VictorJuiz/thesis huggingface dataset:
Perfluoropolyethers: Analytical Method Development for a New Class of Compounds with the Potential to be Long-lived Environmental Contaminants

Perfluoropolyethers (PFPEs) are used in a remarkably large number of industrial applications including thin-film lubricants, greases, heat transfer fluids, cosmetics, and EPA-approved food contact paper coatings and are marketed for their chemical inertness. Although desired industrially, it is also the property of most environmental concern. The lack of literature concerning the environmental impact of these compounds suggests a need to assess and characterize their environmental fate and transport. This work describes efforts to develop methods to characterize, identify and quantify various congeners of PFPEs through chromatographic, mass spectral and nuclear magnetic resonance techniques. The PFPEs exhibited unusual behavior during ionization by ESI, suggesting the possibility of structural lability during analysis. A preliminary assessment of the environmental degradation of a PFPE-phosphate congener is also described, which showed rapid sorption to sewage sludge particulate matter and the possible presence of multiple PFPEs present in the technical product mixture used for analysis.

Keywords: Fluorochemicals
Environmental Chemistry
Advisor: Mabury, Scott A.
Lung Complications in Adenosine Deaminase (ADA) Deficiency: A Mouse Model for the Human Disease

Recently, we discovered patients with inherited adenosine deaminase (ADA) deficiency are predisposed to pulmonary alveolar proteinosis (PAP). PAP is characterized by the accumulation of surfactant in the alveoli. To overcome ethical issues and limited patient samples, animal models are often utilized. Here, I investigated the lung abnormalities in ADA deficient (ADA -/-) mice, which suffer from severe hypoxia, till their death at 3 weeks. I hypothesized that, similar to ADA-deficient patients, ADA -/- mice demonstrate evidence of PAP. Indeed, electron microscopy showed thickening of type I cells, accumulation of apoptotic foamy alveolar macrophages, cholesterol and lipoproteinaceous material that is periodic-acid Schiff (PAS) positive and diagnostic of PAP. Moreover, the pulmonary abnormalities were corrected with supplementation of ADA. In conclusion, we demonstrated evidence of PAP in ADA -/- mice for the first time and their suitability to study pathogenesis of PAP in ADA deficiency.

Keywords: Adenosine Deaminase
SCID
Pulmonary Alveolar Proteinosis
Advisor: Grunebaum, Eyal
Serbian Media & the International Criminal Tribunal for the Former Yugoslavia

The International Criminal Tribunal for the Former Yugoslavia has set for itself goals that go beyond bringing perpetrators of crimes to account. Some of these functions directly depend on the media for their fulfilment, because it is precisely the media who transmits these functions to the public. This ever-increasing reliance on the media brings a need for a minimal standard of balanced reporting,which seems to be lacking in Serbia. I will examine Serbian media reporting and conclude that it does not further the Tribunals purposes, thus negatively affecting the Serbian public. I will contrast Serbian to Rwandan news reporting in order to show that a higher standard can be expected of these news outlets. Nevertheless, regardless of what kind of reporting is prevalent, the effect on the ground may not be negative if it motivates people to access other sources and thus widen their outlooks on the issues.

Keywords: ICTY, media
Advisor: Knop, Karen C.
Biofilm Formation within the Interface of Bovine Root Dentin Treated with Conjugated Chitosan and Sealer Containing Chitosan Nanoparticles

This study assessed biofilm formation within sealer-dentin interfaces of root segments filled with gutta-percha and zinc oxide sealer incorporated with chitosan nanoparticles, without and with canal surface treatments. Bovine root segments were filled using Pulp Canal Sealer incorporating chitosan nanoparticles (CS), or after surface treatment with phosphorylated CS (PHCS), chitosan-conjugated Rose Bengal (CSRB) and a combination of both (RBPH). The control group used unmodified sealer. Specimens were aged 1- or 4-weeks. Enterococcus faecalis biofilms were grown on specimens for 7days and assessed with confocal laser scanning microscopy. In the 4-week aged specimens only, the mean biofilm areas were lower than the control for CS, PHCS and RBPH. Percentage of biofilm-covered interface was lower than the control for CS and PHCS. CS, PHCS and RBPH did not differ. Incorporating chitosan nanoparticles into sealer affected inhibition of biofilm formation within the sealer-dentin interface. This was maintained with PHCS, but moderated by CSRB.

