Digital Commons Network^™

Towards Interpretable Machine Learning With Applications To Clinical Decision Support, Zhicheng Cui

McKelvey School of Engineering Theses & Dissertations

Machine learning models have achieved impressive predictive performance in various applications such as image classification and object recognition. However, understanding how machine learning models make decisions is essential when deploying those models in critical areas such as clinical prediction and market analysis, where prediction accuracy is not the only concern. For example, in the clinical prediction of ICU transfers, in addition to accurate predictions, doctors need to know the contributing factors that triggered the alert, which factors can be quickly altered to prevent the ICU transfer. While interpretable machine learning has been extensively studied for years, challenges remain as among …

Rhodococcus Opacus Pd630 Genetic Tool Development To Enable The Conversion Of Biomass, Drew Michael Delorenzo

McKelvey School of Engineering Theses & Dissertations

The discovery of fossil fuels facilitated a new era in human history and allowed many firsts, such as the mass production of goods, the ability to travel and communicate long distances, the formation of population dense cities, and unprecedented improvements in quality of life. Alternative sources of energy and chemicals are needed, however, as hydrocarbon reserves continue to deplete and the effects of burning fossils on the planet become better understood. Lignocellulosic biomass is the most abundant raw material in the world and a viable alternative to petroleum-derived products. The pre-treatment of lignocellulose (e.g., thermocatalytic depolymerization, enzymatic hydrolysis, pyrolysis, etc.) …

The Role Of Multi-Charged Responses: Construction And Application Of A Tandem Differential Mobility Analyzer (Tdma), Christopher Ray Oxford

McKelvey School of Engineering Theses & Dissertations

Atmospheric aerosols impact health outcomes, visibility, and the energy balance of the earth. The atmosphere contains a variety of compounds, and the volatility (phase change enthalpy and vapor pressure) of each compound determines its partitioning between the gas phase and the particle phase. The hygroscopicity (an aerosol’s affinity for water) of an atmospheric aerosol particle is determined by the many compounds present in the particle, and thus, the volatility impacts hygroscopicity. Changes in hygroscopicity alter the fraction of the aerosol deposited in the lungs and the fraction of the aerosol activated into cloud droplets. Thus, understanding the volatility and hygroscopicity …

Dynamics And Control In Spiking Neural Networks, Fuqiang Huang

McKelvey School of Engineering Theses & Dissertations

In the brain, neurons (brain cells) produce electrical impulses, or spikes, that are thought to be the substrate of information processing and computation. Through enigmatic processes, these spikes are ultimately decoded into perceptions and actions. The nature of this encoding and decoding is one of the most pervasive questions in theoretical neuroscience. In other words, what are the specific functions enacted by neural circuits, through their biophysics and dynamics? This thesis examines the dynamics of neural networks from the perspective of control theory and engineering. The pivotal concept is that of the normative synthesis of neural circuits, wherein neural dynamics …

A Microfluidic Platform To Investigate The Mechanism By Which Gdnf Overexpression In Schwann Cells Causes Neuronal Axon Entrapment, Ze Zhong Wang

McKelvey School of Engineering Theses & Dissertations

Twenty million Americans suffer from peripheral nerve injury (PNI) caused by trauma and medical disorders, with approximately $150 billion spent in annual health-care dollars in the United States. Even with proper surgical reconstruction, less than 50% of the patients achieve satisfactory functional recovery. The gold standard surgical repair for long gaps (>3cm) is the autologous nerve graft, despite its disadvantages such as donor site morbidity, risk of infection, and increased cost. Alternative methods, such as acellular nerve grafts (ANA), are ineffective for large lesion gaps because of the lack of cells and regeneration factors. Recent efforts have been focused …

Three-Dimensional Image Reconstruction In Transcranial Photoacoustic Computed Tomography, Joemini Poudel

McKelvey School of Engineering Theses & Dissertations

Photoacoustic computed tomography (PACT) is an emerging imaging modality that exploitsoptical contrast and ultrasonic detection principles to form images of the photoacousticallyinduced initial pressure distribution within tissue. The PACT reconstruction problemcorresponds to an inverse source problem in which the initial pressure distribution is recoveredfrom measurements of the radiated pressure wavefield. A major challenge in transcranialPACT brain imaging is compensation for aberrations in the measured data due to the presenceof the skull. Ultrasonic waves undergo absorption, scattering and longitudinal-to-shear wavemode conversion as they propagate through the skull. To properly account for these effects, awave-equation-based inversion method should be employed that can …

