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Factors Affecting Transduction Efficiency Of Pseudotyped Viral Vectors Incorporating Alphaviral Glycoproteins, Aditi Kesari

Open Access Dissertations

The genome of an organism has the complete set of biochemical instructions required for sustenance of life. Mutations or abnormalities in this genome lead to genetic disorders. Currently available therapeutic options mostly focus on treating the symptoms, but not curing them. Gene therapy promises to be a curative form of medicine. In gene therapy cells carrying a defective gene are targeted and replaced with a healthy copy of that gene. The vehicles used for delivering this gene are known as vectors. Retroviruses are popularly used gene therapy/transfer vectors. However, retroviruses are limited in the range of cells they can enter …

Learning The Language Of Academic Engineering: Sociocognitive Writing In Graduate Students, Catherine G. P. Berdanier

Open Access Dissertations

Although engineering graduate programs rarely require academic writing courses, the indicators of merit in academic engineering, such as journal publications, successful grants, and doctoral milestones (e.g. theses, dissertations) are based in effective written argumentation and disciplinary discourse. Further, graduate student attrition averages 57% across all disciplines, with some studies classifying up to 50% of these students as “ABD” (All But Dissertation.) In engineering disciplines specifically, graduate attrition rates across the U.S. average 36% (both Master’s and PhD students), according to the Council of Graduate Schools. The lack of socialization is generally noted as a main reason for graduate attrition, one …

Hydrologic And Water Quality Impacts From Perennial Crop Production On Marginal Lands, Qingyu Feng

Open Access Dissertations

Marginal lands are proposed as a viable option for producing biofeedstocks as these lands are not heavily engaged in agricultural production or may not be suitable for intensive row-crop food/feed production. However, meeting biofeedstock production goals will require large amount of marginal lands and the unintended consequences of producing biofeedstocks on marginal lands are not fully clear. The overall goal of this study was to evaluate the productivity of biofeedstocks on marginal lands and the potential impacts on hydrologic and water quality processes from the land use conversion.

This study was conducted in the Upper Mississippi River Basin (UMRB). First, …

Understanding The Communicative Processes Of Baby Boomer Women Adjusting To Retirement: Connecting Micro And Macro Discourses, Patricia E. Gettings

Open Access Dissertations

Baby Boomers are changing the face of retirement in the United States. For example, retirement traditionally refers to the time when an individual who has worked full-time for the majority of her life chooses to entirely and permanently exit the workforce, but now includes a range of formations (e.g., bridge employment). Baby Boomer women are most affected by this “new” retirement because they have worked a broader range of jobs for longer periods of time than ever before. Transitioning to retirement implicates processes of adjusting beyond just a change in one’s employment status as retirees potentially confront instrumental (e.g., where …

Using Information Technology To Model Hand-Washing Behavior And To Improve Policies Impacting Elementary School Absenteeism Due To Influenza, Galina V. Miller

Open Access Dissertations

This dissertation revealed several problems on the analysis of in?uenza propagation by indicating how agent-based modeling can be employed to measure the e?ectiveness of control measures and assist in improving health policy to decrease absenteeism among elementary students. The primary question posed was as following: “What is the e?ect of hand hygiene on the possible incidence rates among school children?” After creating an agent-based model representing the in?uenza transmission dynamic, the incidence rates were calculated based on the hand-washing success rates. The statistical results from the simulation model were displayed in graphical format.

Finally, the author addressed the issue of …

Investigating Physiological Collaborations Between A Lower Termite And Its Symbionts, Brittany F. Peterson

Open Access Dissertations

This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of Reticulitermes flavipes, the eastern subterranean termite. Lower-termites, like R. flavipes, house symbionts from all three domains of life within their hindgut paunch. This intimate association is reflected in nearly every aspect of termite biology. Here, I investigate these physiological collaborations as they relate to digestion and immunity. My efforts focused on 1) quantifying the role of bacteria in wood digestion within the termite gut, 2) evaluating the role of symbionts in protection against pathogens, and 3) identifying gene products that bacterial …

Cognitive Complexity In Carnivora: The Evolutionary Link Between Social Complexity And Cognitive Complexity, Natalia D. Borrego