Keywords: Endodontics
Nanoparticles
Advisor: Kishen, Anil
Investigation of Inhaled Nitric Oxide and Mesenchymal Stromal Cells as Novel Therapeutic Strategies to Improve Clinical Outcome in Experimental Severe Influenza

Severe influenza, recognized as a clinical syndrome characterized by hyper-induction of pro-inflammatory cytokine production, results in approximately 250–500 thousand deaths annually worldwide. Current influenza research is focused on therapeutics to target the influenza virus or modulate influenza virus-induced inflammation as potential treatment options to improve clinical outcome in experimental influenza A (H1N1) virus infection. The goals of this work were: (1) to evaluate the utility of inhaled nitric oxide (iNO) for decreasing influenza virus production in the lungs, and (2) investigate the use of mesenchymal stromal (stem) cells (MSCs) for mitigating deleterious host responses to influenza infection. Here, we report that MSCs and iNO, administered alone either prophylactically or post-influenza virus infection, fail to modulate host inflammation, fail to improve acute lung injury, fail to dampen lung viral load, and fail to improve survival of infected mice.

Keywords: influenza A
mesenchymal stromal cells
inhaled nitric oxide
Advisor: Liles, W. Conrad
Effect of Temperature and Thermal Cycles on PZT Ceramic Performance in Fuel Injector Applications

This thesis presents an experimental analysis of the effect of temperature and thermal cycles on the performance of PZT ceramics in fuel injector applications. Due to the increase in the implementation of piezoceramics in applications such as fuel injection technology, it is imperative to understand how temperature affects piezoceramic performance. In this project, the fundamental piezoelectric properties (d_33, ε_33^T, s_33^E) of bulk PZT samples and high electric-field properties of piezoelectric stack actuators were obtained with respect to temperature and thermal cycles. The results show that increasing temperature will increase the fundamental piezoelectric properties of bulk piezoceramics, capacitance of stack actuators, and the displacement of piezoactuators in the absence of external load. Raising the temperature while applying a constant preload will initially increase piezoactuator displacement, but decrease it at higher temperatures. Temperature had a negative effect on the hysteresis in the displacement-voltage. Additionally, thermal hysteresis decreased significantly in subsequent temperature cycles.

Keywords: Piezoceramic
Temperature
Advisor: Mrad, Ridha Ben
Sinclair, Anthony
He, Siyuan
Eswar, Prasad
Emotion Perception in Borderline Personality Disorder

Borderline personality disorder (BPD) is a serious mental illness characterized by emotion dysregulation. Symptoms related to emotion are thought to contribute to difficulties in perceiving emotional expressions. Individuals with BPD and demographically matched healthy controls completed a task assessing the recognition of happy, sad, and neutral facial expressions at two intensities. Patients with BPD demonstrated comparable performance on the recognition of very happy and very sad facial expression but were significantly less accurate on neutral expressions. Patients with BPD were also significantly worse in recognizing mildly happy facial expressions, however the severity of current depressive symptoms intervened this relationship. There was evidence that perceptual biases within BPD are unique from mood-congruent biases typically found in major depressive disorder. The findings advance research on the topic of emotion perception in BPD and suggest important new lines of investigation that may be useful for delineating the nature of emotion dysregulation in BPD.

Keywords: emotion
perception
Advisor: Ruocco, Anthony Charles
Birds of a Convergent Feather: The Interrelationship between Similarity, Conflict and Cross-group Friendship Potential

I examined whether perceptions of intergroup similarity and conflict interact to predict prejudice and facilitation of an intergroup social interaction as a consequence of physiological linkage – a state correlated with successful social interactions wherein two people's autonomic nervous systems synch-up in time. Studies 1 and 2a, revealed an association between similarity, conflict and low prejudice. In Study 2b participants completed essays priming similarity and conflict in order to test the indirect effect of their interaction with participants' physiological reactivity on the success of a dyadic social interaction. Similarity, conflict and physiological reactivity interacted to predict physiological linkage, which in turn moderated the effects of conflict on the success of the social interaction. These results suggest that physiological and social cognitive processes play key roles in determining the important moment when an outgroup stranger becomes a potential friend.

