VictorJuiz/thesis huggingface dataset:
The Impact of Microbiome Alterations in the NOD Mouse Model of Type 1 Diabetes

Epidemiological and experimental data suggest Type 1 Diabetes (T1D) and gut inflammatory disorders share genetic and environmental risk factors. Genetics and microbiome composition differentiate T1D-prone NOD mice and T1D-resistant NOR mice. In the first part of this study, we examined the possible protective effects of NOR-derived microbiome transplant in NOD mice. We report, despite quantifiable, durable changes in the gut microbiome of NOD recipients of NOR-derived microbiome transplant compared to NOD and NOR controls, these mice were not protected from T1D. Studies have also suggested that probiotic bacteria can have protective effects in T1D and gut inflammatory disorders. In the second part of this study, we examined the possible protective effects of treatment with probiotic microbes in the NOD mice. We report Protecflor probiotic-treated NOD mice showed quantifiable, durable changes in gut microbiome composition, and were protected from autoimmune infiltration of the islets compared to vehicle-treated controls.

Keywords: Microbiota
NOD mouse
Type 1 Diabetes
Advisor: Danska, Jayne S
Earprint: Transient Evoked Otoacoustic Emission for Biometrics

Biometrics is attracting increasing attention in privacy and security concerned issues. However, advanced forgery techniques are threatening the reliability of conventional biometric modalities. This has been motivating our investigation of a novel modality Transient Evoked Otoacoustic Emission (TEOAE), which is an acoustic response generated from cochlea. As a physiological outcome from auditory system, TEOAE is immune to replay and falsification attacks In this work, we derive the time-frequency representation of the signal using wavelet analysis, revealing individual uniqueness. Discriminant analysis is subsequently utilized to reduce intra-subject variability. We also introduce a complete framework of the biometric system in both verification and identification modes, as well as a solution to secure sensitive template data. Comparative experiments on a biometric setting dataset show the merits of the proposed methods. Performance is further improved with fusion of information from both ears, with an average identification rate 99.44% and equal error rate 0.02% achieved.

Advisor: Hatzinakos, Dimitrios
The Roles of Phosphodiesterase (PDE) 3A and 3B as Regulators of Cardiac Function in Disease

Cyclic nucleotide phosphodiesterases (PDEs) are enzymes that hydrolyze the 3'-5'-phosphodiester bonds of cAMP and/or cGMP. PDE3 family variants (PDE3A, PDE3B) are highly expressed in the heart. The roles of PDE3A, and PDE3B as regulators of cardiac function in disease have not been definitively established. We investigated the roles of PDE3A and PDE3B as regulators of cardiac function in the setting of heart failure (HF) of non-ischemic etiology. PDE3A and not PDE3B protein expression was elevated in failing hearts subjected to sustained biomechanical stress (pressure-overload). Chronic ablation of PDE3A and not PDE3B activity attenuated cardiac contractile dysfunction and pathological remodelling induced by pressure-overload. We propose ablation of PDE3A activity to prevent functional deterioration and compensatory remodelling induced by chronic biomechanical stress by stimulating ANP release from cardiac myocytes, and consequently enhancing paracrine and endocrine activities of ANP. Accordingly, we propose PDE3A to negatively regulate ANP release from cardiac myocytes.

Keywords: cAMP/cGMP signaling
Cardiac hypertrophy
Heart failure
Phosphodiesterases
Advisor: Backx, Peter H
Membrane Leakage and Antimicrobial Activity of Nylon-3 Polymers and Surfactants

This study was part of an effort to gain insight into biological modes of action of membrane-active antimicrobial agents with vesicle leakage experiments. Specific systems tackled here were three nylon-3 type polymers, introduced by Prof. S.H.Gellman's group (U of Wisconsin at Madison), which have shown great potential to serve as antibacterials and fungicides. A comprehensive set of vesicle leakage experiments, performed on different lipid models, included (i) the fluorescence lifetime-based leakage assay, which yields not only the active concentration but also the mechanism of leakage (ii) kinetics of leakage, and (iii) concerted action tests with detergents. Results suggest that there are different, characteristic vesicle leakage patterns that can be assigned to specific modes of action. Vesicle data often, but not always, correlates with biological activity. We speculate that the correlation may depend on the type of leakage - some mechanisms of vesicle disruption may be more directly relevant in vivo than others.

