Digital Commons Network^™

Incorporating Ontological Information In Biomedical Entity Linking Of Phrases In Clinical Text, Evan French

Theses and Dissertations

Biomedical Entity Linking (BEL) is the task of mapping spans of text within biomedical documents to normalized, unique identifiers within an ontology. Translational application of BEL on clinical notes has enormous potential for augmenting discretely captured data in electronic health records, but the existing paradigm for evaluating BEL systems developed in academia is not well aligned with real-world use cases. In this work, we demonstrate a proof of concept for incorporating ontological similarity into the training and evaluation of BEL systems to begin to rectify this misalignment. This thesis has two primary components: 1) a comprehensive literature review and 2) …

Modification Of Culture Medium And Identification Of Microbial Contaminants For Improved In Vitro Propagation Of Freshwater Mussels, Raquel M. Wetzell

Theses and Dissertations

In vitro propagation efforts play an essential role in conserving and restoring threatened freshwater mussel populations by circumventing the need for a fish host. Across a broad range of taxa, transformation is induced with an artificial M199 medium and rabbit serum. However, such formulation may not be sufficient in culturing critical species with more specific physiological requirements. In this study, multiple serum mixtures were tested to improve in vitro transformation of two freshwater mussel species: yellow lampmussel (Lampsilis cariosa) and tidewater mucket (Atlantaconcha ochracea). These species were selected because they parasitize similar fish host species but …

A Thematic Analysis Of African American Fathers' Emotion-Related Beliefs And Behaviors, Deon Brown

Theses and Dissertations

This study explored African American fathers’ beliefs about and experiences with their own and their children’s negative emotions (i.e., parental meta-emotion philosophy and parental emotion socialization). Participants included 58 African American fathers in the Midwestern region of the United States between the ages of 29 and 40 (Mage = 30.94). 57 were biological fathers and one was a stepfather to toddlers between 24 and 31 months of age. Participants were invited to complete lab tasks, including the meta-emotion interview (MEI). The MEI is semi-structured interview of parents’ and their children’s negative emotion (i.e., sadness and anger). I selected a subset …

Using Individual Determinants To Predict Behavioral Health Service Use In Integrated Pediatric Primary Care, Alfonso L. Floyd Jr.

Theses and Dissertations

Mental health problems (e.g., attention, externalizing, internalizing) are commonly observed in youth and are often associated with significant impairment and an increased need for mental health services. Conceptual frameworks, such as Andersen’s Behavioral Model of Health Service Utilization, have proposed that several individual determinants (e.g., predisposing, enabling, and need factors) may influence service use for mental health problems among youth. Despite the glaring need for mental health treatment among youth with mental health problems, studies indicate that many affected youths do not receive mental health care. Integrated pediatric primary care (IPPC) settings provide an ideal setting for youth and families …

Investigating The Role Of Nlrp3 Inflammasome In Chemotherapy-Induced Peripheral Neuropathy, Urszula O. Warncke

Theses and Dissertations

Paclitaxel and oxaliplatin are commonly used antineoplastic drugs that cause chemotherapy-induce peripheral neuropathy (CIPN) in up to 90% of patients. The sensory symptoms of CIPN include numbness, loss of proprioception, tingling, spontaneous burning, shooting or electric shock-like pain, mechanical and thermal allodynia, and cold hypersensitivity among others. Affected patients struggle with daily activities, have a low quality of life, and might stop cancer treatment. Unfortunately, there are no effective prophylactic or therapeutic treatments for these side effects. Many studies point to the involvement of inflammation as a major contributor of CIPN pathology. We investigated the effects of genetic (NLRP3 …

Crosstalk Between Hippo And Rb Tumour Suppressor Pathways In Ovarian Cancer, Fatmata Sesay

Theses and Dissertations

The cell cycle is a highly regulated process that ensures the timely and accurate division of cells. Events of the normal cell cycle fall under two categories - positive and negative regulatory mechanisms. The first category, positive regulatory machinery, includes active protein complexes of cyclins in association with their partnering cyclin-dependent kinases (cyclin/CDK), which mediate series of phosphorylation events that relay a cell cycle progression from one stage to the next. The second category, the negative regulatory mechanisms, include the checkpoint controls consisting of the retinoblastoma (RB) family of proteins, some of which can form a transcriptional repressor complex DREAM. …

