Full text for dissertations and theses included in this collection dates back to 2011. For older dissertations, check the library’s catalog CatalogUSMAI or Dissertations and Theses.

Recent Submissions

  • Advancing Drug and Biomaterial Design with Constant pH Molecular Dynamics Simulations

    Tsai, Cheng-chieh; Shen, Jana (2019)
    Molecular dynamics (MD) simulation is a valuable tool for investigating motions of macromolecular systems; however, solution pH, a critical factor for biological and chemical processes, is neglected in conventional MD simulations. To address this weakness, our group developed various continuous constant pH molecular dynamic (CpHMD) tools. In this dissertation, applications and new protocols that utilize CpHMD for drug and biomaterial design are presented. β-secretase 1 (BACE1, implicated in Alzheimers disease) and Src kinase (implicated in cancer) were utilized as model systems for drug design applications. In chapter 2, we applied CpHMD to understand the binding of BACE1 with two small-molecular inhibitors. We discovered that, despite the structural similarity of the two inhibitors, the titration behavior of the protein active site differs and this difference dramatically impacts the protein-ligand interactions and consequently the inhibitor affinity. Further, we tested a new protocol that combines CpHMD titration with free energy simulations to construct the pH-dependent binding free energy profiles. The resulting data showed excellent agreement with experiment and identified one potential allosteric site in BACE1. Next, in chapter 3, we simulated Src kinase to test the capability of CpHMD tostudy kinases. Starting from the crystal structure of the inactive Src, CpHMD can capture the conformational activation along the major inactive states without introducing any biasing potential or mutation. Starting from chapter 4, we studied the chitosan-based hydrogel systems to explore the detailed molecular mechanisms that give rise to macroscopic materials properties. We examined the flexibility of chitosan chains under different environmental conditions such as pH and salt concentration. Simulation data revealed that in addition to electrostatic screening, salt ions enhance the chain flexibility by interrupting the intra-molecular hydrogen bonds and thereby shifting the conformational populations between extended and bent states. In chapter 5, the atomic-level mechanism of pH-responsive chitosan-based hydrogels with switchable mechanical properties was investigated. Our data suggested that the electrostatic crosslinks are formed through the pH-dependent salt-bridge interactions between the chitosan glucosamines and surfactant headgroups. The pKa difference between the chitosan crystallite and the surfactant-bound chitosan is a key for the persistent but erasable gradient in the structural and mechanical properties between the two crosslinked regions. In summary, my work provids insights that will contribute to drug and biomaterial design and highlights the usefulness of CpHMD in these fields.
  • Abutment Material Affects the Attachment of Co-cultured Fibroblasts and Keratinocytes

    Tibbs, Maria; Saito, Hanae (2019)
    Creating a stronger transmucosal seal around the implant abutment may help prevent epithelial downgrowth and resultant crestal bone loss. Most studies focus on titanium and zirconium, but provisional restorations are gaining popularity and these materials require further study. Previous in vitro models utilize a monoculture technique to understand cell behavior, which makes direct intercellular comparisons difficult. Our first aim was to develop a co-culture of human gingival fibroblasts and human oral keratinocytes. Then, cell attachment, proliferation, and migration across six commercially available abutment materials was ascertained and comparisons drawn. Discs made of smooth titanium, (control), rough titanium, CAD/CAM poly (methylmethacrylate), poly ether etherketone, smooth zirconium, and rough zirconium were chosen. Preliminary results indicate that at various time points, significant differences in fibroblast and keratinocyte proliferation and attachment exist among abutment materials.
  • Temporary anchorage devices for ridge preservation after extraction

    Joseph, Dr. Surya Elizabeth; Oh, Se-Lim (2019)
    The objective of this study is to investigate effects of transcortical mini-screws placed in the buccal plate of the extraction socket following tooth extraction in human subjects compared to untreated sockets. Patients planned for extraction of two maxillary premolars were recruited. One mini-screw was placed in the buccal plate of the extraction side on the experimental side. The contralateral extraction side was left untreated as the control side. Intraoral digital scans and clinical photographs were obtained at baseline, 4 months, and 8 months. CBCTs were exposed after the extraction and before mini-screw placement and at 8 months. A considerable decrease in ridge width was observed in all three subjects at experimental and control sides. However, the experimental sides exhibited less bone loss compared to the control sides in two subjects. Transcortical mini-screw placement in the buccal plate might reduce dimensional changes at the extraction side.
  • Developing a patient-driven cost-effectiveness analysis of pharmacological treatments for patients with chronic hepatitis C

