Physical Sciences and Mathematics Commons^™

Investigating Applications Of Deep Learning For Diagnosis Of Post Traumatic Elbow Disease, Hugh James

McKelvey School of Engineering Theses & Dissertations

Traumatic events such as dislocation, breaks, and arthritis of musculoskeletal joints can cause the development of post-traumatic joint contracture (PTJC). Clinically, noninvasive techniques such as Magnetic Resonance Imaging (MRI) scans are used to analyze the disease. Such procedures require a patient to sit sedentary for long periods of time and can be expensive as well. Additionally, years of practice and experience are required for clinicians to accurately recognize the diseased anterior capsule region and make an accurate diagnosis. Manual tracing of the anterior capsule is done to help with diagnosis but is subjective and timely. As a result, there is …

Speeding Up The Quantification Of Contrast Sensitivity Functions Using Multidimensional Bayesian Active Learning, Shohaib Shaffiey

McKelvey School of Engineering Theses & Dissertations

No abstract provided.

Geometric Algorithms For Modeling Plant Roots From Images, Dan Zeng

McKelvey School of Engineering Theses & Dissertations

Roots, considered as the ”hidden half of the plant”, are essential to a plant’s health and pro- ductivity. Understanding root architecture has the potential to enhance efforts towards im- proving crop yield. In this dissertation we develop geometric approaches to non-destructively characterize the full architecture of the root system from 3D imaging while making com- putational advances in topological optimization. First, we develop a global optimization algorithm to remove topological noise, with applications in both root imaging and com- puter graphics. Second, we use our topology simplification algorithm, other methods from computer graphics, and customized algorithms to develop a high-throughput …

Plasmonic Nanomaterials-Based Point-Of-Care Biosensors, Rohit Gupta

McKelvey School of Engineering Theses & Dissertations

Point-of-care (POC) biosensors, although rapid and easy-to-use, are orders magnitude less sensitive than laboratory-based tests. Further they are plagued by poor stability of recognition element thus limiting its widespread applicability in resource-limited settings. Therefore, there is a critical need for realizing stable POC biosensors with sensitivity comparable to gold-standard laboratory-based tests. This challenge constitutes the fundamental basis of this dissertation work– to expand access to quality and accurate biodiagnostic tools. At the heart of these solutions lies plasmonic nanoparticles which exhibit unique optical properties which are attractive for label-free and labelled biosensors.Firstly, we improve the stability and applicability of label-free …

Modeling, Analysis, And Simulation To Reveal The Mechanisms Of Ciliary Beating, Louis Woodhams

McKelvey School of Engineering Theses & Dissertations

Cilia are microscopic cellular appendages that help us breathe by clearing our airways, maintain the health of our central nervous system by circulating cerebrospinal fluid, and allow us to reproduce by transporting eggs and propelling sperm cells. Cilia even determine the asymmetry of our internal organs during embryonic development. However, the mechanisms underlying ciliary beating are not fully understood. Questions remain as to how arrays of the motor protein dynein generate the propulsive waveforms observed in cilia and how structural elements within the cilium and its connection to the cell deform during beating. In the current work, mathematical modeling, analysis, …

Development Of The Assessment Of Clinical Prediction Model Transportability (Apt) Checklist, Sean Chonghwan Yu

McKelvey School of Engineering Theses & Dissertations

Clinical Prediction Models (CPM) have long been used for Clinical Decision Support (CDS) initially based on simple clinical scoring systems, and increasingly based on complex machine learning models relying on large-scale Electronic Health Record (EHR) data. External implementation – or the application of CPMs on sites where it was not originally developed – is valuable as it reduces the need for redundant de novo CPM development, enables CPM usage by low resource organizations, facilitates external validation studies, and encourages collaborative development of CPMs. Further, adoption of externally developed CPMs has been facilitated by ongoing interoperability efforts in standards, policy, and …

Fate Of Metals In Presence Of Minerals And Mineral-Organic Assemblages, Neha Sharma

