Physical Sciences and Mathematics Commons^™

Phylogenetic Reconstruction Analysis On Gene Order And Copy Number Variation, Ruofan Xia

Theses and Dissertations

Genome rearrangement is known as one of the main evolutionary mechanisms on the genomic level. Phylogenetic analysis based on rearrangement played a crucial role in biological research in the past decades, especially with the increasing avail- ability of fully sequenced genomes. In general, phylogenetic analysis aims to solve two problems: Small Parsimony Problem (SPP) and Big Parsimony Problem (BPP). Maximum parsimony is a popular approach for SPP and BPP which relies on itera- tively solving a NP-hard problem, the median problem. As a result, current median solvers and phylogenetic inference methods based on the median problem all face se- rious …

Improving Person-Independent Facial Expression Recognition Using Deep Learning, Jie Cai

Theses and Dissertations

Over the past few years, deep learning, e.g., Convolutional Neural Networks (CNNs) and Generative Adversarial Networks (GANs), have shown promise on facial expression recog- nition. However, the performance degrades dramatically especially in close-to-real-world settings due to high intra-class variations and high inter-class similarities introduced by subtle facial appearance changes, head pose variations, illumination changes, occlusions, and identity-related attributes, e.g., age, race, and gender. In this work, we developed two novel CNN frameworks and one novel GAN approach to learn discriminative features for facial expression recognition.

First, a novel island loss is proposed to enhance the discriminative power of learned deep …

Studies Of Ch Activation In Unsaturated Amides And Esters By Trinuclear Metal Carbonyl Clusters Of Osmium, Morteza Maleki

Theses and Dissertations

The chemistry of the reaction of Os3(CO)10(NCCH3)2 with representatives of unsaturated amides and esters, RCOCHCH2 (R=(CH3)2N, CH3O) has been investigated. In these reactions, it has been observed that a CH bond on the β-carbon atom is readily activated by triosmium carbonyl clusters. The activation of β-carbon C-H bond in unsaturated amides and esters provides a robust platform for studying multicenter C-H bond transformations and for C-C bond formation via hydrogen shift and CO insertion processes. In this work, proposed mechanistic approaches have been taken in order to better understand and study the relationship between the characterized species. In addition, a …

Designing, Constructing, And Employing Two-Dimensional Ultrafast Spectroscopy To Resolve Complex Kinetics, Jason R. Darvin

Theses and Dissertations

Multiple population-period transient spectroscopy (MUPPETS) is a two dimensional ultrafast time resolved spectroscopy technique. MUPPETS uses three pairs of optical pulses over two time periods to separate homogeneous and heterogeneous causes of rate dispersion. This dissertation details improvements to the MUPPETS optical assembly enabling measurements on systems that previously fell outside of the MUPPETS 2-ns time window. In addition, the theoretical groundwork is laid to unveil the hidden coordinate controlling rate exchange using 2D and 3D correlation functions.

The first project details improvements made to the MUPPETS assembly. A detailed method was developed to eliminate astigmatism, coma, and spherical aberration …

Insider’S Misuse Detection: From Hidden Markov Model To Deep Learning, Ahmed Saaudi

Theses and Dissertations

Malicious insiders increasingly affect organizations by leaking classified data to unautho- rized entities. Detecting insiders’ misuses in computer systems is a challenging problem. In this dissertation, we propose two approaches to detect such threats: a probabilistic graph- ical model-based approach and a deep learning-based approach. We investigate the logs of computer-based activities to discover patterns of misuse. We model user’s behaviors as sequences of computer-based events.

For our probabilistic graphical model-based approach, we propose an unsupervised model for insider’s misuse detection. That is, we develop Stochastic Gradient Descent method to learn Hidden Markov Models (SGD-HMM) with the goal of analyzing …

Study Of Transition State Stabilization Using Molecular Rotors, Erik Carl Vik

Theses and Dissertations

Molecular devices that function as rotors and measurement devices are the main topic of this dissertation. Each study contains a device based on an N-phenylimide framework, which has restricted rotation about the N-C (imide-phenyl) single bond due to a steric clash from the imide carbonyl and the phenyl rings ortho substituent. In general, two ground states are observed by 1H NMR, which are separated by a single transition state (TS). Incorporation of non-covalent interactions into the TS led to measurable changes in the rate for rotation. While the molecules in this dissertation revealed details that could not have been predicted, …