Structural And Tissue-Level Adaptations Of Lumbar Intervertebral Discs In Humans With Inducible Low Back Pain Symptoms, Christian Isaiah Weber

McKelvey School of Engineering Theses & Dissertations

Low back pain (LBP) is a devastating musculoskeletal ailment that impacts majority of the global population. Up to 95% of cases are considered nonspecific where the origin is unclear. Although there is a diagnosis with these cases, there lacks specificity that would help individuals with treatment and pain management. Imaging techniques such as magnetic resonance imaging (MRI) are primarily utilized in the diagnosis of LBP as it illuminates internal structures of the spine. One important structure clearly identified with MRI is the intervertebral disc (IVD) that is susceptible to injury and disease. Further, diagnostic imaging is performed lying down where …

Graph Deep Learning: Methods And Applications, Muhan Zhang

McKelvey School of Engineering Theses & Dissertations

The past few years have seen the growing prevalence of deep neural networks on various application domains including image processing, computer vision, speech recognition, machine translation, self-driving cars, game playing, social networks, bioinformatics, and healthcare etc. Due to the broad applications and strong performance, deep learning, a subfield of machine learning and artificial intelligence, is changing everyone's life.Graph learning has been another hot field among the machine learning and data mining communities, which learns knowledge from graph-structured data. Examples of graph learning range from social network analysis such as community detection and link prediction, to relational machine learning such as …

Kernel Methods For Graph-Structured Data Analysis, Zhen Zhang

McKelvey School of Engineering Theses & Dissertations

Structured data modeled as graphs arise in many application domains, such as computer vision, bioinformatics, and sociology. In this dissertation, we focus on three important topics in graph-structured data analysis: graph comparison, graph embeddings, and graph matching, for all of which we propose effective algorithms by making use of kernel functions and the corresponding reproducing kernel Hilbert spaces.For the first topic, we develop effective graph kernels, named as "RetGK," for quantitatively measuring the similarities between graphs. Graph kernels, which are positive definite functions on graphs, are powerful similarity measures, in the sense that they make various kernel-based learning algorithms, for …

A Noncanonical Function Of The Telomerase Rna Component In Human Embryonic Stem Cells, Kirsten Ann Brenner

Arts & Sciences Electronic Theses and Dissertations

Telomeres are stretches of TTAGGG nucleotide repeats located at the ends of linear chromosomes that shorten with progressive cell division and prevent genomic instability at the cost of limiting a cell’s capacity to proliferate. This limitation can be overcome by telomerase, a ribonucleoprotein complex that elongates telomeres via reverse-transcription of the template telomerase RNA component (TERC). Recent studies have reported potential functions of TERC outside of its role in telomere maintenance. These noncanonical functions of TERC are however poorly defined, and the molecular mechanisms and biological relevance behind such functions remain elusive. Here, we generated conditional TERC knock-out human embryonic …

Transcriptional Regulation Of Adipose Tissue Development By Pexrap And Med19, John Dean

Arts & Sciences Electronic Theses and Dissertations

Targeting adipose tissue function to decrease adiposity and improve insulin sensitivity could treat obesity and diabetes. How the nuclear receptor PPARγ regulates the development of two functionally distinct types of adipose tissue, brown and white fat (BAT and WAT), as well as the browning of white fat, remains unclear. Our previous studies suggest that PexRAP, a peroxisomal lipid synthetic enzyme, regulates PPARγ signaling and white adipogenesis.Here, we show that PexRAP is an inhibitor of brown adipocyte gene expression. PexRAP inactivation promoted adipocyte browning, increased energy expenditure, and decreased adiposity. Identification of PexRAP-interacting proteins suggests that PexRAP function extends beyond its …

An Evolving Epigenome That Determines Tissue And Cell Specificity, Renee Louise Sears