McKelvey School of Engineering Theses & Dissertations

Metals can enter aquatic systems from natural and anthropogenic processes associated with weathering, sediment re-suspension, industrial activities, and atmospheric deposition. Metals pose health and environmental risks at high concentrations due to their potential toxicity and bioaccumulation, but many trace metals also serve as essential micronutrients for biogeochemical processes in natural aquatic systems. Biogeochemical processes such as methanogenesis, denitrification, and mercury methylation require transition metals such as nickel (Ni), cobalt (Co), copper (Cu), and molybdenum (Mo) for completion. These biogeochemical processes can be substantial contributors of greenhouse gases, such as methane (CH4) and nitrous oxide (N2O), into the atmosphere. The behavior, …

Environmental Fate Of Rna Interference Biopesticides, Ke Zhang

McKelvey School of Engineering Theses & Dissertations

Emerging agricultural biotechnology uses RNA interference (RNAi) to protect crops from pests. RNAi is a cellular mechanism in which double-stranded RNA (dsRNA) directs the degradation of the homologous messenger RNA (mRNA), leading to gene silencing and preventing the synthesis of essential proteins. As applied to agriculture, dsRNA biopesticides have been developed that can trigger RNAi inside of the pest tissues to cause reduced pest growth and/or increased pest mortality. When dsRNA biopesticides are released to receiving environments (e.g., agricultural soils and surface water), they pose potential ecological risks to non-target organisms. This dissertation aims to advance the understanding of the …

Characterization Of Smoke Particles Toward Improved Remote Sensing Retrievals And Chemical Transport Modeling, Chenchong Zhang

McKelvey School of Engineering Theses & Dissertations

Wildfires increase in extent, intensity, and frequency across the globe over the recent decades. The uncontrolled fires trigger cascading effects on local ecosystems and the fire emissions pose a higher risk to air quality and climate. Wildfire emissions contain a variety of trace gases and particulate matters. The particle-phase emissions, especially those light-absorbing species including black carbon (BC) and brown carbon (BrC), significantly affect the regional and global climate by modulating the radiative transfer phenomena in the atmosphere. A great discrepancy still exists between model- and observation-based estimates of aerosol-radiation interactions (ARI). The discrepancy is partially attributed to the mischaracterizations …

Dynamics Of Spatiotemporal Heterogeneities In Particulate Intercalation Electrodes, Shubham Agrawal

McKelvey School of Engineering Theses & Dissertations

Electrochemical energy systems rely on particulate porous electrodes to store or convert energies. While the three-dimensional porous structures of the electrodes were introduced to maximize the interfacial area for better overall performance of the system, spatiotemporal heterogeneities arising from materials thermodynamics localize the charge transfer processes onto a limited portion of the available interfaces. These reaction heterogeneities may cause local hot and cold spots, and early battery failures. This dissertation focuses on the following three aspects of the dynamic reaction heterogeneities in the particulate cathodes and anodes in the lithium-ion batteries: (i) the real-time evolution of reaction heterogeneities in graphite …

Smart Sensing And Clinical Predictions With Wearables: From Physiological Signals To Mental Health, Ruixuan Dai

McKelvey School of Engineering Theses & Dissertations

Wearable devices such as smartwatches and wristbands are gaining adoption. Recent advances in technology in wearables enable remote health monitoring. However, there are challenges in exploiting wearables in healthcare applications. First, sensor readings from wearables are vulnerable to motion and noise artifacts. A robust pipeline is needed to extract reliable measurements from noisy signals. Second, while wearables support an increasing number of sensing modalities, there is a significant need to generate more clinically meaningful measurements with wearables. Finally, to incorporate wearables into clinical practice, we need to establish the link between wearable measurements and clinical outcomes, thus supporting clinical decisions. …

Dynamic Continuous Distributed Constraint Optimization Problems, Khoi Hoang

McKelvey School of Engineering Theses & Dissertations

The Distributed Constraint Optimization Problem (DCOP) formulation is a powerful tool to model multi-agent coordination problems that are distributed by nature. The formulation is suitable for problems where the environment does not change over time and where agents seek their value assignment from a discrete domain. However, in many real-world applications, agents often interact in a more dynamic environment and their variables usually require a more complex domain. Thus, the DCOP formulation lacks the capabilities to model the problems in such dynamic and complex environments. To address these limitations, researchers have proposed Dynamic DCOPs (D-DCOPs) to model how DCOPs dynamically …

