systems, Nilmi T. Fernando

Chemistry Dissertations

Heptamethine cyanine dyes are attractive compounds for imaging purposes in biomedical applications because of their chemical and photophysical properties exhibited in the near-infrared region. A series of meso amino-substituted heptamethine cyanine dyes with indolenine, benz[e]indolenine and benz[c,d]indolenine heterocyclic moieties were synthesized and their spectral properties including fluorescence quntum yield were investigated in ethanol and ethanol/water mixture. Upon substitution with amines, the absorption maxima of the dyes shifted to the lower wavelength region (~600 nm), showed larger Stokes shifts and stronger fluorescence which can be attributed to an excited state intramolecular charge transfer (ICT). High quantum yields …

Nucleic Acid Substrates: Investigation Of Structural And Dynamic Features That Influence Enzyme Activity, Christopher N. Johnson

Chemistry Dissertations

The previous view of DNA as a linear sequence of bases is evolving to consider structure, topology and dynamics. Sequences surrounding damage lesions have been shown to effect enzyme recognition and processing. Here we present an in depth investigation of subtle structural and dynamical features imparted to nucleic acid duplexes by a designed modification or damage lesions. Highly restrained solution structures were generated and validated utilizing a range of NMR techniques. This allowed for the characterization of multiple features of the nucleic acid duplex; such as base pairing, backbone torsion angles, deoxyribose sugar pucker, and intra and inter nucleotide proton …

Syntactic And Semantic Analysis And Visualization Of Unstructured English Texts, Saurav Karmakar

Computer Science Dissertations

People have complex thoughts, and they often express their thoughts with complex sentences using natural languages. This complexity may facilitate efficient communications among the audience with the same knowledge base. But on the other hand, for a different or new audience this composition becomes cumbersome to understand and analyze. Analysis of such compositions using syntactic or semantic measures is a challenging job and defines the base step for natural language processing.

In this dissertation I explore and propose a number of new techniques to analyze and visualize the syntactic and semantic patterns of unstructured English texts.

The syntactic analysis is …

Statistical Inferences For The Youden Index, Haochuan Zhou

Mathematics Dissertations

In diagnostic test studies, one crucial task is to evaluate the diagnostic accuracy of a test. Currently, most studies focus on the Receiver Operating Characteristics Curve and the Area Under the Curve. On the other hand, the Youden index, widely applied in practice, is another comprehensive measurement for the performance of a diagnostic test. For a continuous-scale test classifying diseased and non-diseased groups, finding the Youden index of the test is equivalent to maximize the sum of sensitivity and specificity for all the possible values of the cut-point. This dissertation concentrates on statistical inferences for the Youden index. First, an …

Whole-Rock Lead-Lead Systematics And Major Element Analyses On The 1.85 Ga. Flin Flon Paleosol, Manitoba, Canada: Implications For Uranium Mobility., Federico Arturo Valencia

Geosciences Theses

The 1.85 Ga Flin Flon paleosol located in Flin Flon, Manitoba, Canada, is studied with the purpose of determining the timing and geochemical trend of uranium migration. Radiometric minimum ages of sediments and paleosols indicates the presence of a post-depositional event, these ages are bracketed by the Trans-Hudson orogeny event (2155–1750 Ma) which resulted in the alteration of κ(Th/U) and µ(U/Pb) ratios by exposing volcanics to the atmosphere and instigating the mobilization of U. The profile shows that the Missi sediments lost Uby 84% average relative to corrected average upper crust value. The upper paleosol gained U by 11% and …

Assessment Of The Sustained Financial Impact Of Risk Engineering Service On Insurance Claims Costs, Bobby I. Parker Mr.

Mathematics Theses

This research paper creates a comprehensive statistical model, relating financial impact of risk engineering activity, and insurance claims costs. Specifically, the model shows important statistical relationships among six variables including: types of risk engineering activity, risk engineering dollar cost, duration of risk engineering service, and type of customer by industry classification, dollar premium amounts, and dollar claims costs.