Keywords: antimicrobial peptide
efflux
fungicide
lipid clustering
liposome
synthetic antimicrobial peptide mimic
Advisor: Heerklotz, Heiko H
Electrochemical Detection of Halides Using a Matrix Containing Silver Nanoparticles

Silver nanoparticles (AgNPs) have many applications in electrochemical studies. Modifying an electrode using AgNPs in a matrix (ie. chitosan) can change the electrochemical properties of a system. In this thesis, we developed an analytical technique based on cyclic voltammetry for the detection of small molecules and halide ions, specifically chloride, in solution using glassy carbon electrodes. Using a more basic fundamental study this technique builds upon work reported by Compton1 on the detection of chloride ions in sweat. After deposition and drying of a chitosan/AgNP film on the electrode, we were able to detect an electrochemical signal change in the presence of various ions at concentrations as low as the nanomolar range. For chloride detection we observed a peak at a potential of ca. 0.3 V while for bromide a similar current appeared at ca. 0.1 V. We investigated the dependence of this technique on the following parameters: pH, analyte concentration, and AgNP morphology.

Advisor: Kraatz, Heinz-Bernhard
Design, Development, and Calibration of a 3D Sensory System for Surface Profiling of 3D Micro-scale Parts

This thesis first presents the development of the SL sensory system and the extensive experiments to verify the use of the SL sensory system for measuring macro-scale 3D parts. This thesis further presents the development of a SL sensor system for Micro-scale applications. A novel calibration method for micro-scale applications is presented to determine the overall SL system calibration parameters. The method includes a novel calibration model which explicitly considers the microscope lenses parameters for the hardware components (camera and projector) as well as addresses the limitation of narrow DOF behaviour of these lenses. The latter is achieved by incorporating an image focus fusion technique. The proposed approach is implemented and tested on a designed SL system. The measurement ability of the SL sensory system was provided by measuring micro-scale features. The measurements results demonstrate great potential for using this sensory system in obtaining 3D information of micro-scale complex parts.

Keywords: 3D Sensing
Analytical Calibration
Micro-scale
Microscope
Phase shifting
Structured Light Technique
Advisor: Nejat, Goldie
The Effect of Adsorption on Energy Transport at a Solid-Vapour Interface

An apparatus was configured to measure steady-state energy transport between ethanol vapour and a polished copper surface. The magnitude of energy transport increased with pressure until the ratio of the vapour pressure to its saturation pressure reached 0.2. The adsorption of ethanol on copper was measured and the energy transport was found to strongly increase with adsorption until approximately 4 mol/m

Keywords: Adsorption
Ethanol
Heat Transfer
Interfacial
Isotherm
Vapour
Advisor: Ward, Charles A
Mechanical Insult Uncouples the Protective Function of PEA15 on Extracellular Matrix Remodeling and Apoptosis

Glaucoma is an optic neuropathy in which the eye's intraocular pressure can become elevated and exert mechanical insult on the optic nerve head (ONH). This leads to dramatic ONH remodeling, astrocyte activation, and retinal ganglion cell death, causing vision loss. Proteomic analysis of human ONH astrocytes exposed to pathologically relevant mechanical insult revealed increased phospho-protein enriched in astrocytes (PEA15). PEA15 plays roles in extracellular matrix (ECM) remodeling and apoptosis, however this has yet to be explored in the context of glaucoma. PEA15 demonstrated protective function by decreasing levels of matrix metalloproteinase 2 (MMP2) and apoptosis. However, mechanical insult uncoupled the protective functions of PEA15 leading to increases in MMP2 and apoptosis. Phosphorylation of serine 104 on PEA15 was shown to be critical in uncoupling these protective functions as mutation of this residue rescued anti-apoptotic activity and suppression of MMP2. Overall glaucomatous mechanical insult appears to abrogate protective functions of PEA15 in apoptosis and ONH remodeling.