Tfa Inference: Using Mathematical Modeling Of Gene Expression Data To Infer The Activity Of Transcription Factors, Cynthia Ma

McKelvey School of Engineering Theses & Dissertations

Transcription factors (TFs) are a set of proteins that play a key role in the information processing system that enables a cell to respond to changes in internal and external state. By binding near a gene in a cell’s DNA, a TF can influence that gene’s expression level, triggering the appropriate increase or decrease in production levels of proteins that are needed to handle stressors like a change in nutrient availability or damage to the cell’s internal structures. Transcription factor activity (TFA) is a measure of how much effect a TF has on its target genes in a given sample …

Evaluation And Clinical Implementation Of A Dual-Energy Ct Stopping-Power Ratio Mapping Technique For Proton-Therapy Treatment Planning, Maria Jose Medrano Matamoros

McKelvey School of Engineering Theses & Dissertations

Proton radiotherapy has the potential to treat tumors with better conformal dose distribution than competing modalities when the rapid dose falloff at the end of the proton-beam range is correctly aligned to the edge of the clinical target volume (CTV). However, its clinical potential is dependent on the accurate localization of the Bragg-peak position from predicted stopping-power ratio maps. The method that is most commonly used in today’s clinical practice for predicting stopping-power ratio (SPR) consists of a stoichiometric calibrationtechnique based on single-energy CT (SECT) for direct estimation of patient-specific SPR distribution from vendor-reconstructed Hounsfield Unit (HU) images. Unfortunately, this …

Human-Centered Machine Learning: Algorithm Design And Human Behavior, Wei Tang

McKelvey School of Engineering Theses & Dissertations

Machine learning is increasingly engaged in a large number of important daily decisions and has great potential to reshape various sectors of our modern society. To fully realize this potential, it is important to understand the role that humans play in the design of machine learning algorithms and investigate the impacts of the algorithm on humans.

Towards the understanding of such interactions between humans and algorithms, this dissertation takes a human-centric perspective and focuses on investigating the interplay between human behavior and algorithm design. Accounting for the roles of humans in algorithm design creates unique challenges. For example, humans might …

Scheduling For High Throughput And Small Latency In Parallel And Distributed Systems, Zhe Wang

McKelvey School of Engineering Theses & Dissertations

Parallel and distributed systems are pervasive, such as web services, clouds, and cyber-physical systems. We often desire high throughput and small latency in the parallel and distributed system. However, since the system is distributed and the input is online, scheduling for high throughput while keeping the latency small is often challenging. In this dissertation, we developed scheduling algorithms, policies, and mechanisms to approach high throughput with small latency in various parallel and distributed applications. First, we developed AMCilk runtime system for running multi-programmed parallel jobs on many-processor machines. When running parallel jobs, the allocation of processors to the parallel jobs …

Design And Analysis Of Strategic Behavior In Networks, Sixie Yu

McKelvey School of Engineering Theses & Dissertations

Networks permeate every aspect of our social and professional life.A networked system with strategic individuals can represent a variety of real-world scenarios with socioeconomic origins. In such a system, the individuals' utilities are interdependent---one individual's decision influences the decisions of others and vice versa. In order to gain insights into the system, the highly complicated interactions necessitate some level of abstraction. To capture the otherwise complex interactions, I use a game theoretic model called Networked Public Goods (NPG) game. I develop a computational framework based on NPGs to understand strategic individuals' behavior in networked systems. The framework consists of three …

Model-Based Deep Learning For Computational Imaging, Xiaojian Xu

McKelvey School of Engineering Theses & Dissertations

This dissertation addresses model-based deep learning for computational imaging. The motivation of our work is driven by the increasing interests in the combination of imaging model, which provides data-consistency guarantees to the observed measurements, and deep learning, which provides advanced prior modeling driven by data. Following this idea, we develop multiple algorithms by integrating the classical model-based optimization and modern deep learning to enable efficient and reliable imaging. We demonstrate the performance of our algorithms by validating their performance on various imaging applications and providing rigorous theoretical analysis.