    Mattingly II, T. Joseph; Mullins, C. Daniel; 0000-0001-7786-5780 (2019)
    Background: Innovations in hepatitis C virus (HCV) drug therapy included in comparative clinical effectiveness evaluations focus on sustained virologic response (SVR) without consideration of socioeconomic or psychological outcomes. This study aimed to identify and prioritize variables important to patients and determine the impact of patient-centered parameters on the cost effectiveness of HCV treatments. Methods: An individual-based state-transition model was developed with the guidance of a patient-centered multi-stakeholder advisory board and patient-only Delphi panel. The model was used to perform a patient-driven cost-effectiveness analysis (CEA) of direct acting antivirals (DAAs) over 10 and 20 year time horizons from both health sector and societal perspectives. The patient-centered model and CEA results were then compared with recently published HCV CEAs. Results: Patients identified treatment effectiveness, longer life, fear of complications, financial issues, quality of life, and impact on society as important factors to include. Fear of harming others was considered more important than physical symptoms in terms of patient-reported problems caused by HCV. Total infected life-years (ILYs) and work days missed were reduced in the treatment group for both 10 and 20 year health sector models in addition to quality-adjusted life-year gains. Compared to no treatment, the incremental cost-effectiveness ratio for treatment would be $3,464/ILYs avoided, $715/work day missed, and $39,086/QALY gained. When costs of absenteeism, presenteeism, and patient/caregiver time were included, the DAA intervention was cost-saving at both 10 and 20 years. Very few traditional economic models for HCV treatments attempt to capture the indirect and non-medical costs or outcomes that may impact HCV patients. Conclusions: Treatment was cost-effective from a health sector perspective and cost-saving when including non-health costs such as patient/caregiver time and productivity. Compared to published HCV CEAs that focused mainly on SVR, our patient-centered CEA provides results that reflect the outcomes of interest informed by direct patient engagement.
  • Drug Repurposing for Lymphatic Filariasis Enabled with Multi-Species Genomics Approaches

    Chung, Matthew; Hotopp, Julie C. Dunning; 0000-0002-9545-523X (2019)
    Filarial diseases affect >200 million individuals worldwide, with another ~800 million individuals at risk across ~50 countries. The causative agents of filariasis are roundworms of the superfamily Filarioidea, also known as filarial nematodes. The most common human filarial disease is lymphatic filariasis, caused by one of three filarial nematodes: Wuchereria bancrofti, Brugia malayi, and Brugia timori. There are four different antihelminthic therapeutics for lymphatic filariasis—albendazole, diethylcarbamazine, ivermectin, and doxycycline. Three are primarily microfilaricidal and have limited efficacy on adult worms. The fourth therapeutic, doxycycline, adulticidal, but causes complications when administered to pregnant women or children <9 years of age. Combined with the emergence of drug resistance in filarial nematodes, new therapeutics are needed for the treatment for lymphatic filariasis. To identify potential drug targets, we conducted a multi-species transcriptomics analysis of B. malayi, its obligate mutualistic endosymbiont Wolbachia endosymbiont wBm, and its laboratory vector host A. aegypti across the entire B. malayi life cycle. We validated the use of the Agilent SureSelect RNA-Seq capture platform to enrich for B. malayi and wBm sequencing reads in low coverage samples, namely those taken during the B. malayi vector life stages in A. aegypti. For the analysis of wBm we developed FADU (Feature Aggregate Depth Utility), a quantification tool designed for prokaryotic RNA-Seq analyses, with an emphasis on accurately quantifying operonic genes. From our transcriptomics analysis, we identified an over-enrichment of the bromodomain and extra-terminal (BET) family of transcription factors, upregulated in the adult female, embryo, and microfilariae life stages. In previous studies, knockdowns of the BET proteins in Caenorhabiditis elegans lead to adult worm sterility and sometimes lethality. We treated adult female B. malayi in vitro with the BET inhibitor JQ1(+) and found that JQ1(+) induced sterility and worm death at lower concentrations than ivermectin, suggesting BET inhibitors may be promising antihelminthics. We also sequenced the genome of the Wolbachia endosymbiont of W. bancrofti, wWb, and used comparative genomics to identify conserved genes between lymphatic filariae Wolbachia. Additionally, we developed an approach for determining species using core genome alignments to reassess the supergroup designations in the genus Wolbachia.
  • Application of Machine Learning Algorithms for Predicting Missing Cost Data