Do Coverage Expansion And Patient-Centeredness Care Delivery Improve Patient Health Outcomes And Care Quality?, Shiva Salehian

Theses and Dissertations

Although correlated, improvement of patient health outcomes and quality of care is a result of health care delivery, performance, and healthcare policies that intend to impact health outcomes (Porter, 2010; AHRQ, 2015). This dissertation focuses on a special model of care delivery (Patient-Centered Medical Homes (PCMH)) and two programs (Addiction and Recovery Treatment Services (ARTS) and Medicaid expansion) to examine the correlation and impact of these programs on cardiovascular-related preventive care, healthcare expenditures, and health behavior hospitalizations as patient outcomes.

Artificial Intelligence-Powered Chronic Wound Management System: Towards Human Digital Twins, Salih Sarp

Theses and Dissertations

Artificial Intelligence (AI) has witnessed increased application and widespread adoption over the past decade. AI applications to medical images have the potential to assist caregivers in deciding on a proper chronic wound treatment plan by helping them to understand wound and tissue classification and border segmentation, as well as visual image synthesis.

This dissertation explores chronic wound management using AI methods, such as Generative Adversarial Networks (GAN) and Explainable AI (XAI) techniques. The wound images are collected, grouped, and processed. One primary objective of this research is to develop a series of AI models, not only to present the potential …

Bioinformatic Pipeline For Determining Terminal Repeats In The Human Cytomegalovirus Genome Assembled With Pacbio Long Read Sequences, Ahmed Al Qaffas

Theses and Dissertations

Human Cytomegalovirus (HCMV) is a member of the betaherpesvirinae subfamily of the Herpesvirus family. HCMV infection is common among adults worldwide, with an estimated seroprevalence of 66 to 95%, depending on the geographic region (Zuhair et al., 2019). Although most of the virus genomic content has been studied extensively, the terminal repeating region sequences remain understudied. Two main challenges hindered the study of the region: a) limitations of sequencing technologies; and b) misassembly of the repeats due to its complex nature. Here I show a novel bioinformatics pipeline that takes advantage of PacBio's long reads to resolve the challenges mentioned …

Effect Of Viscoelasticity On Cellular Morphology And Activity, Thomas J. Petet Jr

Theses and Dissertations

It has been well established that there is a link between substrate stiffness and cellular activities such as proliferation, migration, and differentiation. Less characterized is the link between the time-dependent viscosity of a substrate with those cellular activities. To explore this, PDMS substrates were created with predictably tunable stiffness and viscosity parameters. A simulated model was also developed in parallel to explore the potential effects of viscosity in a computationally predictive way. It was found that the inclusion of viscosity caused a major paradigm shift to a non-zero substrate equilibrium that was sensitive to increases in the substrate stiffness. Finally, …

Structure-Based Drug Discovery And Development Of Protein Structure Prediction Tools Using An Empirical Force Field, Noah B. Herrington

Theses and Dissertations

Traditional drug discovery has rapidly accelerated thanks to development of computational molecular modeling. The crucial component that these computational studies hinge upon is having a well-defined, and energetically favorable structure. Structures of proteins and ligands that meet these criteria are important for accurately simulating models used to study drug binding. To demonstrate the role of accurate structure simulation in the study of these events, this thesis presents, first, a story examining the problem of accurate structure modeling of ionizable residues within protein structures, specifically aspartic acid, glutamic acid, and histidine. I present our method, which uses the HINT force field …

Investigating The Potential Causal Relationship Between Free Will Belief And Well-Being, Courtney J. Alderson

Theses and Dissertations

This multi-study dissertation had four primary aims. My first was to add to the evidence base indicating a positive association between free will belief (FWB) and subjective well-being (SWB). My second aim was to develop a measure to assess the FWB theme referred to as the principle of alternate possibilities (PAP). To achieve the first two aims, I conducted two cross-sectional studies to further establish the FWB-SWB association and start the development and assessment of a new PAP FWB measure. In the first study (N=995), I hypothesized that an EFA of the new PAP items would produce at least a …

Secondary English Teachers’ Experiences Of Agency: Connections To Shifting Educational Contexts During Covid-19, Kristina Lee