Keywords: Apoptosis
Astrocytes
Extracellular Matrix Remodeling
Matrix Metalloproteinase 2
Mechanical Insult
PEA15
Advisor: Sivak, Jeremy M
Microfluidic Bioprinter for Hydrogel Sheet Formation

We present a microfluidic bioprinter that is compatible with a wide range of biopolymers and is able to continuously or periodically produce intact homogeneous or heterogeneous hydrogel sheets in Couette flow condition with different throughputs through different cross-linking mechanisms with control over the sheet geometries and mechanical properties. The printer includes a movable platform to achieve the automated production, collection and transportation of the hydrogel sheets, a microfabricated printing device that defines the geometry and composition of the printed hydrogel sheets, pressure controls upstream for introducing biomaterials with different flow rates, and temperature features to fulfill the thermal requirement during the material processing. According features can be enabled for different gelation mechanisms including ionic cross-linking gelation and thermal gelation. Using the concept of Couette flow with controls over printing parameters, homogenous and heterogeneous hydrogel sheets with different geometries and mechanical properties can be produced as predicted using the theoretical model.

Keywords: biopolymer
bioprinting
gelation
hydrogel
microfluidic
Advisor: Guenther, Axel
Effect of Pulses in a Low Glycemic Index Diet on Renal Function in Participants with Type 2 Diabetes mellitus

Dietary pulses are rich sources of protein, dietary fiber and are amongst the lowest glycemic index (GI) foods. We hypothesized that addition of pulses to a low GI (LGI-pulse) diet in participants with type 2 diabetes mellitus may be associated with improvement in renal markers resulting from replacement of animal by plant (pulse) protein. We attempted to develop a low GI pulse bread for use in therapeutic diets. The pulse bread had a low GI but lacked the required palatability. We determined the effect of increased plant protein intake on markers of renal function. We included 109 participants with type 2 diabetes mellitus who completed the diet. Pulses as part of a low GI diet in participants with type 2 diabetes mellitus did not adversely affect markers of renal function.

Keywords: Dietary pulses
Glycemic index
Renal function
Type 2 diabetes mellitus
Advisor: Jenkins, David JA
Darling, Pauline B
Fluid Dynamics and Biofilm Removal Generated by Syringe-delivered and Two Ultrasonic-assisted Irrigation Methods: A Novel Experimental Approach

Introduction: This study aimed to develop a standardized root canal model to study fluid/irrigation dynamics and biofilm elimination. Methods: A maxillary incisor with an instrumented canal was replicated in soft lithography-based models. Canals were irrigated using a syringe (SI) and two ultrasonic-assisted methods: intermittent (IUAI) and continuous (CUAI). Real-time fluid movement within the apical 3 mm of canals was imaged using micro-particle image velocimetry. Canals were inoculated with Enterococcus faecalis to grow 3-week-old biofilms. Biofilm reduction by irrigation was assessed. Results: CUAI generated the highest overall velocity and shear stress of all the groups in the apical 0-3 mm. Biofilm was significantly reduced compared to the control only by CUAI (p=0.005). Conclusions: CUAI exhibited the highest mechanical effects of fluid flow in the apical 3 mm, which correlated with significant biofilm reduction. The soft lithography-based models provided a novel model/method for study of root canal irrigation.

Keywords: Biofilm
Irrigation
Root canal
Ultrasonic
Advisor: Kishen, Anil
The Role of the ErbB2/Neuregulin Signaling Network in Regulating Acute or Chronic Nerve Regeneration and its Application to the Protection Provided by Side-to-side Nerve `Bridges'

Functional outcomes following peripheral nerve injuries are profoundly inhibited by the harmful consequences of chronic denervation. Surgical strategies that employ side-to-side nerve `bridges' can protect against chronic denervation. We hypothesize that this protection results from the activity of the Schwann cell mitogen Neuregulin-1 and its receptor ErbB2. A detailed histological assessment in the first series of experiments demonstrated typical patterns of axon regeneration, myelination and changes in Schwann cell phenotype, which implicate neuregulin signaling in directing Schwann cell behaviour in the `protected' denervated stump. The second and third experimental series examine regeneration following acute and chronic denervation in the presence of an inhibitor to the neuregulin receptor, ErbB2. Motoneuron and myelinated fiber regeneration is paradoxically enhanced in addition to increased cellular proliferation in the distal nerve. This effect may result from a newly described inhibitory association between ErbB2 and epidermal growth factor receptor (EGFR).