    Rueda, Juan-David; Slejko, Julia; 0000-0002-0907-7106 (2019)
    Objective: To compare new alternatives to estimate health care costs in the presence of missing data using methods based on machine-learning (ML). Introduction: Costs must be correctly estimated for value assessment and budget calculations. Problems arise when they are not correctly estimated. Sometimes costs can be biased and lead to wrong decisions that affect population health. Cost estimation is a challenging task and it is more challenging in the presence of missing data. Methods: We used Surveillance, Epidemiology, and End Results program (SEER)-Medicare including patients with multiple myeloma newly diagnosed from 2007-2013. We explored the problem of missing data using different approaches creating artificial missing data. We hypothesized that the use of ML techniques improves the prediction of mean medical total costs in the presence of missingness. ML methods included support vector machines, boosting, random forest, and classification and regression trees. First, we analyzed the problem considering only one dimension, when one variable is missing in a cross-sectional scenario, using generalized linear models as a comparator against ML. Then, we added time as a factor for missingness, utilizing reweighted estimators against ML. Finally, we explored the different levels of censoring and determined how each censoring level affected our cost estimations. In this case, we created multiple linear spline models to establish the effect of censoring on the bias of the estimator. Results: We demonstrated that ML algorithms had better prediction when data were missing completely at random and missing at random. All the methods performed badly in the missing not at random scenario. In the second aim, we showed that ML-based methods predict just as well as reweighted estimators for the five-year total cost of a patient with multiple myeloma. Lastly, we found that ML methods are consistent and robust at low and moderate levels of censoring; however, we failed to prove that they are better than the reweighted estimators. Conclusions: ML-based methods are a good alternative for the prediction of missing cost data in the case of cross-sectional and longitudinal data.
  • An investigation into the behavioral effects of targeted memory reactivation during sleep on sensorimotor skill performance

    Johnson, Brian Philip; Westlake, Kelly P. (2019)
    Background. Memory consolidation occurs during sleep, providing an opportunity to enhance upper extremity (UE) function in people with residual impairments post-stroke. Targeted memory reactivation (TMR) has been used to enhance this process, which involves pairing auditory cues with task performance and subsequent cue replay during sleep. TMR application during sleep leads to increased task-related brain network connectivity and behavioral performance in healthy young adults. Yet it remains unknown whether TMR can enhance sensorimotor performance in individuals with stroke. Methods. Healthy younger and older adults and individuals with chronic stroke were trained on a non-dominant (or non-paretic) UE throwing task before a period of waking or sleeping consolidation, with some receiving TMR throughout the consolidation period. Study 1 involved the use of TMR throughout the first two slow wave sleep periods over a full night of sleep with young adults. Studies 2, 3, and 4 investigated whether TMR throughout a one-hour nap was sufficient to influence sensorimotor performance in young adults, older adults, and people with a history of stroke, respectively. Results. All studies found that TMR application during sleep enhanced sensorimotor performance. In addition, TMR during wake did not influence sensorimotor performance (Studies 1 and 2), and enhanced performance of a cognitive aspect of the trained task (Study 2). Additional generalization and transfer tests helped to support the hypothesis that TMR enhanced a task-specific motor program, as improvements were seen within the trained task but not un-trained, but similar tasks. Lastly, sleep alone appears to stabilize sensorimotor performance variability, but this process demonstrates an age-related decline. Conclusion. This dissertation has shown that the use of TMR during sleep is a useful method for enhancing sensorimotor performance in healthy young and old adults, as well as individuals with a history of stroke. Future research may lead to an adjunct to traditional physical rehabilitation protocols.
  • Spatiotemporal Regulation of Myosin II Dynamics during Cell Movement