Open Access Dissertations

Traditional views of cognitive evolution favored a simplistic approach in which the evolution of advanced cognition was considered unique to primate lineages. A recent expansion to non-primates indicates that cognition convergently evolved in several lineages. The social intelligence hypothesis attributes the convergent evolution of cognitive complexity to shared selective pressures imposed by social complexity. According to the social intelligence hypothesis, social individuals benefit from cognitive abilities facilitating social life, and the resultant fitness advantage engenders an evolutionary link, whereby social complexity selectively favors cognitive complexity. The social intelligence hypothesis predicts that social species are cognitively advanced. Although several studies support …

Coupling Between Nutrient Availability And Thyroid Hormone Activation, Lattoya Josephine Lartey

Open Access Dissertations

Thyroid hormone is essential for metabolism, growth, development and cognitive function. Thyroid hormone is secreted in two forms, the biologically active 3,5,3’-triiodothyronine (T3) and the inactive thyroxine (T4) that must be converted to T3 in order to gain biological activity. This reaction is catalyzed by type II deiodinase (D2), a thioredoxin-fold containing selenoenzyme; its activity plays an essential role in thyroid hormone activation. The thyroid gland is regulated by the hypothalamic-pituitary-thyroid (HPT) axis. It responds to food availability via leptin induction of thyrotropin releasing hormone (TRH) in the hypothalamus and thyroid stimulating hormone (TSH) in the pituitary. These actions stimulate …

Observations And Modeling Of Exchange And Residence Time In Tidal Inlets, Patrick Forde Rynne

Open Access Dissertations

The exchange of water in a coastal embayment with seawater is forced by tidally driven and gravitational flows. Tidal flows oscillate temporally based on planetary motion, while gravitational flows like those found in rivers act in one direction from high to low altitude. These flows determine the residence time, or the time water will remain within an embayment. At the ocean boundary, many coasts contain barrier islands with inlets through which these flows propagate. The effect that inlets have on the exchange of inland water with the sea has been the subject of research for nearly a century. Residence time …

A Selected Review Of Prevention And Non-Surgical Treatment Options For Musculoskeletal Performance-Related Injuries Common Among Oboists, Sara Lyn Diehl

Open Access Dissertations

Oboe practice and reed making entails persistent and methodical application. This can lead to misuse and overuse, which may cause injuries that could result in early retirement, permanent disfigurement, or both. The purpose of this essay is to catalog the current prevention and non-surgical treatment options for musculoskeletal performance-related injuries common among oboists. The essay will also identify injuries that are frequently found in oboe players, and provide information about the causes of these injuries. It is my hope that this document will become a resource for oboists to use when they are struggling with performance-related injuries and will help …

Designing Prenatal M-Health Interventions Through Transmigrants Reflection On Their Pregnancy Ecology, Hana Aljaberi

Open Access Dissertations

This dissertation presents the findings from three participatory focus group and co-design sessions with Caribbean transmigrant women in the United States. Informed by their focus group discussions regarding their pregnancy experiences in the United States, the participants produced design ideas that reflected on physical, emotional, informational and social gap themes. The purpose of this study was to understand the challenges affecting the women’s prenatal wellbeing practices, and to conceive a set of recommendations and opportunities for mHealth technology design to assist with prenatal preventative care and management. The study uses the theoretical concept of pregnancy ecology to identify gaps in …

Supervised Learning-Based Explicit Nonlinear Model Predictive Control And Unknown Input Estimation In Biomedical Systems, Ankush Chakrabarty

Open Access Dissertations

Application of nonlinear control theory to biomedical systems involves tackling some unique and challenging problems. The mathematical models that describe biomedical systems are typically large and nonlinear. In addition, biological systems exhibit dynamics which are not reflected in the model (so-called 'un-modeled dynamics') and hard constraints on the states and control actions, which exacerbate the difficulties in designing model-based controllers or observers.