We accomplish this by using a large data sample of approximately 15,000 customer-years of insurance coverage, and risk engineering activity. Data sample is from an international casualty/property insurance company and covers four years of operations, 2006-2009. The choice of statistical model is …

The Evolution Of Dwarf-Irregular Galaxy Ngc 1569: A Kinematic Study Of The Stars And Gas, Megan C. Johnson

Physics and Astronomy Dissertations

The evolution and formation of dwarf galaxies has great importance to our knowledge of cosmological history from the Big Bang through the present day structure we observe in our local universe. Dwarf galaxies are believed to be the "building blocks" of larger galaxies, which implies that interactions and mergers of these small systems must have occurred frequently in the early universe. There is a population of starburst dwarf irregular (dIm) galaxies that seem to have characteristics indicative of interactions or mergers. One of these dIm galaxies is the nearby post-starburst NGC 1569. This dissertation project explores the stellar and gas …

A Geochemical Analysis: Application Of A Chelating Agent On Potential Asr Reactive Aggregates, Jennifer N. Garcia

Geosciences Theses

Alkali Silica Reaction (ASR) is a deleterious, expansive reaction in concrete. Several ASTM methods test potential aggregates for ASR risk. One method uses NaOH digestion, followed by spectroscopic methods, to estimate the amount of reactive silica present in an aggregate. NaOH, however, can digest both crystalline (i.e. quartz) and non-crystalline (e.g. opal), or poorly crystalline silica, potentially yielding falsely high estimates of reactive silica. Studies in soil and plant sciences have used Tiron, an alkaline chelating agent (C₆H₄S₂O₈Na₂), as a method of digesting opaline silica for spectroscopic analysis. Here we …

Development Of Boronic Acid Flurescent Reporters, Boronic Acid-Modified Thymidine Triphosphates For Sensor Design And Antagonists Of Bacterial Quorum Sensing In Vibrio Harveyi, Yunfeng Cheng

Chemistry Dissertations

Carbohydrates are known to play important roles in a large number of physiological and pathological processes. Conceivably, “binders” of carbohydrates of biological importance could be used as diagnostic and therapeutic agents. Currently, lectins are the major available tools in research for carbohydrate recognition. However, the available lectins often have cross-reactivity issues, along with the high costs and stability issues. Therefore, there is a critical need to develop alternatives (lectin mimics). In this regard, there have been very active efforts in developing different “binders”, such as small molecule lectinmimics and aptamers. Among all the small molecule lectinbmimics developments, boronic acid stands …

On The 4 By 4 Irreducible Sign Pattern Matrices That Require Four Distinct Eigenvalues, Paul J. Kim

Mathematics Theses

A sign pattern matrix is a matrix whose entries are from the set {+,-,0}. For a real matrix B, sgn(B) is the sign pattern matrix obtained by replacing each positive(respectively, negative, zero) entry of B by + (respectively, -, 0). For a sign pattern matrix A, the sign pattern class of A, denoted Q(A), is defined as {B: sgn(B) = A}.

An n by n sign pattern matrix A requires all distinct eigenvalues if every real matrix whose sign pattern is represented by A has n distinct eigenvalues. In this thesis, a number of sufficient and/or necessary conditions for a …

Analysis Of Faculty Evaluation By Students As A Reliable Measure Of Faculty Teaching Performance, Etienne Twagirumukiza

Mathematics Theses

Most American universities and colleges require students to provide faculty evaluation at end of each academic term, as a way of measuring faculty teaching performance. Although some analysts think that this kind of evaluation does not necessarily provide a good measurement of teaching effectiveness, there is a growing agreement in the academic world about its reliability. This study attempts to find any strong statistical evidence supporting faculty evaluation by students as a measure of faculty teaching effectiveness. Emphasis will be on analyzing relationships between instructor ratings by students and corresponding students’ grades. Various statistical methods are applied to analyze a …