Keywords: intergroup relations
cross-group friendship
similarity
conflict
dyadic
psychophysiology
Advisor: Page-Gould, Elizabeth
Impact and Adhesion of Molten Wax Droplets on Porous Polymer Surfaces

The adhesion of solid wax ink droplets to porous polyethylene and Teflon substrates was studied experimentally. Wax droplets with a diameter of 3 mm and an initial temperature of 110°C were dropped onto test surfaces. As the mean pore diameter increases, the spreading reduces. Increasing the impact velocity maximizes the wetted area of the splat. The detachment force increased with droplet impact velocity. An analytical model was proposed to predict the force attaching the wax splat to the surface. The model comprises summation of two components: An adhesive component, calculated by multiplying the contact area between the splat and substrate by the strength of adhesion; and a cohesive component, calculated by multiplying the area of the pores into which wax penetrates by the ultimate tensile strength of wax. Predictions from the model agreed reasonably well with measurements.

Advisor: Chandra, Sanjeev
Ashgriz, Nasser
Mechanisms for Range Size and Distribution Variation in the Polyploid Complex Black-fruited Hawthorn (Crataegus series Douglasianae): Biogeographic Implications for the Maintenance of Cytotype Diversity

Polyploidization is exceptionally cosmopolitan in plants. One common observation is that polyploids inhabit larger geographic distributions than their diploid progenitors. Differences in distribution between cytotypes are largely attributed to differences in mating system and ecological breadth among cytotypes. In Crataegus series Douglasianae, allopolyploids have larger ranges than their diploid progenitors. Range size increase is coupled with a shift to predominant asexuality in polyploids. This thesis explores 2 additional hypotheses that may contribute to differences in distribution among cytotypes: ecological breadth and dispersal ability. We find evidence that tetraploid C. douglasii occurs in a wider range of habits and has a greater dispersal ability than diploid C. suksdorfii. Overall, we suggest that differences in mating system, ecological breadth, and dispersal ability have contributed individually and collaboratively to differences in distribution among cytotypes of Crataegus series Douglasianae. Large ranges in polyploids may help maintain cytotype diversity by providing buffering capacity against demographic stochasticity.

Keywords: Range Size
Polyploidization
Hawthorn
Ecological Niche
Apomixis
Dispersal Ability
Advisor: Dickinson, Timothy
Stefanovic, Sasa
Quantification of Microvascular Response to Ionizing Radiation with Speckle Variance Optical Coherence Tomography

Cancer cells require access to blood vessels for oxygen and nutrients to enable growth and metastasis, making the tumour vasculature an attractive potential target for cancer therapies. Recent evidence suggests that the tumour vasculature plays a significant role in tumour response to high dose radiation therapy; however this effect is not well characterized due to limitations in quantitative imaging of the microvasculature. Speckle variance optical coherence tomography is an emerging imaging modality capable of 3D, non-invasive imaging of in vivo microvasculature. This thesis outlines the work done to test the hypothesis that svOCT imaging can be used to quantitatively monitor the vascular effects of high dose radiotherapy in a preclinical model. This was achieved through the development of a quantification pipeline for longitudinal 3-D svOCT images of microvascular radioresponse.

Keywords: optical imaging
radiobiology
Advisor: Vitkin, Alex
Non-invasive Measurement of Corticosterone in Food Restricted Rats

Blood CORT is commonly used to assess stress in rodents, but sampling can trigger a rapid stress response. This study aims to identify whether faecal CORT metabolites (FCM) can reflect changes in CORT induced by 7-day food restriction (FR) and an ACTH challenge. Blood and 24hr faecal samples were collected at baseline and Day 7 for control (n=8) and FR (n=10) rats. On Day 8, after a baseline blood sample, an ACTH injection was administered and followed by blood and fecal sampling. Results showed increased serum CORT and FCM in response to FR. Increased adrenal sensitivity with FR was illustrated by a greater increase in serum CORT compared to control in response to ACTH. Lastly, although it appeared that ACTH induced an increase in FCM in FR and control, only the latter reached statistical significance. Thus FCM might be better suited for quantifying chronic rather than acute changes in CORT.