This thesis investigates the design of scalable fast explicit nonlinear model predictive controllers (ENMPCs). The design involves (i) the estimation of a feasible region using Lyapunov stability methods and support vector machines; and (ii) within the estimated feasible …

A Flexible And Versatile Framework For Statistical Design And Analysis Of Quantitative Mass Spectrometry-Based Proteomic Experiments, Meena Choi

Open Access Dissertations

Quantitative mass spectrometry (MS)-based proteomics is an indispensable technology for biological and clinical research. As the proteomics field grows, MS-based proteomic workflows are becoming more complex and diverse. The accuracy and the throughput of the MS measurements and of the signal processing tools dramatically increased. However, many existing statistical tools and workflows have not followed the technological development. Therefore, there is a need for flexible statistical tools, which reflect diverse and complex workflows, are computationally efficient for large datasets, and maximize the reproducibility of the results.

We propose a family of linear mixed effects models, and a split-plot view of …

The Effects Of Acidified Pepsin On Porcine Vocal Fold Tissue: Developing A Porcine Model Of Laryngopharyngeal Reflux Disease, Abigail Cox Durkes

Open Access Dissertations

Approximately 7.5 million Americans are affected by a voice disorder. In the last year, 7.2% of people missed one or more days of work due to a voice problem. For professional voice users, such as teachers, the rate increases to 20% and an annual cost of $2.5 billion. Voice disorders are complex and multi-faceted, as well as difficult to diagnose and treat. Prospective animal studies are necessary to study the pathophysiology of voice disorders, optimize our understanding of laryngeal pathology, and improve treatment outcomes. The pig provides a unique opportunity to test hypotheses relating to laryngeal disease because porcine vocal …

Alternative Splicing Of Drosophila Nmnat: A Neuronal Self-Protection Mechanism, Kai Ruan

Open Access Dissertations

Neurodegenerative diseases triggered by a variety of genetic, epigenetic, and environmental factors are increasingly prevalent worldwide. Maintaining neuronal homeostasis is a prerequisite for proper neurological activity. However, details of mechanisms of neuronal maintenance are largely unknown, and in particular it is unclear whether and how healthy neurons regulate their self-protective activities. Previous work in our laboratory and others has found housekeeping NAD synthetic enzyme NMNAT proteins to be among the most effective and versatile neuroprotective factors in Drosophila and mammals. It has been shown that a stem-loop secondary RNA structure within the Drosophila Nmnat (DmNmnat) intron can modulate its alternative …

The Contribution Of Cancer Associated Fibroblasts In Breast Cancer Progression, Sanket H. Shah

Open Access Dissertations

Cancer Associated Fibroblasts (CAFs) are an integral component of the TME, and the majority of breast tumor stroma is comprised of CAFs. Multiple juxtacrine and paracrine interactions occur between cancer cells and CAFs that direct tumor progression. These interactions occur via soluble agents, including cytokines, hormones, growth factors, and secreted microRNAs. Some of these soluble agents induce MAPK activation in tumor cells. Our lab has established that MAPK activation in tumor cells is one of the key mechanisms involved in repression of ER. MAPK activation in tumor cells leads to alteration in miRNA expression. We previously identified a microRNA signature …

The Impacts Of Bycatch From The Atlantic Tropical Tuna Purse Seine Fishery On Ecosystem Structure And Function, Francesca Cassell Forrestal

Open Access Dissertations

Global catches of tuna have increased steadily in the past several decades and this increase was largely driven by the switch to purse seine gears. Purse seine vessels target tropical tuna species in all the world’s oceans and have two main modes of fishing, catching schools of tuna associated with a floating object (FAD sets) or schools of unassociated tunas (free sets). Both modes of fishing strategies have the potential to catch unintended species, termed bycatch, however larger rates of bycatch are seen from FAD sets. The total amounts of bycatch caught by both fishing strategies can be difficult to …

Complex Resistivity Spectra In Relation To Multiscale Pore Geometry In Carbonates And Mixed-Siliciclastic Rocks, Jan Henrik Norbisrath

Open Access Dissertations

Carbonate rocks are known to have complex and heterogeneous pore structures, which result from their biogenic origin and strong affinity for diagenetic processes that change their pore structure after burial. The combination of sheer endless variations of precursor biogenic material, depositional environments, and diagenetic effects results in rocks that are interesting to study but intricate to understand. Many schemes to categorize the diversity of carbonate rocks are in use today; most are based on the macropore structure and qualitative thin-section analysis. Many studies, however, acknowledge that micropores have a significant influence on the macroscopic petrophysical rock properties, which are essential …