The dissertation evaluates and extends three general frameworks, plug-and-play priors (PnP), regularized …

Integrating Physical Models And Deep Priors For Computational Imaging, Yu Sun

McKelvey School of Engineering Theses & Dissertations

This dissertation addresses integrating physical models and learning priors for computational imaging. The motivation of our work is driven by the recent discussion of learning-based methods that solve the imaging inverse problem by directly learning a measurement-to-image mapping from the existing data: they achieve superior performance over the traditional model-based methods but lack the physical model to impose sufficient interpretation and guarantee of the final image. We adopt the classic statistical inference as the underlying formulation and integrate learning models as implicit image priors, such that our framework is able to simultaneously leverage physical models and learning priors. Additionally, the …

Nanoscale Interfacial Control Of Ion Behaviors And Caco3 Formation In Environmental Systems, Yaguang Zhu

McKelvey School of Engineering Theses & Dissertations

Interfaces in environmental systems can change the distribution of pollutants and nutrients, determine the fate and transport of nanoparticles, and affect the efficiency of engineering projects. Complex interactions, including electrostatic interactions, Van der Waals interactions, chemical interactions, and ion-surface specific interactions, can all contribute to different ion, ion-pair, and nanoparticle formations near interfaces. Although environmental interfaces play critical roles, only a limited number of studies have considered the nanoscale picture of how they control ions and nanoparticles. Thus, this dissertation addresses three research questions: (1) How does sulfate chemically interact with calcium carbonate (CaCO3) during its heterogeneous formation on quartz …

Echoed Sites And The Unknowable Object, Joseph Canizales

MFA in Visual Art

This thesis will discuss the expanded field of sculpture, simulacra, digital technology, and two terms I’ve devised: the unknowable object, and echoed sites. Within these two terms, I’m concerned with the complicated relationship between humans and geology and how we extract material from the ground without reflecting on the geologic history of the site. In echoed sites I create sculptures with and without a geologic site or object, by way of digital technology. These forms display two states paradoxically in balance, where what’s presented leaves more questions than answers. Thus, as part of echoed sites, exists the unknowable object. …

A Nonconforming Finite Element Method For The 2d Vector Laplacian, Mary Barker

Arts & Sciences Electronic Theses and Dissertations

The vector Laplacian presents difficulties in finite element ap- proximation. It is well known that for nonconvex domains, H1- conforming approximation spaces form a closed subspace of the solution space H(div; Ω) ∩ H(curl; Ω). Hence H1-conforming approximations will fail to converge. This is problematic as it is highly difficult to construct more general finite dimensional ap- proximation spaces for this space. We will present an extension of a nonconforming method introduced by Brenner et al. The method was originally given for P1-nonconforming spaces in two dimensions. Our extension is given for degree r polynomials, but which agrees with the …

Some Problems In Reproducing Kernel Spaces, Christopher Felder

Arts & Sciences Electronic Theses and Dissertations

The two chapters of this thesis are comprised of work in the setting of reproducing kernel (Hilbert) spaces. These are Banach (or Hilbert) spaces of functions defined on some set, with the special property that point evaluation, on the underlying set, is bounded.

The first chapter deals with the study of inner functions. These functions have a rich history in function and operator theory in the Hardy spaces of the unit disk. The first section of this chapter studies the relationship between generalized inner functions and optimal polynomial approximants. The second section, which is joint work with Trieu Le, deals …

Electronic, Optical, And Thermal Probes Of The Layered Mott Insulator Α-Rucl3 In The Atomically Thin Limit, Jesse Balgley

Arts & Sciences Electronic Theses and Dissertations

Alpha-ruthenium(III) chloride (α-RuCl3) is a layered Mott insulator and van der Waals material that can be cleaved down to a single atomic layer. This material is a promising candidate to realize the Kitaev quantum spin liquid, a strongly correlated phase of matter expected to host fractionalized quasiparticles and a potential platform for topological quantum computation. When α-RuCl3 is placed in direct contact with the layered semimetal graphene we observe a strong charge transfer between the two materials despite the electrically insulating nature of α-RuCl3, which absorbs ≈ 4 × 10^13 electrons/cm^2 from the graphene. Remarkably, this charge transfer persists and …

