Digital Commons Network^™

Explainable Neural Networks Based Anomaly Detection For Cyber-Physical Systems, Kasun Amarasinghe

Theses and Dissertations

Cyber-Physical Systems (CPSs) are the core of modern critical infrastructure (e.g. power-grids) and securing them is of paramount importance. Anomaly detection in data is crucial for CPS security. While Artificial Neural Networks (ANNs) are strong candidates for the task, they are seldom deployed in safety-critical domains due to the perception that ANNs are black-boxes. Therefore, to leverage ANNs in CPSs, cracking open the black box through explanation is essential.

The main objective of this dissertation is developing explainable ANN-based Anomaly Detection Systems for Cyber-Physical Systems (CP-ADS). The main objective was broken down into three sub-objectives: 1) Identifying key-requirements that an …

Site- And Location-Adjusted Approaches To Adaptive Allocation Clinical Trial Designs, Brian S. Di Pace

Theses and Dissertations

Response-Adaptive (RA) designs are used to adaptively allocate patients in clinical trials. These methods have been generalized to include Covariate-Adjusted Response-Adaptive (CARA) designs, which adjust treatment assignments for a set of covariates while maintaining features of the RA designs. Challenges may arise in multi-center trials if differential treatment responses and/or effects among sites exist. We propose Site-Adjusted Response-Adaptive (SARA) approaches to account for inter-center variability in treatment response and/or effectiveness, including either a fixed site effect or both random site and treatment-by-site interaction effects to calculate conditional probabilities. These success probabilities are used to update assignment probabilities for allocating patients …

Development And Characterization Of Stationary Phase Gradients For High Performance Liquid Chromatography, Anna Forzano

Theses and Dissertations

Choosing a stationary phase is the first step in developing a liquid chromatography (LC) separation method, where the selectivity is governed by the differential interactions of the analytes with the stationary and mobile phases. Introducing a gradient in stationary phase functionality allows for tuning of analyte retention, translating to a possible improvement in selectivity and an increase in resolution versus that offered by uniform stationary phases.

In this work, C₁₈-silica, phenylbutyl-silica, and phenylbutyl-ammonium opposed continuous stationary phase gradients were fabricated using controlled rate infusion (CRI) on particle packed LC columns. Characterization of the stationary phase was carried out …

Determination Of Optimal Parameter Estimates For Medical Interventions In Human Metabolism And Inflammation, Marcella Torres

Theses and Dissertations

In this work we have developed three ordinary differential equation models of biological systems: body mass change in response to exercise, immune system response to a general inflammatory stimulus, and the immune system response in atherosclerosis. The purpose of developing such computational tools is to test hypotheses about the underlying biological processes that drive system outcomes as well as possible real medical interventions. Therefore, we focus our analysis on understanding key interactions between model parameters and outcomes to deepen our understanding of these complex processes as a means to developing effective treatments in obesity, sarcopenia, and inflammatory diseases.

We develop …

Monitoring Software And Charged Particle Identification For The Clas12 Detector, William A. Oliver

Theses and Dissertations

The CEBAF Large Acceptance Spectrometer for the 12 GeV era, known as CLAS12, uses the time of flight (TOF) system to identify charged particles from scattering events between the beam and target. The TOF system is divided into two parts: The Forward time of flight system, and the Central time of flight system. These two sub-systems subtend different polar angles of the detector geometry for wide acceptance of scattered particles. Reconstruction is the service used to identify particles from the interactions between the beam and target, called as a vertex or the point where the interaction occurs. The vertex position …

Methods For Evaluating Dropout Attrition In Survey Data, Camille J. Hochheimer

Theses and Dissertations

As researchers increasingly use web-based surveys, the ease of dropping out in the online setting is a growing issue in ensuring data quality. One theory is that dropout or attrition occurs in phases that can be generalized to phases of high dropout and phases of stable use. In order to detect these phases, several methods are explored. First, existing methods and user-specified thresholds are applied to survey data where significant changes in the dropout rate between two questions is interpreted as the start or end of a high dropout phase. Next, survey dropout is considered as a time-to-event outcome and …

Searching For Clean Observables In $B -> D* /Tau- \Bar{\Nu}_{\Tau}$ Decays, Michael D. Williams Jr.