    Snell, Nicole; Rizzo, Mark A. (2019)
    The goal of this research was to investigate how the phosphorylation of non-muscle myosin II (NMMII) by myosin light chain kinase (MLCK) and myosin light chain phosphatase (MLCP) regulates cell motility. Cellular movement is important to both biological processes such as immune response, organism development, and axon guidance and to diseases such as cancer metastasis and hypertension. Movement requires a complex series of coordinated events involving the simultaneous buildup and tear down of the actomyosin cytoskeleton. The actomyosin cytoskeleton stabilizes cellular protrusions by joining with proteins in the extracellular matrix (EM), like fibronectin, and together they produce stress fibers that allow movement. NMMII regulatory light chain (RLC) phosphorylation at Serine 19 and Threonine 18 helps drive cell movement. Removing NMMII causes cells to lose structure and lose their migratory capabilities. Subsequently, phosphorylation allows NMMII to bind to actin filaments and create actomyosin crossbridges, the structural components, of the leading and lagging edges of moving cells. The dynamic activity of NMMII and MLCK at the leading edge remains undetermined in live cells, and it is also not well understood where MLCP influences cell movement on the motile edge. I investigated the moving edge of the cell using a multiparametric imaging approach with Förster resonance energy transfer (FRET) biosensors for NMMII, MLCK, and MLCP. Transfected NIH3T3 fibroblasts were imaged using fluorescence polarization microscopy. My results suggest that NMMII and MLCK activity are compartmentalized at the leading edge during cell motility and that there are differential phases of activity on a retracting membrane. We aim to understand the spatial relationship of NMMII phosphorylation with its regulators in different areas of the cell during movement. Taken together, this thesis work advances our understanding of non-muscle myosin II phosphorylation and regulation during random cell migration.
  • Computational Modeling of Behavior and Neural Mechanisms of Decision-Making Using Reinforcement Learning Theory

    Pietras, Bradley William; Schoenbaum, Geoffrey; Dayan, Peter, 1965- (2019)
    In the study of learning and decision-making in animals and humans, the field of Reinforcement Learning (RL) offers powerful ideas and tools for exploring the control mechanisms that underlie behavior. In this dissertation, we use RL to examine the questions of (i) how rats represent information about a complex, changing, task; (ii) what are the relevant variables underlying their decision-making processes; and (iii) whether those variables are encoded in the firing rates of neurons in the orbitofrontal cortex (OFC). We addressed these questions by making inquiries across three levels of understanding: computational theory, algorithmic representation, and physical implementation. Within this tri-level framework, we hypothesize that the subjects are engaged in a form of approximately optimal adaptive control. This involves their tracking critical, task-relevant, features of their environment as these features change, and then making appropriate choices accordingly. Two classes of RL algorithms were constructed, embodying different structural assumptions. One class of so-called return-based algorithms is based on elaborations of a standard Q-learning algorithm. The other, novel, class of income-based algorithms is based on a rather weaker notion of action-outcome contingency. Both classes of algorithm were parametrized and other factors were included such as perseveration. We t the algorithms to behavioral data from subjects using complexity-controlled empirical Bayesian inference. Internal variables from our algorithms were then used to predict neural ring rates of OFC neurons that were recorded as subjects performed the task. Linear regression, randomization testing, and false discovery rate analysis were used to determine statistically significant correlations between the predictors and neural activity. We found that income-class algorithms augmented with perseveration offered the best predictions of behavior. For the least restrictive statistical test (linear regression, p < 0.05), as many as 24% of the neurons were significantly correlated with variables associated with the best-fitting algorithm. By contrast, for our most restrictive test (randomized false discovery rate < 0.05), only 3% of the neurons passed as significant for one or more of our predictor variables. Other forms of neuronal dependence were apparent, including neurons that appeared to change their computational function dynamically depending on the state of the task.
  • Therapeutic Evaluation of a Novel Topical Antimicrobial Formulation against Candida-Associated Denture Stomatitis in an Experimental Rat Model

    Sultan, Ahmed; Jabra-Rizk, Mary Ann; 0000-0001-5286-4562 (2019)
    Candida-associated denture stomatitis (DS), caused by the fungal species Candida albicans, is the most common manifestation of oral candidiasis and is prevalent in up to 70% of denture wearers. DS tends to be a persistent and recurrent oral condition as a consequence of the ability of C. albicans to adhere to denture material and invade associated palatal tissue. There are currently no effective therapeutic strategies targeting DS, and despite antifungal therapy, infection is often re-established after treatment ceases. Therefore, it has become crucial to identify novel therapeutic approaches. Antimicrobial peptides have attracted significant attention as candidates for drug development due to their potent antimicrobial and anti-inflammatory properties, lack of toxicity and lack of development of drug resistance. Specifically, histatin-5 (Hst-5), naturally produced and secreted by host salivary glands, has demonstrated potent antifungal activity, including against strains resistant to traditional antifungals. However, our laboratory has previously demonstrated vulnerability for Hst-5 to proteolysis by C. albicans secreted proteolytic enzymes at specific amino acid residues. Therefore, to generate a resistant derivative of Hst-5, we engineered a variant (K11R-K17R) with substitutions in the amino acid residues at the cleavage sites. The new peptide proved to be more stable, and unlike the native Hst-5, resistant to proteolysis by C. albicans proteases. Importantly, for clinical application, we designed a polymer-based bioadhesive hydrogel as a delivery system for the peptide and developed a therapeutic formulation specifically designed for oral topical application. The potency of the new formulation in inhibiting C. albicans adherence and biofilm formation on denture acrylic material was demonstrated in vitro indicating a potential clinical applicability against DS. To that end, using 3D digital design and printing technology, we engineered and fabricated a universal intraoral device that was successfully used in the animals to develop clinical disease mimicking DS as in humans. Using the novel animal model, we established the clinical utility of the formulation for the prevention of biofilm formation on denture device and DS development. Importantly, in addition to DS, the formulation can also be used for treatment of other forms of candidiasis as well as serve in augmenting host natural immune defenses.
  • Neonatal Nurses' Work in a Single Family Room NICU