Keywords: ErbB2
Herceptin
Nerve Regeneration
Neuregulin
Peripheral Nerve
Side-to-Side Nerve Bridges
Advisor: Borschel, Gregory H
Gordon, Tessa
Palladium-catalyzed Carbohalogenation of Sterically Congested Alkynes: An Intramolecular Approach to the Synthesis of Vinyl Halides

Pd catalyzed cross coupling reactions are extensively used to effect a multitude of organic transformations. The recent advent of carbon-halogen reversible oxidative addition has introduced C-X bond forming as a viable catalytic process. These carbohalogenation reactions are ideal because the reactive halide functionalities are retained in the products, however several limitations in the methodology still remain. Specifically, carbohalogenations using aryl bromides and chlorides and the formation of vinyl halide products are desirable transformations that have been elusive. Cyclopropene substrates were initially examined as intermolecular carbohalogenation coupling partners but these substrates were not found to be amenable to carbohalogenation. The focus shifted to using alkynes as intramolecular coupling partners. These substrates were found to successfully undergo cyclization, forming vinyl halide products. Additionally, aryl iodides, bromides and chlorides all react to form the corresponding vinyl halides. The reaction parameters were examined, a substrate scope was developed and mechanistic studies were performed.

Keywords: Carbohalogenation
Catalysis
Palladium
Steric Bulk
Advisor: Lautens, Mark
Contribution of Rare Copy Number Variants to the Development of Autism Spectrum Disorder in High-risk Siblings

As microarrays are commonly used to identify the causes of autism spectrum disorder (ASD) we are investigating whether genetic testing in young children can predict ASD status prior to the typical age of onset of symptoms. A total of 441 individuals (190 probands, 88 siblings with ASD, 163 unaffected siblings) from the Infant Siblings Research Consortium were genotyped on the high-resolution Affymetrix CytoScan HD platform. De novo and inherited presumed pathogenic CNVs were identified in 23/199 families (11.4%). In 6 of these families, the index case and one or more siblings carried the presumed pathogenic CNV; in every such case the carrier individual either had ASD (4) or had a subclinical form of ASD (2). There were 6 additional families in which CNV data would have been informative for early ASD diagnosis or detection of developmental delay. Our results suggest CNVs may serve as biological markers for ASD.

Keywords: Autism
Copy Number Variation
High-Risk Siblings
Microarray
Advisor: Scherer, Stephen W
Hippocampal Subfield Volumes and Relations to Associative Memory in Children and Adolescent Survivors of Pediatric Brain Tumors

Pediatric brain tumor survivors (PBTS) treated with cranial radiation therapy (CRT) experience debilitating cognitive deficits, including impaired learning and memory. These impairments may be linked to volume abnormalities in the hippocampus. Animal studies suggest that radiation induces memory impairments in part, by disrupting neurogenesis in the hippocampal dentate gyrus. However, the effects of CRT on hippocampal subfields and relations to impaired memory in humans remain unknown. We used MRI and segmented hippocampal subfields (CA1, CA2/3, dentate gyrus/CA4, stratum radiatum, lacunosum, moleculare (SR/SL/SM) and subiculum) in PBTS and typically developing children using an automated segmentation tool. Hippocampal subfield volumes in PBTS were assessed in relation to memory performance. We observed that PBTS displayed smaller dentate gyrus/CA4, CA1, and SR/SL/SM volumes compared to typically developing children. Moreover, smaller dentate gyrus/CA4 and SR/SL/SM volumes correlated with lower memory performance. These findings suggest that damage to hippocampal subfields may in part underlie memory deficits in PBTS.

Keywords: associative memory
cranial radiation
hippocampal subfields
neurodevelopmental abnormalities
pediatric brain tumor survivors
Advisor: Mabbott, Donald J
Coping Strategies and Skills Through Adjustment and Transition: A Study of New and Professional Immigrants in Canada

The present study explored the lived experience of new and professional immigrants in Canada, and the coping skills and strategies they employed through life-career adjustment and transition. A qualitative methodology examined in-depth transcripts that were analyzed using a grounded theory approach to data analysis. The findings reflected the use of engagement coping, which included primary control coping (i.e. social support and action-taking â networking, retraining/re-education, seeking out resources), secondary control coping (i.e. adaptability and positivity), as well as proactive coping, religious coping and an external form of coping (i.e. luck). The implications of these findings extend to the field of coping psychology, immigrant adjustment and vocational psychology. Moreover, this research applies to those in helping professions (i.e. counsellors) who can better facilitate the population of new and professional immigrants with an increased understanding of the challenges they face and the coping strategies that facilitate their transitional process.