Theses and Dissertations

In this thesis, the clean angular observables in the $\bar{B} \to D^{*+} \ell^- \bar{\nu}_{\ell}$ angular distribution is studied. Similar angular observables are widely studied in $B \to K^* \mu^+ \mu^-$ decays. We believed that these angular observables may have different sensitivities to different new physics structures.

Expansion Of The Genetic Code To Include Acylated Lysine Derivatives And Photocaged Histidine, William D. Kinney

Theses and Dissertations

The genetic code of all known organisms is comprised of the 20 proteinogenic amino acids that serve as building blocks on a peptide chain to form a vast array of proteins. Proteins are responsible for virtually every biological process in all organisms; however, the 20 amino acids contain a limited number of functional groups that often leaves much to be desired. The lack of diversity addresses the need to increase the genetic repertoire of living cells to include a variety of amino acids with novel structural, chemical, and physical properties not found in the common 20 amino acids. In order …

Distributed Multi-Label Learning On Apache Spark, Jorge Gonzalez Lopez

Theses and Dissertations

This thesis proposes a series of multi-label learning algorithms for classification and feature selection implemented on the Apache Spark distributed computing model. Five approaches for determining the optimal architecture to speed up multi-label learning methods are presented. These approaches range from local parallelization using threads to distributed computing using independent or shared memory spaces. It is shown that the optimal approach performs hundreds of times faster than the baseline method. Three distributed multi-label k nearest neighbors methods built on top of the Spark architecture are proposed: an exact iterative method that computes pair-wise distances, an approximate tree-based method that indexes …

Pharmacodynamics Of Monoamine Transporter Releasing Agents And Reuptake Inhibitors, Alexa Holloway

Theses and Dissertations

Ligands of the human monoamine transporters encompass a wide range of both illicit and therapeutic drugs that act upon neural circuitry related to reward, motivation, and the processing of salient stimuli. The present study utilizes two methods for analyzing transporter substrates and inhibitors in order to characterize activity and assess potency. The first measures transient changes in intracellular calcium as a surrogate for transporter activity by harnessing the electrical coupling of monoamine transporters and L-type calcium channels. This is used to analyze novel chimera of the strong hDAT inhibitors methylphenidate and ��-PPP in order to assess the contribution of specific …

An Introduction To Supersymmetric Quantum Mechanics, Vincent R. Siggia

Theses and Dissertations

In this thesis, the general framework of supersymmetric quantum mechanics and the path integral approach will be presented (as well as the worked out example of the supersymmetric harmonic oscillator). Then the theory will be specialized to the case of supersymmetric quantum mechanics on Riemannian manifolds, which will start from a supersymmetric Lagrangian for the general case and the special case for S2. Afterwards, there will be a discussion on the superfield formalism. Concluding this thesis will be the Hamiltonian formalism followed by the inclusion of deforma- tions by potentials.

Biometal-Induced Structural Consequences Of Α-Synuclein – The Parkinson’S Disease Protein, Dinendra L. Abeyawardhane

Theses and Dissertations

The pre-synaptic protein α-Synuclein (αS) is often linked to the pathology of Parkinson’s disease (PD), an age-related neurodegenerative disorder. Lewy bodies, the cytopathological hallmarks of PD, are found to be rich in aggregates of misfolded αS protein. Metal dyshomeostasis has also been linked to PD due to the accumulation of iron in the substantia nigra pars compacta, and diminished copper levels reported in this same region. Metal dyshomeostasis in the brain coupled with oxidative stress can enhance the aggregation of αS. Recently, it was confirmed that mammalian αS is universally acetylated at the N-terminus, a common post-translational modification in …