Studies On The Mechanism And Application Of Steam Thermography, Raymond Gerard Belliveau Iii

Theses and Dissertations

The detection of blood on fabrics for forensic purposes is a widely studied topic in forensic science, and to that end, effort in this laboratory has been devoted to developing a thermal imaging method called steam thermography. Steam thermography is a method used to enhance chemical contrast in thermographic images by exposing a surface to water vapor during imaging. The exposure of water vapor to the surface generates heat, and can differentially increase the thermographically measured apparent temperature of imaged surfaces. This can result in thermographic contrast between surfaces with different chemical properties. Previously reported proposed mechanisms to describe the …

A Spatial Heterodyne Spectrometer For Raman Imaging And Remote Spectroscopy, Ashley Nicole Allen

Theses and Dissertations

Raman and Laser-Induced Breakdown Spectroscopy (LIBS) are optical techniques that provide information about the chemical makeup of a sample without any preparation or physical contact with it. For this reason, Raman and LIBS spectrometers are among the instruments selected for NASA’s Mars 2020 rover mission and are being considered for future missions to the Jovian moons, asteroids and comets. Such future missions will require smaller, more ruggedized Raman and LIBS spectrometers, and the new type of spectrometers discussed here, the spatial heterodyne Raman and LIBS spectrometers are being developed for this purpose. The SHS is a wide-field, Fourier transform, stationary …

Properties, Learning Algorithms, And Applications Of Chain Graphs And Bayesian Hypergraphs, Mohammad Ali Javidian

Theses and Dissertations

Probabilistic graphical models (PGMs) use graphs, either undirected, directed, or mixed, to represent possible dependencies among the variables of a multivariate probability distri- bution. PGMs, such as Bayesian networks and Markov networks, are now widely accepted as a powerful and mature framework for reasoning and decision making under uncertainty in knowledge-based systems. With the increase of their popularity, the range of graphical models being investigated and used has also expanded. Several types of graphs with dif- ferent conditional independence interpretations - also known as Markov properties - have been proposed and used in graphical models.

The graphical structure of a …

Cationic Cobaltocene Derivatives And Polyelectrolyte Membranes For Energy Storage Applications, Tianyu Zhu

Theses and Dissertations

Metal-containing polyelectrolytes (or metallo-polyelectrolytes) represent a new class of polymeric materials with distinct properties compared to traditional organo- polyelectrolytes or neutral metallopolymers. This emerging class of synthetic materials is ubiquitous for a myriad of utilities ranging from traditional electrolyte chemistry to biomedicals to sustainable applications, to name just a few. This dissertation work is focused on the design, synthesis, characterization and application of advanced metallo- cations and metallo-polyelectrolytes for energy storage applications. First, a template method to prepare metallo-polyelectrolytes based on cationic cobaltocene and polyethylene backbone was described. The resulting membranes are mechanically tough, ionically conductive and chemically inert. Second, …

Elucidating The Mechanism Of Bone Morphogenetic Protein (Bmp) -Mediated Sox2 Downregulation In Ovarian Cancer, Zainab Motolani Shonibare

Theses and Dissertations

Sex determining region Y-box 2 (Sox2) is a transcription factor essential for maintaining self-renewal and pluripotency of undifferentiated embryonic stem cells. Sox2 is involved in multiple processes of cancer cells, however, regulation of Sox2 expression and the consequences of that regulation in cancer remains elusive. Previously, we demonstrated that BMP9/GDF2 is significantly reduced in expression in ovarian cancer (OVCA) cells, methylated in patient tumors and, promoted anoikis resistance in both breast and OVCA cell lines. In an attempt to identify genes downstream of BMP9 that may provide anoikis resistance, transcriptomics was performed leading to the identification of Sox2, a developmental …

Green Forest Businesses As A Method To Improve Communities In Unesco’S East Usambara Biosphere Reserve In Tanzania, Myoung Su Ko

Theses and Dissertations

A number of developing countries, especially those in Africa which have experienced former colonization, are still struggling with exploitation of their natural resources. Throughout the development of environmental management, the strategy of natural resource management has evolved from mistreating the environment for economic and social development, to separating human activities from the environment for extreme environmental protection, to ensuring the interaction between human life and environment for sustainable development. Although an abundance of natural resources, and particularly forests, exist in the protected areas, the residents in communities surrounding protected areas are usually economically and socially poor.