Low-Temperature Plasticity Of Rock-Forming Minerals, Michael Keith Sly

Arts & Sciences Electronic Theses and Dissertations

The rheology of the Earth’s crust and mantle is in part governed by the physical and mechanical properties of feldspar, quartz, calcite, and olivine. Over the past several decades a significant number of experimental studies have been performed on these minerals. Conventional experiments are generally performed at elevated temperatures because much of the viscoplastic deformation of these minerals is accommodated by high-temperature mechanisms. There is, however, evidence of viscoplastic deformation at lower temperatures (T ≤ 0.3Tm) in the uppermost mantle and throughout the crust. Micromechanical experimental techniques, including nanoindentation and micropillar deformation, can be used to achieve plastic deformation at …

Exploring The Solar System Through Space And Time Via Laboratory Investigations Of Extraterrestrial Material, Kainen Lee Utt

Arts & Sciences Electronic Theses and Dissertations

This dissertation reports the results of laboratory studies of lunar soil samples, gas-to-solid filamentary enstatite grains from a likely-cometary interplanetary dust particle (IDP), and exogenous clasts in the CH3 chondrite Acfer 182 that likely originated from a differentiated basaltic planetesimal. These studies were performed using multi-instrument analyses involving high-resolution scanning and transmission electron microscopy (SEM/TEM) techniques, nanoscale secondary ion mass spectrometry (NanoSIMS), synchrotron infrared nanospectroscopy (SINS), electron probe microanalysis (EPMA), and Raman spectroscopy. The results of these analyses are used to examine space weathering phenomena, energetic processing and radial transport in the protoplanetary disk, and the origins of igneous inclusions …

The Evaluation Of Radiometal Labeled Biomolecules For Imaging And Therapeutic Applications, Truc Huynh

Arts & Sciences Electronic Theses and Dissertations

Radiometals play a crucial role in nuclear medicine for the diagnosis and therapy of various diseases including cancer and neurological disorders. In fact, there is a broad range of radiometals that are currently in use for imaging and therapy such as 99mTc, 89Zr, 68Ga, 177Lu, and 64/67Cu. Radiometal use in nuclear medicine has been stimulated by advances in radionuclide production that allow for fast, reliable, and cost-efficient production and an extensive understanding of molecular targets and tumor biomarkers. In recent years, there has been a growing interest in theranostics - the combination of imaging and therapy related to the same …

Classical And Quantum Markov Chains Derived From Billiard-Like Systems, Joshua Covey

Arts & Sciences Electronic Theses and Dissertations

Random billiards are a class of random dynamical systems related to dynamical billiards. We extend the study of random billiards and their associated Markov chains in two new directions. First, we introduce a new class of billiard-like systems called lensed billiards, which introduce a step potential to the usual billiard set-up, and conduct an exploratory study of random lensed billiards where we are mainly interested in how the newly-introduced potential parameter relates to the spectral gap and set of moments of the Markov operator associated to the random lensed system.

Second, we recast the mathematical set-up of random billiards to …

Trace Metal Speciation And Impacts On Iron Oxide Transformations And Biogeochemical Cycling, Jinshu Yan

Arts & Sciences Electronic Theses and Dissertations

Trace metals in anoxic aquatic systems are of great importance for iron oxide transformations and biogeochemical cycling. The presence of trace metal can alter iron oxide transformations under anoxic conditions. Trace metals are also essential for microbially-mediated biogeochemical processes occurring in anoxic wetland soils and stream bed sediments, but low availability of these elements may inhibit anaerobic element cycling and transformations. Trace metal speciation is also vital for understanding the environmental control on nutrients and contaminants. Three projects were conducted to explore trace metal speciation and its associated effect on iron oxide transformations and biogeochemical cycling. First, the Fe(II)-promoted conversion …

Contribution To Data Science: Time Series, Uncertainty Quantification And Applications, Dhrubajyoti Ghosh

Arts & Sciences Electronic Theses and Dissertations

Time series analysis is an essential tool in modern world statistical analysis, with a myriad of real data problems having temporal components that need to be studied to gain a better understanding of the temporal dependence structure in the data. For example, in the stock market, it is of significant importance to identify the ups and downs of the stock prices, for which time series analysis is crucial. Most of the existing literature on time series deals with linear time series, or with Gaussianity assumption. However, there are multiple instances where the time series shows nonlinear trends, or when the …