Metal Nanoparticle Synthesis By Photochemical Reduction With A High-Intensity Focused Laser Beam, Victoria K. Meader

Theses and Dissertations

Colloidal, metallic nanoparticles have myriad applications, but they are most ideal when they are monodisperse, and demonstrate maximum catalytic utility when they are small (< 5 nm) and uncoated; because their surface area is accessible and maximized. Laser- assisted metal nanoparticle synthesis is a ‘green’ method that has become a topic of active research because it is able to produce uncoated or ‘naked’ products. The nanoparticles synthesized in this work were formed through the reduction of metal salts in aqueous solutions; but the reducing agent is an electron-dense microplasma generated by the laser pulse interacting with the media. Because no chemical reducing agents or stabilizers are needed, the products have no surfactants.

The underlying reaction mechanisms that drive this type of synthesis are generally understood, however, there is insufficient detail that would allow control over the formation of ultimate product morphologies and size distributions. The metals examined in this thesis are: gold, whose formation follows an autocatalytic rate law; and silver, whose formation follows a first-order rate law. Through my research, I was able to …

Theoretical Studies Of The Structure And Stability Of Metal Chalcogenide Crntem (1≤N≤6, 1≤M≤8) Clusters, Fnu Sweta Prabha

Theses and Dissertations

In the presented work, first principle studies on electronic structure, stability, and magnetic properties of metal chalcogenide, Cr_nTe_m clusters have been carried out within a density functional framework using generalized gradient functions to incorporate the exchange and correlation effects. The energetic and electronic stability was investigated, and it was found that they are not always correlated as seen in the cluster Cr₆Te₈ which has smaller gap between its HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) and a high electron affinity of 3.39 eV indicating lower electronic stability whereas higher fragmentation …

Assessing The Impact Of Incorporating Residential Histories Into The Spatial Analysis Of Cancer Risk, Anny-Claude Joseph

Theses and Dissertations

In many spatial epidemiologic studies, investigators use residential location at diagnosis as a surrogate for unknown environmental exposures or as a geographic basis for assigning measured exposures. Inherently, they make assumptions about the timing and location of pertinent exposures which may prove problematic when studying long latency diseases such as cancer.

In this work we explored how the association between environmental exposures and disease risk for long-latency health outcomes like cancer is affected by residential mobility. We used simulation studies conditioned on real data to evaluate the extent to which the commonly held assumption of no residential mobility 1) affected …

Methods For Joint Normalization And Comparison Of Hi-C Data, John C. Stansfield

Theses and Dissertations

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing …

Evaluation Of Private Landowner Intention To Create Early Successional Habitat In Virginia's Appalachian Region, Hannah M. Coovert

Theses and Dissertations

As human land uses continue to expand rapidly across the landscape, the management practices of private landowners are an essential part of effective conservation of biodiversity. Conservation of early successional habitats (ESH) and the species that depend on them is a priority in the eastern United States, and efforts to create more ESH on private lands has primarily focused on forest landowners and the harvesting of timber. Private lands with significant pasture cover in a forested landscape present an additional opportunity to create and maintain ESH, yet our understanding of landowner values and attitudes about management strategies in pastures (i.e., …

Straintronic Nanomagnetic Devices For Non-Boolean Computing, Md Ahsanul Abeed

Theses and Dissertations

Nanomagnetic devices have been projected as an alternative to transistor-based switching devices due to their non-volatility and potentially superior energy-efficiency. The energy efficiency is enhanced by the use of straintronics which involves the application of a voltage to a piezoelectric layer to generate a strain which is ultimately transferred to an elastically coupled magnetostrictive nanomaget, causing magnetization rotation. The low energy dissipation and non-volatility characteristics make straintronic nanomagnets very attractive for both Boolean and non-Boolean computing applications. There was relatively little research on straintronic switching in devices built with real nanomagnets that invariably have defects and imperfections, or their adaptation …

Genome-Wide Systems Genetics Of Alcohol Consumption And Dependence, Kristin Mignogna

Theses and Dissertations

Widely effective treatment for alcohol use disorder is not yet available, because the exact biological mechanisms that underlie this disorder are not completely understood. One way to gain a better understanding of these mechanisms is to examine the genetic frameworks that contribute to the risk for developing this disorder. This dissertation examines genetic association data in combination with gene expression networks in the brain to identify functional groups of genes associated with alcohol consumption and dependence.