Theses and Dissertations

The COVID-19 pandemic caused schools around the world to enter uncharted territory. Due to the unprecedented nature of the educational crisis, it was important to examine how teacher agency may have been affected. Teacher agency can have important implications for school climate, policy, and the experience of stakeholders. The main focus of this study was to cultivate an understanding of secondary English teachers’ perceptions of agency as they navigated teaching throughout the COVID-19 pandemic. An ecological framework was used to examine teachers’ experiences of agency in the context of COVID-19. The study utilized a basic qualitative design with in-depth interviews …

Assessing Medical Discrimination, Mistrust, And Healthcare Engagement As Predictors Of Covid-19 Vaccination Among Transgender And Gender Diverse Individuals, Shelby A. Smout

Theses and Dissertations

As of March 11^th 2020, the World Health Organization (WHO) declared COVID-19 a global pandemic. Early studies conducted among LGBT+ communities indicated that individuals of color and transgender individuals were more likely to express hesitation towards a possible COVID-19 vaccine. Such hesitation can be explained by historical medical mistreatment of people of color and LGBT+ communities which contributes to higher medical mistrust within these populations. The present study assessed vaccination behaviors among a sample of transgender and gender diverse individuals (N=385) and results indicated an association amongst experiences of discrimination in healthcare, medical mistrust, COVID-19 mistrust, barriers to vaccination, …

“There Was Some Sort Of Missing Middle”: Lived Experiences Of Jewish Youth With Intellectual And Developmental Disabilities, Aliza Lambert

Theses and Dissertations

Though religion and spirituality contribute to overall well-being (Koenig, 2012; Koenig & Cohen, 2002), social support (Biggs & Carter, 2016; Koenig & Cohen, 2002; Taub & Werner, 2016), quality of life (QOL; Myers & Sweeney, 2000), coping strategies (Krok, 2008), and lower rates of depression and anxiety (Brown et al., 2013; Young et al., 2000), religion and spirituality are seldom included in curriculum in counselor education and supervision doctoral programs (Adams et al., 2015; Henriksen et al., 2015). In the present study, the researcher uses a multiple-case study design to describe the lived experiences of Jewish youth with intellectual and …

Predicting Medication Adherence Patterns During The Maintenance Phase Of Treatment For Pediatric Leukemia And Lymphoma: A Model Of Individual- And Family-Level Factors, Stephanie M. Romo

Theses and Dissertations

Adherence during the maintenance phase of pediatric cancer treatment is critical to prevent relapse and ensure long-term, event-free survival. Yet, little research has been done to examine individual- and family-level factors that may relate to adherence during the maintenance phase of treatment, particularly among Latinx patients. This is surprising given findings demonstrating that children who miss more than 5% of their prescribed oral chemotherapy medicine, most commonly 6-mercaptopurine (6MP), are 2.5-2.7 times more likely to relapse than children who take 95% or more of their prescribed 6MP. Pediatric cancer patients face unique adherence challenges given the importance of family involvement …

Protein Structure And Interaction: The Role Of Aromatic Residues In Protein Structure And Interactions Between Pyridoxine 5'-Phosphate Oxidase/Dopa Decarboxylase, Mohammed H. Al Mughram

Theses and Dissertations

Naturally developed proteins are capable of carrying out a wide variety of molecular functions due to their highly precise three-dimensional structures, which are determined by their genetically encoded sequences of amino acids. A thorough knowledge of protein structures and interactions at the atomic level will enable researchers to get a deep foundational understanding of the molecular interactions and enzymatic processes required for cells, resulting in more effective therapeutic interventions. This dissertation intends to use structural knowledge from solved protein structures for two distinct objectives.

In the first project, we conducted a bioinformatics structural analysis of experimental protein structures using our …

Perceived Discrimination And Mental Health Outcomes In College Students: The Mediating Role Of Preventive Health Behaviors And Social Support, Sarah C M Morton

Theses and Dissertations

Perceived discrimination has been linked to adverse mental health outcomes, increased risk-taking behaviors, and poor engagement in health promoting behaviors. College students may be especially susceptible to negative mental health outcomes associated with discrimination due to the unique stressors faced by young adults (e.g., prolonged transition to adulthood, onset of mental health disorders, changes in social support). The current study examined the mediating and moderating roles of health behaviors and social support on the association between perceived discrimination and mental health outcomes (e.g., anxiety, depression, suicidality) in college students. A total of 709 college students (42.8% White; 72.2% female; 30.2% …