Keywords: methodology
stress measurements
Advisor: Amara, Catherine
Freight on Transit Delphi Study

The Freight on Transit Delphi Study was conducted to explore the concept of freight on transit – using public transit vehicles and infrastructure for transporting things other than people. Three rounds of web based surveys were conducted with a panel of 34 transportation experts to explore the main issues related to freight and transit integration and to build and evaluate potential freight on transit operations. Survey results were consistent with previous investigations and suggest that organizational disputes are a larger barrier to implementation than technical challenges. Traditional Delphi questions were used to determine the most important positive impacts, negative impacts, and challenges of moving freight on transit networks while survey responses combined with scenario building techniques were used to build and evaluate five potential freight on transit operating strategies using public transit networks in the GTHA.

Keywords: Freight
Public Transit
Delphi
Urban Goods
Freight on Transit
Advisor: Roorda, Matthew J.
Shalaby, Amer Saïd
Modelling Forest Fire Initial Attack Airtanker Operations

The Ontario Ministry of Natural Resources uses airtankers for forest fire suppression that now have onboard GPS units that track their real-time location, velocity and altitude. However, the GPS data does not indicate which fire is being fought, the time each airtanker spends travelling to and from each fire or the time each airtanker spends flying between each fire and the lake from which it scoops water to drop on the fire. A pattern recognition algorithm was developed and used to determine what was happening at each point along the airtanker’s track, including the time and location of every water pickup. This pre-processed data was used to develop detailed models of the airtanker service process. A discrete-event simulation model of the initial attack airtanker system was also developed and used to show how service process models can be incorporated in other models to help solve complex airtanker management decision-making problems.

Keywords: Operations Research
Forest Fire Management
Advisor: Martell, David Lee
Learning Patch-based Structural Element Models with Hierarchical Palettes

Image patches can be factorized into ‘shapelets’ that describe segmentation patterns, and palettes that describe how to paint the segments. This allows a flexible factorization of local shape (segmentation patterns) and appearance (palettes), which we argue is useful for tasks such as object and scene recognition. Here, we introduce the ‘shapelet’ model- a framework that is able to learn a library of ‘shapelet’ segmentation patterns to capture local shape, and hierarchical palettes of colors to capture appearance. Using a learned shapelet library, image patches can be analyzed using a variational technique to produce descriptors that separately describe local shape and local appearance. These descriptors can be used for high-level vision tasks, such as object and scene recognition. We show that the shapelet model is competitive with SIFT-based methods and structure element (stel) model variants on the object recognition datasets Caltech28 and Caltech101, and the scene recognition dataset All-I-Have-Seen.

Keywords: Computer vision
Object recognition
Advisor: Frey, Brendan J.
Temporal Integration of English Words: Evidence for a Processing Hierarchy in Visual Word Recognition

Several models of visual word recognition suggest a processing hierarchy; basic orthographic features are processed early and whole-word representations are processed late in the hierarchy. Unfortunately, given the extreme efficiency of the visual word recognition system, studies typically focus on one specific level of the processing hierarchy (e.g., orthographic, phonological and/or semantic processing). Furthermore, different paradigms are used to study different levels of the hierarchy. Fortunately, data across different studies in the literature do converge to two distinct temporal thresholds for letter perception and whole-word integration. The current experiments assessed the temporal thresholds for both letter perception and whole-word integration using a single novel paradigm. The results demonstrated distinct temporal thresholds for letter perception and whole-word integration which agree with those reported in the literature. Thus, the current experiments provide further behavioral evidence that the visual word recognition is a hierarchical process.