Advisor: Chen, Charles P
Auto-tuned Near Minimum-deviation Digital Controller for Hard Switching DC-DC Converters

This thesis presents a practical auto-tuned digital controller applicable to various kinds of hard switching dc-dc converters. Controller consists of three main functional blocks: i) an output current estimator which can obtain the instantaneous load current value for both direct and indirect energy transfer converters, ii) a conventional digital compensator for steady state regulation and, iii) a nonlinear digital module for fast transient response to minimize voltage deviation.

Keywords: controller
Converters
dc-dc
deviation
digital
mixed-signal
Advisor: Prodic, Aleksandar
The Effects of Matrix Metalloproteinases on Fetuin's Role as an Inhibitor of Transforming Growth Factor-beta1

Periodontitis may increase the risk of developing cardiovascular diseases, yet mechanisms of this association are undefined. Transforming growth factor beta-1 (TGF-β1) has both atheroprotective and atherogenic roles. Fetuin, a serum glycoprotein, binds and inhibits TGF-β1, which may affect atheroma formation. Some matrix metalloproteinases (MMP) elevated in periodontitis are known to cleave fetuin. We hypothesized that fetuin cleavage by MMPs may reduce fetuin’s ability to inhibit TGF-β1. SDS-PAGE, densitometry and mass spectrometry confirmed bovine fetuin was degraded by MMP-2, 3, 7, and 9 (MMP:fetuin=1:60), identifying unique cleavages. TGF-β1 activity at 2ng/mL was assessed with intact or MMP-cleaved fetuin utilizing a cell growth assay. TGF-β1 inhibited cell growth by 28.6%. Intact fetuin, at 1mg/mL and higher, reduced TGF-β1 inhibition of cell growth to 19.8%. MMP-7-cleaved fetuin, at 0.2mg/mL, significantly reduced the TGF-β1 inhibition to 8.6%. Thus, MMP-7 cleavage of fetuin enhances fetuin’s ability to inhibit TGF-β1.

Keywords: BMP
Cardiovascular
Fetuin
Periodontitis
TGF-beta
Advisor: Peel, Sean
Proton Conducting Ionic Liquid-polymer Electrolytes for Solid Electrochemical Capacitors

Electrochemical capacitors (ECs) are energy storage devices with high power density and high efficiency, but their liquid electrolytes can contain environmentally unfriendly compounds and are vulnerable to leakage. Ionic liquids (ILs) provide non-volatile ionic conductivity in flexible polymer electrolytes, which can alleviate these issues. The ILs 1-ethyl-3-methylimidazolium hydrogen sulfate (EMIHSO4) and 1-methylimidazolium hydrogen sulfate (MIHSO4) were combined into a binary mixture with a deeply depressed melting point, and a phase diagram was constructed after thermal analysis. On ruthenium dioxide electrodes, 70-30 wt% EMI-MIHSO4 showed an increase in capacitance of about 75% over that of neat EMIHSO4, demonstrating its proton activity. The binary IL mixture was incorporated into a polyvinyl pyrrolidone polymer matrix to form polymer electrolytes that showed good electrochemical performance and rate capability under electrochemical impedance spectroscopy and cyclic voltammetry. On ruthenium dioxide electrodes, the PVP-EMI-MIHSO4 electrolyte showed a 30% improvement in capacitance over PVP-EMIHSO4.

Keywords: electrochemical capacitor
energy storage
ionic liquid
polymer electrolyte
pseudocapacitor
supercapacitor
Advisor: Lian, Keryn
Forms of Technology-facilitated Sexual Violence and University Women's Psychological Functioning

Technology-facilitated sexual violence (TFSV) is an emerging social and public health issue that can significantly impact those who experience it, yet our knowledge and understanding of this issue is limited. Despite the abundance of research addressing offline sexual violence, comparatively little attention has been paid to online sexual violence. With a growing emphasis on the use of technology on campuses and university women being both avid users of technology and overrepresented as victims of sexual violence (Stermac, Del Bove, Brazeau, Bainbridge, 2006), university women are at an increased risk of experiencing TFSV. Using an online self-guided study, this research investigated the forms and characteristics of TFSV being experienced by university women and their association with womenâ s wellbeing. Results indicate that technologies are being used to victimize women in a variety of ways and these experiences are associated with feelings of depression, anxiety, stress and symptoms of post-traumatic stress disorder.

Advisor: Stermac, Lana