    Doede, Megan; Trinkoff, Alison M. (2019)
    Background: In the past twenty years, neonatal intensive care units (NICUs) have undergone changes in layout from open-bay (OPBY) to single family room (SFR). SFR layout may be advantageous to nurses’ work in that it improves the quality of the physical environment, patient care, and parent-nurse interactions. SFR layout may disadvantage nurses’ work in terms of decreased interaction among the NICU patient care team, increased nurse workload, and decreased visibility on the unit. It is unclear exactly how SFR layout is producing these changes. Purpose: This study asked: what is it like for neonatal nurses to work in a SFR NICU? Methods: Interpretive description, a qualitative methodology, guided this study. Interviews and observations were conducted in one SFR NICU over a six-month period. Data were coded broadly, then collapsed into themes as patterns within the data emerged. The Systems Engineering Initiative for Patient Safety model aided interpretation of nurses’ job demands. Emotional work was conceptualized as being preceded by emotional demands and anteceded by stress and burnout. Results: A total of 15 nurses participated. Overall, privacy, visibility, and proximity were integral in shaping nurses’ work. Regarding job demands, four themes emerged: challenges in infant surveillance and informal communication, alarm fatigue, and increased walking distances. Regarding emotional work, four themes emerged: families “living on the unit,” isolation of infants, ability to form trust and bonds, and sheltering. Emotional demands increased when families were living on the unit or when infants were left in isolation but were absent when nurses were able to form trusting relationships with parents and shelter them. Privacy gains on SFR NICUs may serve to balance losses in visibility and proximity for nurses. Conclusions: NICU layout impacts nurses’ job demands and emotional work. Future research should investigate unit layouts that maximize visibility and proximity for nurses while maintaining privacy. Neonatal clinicians transitioning to SFR layout should consider overall visibility and proximity of patients, equipment, and staff members from any point on the unit as a primary avenue for decreasing nurses’ work demands. Neonatal nurses will benefit from tactics that improve their communication skills with families.
  • Neuroprotective role of nicotinamide adenine dinucleotide precursor in modulation of mitochondrial fragmentation and brain energy metabolism

    Klimova, Nina; Kristian, Tibor (2019)
    Nicotinamide adenine dinucleotide (NAD+) is a central signaling molecule and enzyme cofactor that is involved in a variety of fundamental biological processes. NAD+ levels decline with age, neurodegenerative conditions, acute brain injury, and in obesity or diabetes. Loss of NAD+ results in impaired mitochondrial and cellular functions. Administration of NAD+ precursor, nicotinamide mononucleotide (NMN), has shown to improve mitochondrial bioenergetics, reverse age associated physiological decline, and inhibit post-ischemic NAD+ degradation and cellular death. In this work we identified a novel link between NAD+ metabolism and mitochondrial dynamics. A single dose (62.5mg/kg) of NMN, administered in naïve animals and after animals are subjected to transient forebrain ischemia, increases hippocampal mitochondria NAD+ pools and drives a sirtuin 3 (SIRT3) mediated global decrease in mitochondrial protein acetylation. This results in a reduction of hippocampal reactive oxygen species (ROS) levels via SIRT3 driven deacetylation of mitochondrial manganese superoxide dismutase. Consequently, mitochondria in neurons become less fragmented due to lower interaction of phosphorylated fission protein, dynamin-related protein 1 (pDrp1 (S616)), with mitochondria. In conclusion, manipulation of mitochondrial NAD+ levels by NMN results in metabolic changes that protect mitochondria against ROS and excessive fragmentation, offering therapeutic approaches for pathophysiologic stress conditions.
  • The Effects of Glossectomy on Airway to Tongue Ratio and Mandibular Morphology Using MRI