Arts & Sciences Electronic Theses and Dissertations

Understanding the mechanisms driving phenotypic variation is a major goal of biology that unifies classical genetics with the emerging fields of genomics and epigenomics. Human and mouse share over 90% of genes and global tissue-specific patterns of expression are maintained between the species. Thus, it is hypothesized that gene expression is influenced through distinctive regulation among species in order to account for the unmistakable phenotypic divergence. DNA methylation, histone modifications, open chromatin patterns, transcription factor binding, and other epigenetic factors are all associated with shaping, maintaining, and repressing regulatory regions which in turn coordinate gene expression. It is vital to …

Homeland Insecurity, Amy Chen

Bachelor of Fine Arts Senior Papers

Homeland Insecurity is a project born out of a life’s worth of marginalization, internalized racism, and forced assimilation. It presents common experiences and emotions that are located between cultures, questioning what it means to inhabit a homeland that exists as a hybrid mental space. As I progress through life, my parents’ culture—my heritage—becomes more and more distant, yet like many non-white children of immigrants, I will continue to carry it in my face as a physical reminder of a life I do not know. Influenced by acculturation theory, my work explores this culture that never quite belonged to me to …

Enhanced Heat Transfer Performance By Shape Optimization Of A Non-Axisymmetric Droplet Evaporating On A Heated Micropillar, Haotian Wu

McKelvey School of Engineering Theses & Dissertations

Abstract

Enhanced Heat Transfer Performance by Shape Optimization of a Non-axisymmetric Droplet Evaporating on a Heated Micropillar

By

Haotian Wu

Department of Mechanical Engineering and Materials Science

Washington University in St. Louis, 2019

Research Advisor: Professor Damena Agonafer

The stacked multilayer 3D IC structure used in next generation high-powered electronics poses great challenges in dissipating their large heat flux, which causes extreme difficulties for traditional cooling technologies. In response, more advanced two-phase liquid cooling technologies, such as droplet evaporation, which utilizes the latent heat of vaporization to remove excessive heat, have been widely investigated. Compared to traditional single-phase cooling techniques, …

Expanding The Palette: Synthesizing Microencapsulated Organic Phase Change Materials In Metallic Matrices For Transient Thermal Applications, Melissa Kate Mccann

McKelvey School of Engineering Theses & Dissertations

As the demand for smaller and faster electronics increases, it becomes increasingly challenging to effectively manage the generated heat without hindering device performance in applications whose thermal profiles are dominated by pulsed thermal loads. Heat propagation in a system can be characterized by steady or transient state heat transfer. In steady state, the temperature at any particular point remains constant after thermal equilibrium is reached. In a transient state, the temperature within a system varies over time. The changing parameters and time dependency associated with a transient regime make heat transfer calculations far more complex than in a steady state. …

Ph-Sensitive Oxygen Release Microspheres To Enhance Cell Survival In Ischemic Condition, Zhongting Liu

McKelvey School of Engineering Theses & Dissertations

Ischemic diseases such as myocardial infarction, stroke and limb ischemia are severe cardiovascular diseases with high rate of death and millions of people suffered from these diseases. Under ischemic environment, cells die due to deficient supply of nutrient and oxygen. To regenerate ischemic tissues, stem cell therapy is a promising approach because stem cells can differentiate into cells necessary for the regeneration. However, stem cell therapy has limitations. For example, few cells can survive under harsh ischemic environment. To enhance stem cells survival, implantation of oxygen release microspheres to sustained supply cells with oxygen represents an effective strategy. Previously, our …

Molecular Dynamics Studies Of Thin-Film Evaporation: The Effect Of Graphene-Coated Silicon On Water Evaporation Behavior, Rui Zhou

McKelvey School of Engineering Theses & Dissertations

Conventional single-phase air or liquid cooling methods are insufficient to dissipate the high heat flux of next-generation electronic systems. Thin-film evaporation is one of the most promising solutions, because it takes advantage of the large amount of latent heat in the phase change process. It is important to understand the relationship between interfacial thermal resistance, surface wettability, and thin-film evaporation behavior. In this study, non-equilibrium molecular dynamics simulations are used to study mass and heat transfer in thin-film evaporation of water on a silicon substrate, and equilibrium molecular dynamics simulations are used to study the surface wettability by measuring contact …

The Biomedical Application Of Chimeric Antigen Receptor T Cell Therapy, Jessica Devenport

Arts & Sciences Electronic Theses and Dissertations

No abstract provided.