Development And Optimization Of A Low Volume Air-Jet Dry Powder Inhaler (Dpi) Platform For The Delivery Of High Dose Aerosolized Powder To Infants, Connor Howe

Theses and Dissertations

The goal of this research project was to develop an infant air-jet dry powder inhaler (DPI) platform for high-efficiency nose-to-lung (N2L) aerosol administration to infants through optimization of individual system components followed by expansion of the system to higher doses and different formulations using a new approach. Primary challenges associated with aerosol delivery to infants using the N2L route include the extremely narrow extrathoracic airways, short inspiratory times (~0.2 sec), low safe airway pressure (H₂O), and very low volumes of air (~10 mL) available to form the aerosol. The infant air-jet DPI system was comprised of three main …

An Analysis Of The Special Focus Facility Program And Nursing Home Quality, Annie S. Rhodes

Theses and Dissertations

The Special Focus Facility Program is an intensive program meant to rapidly support 88 of the lowest quality nursing homes in the United States, as determined by the Five-Star Quality Ranking system. There are also 435 facility candidates which are similarly low performing but not enrolled in the program. Academic literature has largely ignored this program, and the existing grey literature is more than a decade old and does not include COVID-19 data. Applying a political economy of aging framework and using a case matching methodology, Special Focus Facilities (SFF), Special Focus Facility Candidate (SFFc) nursing homes, and 5-star nursing …

Behavioral Screening And Chiral Bioanalysis Of Emerging Stimulant-Type Drugs In Rats, Tyson R. Baird

Theses and Dissertations

The epidemic of drug use in the United States and elsewhere in the world has resulted in tragic loss of life and substantial economic costs. Novel psychoactive substances (NPS) are one of the contributors to this problem, and the lack of information about many of these drugs compounds their risk. This dissertation proposes a strategy to use intracranial self-stimulation (ICSS) as a behavioral screening tool to assess emerging drugs of abuse for their abuse potential in order to generate a proactive threat assessment. A series of stimulant-type drugs including methcathinone, α-pyrrolidinohexanophenone (α-PHP), cocaine, and the phenyltropane analogs of cocaine WIN35428 …

Sleep Self-Efficacy, Loneliness, And Physical Activity: Assessing The Pathways Between Sleep Quality And Mental Health Using Structural Equation Modeling, Amber M. Fox

Theses and Dissertations

Although there is robust empirical support that poor sleep contributes to declines in mental health, explanations of this relationship remain unclear. The purpose of the present study was to examine the pattern of associations between sleep quality, sleep self-efficacy, loneliness, physical activity, and mental health among U.S. adults across the lifespan, and whether they differed by gender or age group. A structural equation model with invariance analysis was developed and examined data from 2,300 adults (M_age = 44.1, SD = 16.78) participating in the online study Investigating Sleep Longitudinally Across Normal Development (ISLAND). Sleep quality was measured by …

Sleepiness: Clinical Correlates, Association With Performance, And Effects Of Performance Feedback, Spencer Nielson

Theses and Dissertations

Background: Daytime sleepiness is a common and debilitating phenomenon. Sleepiness is associated with increased symptoms of insomnia, depression, anxiety, and fatigue. Daytime sleepiness is commonly associated with cognitive performance, including performance on the Psychomotor Vigilance Test (PVT). The PVT includes performance feedback, and that feedback may influence an individual’s report of their sleepiness. Whether the feedback on the PVT influences an individual's self-reported sleepiness is unknown. This study sought to investigate how sleepiness was associated with clinical symptoms and performance, whether there are sex differences in sleepiness, and whether manipulating feedback on the PVT influenced an individual’s self-reported sleepiness. …

Examination Of Common And Rare Variant Genetic Architecture Of Psychiatric Disorders, Mohammad Ahangari

Theses and Dissertations

Psychiatric disorders are often heterogenous in their manifestation and genome-wide association studies have identified many common risk variants involved in their polygenic architectures with varying degrees of pleiotropy. In recent years, large-scale biobanks have also begun sequencing the genome of their participants to elucidate the role of rare risk variation in the genetic architecture of complex phenotypes, including psychiatric traits. This dissertation sought to better understand the role of both common and rare risk variation in the genetic architecture of psychiatric disorders with a particular focus on schizophrenia and alcohol problems. In the first three analyses, we focused on characterizing …