    Kim, Eric J.; Stone, Maureen L. (2019)
    Purpose: This study asked if glossectomy surgery causes anatomical changes of the surrounding structures and the airway by altering the balance of forces in the oral cavity. We predict that glossectomy patients will have proportionately larger pharyngeal air spaces than controls relative to the hard and soft structures around the mandible. Materials and Methods: Twenty subjects were studied, ten T1 or T2 SCC glossectomies and ten controls. The gathered MRI data sets were reconstructed into 3D volumes. Results: Mid-sagittal transpalatal airway lengths were significantly shorter for the glossectomy subjects. All other measurements were not statistically significant between the two groups. Discussion: A person may compensate for the reduction of tongue size following glossectomy, which may contribute to a shorter A-P airway distance at the transpalatal level. However, all other tests were not statistically significant, including the transpalatal area inidicating that objects in the oral cavity adapt to the reduction in tongue size and does not affect the established equilibrium. The overall transpalatal airway size may be maintained in post-glossectomy speakers by lateral expansion of the airway at the transpalatal level. Conclusion: This study concluded that the spatial relationships between airway and oral structures may change in dimension, but not in balance of forces following glossectomy. Second conclusion was that a 3-dimensional imaging is required for evaluation of the airway.
  • Alveolar Bone Height Changes in Patients Treated with Conventional and Damon Brackets

    Akinwande, Akinwale Banji; Schneider, Monica, D.D.S., M.S. (2019)
    Objective: To compare the distance between the cementoenamel junction (CEJ) and marginal alveolar bone (MAB) on the buccal root surfaces of the maxilla and mandible after orthodontic treatment using Conventional bracket system (CS) and Damon bracket system (DS). Methods: The sample included 30 patients, 14- 46 years of age (13 treated with CB and 17 with DB) with moderate to severe crowding treated nonextraction. We compared pre and post-alignment cone beam computed tomography (CBCT) images to measure the bone height (BH) changes of 24 buccal surfaces for each subject. Results: Even though we found great variability in BH levels, there was a statistically significant difference (Paired t-test: p value ≤ 0.05) between pre and post- alignment CBCT images of teeth in both Conventional and Damon groups. There was no statistically significant difference (independent t-test: p value ≤ 0.05) in BH changes when comparing the 2 bracket systems. Conclusion: The bone height levels changed after orthodontic treatment with both Conventional and Damon bracket systems, but there appears to be no significant difference in alveolar bone height changes between the two brackets in this study.
  • The Effect of Malocclusion Severity and Treatment Duration on Patient Satisfaction with Clear Aligner Therapy

    Wiese, Lauren Elizabeth; Bosio, Jose A.; Williams, Robert E., D.M.D., M.A.; 0000-0003-0335-7606 (2019)
    Objective: Determine if a patient’s initial malocclusion and treatment duration influenced satisfaction with clear aligner (Invisalign®) therapy. Methods: Thirty-three orthodontic patients treated with clear aligners responded to a satisfaction questionnaire containing twenty-one questions relating to their satisfaction with treatment, approximately two years after completing treatment. Overjet, overbite, and maxillary and mandibular anterior crowding/spacing were measured to determine the initial severity of their malocclusion. Logistic regression analyses with satisfaction factors as the dependent variable were used to quantify associations between patient satisfaction regarding both the initial severity of malocclusion and treatment duration. Results: Overall, patients were satisfied with aligner treatment. However, no significant associations were observed between patient satisfaction and either the initial severity of the malocclusion or treatment duration. Conclusion: The current study does not find that initial malocclusion or treatment duration significantly affects patient satisfaction. Patient satisfaction with clear aligner therapy is generally very high, and multi-factorial.
  • Development of the Drude Polarizable Force Field for Molecular Dynamics Simulation