Optical Spectroscopy Of Massive Binary Stars, Stephen J. Williams

Physics and Astronomy Dissertations

This is a spectroscopic and photometric study of suspected close binary systems among the massive stars. The stars studied here include stars with temperatures ranging from 45,000 Kelvin (K) to 15,000 K, corresponding to spectral types ranging from O3 V to B5 III, masses between 47 Solar Masses and 5 Solar Masses, and absolute V magnitudes from -6.28 to -2.0. I categorize 30 targets according to my spectroscopic observations into groups with no radial velocity variability, single-lined, and double-lined variability. My analysis of the 18 constant velocity stars results in estimates of stellar effective temperature, T_eff, gravity, log …

I. Synthesis Of Anthraquinone Derivatives For Electron Transfer Studies In Dna. Ii. Characterization Of The Interaction Between Heme And Proteins., Yu Cao

Chemistry Dissertations

Anthraquinone (AQ) derivatives with relatively high reduction potentials have been synthesized to afford good candidates for electron transfer studies in DNA. Electron withdrawing groups on the anthraquinone ring gave derivatives with less negative reduction potentials. The anthraquinone imide (AQI) derivatives had reduction potentials less negative than AQ derivatives. The AQI ring system was subject to base-induced hydrolysis.

Water-soluble sulfonated tetraarylporphyrins have been studied in a wide variety of contexts. Herein, we report the first synthesis of a pentasulfonated porphyrin bearing an internal cyclic sulfone ring. Treatment of 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (TPPS4) with fuming H₂SO₄ gave a structure consistent with …

Tuning Calcium Bindging Affinities With Related Biological Functions Of Calmodulin And Designing Protein Based Contrast Agent, Jie Jiang

Chemistry Dissertations

Calmodulin (CaM) is a ubiquitous intracellular protein that regulates biological activities of numerous enzymes and ion channels. Upon responding Ca²⁺ concentration change, Ca²⁺- dependent CaM activates the hydrolyzation of cGMP by PDE and Ca²⁺ releasing channel activity of ryanodine receptor. In this dissertation, a series of CaM variants were engineered to enhance Ca²⁺ binding affinities by increasing the number of negative charged residues in individual EF-hand. The capability of shifting the biphasic Ca²⁺-activation profile of RyR1 is significantly altered by changing Ca²⁺ binding affinity of CaM at the C-terminal. This indicates that …

Mechanistic Studies Of Two Selected Flavin-Dependent Enzymes: Choline Oxidase And D-Arginine Dehydrogenase, Hongling Yuan

Chemistry Dissertations

Choline oxidase catalyzes the flavin-dependent, two-step oxidation of choline to glycine betaine via the formation of an aldehyde intermediate. The oxidation of choline includes two reductive half-reactions followed by oxidative half-reactions. In the first oxidation reaction, the alcohol substrate is activated to its alkoxide via proton abstraction and oxidized via transfer of a hydride from the alkoxide α-carbon to the N(5) atom of the enzyme-bound flavin. In the wild-type enzyme, proton and hydride transfers are mechanistically and kinetically uncoupled.

The role of Ser101 was investigated in this dissertation. Replacement of Ser101 with threonine, alanine, cysteine, or valine demonstrated the importance …

Stakeholders' Perceptions Of Risk For Gentrification In Atlanta's Pittsburgh Neighborhood, David C. Holmes

Geosciences Theses

The 2008-2010 foreclosure crisis and the Beltline project present two significant forces shaping neighborhoods throughout Atlanta. Both the high foreclosure rates and the promise of public and private investment create conditions for the displacement of existing residents and for the gentrification of the southwest Atlanta neighborhood of Pittsburgh in particular. Through qualitative analysis, including interviews with residents, community leaders, and government officials, the development of overlay analysis maps of Pittsburgh, as well as studying the various stakeholders' perception of risk for gentrification in Pittsburgh, this research examines how and why these stakeholders' perception of the risk of gentrification in Pittsburgh …

Assessment Of Watershed Model Simplification And Potential Application In Small Ungaged Watersheds: A Case Study Of Big Creek, Atlanta, Ga, Zoia A. Comarova Ms