Lfda: A Probabilistic Graphical Model For The Study Of Excitation Emission Matrices, Oscar Luis Martinez

Open Access Dissertations

Traditional classification techniques assume samples are described by vectors of features. However, in some domains samples are gathered by measuring a variable with respect to two or more other variables: for a given value of x and y measure z. In such domains, samples are more naturally described by matrices or by higher dimensional arrays. We present a novel latent Dirichlet allocation (LDA)-based approach for modeling and analyzing fluorescent spectroscopy excitation-emission Matrices (EEMs) and other three way datasets. We introduce parallels between topic modeling and three-way arrays which allow us to create adaptations to use LDA-based methods in latent fluorophore …

Characterization Of Novel Neurodegenerative Genes Implicated In Mitochondrial Dynamics, Alexander J. Abrams

Open Access Dissertations

Mitochondria are dynamic organelles undergoing constant fusion, fission, and migration within cells. The mobile nature of the mitochondria is essential for nerve health, as mutations in two of the major mitochondrial fusion genes, MFN21 and OPA12,3, cause axonal peripheral neuropathy (Charcot-Marie-Tooth Type 2, CMT2), and dominant optic atrophy (DOA) respectively. Through collaborative exome sequencing and data sharing, we identified four families with recessive mutations in the nuclear encoded mitochondrial gene, SLC25A46 (Chapter 2). The patients in these families present a clinical spectrum of features ranging from optic atrophy, spasticity, peripheral neuropathy, and ataxia, to lethal infantile neurodegeneration. SLC25A46 is one …

Physiological Downstream Consequences And Tradeoffs Associated With Co2 Compensation In Marine Fish, Rachael M. Heuer

Open Access Dissertations

Fish are renowned for their ability to defend blood pH following exposure to elevated ambient CO2, a trait that has undoubtedly led to their ability to thrive successfully in a wide variety of habitats. While the defense of internal pH is critical for survival, the sustained elevation of HCO3- and PCO2 that occurs as a part of this compensatory response could potentially lead to sub-lethal impacts. This point is underscored by a growing number of studies demonstrating negative effects of CO2, even at relatively low CO2 tensions. The goal of this dissertation was to assess potential downstream consequences and/or tradeoffs …

Interfacial Mechanical Strength Characterization In Multilayered Materials Via Nanoscale Impact And Nano Mechanical Raman Spectroscopy Experiments, Devendra Verma

Open Access Dissertations

A composite materials strength can significantly depend on the constitutive description of interfaces. A computational model of composite deformation should, therefore, incorporate interface constitutive behavior. These interfaces poses several challenges in studying them due their length scales of micrometer to nanometer as well the coupling of other factors such as confinement during the loading. Thus, separating main phase constitutive behavior from interface constitutive behavior in mechanical property measurement experiments is an arduous task. In this work, an epoxy interface between glass plates is analyzed under quasistatic and dynamic loading conditions to obtain a description of interfacial constitutive response at strain …

Exiles Of Heteronormativity: Queer Reproduction And Female Same-Sex Families In Singapore, Nur Adlina B. Maulod

Open Access Dissertations

In Singapore, same-sex desires and practices are treated as antithetical to the Family. This dissertation challenges the rhetorical monolith of the traditional family by documenting intimate stories of alternative reproduction from the experiences of female citizens who have been treated as exiles of heteronormative kinship.

Targeting Multi-Drug Resistant Pathogens With Novel Antimicrobial Peptides, Mohamed F. Mohamed

Open Access Dissertations

The emergence of antibiotic resistance is a notorious problem worldwide. In the United States alone, antibiotic-resistant bacteria infect at least two million people and kill around 23,000 patients each year. Half of these infections are attributed to the bacterial pathogen, methicillin resistant Staphylococcus aureus (MRSA) according to a report published in 2013 by the Centers for Disease Control and Prevention (CDC). Similarly, S. pseudintermedius is a leading cause of opportunistic infections in pet animals and has zoonotic potential. Furthermore, the marked increase in the incidence of infections due to extensively drug-resistant and pandrug-resistant isolates of Pseudomonas aeruginosa and Acinetobacter baumannii …

Quantitative Modeling Of Scaling Of Patterns And Receptor Signaling In Morphogenesis, Md Shahriar Karim

Open Access Dissertations

Organs and tissue development often experience perturbations, but developmental processes seem to replicate a common body template to maintain appropriate proportions and positions. The key signaling factors that guide a number of those processes are known as morphogens. Developing cells sense their respective positional information from a graded morphogen profile, and differentiate into patterns. Remarkably, patterns are highly robust and reproducible among species, and the underlying mechanisms associated with such high degrees of precision are still enigmatic. In addition, details of the signal, such as the Bone Morphogenetic Protein (BMP) signal, that transmit patterning information to a group of homogenous …

Efficient Sparse Bayesian Learning Using Spike-And-Slab Priors, Syed Abbas Zilqurnain Naqvi Zilqurnain Naqvi

Open Access Dissertations

In the context of statistical machine learning, sparse learning is a procedure that seeks a reconciliation between two competing aspects of a statistical model: good predictive power and interpretability. In a Bayesian setting, sparse learning methods invoke sparsity inducing priors to explicitly encode this tradeoff in a principled manner.

Unique Allosteric Mechanism Regulating Protein-Protein Interaction Through Phosphorylation: A Case Study Of The Conformational Changes In The Syk Tandem Sh2 Protein, Duy Phuong Hua

Open Access Dissertations

Spleen tYrosine Kinase (Syk) is one of the crucial signaling proteins involved in the development of immune cells and the initiation of inflammatory responses. Syk is a 72-kDa kinase comprising three folded domains: two SH2 domains and a catalytic domain. The tandem SH2 domains connected by linker A are key to the regulation of Syk activity. Immune signaling through Syk is initiated by the binding of the tandem SH2 to the dpITAMs found on immune cell receptors. The high-affinity, bifunctional binding of Syk tandem SH2 to the immunoreceptor requires that the two phosphotyrosines (pTyr) of the dpITAM fit the spacing …

Graph Diffusions And Matrix Functions: Fast Algorithms And Localization Results, Kyle Kloster

Open Access Dissertations

Network analysis provides tools for addressing fundamental applications in graphs such as webpage ranking, protein-function prediction, and product categorization and recommendation. As real-world networks grow to have millions of nodes and billions of edges, the scalability of network analysis algorithms becomes increasingly important. Whereas many standard graph algorithms rely on matrix-vector operations that require exploring the entire graph, this thesis is concerned with graph algorithms that are local (that explore only the graph region near the nodes of interest) as well as the localized behavior of global algorithms. We prove that two well-studied matrix functions for graph analysis, PageRank and …

Studies Of Nicotinic Acetylcholine Receptors Containing Α4 And Α6 Subunits In Nicotine-Induced Synaptic Plasticity In Brain Reward Areas, Staci Engle

Open Access Dissertations

Tobacco addiction is a serious threat to public health in the United States and abroad, and development of new therapeutic approaches is a major priority. Nicotine, the primary psychoactive compound in tobacco smoke, activates and/or desensitizes nicotinic acetylcholine receptors (nAChRs) throughout the brain. nAChRs in ventral tegmental area (VTA) dopamine (DA) neurons are crucial for the rewarding and reinforcing properties of nicotine. Nicotine causes cellular changes in VTA DA neurons, including the enhancement of AMPA receptor (AMPAR) function. This enhancement sensitizes the VTA to excitatory input and promotes drug seeking in animal models. However, which nAChR subtype(s) are responsible for …

Integrated Aquifer Vulnerability Assessment Of Nitrate Contamination In Central Indiana, Won Seok Jang

Open Access Dissertations

Groundwater is not easily contaminated, but it is difficult to restore once contaminated. Therefore, groundwater management is important to prevent pollutants from reaching groundwater. A common step in developing groundwater management plans is assessment of aquifer risk using computational models. Groundwater modeling with a geographic information system (GIS) for efficient groundwater management can provide maps of regions where groundwater is contaminated or may be vulnerable and also can help select the optimal number of groundwater monitoring locations.