    Lin, Fang-Yu; MacKerell, Alexander D., Jr.; 0000-0003-0103-0167 (2019)
    Molecular dynamics (MD) simulations have been widely applied to study biomolecular systems. While MD simulations have been used in a variety of applications, the accuracy of the results depends strongly on the force field (FF) used. The commonly used FFs are additive or non-polarizable FFs. However, one limitation of the additive FFs is the lack of electronic polarizability to treat molecules. To overcome this, an attractive approach is to introduce the explicit treatment of electronic polarizability into the potential energy function known as polarizable FFs. In Chapter 1, an overview of the CHARMM empirical FF as well as the development and application of the polarizable CHARMM FF based on the classical Drude oscillator is presented. As noncovalent halogen bonding interactions between halogenated ligands and proteins are important in drug design, a well-parametrized polarizable FF for halogen containing compounds is required to perform more accurate modeling of halogenated molecules. During the course of this development, a significant contribution of halogen-hydrogen bond donor (X-HBD) interactions to ligand-protein complexes was uncovered in addition to halogen bond (XB) interactions (Chapter 2). In Chapter 3, the development of halogen polarizable FF to both aliphatic and aromatic systems using halogenated ethane and benzene model compounds is illustrated, with emphasis on optimizing both X-HBD and XB interactions as discussed in Chapter 2. To assure good reproduction of X-HBD interactions with proteins, further optimization of atom pair-specific Lennard-Jones (LJ) parameters is required for both the polarizable and non-polarizable halogen FFs (Chapter 4). Finally, Chapter 5 presents the current optimization of polarizable protein FF to yield a more accurate description of the polarization response in simulations. The resulting protein FF, referred to as Drude-2019, will be more applicable in the study of biomolecular systems. Overall, the advances made in this dissertation will facilitate important discoveries of a range of chemical and biological phenomena.
  • Examining Dietary Patterns and Relationship to Caloric Intake in a Sample of Youth with Antipsychotic Induced Weight Gain

    Bussell, Kristin Lynn; Scrandis, Debra; Friedmann, Erika; 0000-0002-3128-0178 (2019)
    ABSTRACT BACKGROUND: Antipsychotic medication (APM) treatment has risen dramatically over the past 15 years in children/adolescents with serious mental illness, increasing risk for serious cardiometabolic sides effects such as rapid weight gain, increased lipids/triglycerides, reduced insulin sensitivity and hyperglycemia. Given the long-term nature of childhood onset mental illness these youths are at considerable high risk for early onset diabetes, cardiovascular disease, chronic morbidity and shortened lifespan. Although clinical practice guidelines for assessment/monitoring have been established none have been developed for dietary assessment/interventions in weight management. Studies examining APM effects eating behaviors and nutritional composition/adequacy are lacking. METHODS: This dissertation includes a literature review related to weight loss strategies in youth treated with APM. Next a secondary analysis of dietary data collected from 117 overweight/obese youth treated with APM was conducted to examine baseline dietary status and change over 6 months after 8 session of healthy lifestyle education. Lastly, qualitative data collected from the parent/child regarding facilitators/barriers to healthy eating was analyzed. RESULTS: Literature review found primarily intervention studies with metformin, which was moderately effective, but without examining diet/exercise. Several dietary/exercise studies reported decreased weight/BMI but did not report dietary intake. Analysis in this study found excess consumption of carbohydrates, protein, fat and total/added sugar while deficient in fruits, vegetables, whole grains, fiber and water when compared to the USDA recommended daily allowance. Change in dietary intake over 6 months found significant decreases in calories, carbohydrates, protein, total/saturated/solid fat, total/added sugar, refined grains, total dairy and cheese with small increases in whole fruit, total vegetables and dark green/orange vegetables, although not statistically significant. Qualitative responses from youths/parents on barriers/facilitators to healthy eating identified barriers as excessive appetite/cravings for sweets, junk food in the home, fast food, disliking fruits/vegetables, and lack of meal planning and food shopping/preparation. Facilitators included encouragement from family, removing junk foods, eating home more, making healthy foods tasteful and including the child in meal planning. CONCLUSIONS: This study provides new information which contributes to understanding dietary intake/eating behaviors in youth treated with APM. Findings suggest a possible influence of a simple dietary intervention on changes in food intake.
  • The impact of organizational culture and climate in child welfare agencies on outcomes for children involved in the child welfare system: A multi-level analysis of a nationally representative sample