Geosciences Theses

Technological and methodological advances of the past few decades have provided hydrologists with advanced and increasingly complex hydrological models. These models improve our ability to simulate hydrological systems, but they also require a lot of detailed input data and, therefore, have a limited applicability in locations with poor data availability. From a case study of Big Creek watershed, a 186.4 km² urbanizing watershed in Atlanta, GA, for which continuous flow data are available since 1960, this project investigates the relationship between model complexity, data availability and predictive performance in order to provide reliability factors for the use of reduced …

A Study Of The Lhires Iii Spectrograph On The Hard Labor Creek Observatory 20 Inch Telescope, Benjamin G. Jenkins

Physics and Astronomy Theses

I present a study done to determine the characteristics of the LHIRES III spectrograph on the 20 inch RC Optics telescope at Hard Labor Creek Observatory. I describe the settings of three different diffraction gratings, collimation and focus issues, and practical aspects of use. The spectrograph was used with a SBIG ST-8XME camera for all studies. Data collection was accomplished with the Maxim DL software package and analysis was completed with IRAF. Solutions for the dispersion relation with all three diffraction gratings were found. Several projects are underway with this instrument. I present time series spectra of α Vir to …

Discrimination Of High Risk And Low Risk Populations For The Treatment Of Stds, Hui Zhao

Mathematics Theses

It is an important step in clinical practice to discriminate real diseased patients from healthy persons. It would be great to get such discrimination from some common information like personal information, life style, and the contact with diseased patient. In this study, a score is calculated for each patient based on a survey through generalized linear model, and then the diseased status is decided according to previous sexually transmitted diseases (STDs) records. This study will facilitate clinics in grouping patients into real diseased or healthy, which in turn will affect the method clinics take to screen patients: complete screening for …

The Path From Foster Care To Permanence: Does Proximity Outweigh Stability?, Michael Fost

Mathematics Theses

This thesis investigates the relationship between foster care placement settings and discharges. Placement settings are where foster children live: foster homes, group homes, etc. There may be one or several placements for any individual child. In the interest of stability, federal funding to states depends in part on low numbers of placement moves. Federal reviews, however, do not consider whether the placement settings resemble permanent family life (foster homes compared to congregate care) or the direction of placement moves. Competing risks regression was used to analyze time to discharge data of foster children in Georgia. Discharges (competing risks) were compared …

Revisiting The Dimensions Of Residential Segregation, Harry Sharp

Mathematics Theses

The first major work to analyze the dimensions of segregation, done in the late 1980s by Massey and Denton, found five dimensions which explained the phenomenon of segregation. Since the original work was done in 1988 it seems relevant to revisit the issue with new data. Massey and Denton used the technique of factor analysis to identify the latent structure underlying the phenomenon. In this research their methodology is applied to a more complete data set from the 1980 Census to confirm their results and extend the methodology. Due to problems identified during the analysis confirmation was not possible. However, …

Testing An Assumption Of Non-Differential Misclassification In Case-Control Studies, Qin Hui

Mathematics Theses

One of the issues regarding the misclassification in case-control studies is whether the misclassification error rates are the same for both cases and controls. Currently, a common practice is to assume that the rates are the same (“non-differential” assumption). However, it is suspicious that this assumption is valid in many case-control studies. Unfortunately, no test is available so far to test the validity of the assumption of non-differential misclassification when the validation data are not available. We propose the first such method to test the validity of non-differential assumption in a case-control study with 2 × 2 contingency table. First, …

Analysis Of Dependently Truncated Sample Using Inverse Probability Weighted Estimator, Yang Liu

Mathematics Theses

Many statistical methods for truncated data rely on the assumption that the failure and truncation time are independent, which can be unrealistic in applications. The study cohorts obtained from bone marrow transplant (BMT) registry data are commonly recognized as truncated samples, the time-to-failure is truncated by the transplant time. There are clinical evidences that a longer transplant waiting time is a worse prognosis of survivorship. Therefore, it is reasonable to assume the dependence between transplant and failure time. To better analyze BMT registry data, we utilize a Cox analysis in which the transplant time is both a truncation variable and …

Minimum Degree Conditions For Tilings In Graphs And Hypergraphs, Andrew Lightcap

Mathematics Theses

We consider tiling problems for graphs and hypergraphs. For two graphs and , an -tiling of is a subgraph of consisting of only vertex disjoint copies of . By using the absorbing method, we give a short proof that in a balanced tripartite graph , if every vertex is adjacent to of the vertices in each of the other vertex partitions, then has a -tiling. Previously, Magyar and Martin [11] proved the same result (without ) by using the Regularity Lemma.