Investigating The Relationship Between Gaze Behavior And Audiovisual Benefit Across Various Speech-To-Noise Ratios, Lauren Gaunt

Arts & Sciences Electronic Theses and Dissertations

Speech perception improves when listeners are able to see as well as hear a talker, compared to listening alone. This phenomenon is commonly referred to as audiovisual (AV) benefit (Sommers et al., 2005). According to the Principle of Inverse Effectiveness (PoIE), the benefit of multimodal (e.g. audiovisual) input should increase as unimodal (e.g. auditory-only) stimulus clarity decreases. However, recent findings contradict the PoIE, indicating that it should be reassessed. One method for investigating the factors that contribute to AV speech benefit is to examine listeners’ gaze behavior with eye tracking. The present study compared young adults’ (N=50) gaze …

Modeling The Effects Of Distribution System Topology On Water Quality, Chun-Ying Chao

McKelvey School of Engineering Theses & Dissertations

Inadequate treatment of drinking water causes the formation of disinfection by-products and the regrowth of harmful microbial species. Various studies have addressed the problem of water quality monitoring, but very few have employed topological analysis, a valuable mathematical tool widely applied in biological, business, and social research. This thesis examines the relationship between the topological properties of water distribution systems and water-quality models. In particular, the research proposes a novel framework for mapping network topological attributes to water-quality models. This research adopts topological metrics to assess the accuracy of the predictions of chlorine concentrations in dead ends. It examines four …

Finding And Analyzing De Novo Mutations In The Exomes Of Parent-Offspring Trios Of Spontaneous Chiari Malformation Type 1 Patients, Brian Leon Ricardo

Arts & Sciences Electronic Theses and Dissertations

Chiari Malformation Type 1 (CM1) is a neurodevelopmental disorder that occurs when one of the cerebellar tonsils herniates past the foramen magnum causing headaches, motor or sensory deficits, sleep apnea, and difficulty swallowing. This disorder is estimated to affect 1% of the population but due to the need of neuroimaging for diagnosis and the presence of asymptomatic patients there is still uncertainty about the exact proportion of the population affected. CM1 often presents itself with other neurodevelopmental disorders such as syringomyelia, scoliosis, and known genetic syndromes such as Klippel-Feil and Marfan syndromes. Twin, family, and familial clustering studies have established …

Double Trouble: How Children And Adults Decide When To Use Double Consonants, Ruth Caputo

Arts & Sciences Electronic Theses and Dissertations

Consonant doubling is a difficult pattern in the English writing system to master because it is inconsistent. In English two-syllable words, consonants are typically doubled after short vowels, a phonological context, but not after any vowel spelled with more than one letter, a graphotactic context. Knowledge about these contexts may help children learn when to use a single or double consonant. Previous theories on spelling development argue that children learn to spell in stages, without learning about phonological or orthographic context until late in the learning process. This study builds on previous research suggesting that children learn spelling patterns through …

Neuroticism And Stressful Life Events: Probing Mechanisms Underlying Vulnerability To Stress-Related Depression, Erin Bondy

Arts & Sciences Electronic Theses and Dissertations

Elevated neuroticism (N) potentiates the depressogenic effects of stressful life events (SLEs). We first replicate this association using longitudinal data (N=971 older adults) from the St. Louis Personality and Aging Network (SPAN) study. Here, SLEs prospectively predicted future depressive symptoms, especially among those reporting elevated N, even after accounting for prior depressive symptoms and previous SLE exposure (NxSLE interaction: p=0.016, ΔR²=0.003). These findings were further replicated in cross-sectional analyses of the Duke Neurogenetics Study (DNS), a young adult college sample with neuroimaging data (n=1,343: NxSLE interaction: p=0.019, ΔR²=0.003). Because evidence suggests that stress may promote depression …

Associations Between Prenatal Selective Serotonin Reuptake Inhibitor Exposure, Depression And Brain Morphology In Middle Childhood, Allison Moreau