    Goering, Emily Smith; Hopkins, Karen M., 1954- (2019)
    Child welfare organizations in the U.S. are tasked with the overarching goal of protecting children from abuse and neglect. The achievement of this goal has been found to be difficult and some child welfare organizations seem to be more effective at reaching this goal than others. A dearth of empirical literature exists in understanding how child welfare organizational functioning impacts its ability to achieve positive outcomes for the children who come into contact with their local child welfare system. An extensive review of the literature revealed that culture and climate of organizations may play an important role, but the existing research is unclear about the extent and direction of that role. Additionally, methodological issues with the existing studies threaten the validity of the results. The present dissertation builds on existing research and conducts secondary analysis using a nationally representative sample. The study applied theories of organizational social context and ecological model to answer the research question: When controlling for risk factors related to child characteristics and organizational contextual characteristics, to what extent do the culture and climate of the child welfare agency impact child-level outcomes? Using the National Survey of Child and Adolescent Wellbeing (NSCAW II), bivariate and multivariate analyses were conducted to answer the research question. Results indicate that individual, agency, and local context characteristics impact recurrence of abuse during the study period. At the individual level, living in a poor household and having prior substantiated maltreatment increased the odds of recurrence. At the agency-level, of the six culture and climate variables, only the climate score of functionality had an impact on risk of recurrence. The agency-level local context variable of county child poverty had the largest effect on recurrence and added explained variance to the model. However, both significant agency-level variables did not impact recurrence in the expected direction. Future research should continue to focus on research methods, better conceptualization and measurement of organizational constructs, and utilize an ecological perspective approach.
  • A Comparison of the Levels of Salivary Biomarkers between Conventional Smokers and Electronic Cigarette Users (A Pilot Study)

    Faridoun, Afnan; Meiller, Timothy F. (2019)
    Cigarette smoking is known to alter host response and the release of inflammatory mediators and cytokines in the body. Electronic cigarettes were marketed to provide the same sensation of conventional smoking without detrimental health consequences; however, the safety of their use is an area where more research is needed. Utilizing saliva as a diagnostic medium has been rising, however, there is a lack of studies investigating the effect of e-cigarettes on the salivary biomarker profile. The purpose of this pilot project was to evaluate the salivary cytokines, associated with inflammation, and CRP profile in e-cigarette users, and compare that to cigarette smokers and controls in an attempt to assess the influence of the use of e-cigarettes on salivary biomarkers. Statistically significant elevated levels of IL- 1β accompanied by lower mean levels of IL-1RA in e-cigarette users were detected. TNF- α showed elevated values in e-cigarette users similar to conventional smokers.
  • Molecular Mechanisms Underlying the Metastasis Suppressor Activity of NME1 in Malignant Melanoma

    Pamidimukkala, Nidhi Vela; Kaetzel, David M. (2019)
    Metastatic melanoma is exceedingly lethal and is responsible for the majority of skin cancer related deaths. Impactful research on melanoma metastasis is crucial to improving prognosis. The discovery of metastasis suppressor genes, genes that inhibit metastasis but do not affect tumor growth, have advanced the field of metastasis research. NME1 (also referred to as NDPK-A or NM23-H1) was the first identified metastasis suppressor gene. NME1 is a multifaceted molecule, executing numerous cellular functions which are attributable to the suppressor phenotype. Our lab previously identified a signature of NME1-regualted genes which have prognostic value in human melanoma. As such, we hypothesize that NME1 possess an understudied transcriptional activity to regulate one or more of these signature genes. In the present study, we identified Aldolase C (ALDOC) from the gene signature as an ideal candidate to assess NME1 transcriptional activity. NME1 induced mRNA and protein expression of ALDOC in multiple melanoma cell lines. Transcriptional regulation was evidenced by elevated expression of ALDOC pre-mRNA and activation of the ALDOC promoter in NME1-expressing melanoma cells. Employing chromatin immunoprecipitation, we demonstrated NME1 localizes to the ALDOC gene and enriches the presence of active transcription indicators at the ALDOC promoter. Together, we provide novel systematic evidence for NME1 transcriptional activity, which may further be explored as a mechanism for the metastasis suppressor function. Furthermore, we establish unequivocal metastasis suppressor capability of NME1 using a transgenic mouse model susceptible to developing melanoma upon exposure to ultraviolet (UV) radiation. Mice deficient in NME1 expression experienced significantly increased melanoma metastases to the lung and lymph nodes compared to wild-type mice. Taken together, our studies demonstrate NME1 as a robust metastasis suppressor of UV-induced melanoma, and provide evidence for novel transcription factor activity of NME1. We aim to enhance our understanding of melanoma metastasis through our continued research of the metastasis suppressor gene, NME1.

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