With this situation, the …

Time Series Analysis Of Weather Data In South Carolina, Geophrey Odero

Theses and Dissertations

This thesis discusses time series analysis of weather data in South Carolina for the last fifteen years (January 2003 to December 2017) for Columbia, Greenville and North Myrtle Beach. The first part presents a brief overview of different variables that are used in the analysis. That is, temperature, dew point, humidity and sea level pressure. A short discussion of time series data is also introduced. The second part is about modeling the variables. The models of choice are presented, fitted and model diagnostics is carried out. In the third part, we discuss background on climates of the cities and model …

Investigation Of Electrostatic Interactions Towards Controlling Silylation-Based Kinetic Resolutions And Exploring The Effect Of The Polymer Backbone On Silylation-Based Kinetic Resolutions Employing A Polymer-Supported Triphenylsilyl Chloride, Tian Zhang

Theses and Dissertations

This dissertation focuses on studies of silylation-based kinetic resolution methodology developed by the Wiskur group, which is a powerful method for the separation of a single enantiomer from a mixture of racemic secondary alcohols. Chapter 1 introduces the background of our silylation-based kinetic resolution..

Chapter 2 involves mechanistic studies of electrostatic interactions in controlling enantioselectivities of our silylation-based kinetic resolution. Electrostatic interactions between a silylated isothiourea intermediate and an ester π system is determined via linear free energy relationship study. To be specific, how variations in sterics and electronics affect the selectivity of a silylation-based kinetic resolution.

Chapter 3 is …

Cybersecurity Issues In The Context Of Cryptographic Shuffling Algorithms And Concept Drift: Challenges And Solutions, Hatim Alsuwat

Theses and Dissertations

In this dissertation, we investigate and address two kinds of data integrity threats. We first study the limitations of secure cryptographic shuffling algorithms regarding preservation of data dependencies. We then study the limitations of machine learning models regarding concept drift detection. We propose solutions to address these threats.

Shuffling Algorithms have been used to protect the confidentiality of sensitive data. However, these algorithms may not preserve data dependencies, such as functional de- pendencies and data-driven associations. We present two solutions for addressing these shortcomings: (1) Functional dependencies preserving shuffle, and (2) Data-driven asso- ciations preserving shuffle. For preserving functional dependencies, …

Challenges In Large-Scale Machine Learning Systems: Security And Correctness, Emad Alsuwat

Theses and Dissertations

In this research, we address the impact of data integrity on machine learning algorithms. We study how an adversary could corrupt Bayesian network structure learning algorithms by inserting contaminated data items. We investigate the resilience of two commonly used Bayesian network structure learning algorithms, namely the PC and LCD algorithms, against data poisoning attacks that aim to corrupt the learned Bayesian network model.

Data poisoning attacks are one of the most important emerging security threats against machine learning systems. These attacks aim to corrupt machine learning models by con- taminating datasets in the training phase. The lack of resilience of …

Person Identification With Convolutional Neural Networks, Kang Zheng

Theses and Dissertations

Person identification aims at matching persons across images or videos captured by different cameras, without requiring the presence of persons’ faces. It is an important problem in computer vision community and has many important real-world applica- tions, such as person search, security surveillance, and no-checkout stores. However, this problem is very challenging due to various factors, such as illumination varia- tion, view changes, human pose deformation, and occlusion. Traditional approaches generally focus on hand-crafting features and/or learning distance metrics for match- ing to tackle these challenges. With Convolutional Neural Networks (CNNs), feature extraction and metric learning can be combined in …

Moving Off Collections And Their Applications, In Particular To Function Spaces, Aaron Fowlkes

Theses and Dissertations

The main focus of this paper is the concept of a moving off collection of sets. We will be looking at how this relatively lesser known idea connects and interacts with other more widely used topological properties. In particular we will examine how moving off collections act with the function spaces Cp(X), C0(X), and CK (X). We conclude with a chapter on the Cantor tree and its moving off connections.