Arts & Sciences Electronic Theses and Dissertations

Objective: Selective Serotonin Reuptake Inhibitors (SSRIs) are one of the most widely used prescribed medicine by pregnant women. A mixed literature suggests that prenatal SSRI exposure may increase depression risk among offspring. Method: Using data from children (n=11,076) who completed the baseline session of the Adolescent Brain and Cognitive Development (ABCD) study, we examined whether prenatal exposure to SSRIs is associated with child depression and variability in depression-related brain structures (i.e., hippocampus, amygdala, nucleus accumbens, caudate, putamen; rostral anterior cingulate; rostral and caudal middle frontal, superior frontal, and lateral and medical orbitofrontal cortices). Analyses were cross-sectional and included the following …

Functional Dissociations Revealed By Representational Similarity Analysis Of Color-Word Stroop, Michael Freund

Arts & Sciences Electronic Theses and Dissertations

The color-word Stroop task is often used in cognitive neuroscience as a common platform for both theoretical and experimental approaches to cognitive control. Yet traditionally, there has been tension between these two approaches. Theoretical models of Stroop have focused on representation: for example, how distributed and overlapping representations of the two stimulus dimensions (color, word) are prioritized, and how conflict between these dimen- sions is represented and used to regulate control. In contrast, neuroimaging experiments have primarily focused on ‘univariately’ (uniformly) mapping the effects of conflict to par- ticular brain regions. This focus on univariate changes in brain activity limits …

Event Reconstruction In The Advanced Particle-Astrophysics Telescope, Emily Ramey

McKelvey School of Engineering Theses & Dissertations

The Advanced Particle-Astrophysics Telescope (APT) is a concept for a gamma-ray space telescope operating in the keV to MeV energy range. Due to the nature of the telescope and the physics of detection, reconstructing initial photon trajectories can be very computationally complex. This is a barrier to the real-time detection of astrophysical transient phenomena such as Gamma Ray Bursts (GRBs), and a faster reconstruction algorithm is needed in order to effectively study them. In this project, we develop such an algorithm based on Boggs & Jean (2000) and discuss the effects of certain algorithmic parameters on computational performance. For testing, …

The Unique Effects Of Relatively Recent Conflict On Cognitive Control, Jackson Colvett

Arts & Sciences Electronic Theses and Dissertations

In tasks such as Stroop, our past experiences with conflict influence our ability to attend to goal-relevant information and ignore irrelevant information. There exists evidence that conflict experiences on at least two timescales affect cognitive control. The “immediate” timescale is evidenced by congruency sequence effects while the “long” timescale is evidenced by list-wide proportion congruence effects. What remains underspecified is whether relatively recent experiences with conflict may also uniquely influence cognitive control and how experiences on different timescales are weighted. The present, pre-registered experiments aimed to assess the role of relatively recent conflict by examining the potential effects of an …

Retrieval Of Past Events During Change Experience Is Associated With Memory For Change, Mary Hermann

Arts & Sciences Electronic Theses and Dissertations

A novel theory has emerged that examines how people process and comprehend change. Two experiments examined these theoretical mechanisms used to detect and recollect changes in everyday activities. Participants viewed movies of an actor performing narrative activities across two fictitious days. During the second movie, participants also completed a prediction task in which they were asked to predict what they thought was going to happen next. In Experiment 1, some activities repeated identically across the two days, some were repeated but changed on a critical feature (e.g. waking up to an alarm from a clock or a phone), and …

Determining The Genetic Contributions Of The Williams Syndrome Critical Region To Behavior Using Mouse Models And Human Genetics, Nathan David Kopp

Arts & Sciences Electronic Theses and Dissertations

Williams syndrome is a neurodevelopmental model caused by the deletion of 26-28 genes on chr7q11.23. The loss of these genes affects multiple organ systems resulting in severe cardiovascular disease, craniofacial dysmorphology, intellectual impairment, a specific Williams syndrome cognitive profile made up of deficits in visual-spatial processing with preserved language skills, and a characteristic hypersocial personality. The reciprocal duplication occurs at a lower frequency and manifests with diametric phenotypes to the deletion. This suggests that this locus harbors dosage sensitive genes that play a role in neurodevelopment. Large efforts have been taken to identify which genes are responsible for causing the …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.

Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …