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Peridynamic Modeling Of Coupled Mechanical Deformations And Transient Flow In Unsaturated Soils, Rami Jabakhanji

Open Access Dissertations

A coupled peridynamic model for mechanical deformations and transient moisture flow in unsaturated soils is developed. The model is capable of simulating the emergence and evolution of cracks triggered by volumetric strains in the soil which are associated with changes in moisture content. The development of our model is motivated by the need for a tool to analyze and evaluate the impact of dessication cracks on the movement of moisture and the mechanical properties of soils at the field scale. The model is based on the peridynamic reformulation of elasticity proposed by Silling for simulating the deformation of bodies with …

Developing A Drug Delivery System For Treatment Of Vocal Fold Scarring, Aaron Michael Kosinski

Open Access Dissertations

Vocal fold scarring is an affliction that results in the formation of a disorganized and stiff extracellular matrix (ECM) with abnormal ECM component densities & structures including a significant increase in collagen deposition. It is caused by improper healing post injury and results in profound changes in the biomechanical properties of the vocal folds impairing their ability to generate a normal mucosal wave during phonation.

Finding an effective treatment for vocal fold scarring has been elusive. Currently, treatments seek temporary solutions that correct glottal incompetence and reduce stiffness caused by the scar through the augmentation of the vocal folds using …

Characterization Of The Specificity And Functions Of The Protein Phosphatase Cdc14, Christie Eissler

Open Access Dissertations

Protein phosphorylation is perhaps the most ubiquitous posttranslational modification in eukaryotes and recent studies suggest that upwards of 75% of human proteins are phosphorylated. Many proteins are phosphorylated at multiple sites, often controlled by multiple kinases and phosphatases. Multisite phosphorylation can differentially affect the functional and regulatory cellular outcomes. For example, dephosphorylation of a protein at a particular site may inhibit nuclear localization of a protein while dephosphorylation of a different site may be necessary for enzymatic activation of a protein. Thus, multisite protein phosphorylation can complicate our understanding of the biological significance and the functional consequences of protein phosphorylation. …

Ozonation Systems As A Non-Chemical Alternative For Stored Grain Protection, Carlos A. Campabadal

Open Access Dissertations

The use of ozone as a non-chemical alternative in stored grain protection was studied by conducting scale-up demonstrations using a fixed bed ozonation system and developing a semi-continuous counterflow and a continuous flow ozonation treatment system. The objectives of this research were to determine the efficacy of ozonation to control insect pests without affecting end-use quality; to prove the concept of the semi-continuous counterflow ozonation system to ozonate grain at a faster rate and quantify its effect on mold growth reduction; to evaluate the efficacy of a modified screw conveyor for pest control by treating grain in a continuous-flow ozonation …

Advanced Control Strategies For Mobile Hydraulic Applications, Davide Cristofori

Open Access Dissertations

Mobile hydraulic machines are affected by numerous undesired dynamics, mainly discontinuous motion and vibrations. Over the years, many methods have been developed to limit the extent of those undesired dynamics and improve controllability and safety of operation of the machine. However, in most of the cases, today's methods do not significantly differ from those developed in a time when electronic controllers were slower and less reliable than they are today.

This dissertation addresses this aspect and presents a unique control method designed to be applicable to all mobile hydraulic machines controlled by proportional directional valves. In particular, the proposed control …

Continued Progress Towards Efficient Syntheses Of Cephalostatin North 1 Analogs, Daniel Preston Jamieson

Open Access Dissertations

Jamieson, Daniel P. Ph.D., Purdue University, December 2013. Continued Progress Towards Efficient Syntheses of Cephalostatin North 1 Analogs. Major Professor: PhilipL. Fuchs.

The cephalostatins and ritterazines represent an intriguing class of marine natural products in both structure and biological activity, and the progress towards the synthesis of high valued analogs with a focus on process orientated methodology is described herein. Included in the pages to follow, is the further advancement of the `Red-Ox' strategy toward the highly efficient synthesis of 25-epi-4,15-dihydro-North 1, Chapter 2. A short review focusing on the earlier efforts toward the main synthetic challenges of North 1 …

Fluorous- Phase Synthesis Of Heparan Sulfate Disaccharides & Low-Molecular Weight Additives For Enhancing The Performance Of Lithium-Ion Batteries., Matthew Daniel Casselman

Open Access Dissertations

Heparan sulfate is a complex cell-surface proteoglycan that serves many important roles in biology, such as growth and development, immune response and pathogenesis. Heparan sulfate is structurally heterogeneous due to the variable post- glycosylation modifications, particularly the generation of diverse sets of sulfate esters (sulfoforms) for any given disaccharide unit. In order to establish useful relationships between heparan sulfate structure and biological activity, a set of well-defined sulfoforms is necessary to support binding affinity screening. In this thesis, we describe the generation of diverse sulfoforms from heparan disaccharides using a fluorous tag to facilitate purification of highly charged intermediates, and …

Numerical Techniques For The Noninvasive Assessment Of Material Properties And Stresses In Soft Biomaterials, Kent David Butz

Open Access Dissertations

The noninvasive measurement of finite displacements and strains in biomaterials by magnetic resonance imaging (MRI) may be shown to enable mathematical estimates of stress distributions and material properties within structures of the body such as articular cartilage or the intervertebral disc. Such methods will allow for non-contact and patient-specific modeling in a manner not currently possible with traditional mechanical testing or finite element techniques. Therefore, the objective of this thesis was to develop computational methods incorporating imaging-based measures of deformation, composition, and local microstructure to permit nondestructive analysis of a range of complex biomechanical systems.

Finite strain-based models were developed …

An Epidemic Model Structured By The Time Since Last Infection, Jorge Alturo Alfaro Murillo

Open Access Dissertations

Epidemiological models structured by time since infection have their origin in the seminal work of 1927 by Kermack and McKendrick. Compared to ordinary differential equations (ODE) models, they are able to capture differences in infectivity of the individuals in a more suitable manner. Their use declined in the second half of the 20th century, probably because the theory for ODE models is more robust, complete and has proved successful in providing insights and predictions for many epidemiological problems. Nevertheless, it is important to understand in what occasions the inclusion of time since infection may alter the outcomes in a significant …

Direct And Indirect Greenhouse Gas Emissions From Biomass Storage: Implications For Life Cycle Assessment Of Biofuels, Isaac Robert Emery

Open Access Dissertations

Ethanol and other biofuels from cellulosic feedstocks are currently the most promising candidates to replace a large fraction of gasoline consumption in the United States and reduce greenhouse gas emissions. Gaps in current approaches to estimating the net greenhouse gas emissions from second-generation biofuels may lead to underestimation of the carbon intensity of these fuels. Current life cycle assessment models of biofuels do not sufficiently account for biomass losses and emissions associated with the harvest and storage of biomass feedstocks, which can require additional fuel and materials use on the farm as well as reducing the effective yield of a …

Multiscale Modeling Of The Hierarchical Structure Of Cellulose Nanocrystals, Fernando Luis Dri

Open Access Dissertations

Cellulose constitutes the most abundant renewable polymeric resource available today. It considered an almost inexhaustible source of raw material, and holds great promise in meeting increasing demands for environmentally friendly and biocompatible products. Key future applications are currently under development for the automotive, aerospace and textile industries. When cellulose fibers are subjected to acid hydrolysis, the fibers yield rod-like, highly crystalline residues called cellulose nanocrystals (CNCs). These particles show remarkable mechanical and chemical properties (e.g. Young Modulus ~200 GPa) within the range of other synthetically-developed reinforcement materials. Critical to the design of these materials are fundamental material properties, many of …

Effects Of Hearing Aid Amplification On Robust Neural Coding Of Speech, Jonathan Daniel Boley

Open Access Dissertations

Hearing aids are able to restore some hearing abilities for people with auditory impairments, but background noise remains a significant problem. Unfortunately, we know very little about how speech is encoded in the auditory system, particularly in impaired systems with prosthetic amplifiers. There is growing evidence that relative timing in the neural signals (known as spatiotemporal coding) is important for speech perception, but there is little research that relates spatiotemporal coding and hearing aid amplification.

This research uses a combination of computational modeling and physiological experiments to characterize how hearing aids affect vowel coding in noise at the level of …

Environmental Tradeoffs In Bioenergy Production And Agricultural Practices, Alicia Lynn English

Open Access Dissertations

The focus of this dissertation is the environmental tradeoffs of stover removal within the Corn Belt. The environmental tradeoffs considered are mainly concerned with managing soil erosion and soil quality. The analysis layers soil characteristics, management strategies and per acre costs using an integrated RUSLE2/WEPS model and an economic optimization model to illuminate a lower bound supply response. Different assumptions were tested in regards to sustainability, prices, and market integration for five states and 18,760 soil types throughout the Corn Belt. Sustainability was defined to limit soil erosion from wind and water to 5 tons/acre/year and the soil organic matter …

Brain Bioavailability Of Polyphenols: Implications For Delivery Of Brain Health Benefits, Tzu-Ying Chen

Open Access Dissertations

Consumption of fruits and vegetables has been associated with neuroprotection and cognitive benefits throughout the life span. These associations have sparked interest in plant-derived polyphenols as biologically active agents with potential for targeting brain benefits. However, little is known regarding the ability of the polyphenols or their metabolites from polyphenol-rich products to cross the blood-brain-barrier, and be available for biological action. Furthermore, additional insight is needed on factors affecting the absorption and brain distribution of polyphenol metabolites in vivo. To fill gap in current knowledge, this thesis will focus on the effects of diabetogenic diet and diabetic state which have …

Nanoscale Semiconductor Materials And Devices Employing Hybrid 1d And 2d Structures For Tunable Electronic And Photonic Applications, Suprem Ranjan Das

Open Access Dissertations

Das, Suprem R. Ph.D., Purdue University, December 2013. Nanoscale Semiconductor Materials and Devices employing Hybrid 1D and 2D structures for Tunable Electronic and Photonic Applications. Major Professor: Dr. David B. Janes.

Continued miniaturization of microelectronic devices over past decades has brought the device feature size towards the physical limit. Likewise, enormous `waste energy' in the form of self-heating in almost all of the electronic and optoelectronic devices needs an `energy-efficient low power' and `high performance' material as well as device with alternate geometry. III-V semiconductors are proven to be one of the alternate systems of materials for various applications including …

Osmium Catalyzed Dihydroxylation And Oxidative Cleavage Of Vinyl Sulfone And Elucidation Of The Vinylsulfone Polypropionate Methodology For The Synthesis Of The C32 Des-Methyl C28-C34 Actin Binding Tail Of Aplyronine A, Thomas Paul Bobinski

Open Access Dissertations

A general methodology for the generation of dipropionate functionalities using cyclic 7-membered vinylsulfones has been devised for the purpose of synthesizing polyketide natural products such as aplyronine A. Final oxidative cleavage via ozonolysis has been shown to be difficult providing variable yields. Furthermore, elegant synthesis of the C28-C34 segment of the aplyronine A actin binding tail has proved elusive. Utilization of OsO4 and catalytic citric acid has led to a methodology whereby harsh ozonolysis procedures can be mostly avoided. A reengineering of the vinylsulfone polypropionate methodology in conjunction with osmylation has been found to provide the actin binding tail under …

Structural And Functional Characterization Of The Endosome-Associated Deubiquitinating Enzyme Amsh, Christopher Williamson Davies

Open Access Dissertations

The endosomal sorting complexes required for transport (ESCRT) machinery is a ubiquitin-dependent molecular mechanism made of up of four individual complexes: ESCRT-0, -I, -II, III, that is necessary for regulating the degradation of cell surface receptors directed towards the lysosome. Not only are the ESCRTs implicated in endosomal sorting and trafficking of proteins, its members also have roles in other important biological processes such as: cytokinesis, HIV budding, transcriptional regulation, and autophagy. As a function of its involvement in several processes throughout the cell, the ESCRT machinery is implicated in a wide variety of diseases including cancer, neurological disease, bacterial …

Novel Modulation Of Adenylyl Cyclase Type 2, Jason Michael Conley

Open Access Dissertations

Adenylyl cyclase isoforms are distinctly modulated by G protein subunits and are therefore hypothesized to be uniquely regulated by proteins that influence G protein signaling. Activator of G protein signaling 3 (AGS3) is a G protein modulator that binds Gαi subunits in the GDP-bound state, implicating AGS3 as an important regulatorof Gi-coupled receptor signaling. We studied the ability of AGS3 to modulate recombinant adenylyl cyclase(AC) type 1 and 2 signaling in HEK293 cells following both acute and persistent activation of the D _2Ldopamine receptor (D_2L DR). AGS3 expression modestly enhanced the potency of acute quinpirole-induced D _2LDR …

Hypothesize-And-Verify Based Solutions For Place Recognition And Mobile Robot Self-Localization In Interior Hallways, Khalil Mustafa Ahmad Yousef

Open Access Dissertations

There is much research interest currently in having mobile robots build accurate and visually dense models ofinterior space as they traverse through such spaces. One of the interesting problems that has came out of this research is that of visual place recognition and self-localization. This is the problem that forms the focus of the present dissertation. We show how dense and accurate 3D models of the interior space can be constructed using a hierarchical sensor-fusion architecture. Our system fuses images from a single photometric camera with range data from a laser scanning sensor. The range data used is rudimentary--the range …

Disk Diffusion Breakpoint Determination Using A Bayesian Nonparametric Variation Of The Errors-In-Variables Model, Glen Richard Depalma

Open Access Dissertations

Drug dilution (MIC) and disk diffusion (DIA) are the two most common antimicrobial susceptibility tests used by hospitals and clinics to determine an unknown pathogen's susceptibility to various antibiotics. Both tests use breakpoints to classify the pathogen as either susceptible, indeterminant, or resistant to each drug under consideration. While the determination of these drug-specific MIC classification breakpoints is straightforward, determination of comparable DIA breakpoints is not. It is this issue that motivates this research.

Traditionally, the error-rate bounded (ERB) method has been used to calibrate the two tests. This procedure involves determining DIA breakpoints which minimize the observed discrepancies between …

A Novel Multiblock Immersed Boundary Method Enabling High Order Large Eddy Simulation Of Pathological And Medical Device Hemodynamics, Anupindi Kameswararao

Open Access Dissertations

Computational fluid dynamics (CFD) simulations are becoming a reliable tool in understanding disease progression, investigating blood flow patterns and evaluating medical device performance such as stent grafts and mechanical heart valves. Previous studies indicate the presence of highly disturbed, transitional and mildly turbulent flow in healthy and pathological arteries. Accurate simulation of the transitional flow requires high order numerics together with a scale resolving turbulence model such as large eddy simulation (LES). This in turn limits one to use a structured fluid flow solver on which complex, branching arterial domains that are typical in the human blood circulatory system could …

Measuring And Modeling The Response Characteristics Of The Environmental Phosphate Transducer In Escherichia Coli, Chetan Sood

Open Access Dissertations

The PhoR/PhoB two-component system in Escherichia coli is a biological transducer that senses the limitation of environmental inorganic orthophosphate, the bacteria's preferred source of the essential nutrient phosphate, and transmits that information to the interior of the cell initiating a response that mitigates phosphate starvation. In the first part of this study, we present and apply a fluorescence microscopy technique to measure, in vivo, the dynamic response characteristics of the transducer with single-cell resolution. We report that the transience in the PhoR/PhoB TCS response is consistent with the transducer having a threshold sensitivity to the concentration of environmental phosphate, …

Molecular Investigations Into The Interplay Between Development And Axon Growth And Regeneration, Ephraim F. Trakhtenberg

Open Access Dissertations

A major reason why central nervous system (CNS) trauma and many neurodegenerative diseases demonstrate only limited endogenous repair is the failure of CNS axons to regenerate. Extracellular factors and developmental changes in maturing CNS neurons regulate CNS axon regeneration. The aim of this thesis was to investigate how molecular changes in maturing neurons affect axon growth and regenerative capacity. We found that regulation of subcellular localization of Set-β protein, which is developmentally upregulated in neuronal nuclei, toggles its function between inhibiting and promoting axon growth and regeneration. We also found that developmentally upregulated serotonin receptor 2C suppresses neurite growth and …

The Role Of Flow Sensing By The Lateral Line System In Prey Detection In Two African Cichlid Fishes, Margot Anita Bergstrom Schwalbe

Open Access Dissertations

The mechanosensory lateral line system is found in all fishes and mediates critical behaviors, including prey detection. Widened canals, one of the four patterns of cranial lateral line canals found among teleosts, tend to be found in benthic fishes and/or fishes that live in hydrodynamically quiet or light-limited environments, such as the deep sea. Little is known about the functional significance of widened canals because most fishes with this morphology are inaccessible for laboratory study. A representative of one genus of Lake Malawi cichlid fishes, Aulonocara, has widened canals and provides an opportunity to investigate the role of widened …

Exploitation Of Androgen Receptor Signaling By Guanine Nucleotide Exchange Factor Vav3 In Castration Resistant Prostate Cancer, Stephanie Peacock

Open Access Dissertations

Advanced or metastatic prostate cancer is treated by androgen deprivation; however, patients inevitably relapse with castration resistant prostate cancer (CRPC). CRPC remains dependent on androgen receptor (AR) signaling, which may include constitutive, ligand-independent action of naturally occurring AR splice variants. For example, the AR splice variant AR3 (also termed AR-V7) is expressed in CRPC and is linked to poor prognosis. Vav3, a Rho GTPase guanine nucleotide exchange factor, is an AR coactivator that is up-regulated in human prostate cancer, compared to benign tissue, and in pre-clinical models of CRPC. Vav3 confers castration-resistant growth to androgen-dependent human prostate cancer cells. Despite …

Mir-23b/-27b Cluster Suppresses The Metastatic Phenotype Of Aggressive Prostate Cancer Cells, Reema A. Ishteiwy

Open Access Dissertations

MicroRNAs (miRs) are small, endogenous, non-coding RNAs that regulate gene expressing by inhibiting the stability and/or translation of complementary mRNA targets. Expression of miR-23b/-27b, which are encoded in tandem as a cluster on chromosome 9, are specifically downregulated in metastatic prostate cancer tissue samples compared to benign prostate. MiR-23b/-27b levels are also lower in aggressive prostate cancer cell lines compared to more indolent cells. We show miR-23b/-27b suppress migration and invasion of two aggressive human prostate cancer cell lines. Furthermore, inhibition of miR-23b/-27b increases the migration and invasion potential of a less aggressive prostate cancer cell line. Interestingly, we found …

The Relationship Of Temporal Discounting And Working Alliance To Substance Abuse Treatment Process In Hispanic Adolescents, James John Weidel

Open Access Dissertations

The association between impulsivity and substance abuse has important implications in the clinical substance abuse treatment field. Adolescents who are characteristically more impulsive by nature of their developmental may be more at risk for treatment failure. The inclination by which individuals devalue future rewards in favor of more immediate rewards with lower monetary values is a type of impulsivity that has received much attention in the substance abuse research field. Identified as temporal discounting (TD) or delay discounting, this phenomenon is not only a factor that influences substance abuse, but also may be a factor that leads to failure in …

Interactive Effects Of Ethnic Identity And A Cognitive Behavioral Stress Management Intervention On Subjective And Objective Stress In Low-Income Minority Women Living With Hiv, Corina Reyes Lopez

Open Access Dissertations

The HIV/AIDS epidemic is more prevalent among minority ethnic groups, with mortality rates highest among African-American women. Additionally, low-income minority women with a positive HIV diagnosis experience a variety of stressors that influence their psychological and physical well-being. Research has found that ethnic identity, an intrapersonal resiliency factor, is associated with lower perceived stress in low-income minority women living with HIV, in part through greater levels of coping self-efficacy and social support. Given the benefits of group-based interventions in reducing stress in HIV positive populations, it is important to understand whether ethnic identity influences the efficacy of these interventions in …

Understanding Nocturnal Ambulatory Blood Pressure In Youth, Katie E. Chipungu

Open Access Dissertations

In adolescents, nocturnal ambulatory blood pressure (ABP) provides a rich and informative picture of cardiovascular health and risk. This study modeled nocturnal ABP taken during one night using multi-level growth modeling. A combination of demographic, daytime, clinical, and sleep related variables were also included as inter-individual predictors of nighttime blood pressure regulation. Adolescents (N = 252) were obtained from three larger studies addressed cardiovascular risk in youth attending public high schools in Miami-Dade County. Participants included in this study completed a baseline medical screening, initial ABP assessment visit and had at least one ABP reading taken during sleep. Within a …

Catalytic Applications Of Bio-Inspired Nanomaterials, Dennis Kien Balaong Pacardo

Open Access Dissertations

The biomimetic synthesis of Pd nanoparticles was presented using the Pd4 peptide, TSNAVHPTLRHL, isolated from combinatorial phage display library. Using this approach, nearly monodisperse and spherical Pd nanoparticles were generated with an average diameter of 1.9 ± 0.4 nm. The peptide-based nanocatalyst were employed in the Stille coupling reaction under energy-efficient and environmentally friendly reaction conditions of aqueous solvent, room temperature and very low catalyst loading. To this end, the Pd nanocatalyst generated high turnover frequency (TOF) value and quantitative yields using ≥ 0.005 mol% Pd as well as catalytic activities with different aryl halides containing electron-withdrawing and electron-donating groups. …