The first study took advantage of the behavioral complexity of human samples, and experimental capabilities provided by mouse models, by co-analyzing gene expression networks …

Metallic Systems At The Nano And Micro Scale: Bimetallic Nanoparticles As Catalysts And Mcraly Bond Coats In Thermal Barrier Coatings, Kenneth Kane

Theses and Dissertations

The dissertation is split into two parts. The first part will be focused on changes in material properties found at the nanoscale, as miscibility and electronic structure can change significantly with size. The formation of classically-immiscible bimetallic nanoparticles (BNPs) becomes favorable at the nanoscale and novel catalytic properties can emerge from the bimetallic alloying. The formation of alloyed and non-alloyed BNPs is achieved through pulse laser ablation (PLA) and a significant increase in catalytic activity is observed for both. Recently discovered, the increased activity in the non-alloyed BNPs, deemed multicomponent photocatalysis, is examined and the proposed mechanism discussed. The second …

Bayesian Nonparametric Analysis Of Longitudinal Data With Non-Ignorable Non-Monotone Missingness, Yu Cao

Theses and Dissertations

In longitudinal studies, outcomes are measured repeatedly over time, but in reality clinical studies are full of missing data points of monotone and non-monotone nature. Often this missingness is related to the unobserved data so that it is non-ignorable. In such context, pattern-mixture model (PMM) is one popular tool to analyze the joint distribution of outcome and missingness patterns. Then the unobserved outcomes are imputed using the distribution of observed outcomes, conditioned on missing patterns. However, the existing methods suffer from model identification issues if data is sparse in specific missing patterns, which is very likely to happen with a …

Optimizing Gas Mixture Composition For The Rtpc Detector For Bonus 12 At Jefferson Lab., Joshua H. Lehman

Theses and Dissertations

The main objective of this thesis is to perform a study of and optimize the most direct and practical gas mixture composition inside the Radial Time Projection Chamber for the Barely-Offshell Nucleon Structure (BONuS 12) detector for use in the CLAS 12 detector in Experimental Hall B at Thomas Jefferson National Accelerator Facility (JLab). The optimization of these conditions will enhance the performance and resolution of the detector. The original BONuS 6 experiment utilized a gas composition of 80 % He and 20% Dimethyl Ether (DME). With the extensive 12 GeV energy upgrade constructed at JLab and the new BONuS …

The Structure And Stability Of Cationic Metal-Benzene Clusters, Daniel P. Rabayda

Theses and Dissertations

We have investigated the size-dependent stability and structure of benzene, aluminum-benzene, and vanadium-benzene clusters. Motivated by gas-phase experimental studies performed by an experimental collaborator, we have used first-principle electronic structure methods to identify the structure of Al⁺(Bz)_n, V⁺(Bz)_n, and Bz_n clusters. Our studies reveal that cationic aluminum-benzene clusters have a magic number of 13, and that its high stability may be understood by analyzing the structure of the cluster. We also investigate the structure of vanadium-benzene clusters which have a magic number of 2. Here I examine the benzene-cation and benzene-benzene …

Electronic Structure Of Cathode Materials In Lithium Ion Batteries, John M. Swanlund