Many of the discussions of important theorems in the literature are expressed in terms that do not suggest the concept …

Semantic Segmentation Considering Image Degradation, Global Context, And Data Balancing, Dazhou Guo

Theses and Dissertations

Recently, semantic segmentation – assigning a categorical label to each pixel in an im- age – plays an important role in image understanding applications, e.g., autonomous driving, human-machine interaction and medical imaging. Semantic segmentation has made progress by using the deep convolutional neural networks, which are sur- passing the traditional methods by a large margin. Despite the success of the deep convolutional neural networks (CNNs), there remain three major challenges.

The first challenge is how to segment the degraded images semantically, i.e., de- graded image semantic segmentation. In general, image degradations increase the difficulty of semantic segmentation, usually leading to …

Toward Greater Reproducibility Of Undergraduate Behavioral Science Research, Bruce Evan Blaine

Mathematical and Computing Sciences Faculty/Staff Publications

Reproducibility crises have arisen in psychology and other behavioral sciences, spurring efforts to ensure research findings are credible and replicable. Although reforms are occurring at professional levels in terms of new publication parameters and open science initiatives, the credibility and reproducibility of undergraduate research deserves attention. Undergraduate behavioral science research projects that rely on small convenience samples of participants, overuse hypothesis testing for drawing meaning from data, and engage in opaque statistical computing are vulnerable to producing nonreproducible findings. These vulnerabilities are reviewed, and practical recommendations for improving the credibility and reproducibility of undergraduate behavioral science research are offered.

Fractals As Basis For Design And Critique, John Charles Driscoll

Dissertations and Theses

The design profession is responding to the complex systems represented by architecture and planning by increasingly incorporating the power of computer technology into the design process. This represents a paradigm shift, and requires that designers rise to the challenge of both embracing modern technologies to perform increasingly sophisticated tasks without compromising their objective to create meaningful and environmentally sensitive architecture. This dissertation investigated computer-based fractal tools applied within a traditional architectural charette towards a design process with the potential to address the complex issues architects and planners face today. We developed and presented an algorithm that draws heavily from fractal …

Application Of 3d Salt Modeling: An Example From The Northeastern Gulf Of Mexico, Adam Mattson

Masters Theses & Specialist Projects

Salt tectonics has important implications for hydrocarbon exploration in saltbearing basins since salt deformation can directly or indirectly form hydrocarbon traps, influence hydrocarbon migration, and can control deepwater depositional systems. In various basins around the globe, extensive research has been conducted on initiation of salt mobilization, subsequent deformation, and eventual cessation, mostly from subsurface two-dimensional (2D) sections. However, 3D seismic data has dominated the petroleum industry for the last 30 years. Despite the plethora of 3D seismic data acquired in salt-bearing basins, there has been hardly any published work on the 3D geometries of complex salt bodies. 3D salt mapping …

Influence Of Spring Flow Reversals On Cave Dissolution In A Telogenetic Karst Aquifer, Mammoth Cave, Ky, Chelsey Kipper

Masters Theses & Specialist Projects

An often overlooked connection between karst groundwater systems and surface water is spring flow reversal, the flow of river water into karst springs caused by changes in hydraulic gradient. Karst aquifers are subject to the intrusion of river water when the hydraulic head of a base level river is higher than the hydraulic head of a base level spring. When this occurs, the flow out of the spring reverses, allowing river water to enter base level conduits. River water thus becomes a source of recharge into karst basins, transporting both valuable nutrients and harmful contaminants into karst aquifers. The rapid …

Synthesis Of Bis(Imino)Pyridine Iron(Ii) Complexes And Development Of Bis(Imino)Pyridine Iron(Ii) Catalyzed Carbene Transfer Reactions, Ban Wang

Masters Theses & Specialist Projects

Metal catalysis of symmetric and asymmetric carbene transfer reactions has been widely applied in natural product synthesis and material science over years. Metal carbene can be easily generated from the extrusion of nitrogen under the catalysis of metal complexes to further undergo various organic reactions, O/N/C-H insertions, cycloadditions, and ylide formations. Currently, the dominant effective catalysts for carbene reactions are built with expensive precious metal, for example, rhodium, ruthenium, palladium, gold. Notably, the effective reactivity and enantioselectivity of the dirhodium(II) catalysts are researched and established over the decades. However, the use of precious metal catalysts is the major source of …