Keywords: Word Recognition
Perception
Advisor: Joordens, Steve
Invasive Earthworm (Oligochaeta: Lumbricidae) Populations in varying Vegetation Types on a Landscape- and Local-scale

There have been no landscape-scale studies on earthworm populations in Canada comparing vegetation types; previous studies on edge habitats have been conducted in agricultural systems. I examined the spatial variations of earthworm populations by measuring abundance based on regional municipality, vegetation type, and edge habitat. Earthworms were sampled throughout the season across a gradient of vegetation types including meadow, forest edge, and interior at a local-scale; and at the landscape level with vegetation types including meadow, deciduous forest, pine plantation and mixed forest. Regional effects were more significant than vegetation type likely due to a gradient of soil characteristics in southern Ontario; edges had intermediate earthworm abundance and a higher proportion of epigeic species. My research provides insight into the patterns of earthworm populations in southern Ontario and the possible effects of edge creation through landscape fragmentation. Field sampling of earthworm parasitoid cluster-flies (Calliphoridae: Pollenia) using synomones was also discussed.

Keywords: invasive earthworms
Lumbricidae
vegetation type
Pollenia
Calliphoridae
regional
forestry
soil
ecotone
spatial
Advisor: Smith, Sandy
Whole Transcriptome Analysis Reveals Established and Novel Associations with TMPRSS2:ERG Fusion in Prostate Cancer

Shortcomings of current methods of prostate cancer detection draw attention to a need for improved biomarkers. The TMPRSS2:ERG gene fusion leads to the overexpression of ERG, an ETS family transcription factor, and is the most prevalent genetic lesion in prostate cancer, but its clinical utility remains to be defined. Two radical prostatectomy samples were analysed by next-generation whole transcriptome sequencing. The chosen samples differed in fusion gene status, as previously determined by RT-PCR. The involvement of novel and previously reported prostate cancer-related transcripts, Wnt signalling, p53 effector loss and several ETS-regulated pathways was identified in the prostate cancer cases examined. ERG was found to directly transactivate RhoGDIB, a gene associated with fusion-positive prostate cancer. Overexpression of RhoGDIB elicited spindle-shaped morphology, faster cell migration and increased cell proliferation, phenotypic changes suggestive of cancer progression. The present findings confirm the value of comprehensive sequencing for biomarker development and indicate avenues of future study.

Keywords: TMPRSS2:ERG
fusion gene
whole transcriptome analysis
RNA sequencing
prostate cancer
RhoGDIB
Advisor: Seth, Arun
Enabling Hardware/Software Co-design in High-level Synthesis

A hardware implementation can bring orders of magnitude improvements in performance and energy consumption over a software implementation. Hardware design, however, can be extremely difficult. High-level synthesis, the process of compiling software to hardware, promises to make hardware design easier. However, compiling an entire software program to hardware can be inefficient. This thesis proposes hardware/software co-design, where computationally intensive functions are accelerated by hardware, while remaining program segments execute in software. The work in this thesis builds a framework where user-designated software functions are automatically compiled to hardware accelerators, which can execute serially or in parallel to work in tandem with a processor. To support multiple parallel accelerators, new multi-ported cache designs are presented. These caches provide low-latency high-bandwidth data to further improve the performance of accelerators. An extensive range of cache architectures are explored, and results show that certain cache architectures significantly outperform others in a processor/accelerator system.

Keywords: FPGA
high-level synthesis
hardware/software co-design
LegUp
Advisor: Brown, Stephen
Anderson, Jason
GLUT2 and TAS1R2 Genotype and Risk of Dental Caries

To determine whether polymorphisms in the GLUT2 and TAS1R2 genes are associated with dental caries, 80 Caucasian individuals were recruited. A clinical and radiographic examination determined 3 caries scores: DMFT (decayed, missing and filled teeth), DMFT+radiographs and ICDAS (International Caries Detection and Assessment System). Associations between genotype(s) and caries scores were analysed. A significant increase in DMFT scores was shown in GLUT2 polymorphism carriers (i.e. GLUT2 risk). Carriers of the TAS1R2 gene polymorphism (i.e. TAS1R2 resistant) consistently demonstrated lower caries scores. Caries scores were significantly decreased in the GLUT 2 Resistant/ TAS1R2 Resistant combined group as compared to the GLUT2 Risk/ TAS1R2 Risk combined groups. Variations in GLUT2 and TAS1R2 genes are associated with risk of dental caries. A possible compounded effect of having both genetic polymorphisms is suggested.

Keywords: genetic
dental caries
Advisor: Kulkarni, Gajanan