Theses and Dissertations

Lithium ion batteries are ubiquitous in modern life, from powering hand-held electronic devices to electric vehicles. And with the necessary drive toward renewable energy sources like solar and wind, electricity storage for the grid promises to drive up the demand for higher performing, less expensive, safer, and more environmentally friendly secondary batteries. Recent research has theorized that replacing halogens in batteries’ electrolytes with non-halogens can yield desirable performance characteristics while eliminating the most dangerous and problematic chemicals. This thesis explores the possibility that a similar approach can be taken with the cathodes of lithium ion batteries. The active material in …

Indirect Relatedness, Evaluation, And Visualization For Literature Based Discovery, Sam Henry

Theses and Dissertations

The exponential growth of scientific literature is creating an increased need for systems to process and assimilate knowledge contained within text. Literature Based Discovery (LBD) is a well established field that seeks to synthesize new knowledge from existing literature, but it has remained primarily in the theoretical realm rather than in real-world application. This lack of real-world adoption is due in part to the difficulty of LBD, but also due to several solvable problems present in LBD today. Of these problems, the ones in most critical need of improvement are: (1) the over-generation of knowledge by LBD systems, (2) a …

Some Intuition Behind Large Cardinal Axioms, Their Characterization, And Related Results, Philip A. White

Theses and Dissertations

We aim to explain the intuition behind several large cardinal axioms, give characterization theorems for these axioms, and then discuss a few of their properties. As a capstone, we hope to introduce a new large cardinal notion and give a similar characterization theorem of this new notion. Our new notion of near strong compactness was inspired by the similar notion of near supercompactness, due to Jason Schanker.

Assessing The Quality Of Software Development Tutorials Available On The Web, Manziba A. Nishi

Theses and Dissertations

Both expert and novice software developers frequently access software development resources available on the Web in order to lookup or learn new APIs, tools and techniques. Software quality is affected negatively when developers fail to find high-quality information relevant to their problem. While there is a substantial amount of freely available resources that can be accessed online, some of the available resources contain information that suffers from error proneness, copyright infringement, security concerns, and incompatible versions. Use of such toxic information can have a strong negative effect on developer’s efficacy. This dissertation focuses specifically on software tutorials, aiming to automatically …

2nd Tier Assay For The Detection Of Congenital Adrenal Hyperplasia By Virginia’S Newborn Screening Laboratory: Steroid Profile By Hplc-Ms/Ms, Christopher E. Nixon

Theses and Dissertations

Congenital Adrenal Hyperplasia (CAH) encompasses several disorders related to disruptions in the adrenal steroid production pathway. These disruptions may cause virilization of the external female sex organs, incorrect gender assignment, precocious puberty, and in the most severe form, may cause life-threatening salt wasting and adrenal crisis if not detected and treated early in the newborn period.

17α-Hydroxyprogesterone (17-OHP) is the primary target for immunofluorescence detection of CAH from dried blood spots in newborn screening (NBS). Unfortunately, current immunoassay techniques for the detection of CAH suffer from high false positive rates. The primary factors contributing to false positive determinations can include …

Adhesion At Solid/Liquid Interfaces, Neda Ojaghlou

Theses and Dissertations

The adhesion at solid/liquid interface plays a fundamental role in diverse fields and helps explain the structure and physical properties of interfaces, at the atomic scale, for example in catalysis, crystal growth, lubrication, electrochemistry, colloidal system, and in many biological reactions. Unraveling the atomic structure at the solid/liquid interface is, therefore, one of the major challenges facing the surface science today to understand the physical processes in the phenomena such as surface coating, self-cleaning, and oil recovery applications. In this thesis, a variety of theory/computational methods in statistical physics and statistical mechanics are used to improve understanding of water adhesion …

Kings In The Direct Product Of Digraphs, Morgan Norge

Theses and Dissertations

A k-king in a digraph D is a vertex that can reach every other vertex in D by a directed path of length at most k. A king is a vertex that is a k-king for some k. We will look at kings in the direct product of digraphs and characterize a relationship between kings in the product and kings in the factors. This is a continuation of a project in which a similar characterization is found for the cartesian product of digraphs, the strong product of digraphs, and the lexicographic product of digraphs.