In a 3-uniform hypergraph , let denote the minimum number of edges that contain for all pairs of vertices. …

Critical Thresholds For Sediment Mobility In An Urban Stream, Ross H. Martin

Geosciences Theses

Bed load transport measurements were made in a small urban stream in Decatur, GA, from which thresholds for motion were calculated using methodologies from the published literature. These methodologies are discussed in terms of their limitations and assumptions. Mobility frequencies were calculated for single grains of each grain size fraction to illustrate the transition from size selective transport to equal mobility. In general, urban streams behave differently than many gravel rivers in non-urban settings because of differences in the availability and character of sediment sources and altered flow hydrographs. This comparison allows for discussion about the way sediment is transported …

Jackknife Empirical Likelihood For The Accelerated Failure Time Model With Censored Data, Maxime K. Bouadoumou

Mathematics Theses

Kendall and Gehan estimating functions are used to estimate the regression parameter in accelerated failure time (AFT) model with censored observations. The accelerated failure time model is the preferred survival analysis method because it maintains a consistent association between the covariate and the survival time. The jackknife empirical likelihood method is used because it overcomes computation difficulty by circumventing the construction of the nonlinear constraint. Jackknife empirical likelihood turns the statistic of interest into a sample mean based on jackknife pseudo-values. U-statistic approach is used to construct the confidence intervals for the regression parameter. We conduct a simulation study …

Prevalence Of Chronic Diseases And Risk Factors For Death Among Elderly Americans, Guangming Han

Mathematics Theses

The main aim of this study is to explore the effects of risk factors contributing to death in the elderly American population. To achieve this purpose, we constructed Cox proportional hazard regression models and logistic regression models with the complex survey dataset from the national Second Longitudinal Study of Aging (LSOA II) to calculate the hazard ratios (HR)/odds ratios (OR) and confidence interval (CI) of risk factors. Our results show that in addition to chronic disease conditions, many risk factors, such as demographic factors (gender and age), social factors (interaction with friends or relatives), personal health behaviors (smoking and exercise), …

Estimation Algorithm For Mixture Of Experts Recurrent Event Model, Timesha U. Brooks

Mathematics Theses

This paper proposes a mixture of experts recurrent events model. This general model accommodates an unobservable frailty variable, intervention effect, influence of accumulating event occurrences, and covariate effects. A latent class variable is utilized to deal with a heterogeneous population and associated covariates. A homogeneous nonparametric baseline hazard and heterogeneous parametric covariate effects are assumed. Maximum likelihood principle is employed to obtain parameter estimates. Since the frailty variable and latent classes are unobserved, an estimation procedure is derived through the EM algorithm. A simulated data set is generated to illustrate the data structure of recurrent events for a heterogeneous population.

Three Topics In Analysis: (I) The Fundamental Theorem Of Calculus Implies That Of Algebra, (Ii) Mini Sums For The Riesz Representing Measure, And (Iii) Holomorphic Domination And Complex Banach Manifolds Similar To Stein Manifolds, Panakkal J. Mathew

Mathematics Dissertations

We look at three distinct topics in analysis. In the first we give a direct and easy proof that the usual Newton-Leibniz rule implies the fundamental theorem of algebra that any nonconstant complex polynomial of one complex variable has a complex root. Next, we look at the Riesz representation theorem and show that the Riesz representing measure often can be given in the form of mini sums just like in the case of the usual Lebesgue measure on a cube. Lastly, we look at the idea of holomorphic domination and use it to define a class of complex Banach manifolds …