Validation Of Neutrino Energy Estimation Using Electron Scattering Data, Mariana Khachatryan

Physics Theses & Dissertations

To study neutrino oscillations, the knowledge of the initial neutrino energy is required. This energy cannot be determined directly because neutrino beams have a broad energy distribution. Instead, the initial energy for each event is estimated from the final state particles of a neutrino-nucleus interaction using two main approaches. It can be determined either from the total energy of all the final state particles or, if the neutrino scatters quasi-elastically from a bound nucleon, then the initial energy can be calculated approximately using the scattered angle and energy of the outgoing charged lepton. This requires a detailed understanding of neutrino-nucleus …

Organic Chemistry Ii Lab Manual, Caitlyn Bailey

Senior Honors Theses

This project aims to supply a full lab manual and grading key for Organic Chemistry II, a class often taken by sophomores in Liberty University’s science degree programs. Properly applied laboratory experiments create a beneficial learning environment for science students by using hands-on procedures to transform intangible lecture concepts into concrete demonstrations. Lab work also fosters the development of problem-solving and critical-thinking skills that students need in research and the workplace. Thus, having a comprehensive lab manual is critical to students’ success and understanding in this upper-level class. This project adds to the experiments of Organic Chemistry II lab through …

Preparation And Detailed X-Ray Photoelectron Spectroscopy And Spectroscopic Ellipsometryanalysis Of Ultrathin Protective Coatings, Brian Ivins Johnson

Theses and Dissertations

Ultra-thin films (UTFs) are important in many applications, seen in the semiconductor industry, in chromatography, in sensing, in microfluidics, in aerospace, and in robotics. They also protect materials from corrosion, change surface energies, limit water intrusion into materials, allow material self-cleaning and self-healing, provide scratch resistance, and impart other specific chemical properties. In many cases, UTFs drastically alter surface properties and therefore their applications. It is imperative that proper and consistent characterization be performed on coatings to confirm and understand their desired properties. In Chapter two, Al oxidation under MgF2 protective layers is studied using real time X-ray photoelectron spectroscopy …

Making Sense Of The Equal Sign In Middle School Mathematics, Chelsea Lynn Dickson

Theses and Dissertations

One of the main reasons that students struggle as they transition from arithmetic to algebra in the middle grades is that they fail to develop the appropriate understanding of the equal sign. Previous research has suggested that students need to move past an operational understanding and develop a relational understanding of the equal sign in order to work with algebraic equations successfully. Other research has suggested that the way that we interpret and utilize the equal sign is based on three main factors: multiple meanings of the equal sign, equation types, and structural conventions. This study extends both areas of …

A Cfd Study Of Steady Fully Developed Laminar Flow Through A 90-Degree Bend Pipe With A Square Cross-Sectional Area, Subodh Sushant Toraskar

Mechanical & Aerospace Engineering Theses & Dissertations

Fluid flow through a closed curved conduit has always been a topic of extensive research, as it has many practical and industrial applications. The flow is generally characterized by a presence of secondary flow, vortical motions and pressure losses for different flow regimes. These observed irregularities may positively or negatively impact the flow. They are beneficial for cases where mixing of fluids is required, usually observed for multiphase flow regimes or detrimental for cases involving particles in the fluid. There are also instances where a particle-laden fluid transported through the curved pipe was directly related to corrosion- erosion related problems. …

Computational Analysis Of Antipode Algorithms For The Output Feedback Hopf Algebra, Lance Berlin

Electrical & Computer Engineering Theses & Dissertations

The feedback interconnection of two systems written in terms of Chen-Fliess series can be described explicitly in terms of the antipode of the output feedback Hopf algebra. At present, there are three known computational approaches to calculating this antipode: the left coproduct method, the right coproduct method, and the derivation method. Each of these algorithms is defined recursively, and thus becomes computationally expensive quite quickly. This motivates the need for a more complete understanding of the algorithmic complexity of these methods, as well as the development of new approaches for determining the Hopf algebra antipode. The main goals of this …