Smart City Management Using Machine Learning Techniques, Mostafa Zaman

Theses and Dissertations

In response to the growing urban population, "smart cities" are designed to improve people's quality of life by implementing cutting-edge technologies. The concept of a "smart city" refers to an effort to enhance a city's residents' economic and environmental well-being via implementing a centralized management system. With the use of sensors and actuators, smart cities can collect massive amounts of data, which can improve people's quality of life and design cities' services. Although smart cities contain vast amounts of data, only a percentage is used due to the noise and variety of the data sources. Information and communication technology (ICT) …

Training Needs And Challenges In Supporting Young Adults With Autism To Access Integrated Employment, Whitney A. Ham

Theses and Dissertations

The purpose of this study was to conduct a needs assessment identifying the current level of training, training needs, and challenges to supporting adults with autism and significant support needs, such as challenging behavior, to access integrated employment. Foundational literature in employment indicates that employment service providers must possess an expansive skillset in order to perform the expectations of their profession. Research on supporting adults with autism to access employment indicates that skills above the traditional employment skills may be needed in order to obtain and maintain employment. This was one of the first studies to assess the needs of …

Effects Of A Video Based Intervention On Job Interview Skills Of Youth With Autism, Kelsey T. Dunn

Theses and Dissertations

In this dissertation, I conducted a multiple-probe-across-participants design to examine the impact of a video-based intervention on interview skills of youth with autism. First, I conducted a systematic literature review of interview interventions. Results were used to guide the development of this study’s measure and procedures. Finding that previous literature relied on rubric measures to rate interview skill behaviors, I developed and piloted a primary measure for examining direct speech production. Using transcripts and video analysis, this study captures the construct of interview skills using both quantity (frequency of relevant/irrelevant c-units) and quality (interview skills rubric score). The intervention consisted …

Disparities Between Native Americans And Whites In Trajectories Of Functional Independence And Life Satisfaction Over The 5 Years After Traumatic Brain Injury, Jack Watson

Theses and Dissertations

A traumatic brain injury (TBI) can have a host of negative consequences including impairments to motor and cognitive function and can result in a decrease in quality of life (i.e., life satisfaction). TBI is one of the leading causes of death and disability worldwide and disproportionately affects Native Americans, who have the highest rates of TBI among all races in the U.S. and elevated likelihood for fatality and severe complications. The current study used a subsample of the national TBI Model Systems Database of 80 demographically and injury severity matched Native American and White individuals (total n = 160) to …

Computational Analysis Of Drug Targets And Prediction Of Protein-Compound Interactions, Sina Ghadermarzi

Theses and Dissertations

Computational prediction of compound-protein interactions generated a substantial amount of interest in the recent years owing to the importance of the knowledge of these interaction for drug discovery and drug repurposing efforts. Research suggests that the currently known drug targets constitute only a fraction of a complete set of drug targets, limiting our ability to identify suitable targets to develop new drugs or to repurpose current drugs for new diseases. These efforts are further thwarted by our limited knowledge of protein-drug (and more generally protein-compound) interactions, where only a subset of drug targets is typically known for the currently used …

Asymmetric Cuh-Catalyzed Reductive Coupling Of Alleneamides With Carbonyl Electrophiles And The Mechanistic Investigation Into The Suzuki-Miyaura Cross-Couplings Of Electron-Deficient Systems, Samantha L. Gargaro

Theses and Dissertations

Most natural products and other biologically active small molecules contain multiple stereogenic heteroatoms throughout their carbon scaffold. As a result, methods to install these multi-heteroatom functionalities efficiently are highly desirable. Reductive coupling reactions have been studied extensively, and reductive allylation has been a key method for generating chiral secondary and tertiary allylic alcohols. This work focuses on utilizing naturally abundant and inexpensive Cu for the asymmetric reductive coupling of alleneamides with carbonyl electrophiles to access highly functionalized multi-heteroatom scaffolds that are difficult to produce via traditional methods. Described herein are methods for these asymmetric reductive coupling reactions. Chapter 1 describes …