VictorJuiz/thesis huggingface dataset:
Investigating the Validity of UV Reactor Additivity

Ultraviolet (UV) light reactors or banks are often arranged in series in order to meet microbial inactivation credit requirements. It has been assumed that UV doses given by each reactor in series are mathematically additive, though work done to substantiate the hypothesis has been inconsistent. Based on previously developed theory of reactor additivity and the reactor additivity factor (RAF), three types of UV reactors are modelled using computational fluid dynamics and their RAFs are computed. It is noted that the assumption of perfect mixing may not be valid depending on the distance between reactors in series. It is discussed that the original formulation of the RAF is inadequate when dealing with wastewater. It is shown unexpectedly that even with perfect mixing performance, worse than additivity would be achieved. A new performance factor (PF) is introduced and the implications of this are further discussed in the context of UV reactor validation.

Keywords: uv reactor performance
reactor additivity
Advisor: Lawryshyn, Yuri Andrew
Deep Grey Matter Growth and Neurodevelopmental Outcomes in Very Preterm Children

Definition of neurodevelopmental outcome from early brain imaging remains a priority for survivors of very preterm (VPT) birth given their persistently high rates of cognitive and motor difficulties. Volumes of the deep grey matter (DGM) structures were measured longitudinally using magnetic resonance imaging from 96 VPT infants studied within 2 weeks of birth and 70 at term-equivalent age. At 4 years of age, 36 children returned for neuropsychological assessments evaluating IQ, language function, and visual motor integration. Multiple hierarchical regressions examined associations of DGM growth with neuropsychological measures. Overall DGM growth, primarily attributed to the caudate and thalamus, predicted Full Scale IQ, core language and VMI scores after controlling for sex and total brain volume. Thalamic growth was additionally associated with measures of neonatal clinical severity, bronchopulmonary dysplasia, and white matter lesions. Longitudinal growth of the DGM, particularly the caudate and thalamus were established as early markers of long-term outcomes.

Keywords: Magnetic Resonance Imaging
Preterm birth
Cognition
Advisor: Taylor, Margot
Functional Expression of a Blue Fluorescent Protein - Photoactive Yellow Protein Fusion in HEK293 and E. coli

Photocontrol, the use of light-sensitive proteins to control events within living tissue, allows complex processes in higher organisms to be studied. The Halorhodospira halophila photoactive yellow protein (PYP) can be used to regulate transcription factor activity with blue light. Before any PYP-based system can probe complex processes in higher organisms, proof of functional expression in vivo is required. We linked d25 PYP to the C-terminus of blue fluorescent protein (BFP) and expressed variants of the fusion protein (BFPd25PYP) in E. coli and human embryonic kidney (HEK293) cells. Expression of BFPd25PYP in E. coli verified in vitro photoswitching. The fusion protein was successfully expressed in HEK293. Fluorescence studies of intact cells indicated chromophore uptake and incorporation into PYP in HEK293, while photoswitching of PYP was measured in protein isolated from HEK293. These findings are promising for the development of applications using PYP for in vivo mammalian photocontrol of biological events.

Keywords: Photoactive Yellow Protein
PYP
BFP-fusion
Photo-control
Fluorescence quenching
Mammalian expression
Advisor: Woolley, Andrew
Dodec: A Random-link Approach for Low-radix On-chip Networks

Network topologies play a vital role in chip design; they largely determine the cost of the network and significantly impact performance in many-core architectures. We propose a novel set of on-chip networks, dodecs, and illustrate how they reduce network diameter with randomized low-radix router connections. In addition, we design an adaptive routing algorithm for dodec networks to achieve high throughput. By introducing randomness, dodec networks exhibit more uniform message latency. By using low-radix routers, dodec networks simplify the router microarchitecture and attain 20% area and 22% power reduction compared to mesh routers while delivering the same overall application performance for PARSEC. We compare our dodec network to alternative low-radix network topologies and show that at the same cost, dodec networks increase the throughput up to 50% while reducing average latency by 10% compared to a mesh.

Keywords: on-chip network
network topology
random-link
low-radix
Advisor: Jerger, Natalie Enright
Systematic Analysis of Suppressor Mutations in S. cerevisiae Strains with Deleted Genome Integrity Genes

The effects of a mutation in one gene can occasionally be suppressed by mutation in another gene. Genetic suppression indicates functional relationships and provides clues about the mechanism and order of action in genetic pathways. Here I explored the existing yeast deletion collection to identify suppressor relationships. The collection was released in 2000 and it is known that some strains in the collection have acquired mutations. Whole genome sequencing of 48 yeast deletion strains corresponding to 26 genome integrity genes was performed. High-throughput sequencing revealed a broad mutational spectrum including point mutations, indels, and copy number variations. I identified and experimentally validated two new suppressor mutations (sgs1 mutations in both top3Δ and rmi1Δ strains) corresponding to gene pairs with previously known suppressor relationships. Thus, high-throughput sequencing and analysis of yeast deletion strains can identify suppressor mutations. The resulting genome sequences also provide a baseline for future laboratory evolution experiments.

Keywords: suppressor mutation
next-generation sequencing
deletion strain
DNA repair
mutation spectrum
Advisor: Roth, Frederick
Towards Application of Selectively Transparent and Conducting Photonic Crystal in Silicon-based BIPV and Micromorph Photovoltaics

Selectively-transparent and conducting photonic crystals (STCPCs) made of alternating layers of sputtered indium-tin oxide (ITO) and spin-coated silica (SiO2) nanoparticle films have potential applications in micromorph solar cells and building integrated photovoltaics (BIPVs). In this work, theoretical calculations have been performed to show performance enhancement of the micromorph solar cell upon integration of the STCPC an intermediate reflector. Thin semi-transparent hydrogenated amorphous silicon (a-Si:H) solar cells with STCPC rear contacts are demonstrated in proof-of-concept devices. A 10% efficiency increase in a 135nm thick a-Si:H cell on an STCPC reflector with Bragg peak at 620nm was observed, while the transmitted solar irradiance and illuminance are determined to be 295W/m2 and 3480 lux, respectively. The STCPC with proper Bragg peak positioning can boost the a-Si:H cell performance while transmitting photons that can be used as heat and lighting sources in building integrated photovoltaic applications.

Keywords: amorphous silicon solar cell
one dimensional photonic crystal
bragg reflector
building integrated photovoltaics
micromorph
Advisor: Kherani, Nazir P.
Modeling, Fabrication, and Characterization of a Bragg Slot Waveguide with a Cavity

This thesis encompasses a theoretical analysis, the fabrication, and optical characterization of a novel compact Bragg Slot Waveguide with a Cavity (BSWC). Strong light confinement in the low refractive index slot region formed by two silicon slabs on a silicon dioxide substrate [1] makes this structure useful for optofluidic, sensing, and optical trapping applications. The transmission spectrum of the BSWC can be engineered through the dimensional variations of the waveguide and through the refractive index change of the surrounding medium. BSWC is compact and can be integrated with various components on a chip for increased functionality. The results in this thesis show a good agreement between analytical and experimental results, while emphasizing the increasing importance of atomic-scale imperfections as a result of fabrication on the nano-scale. The impact of the slot width, slab width, and the cavity length on the waveguide transmission spectrum is investigated.

Keywords: slot waveguide
photonics
Advisor: Aitchison, J. Stewart
The Maternal Immune Activation Mouse Model of Autism Spectrum Disorders

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social interaction and communication as well as ritualistic repetitive behaviors. Epidemiological studies suggest that maternal immune activation (MIA) during pregnancy may be a risk factor for ASD. To study MIA in a laboratory setting, we injected mouse dams (C57BL/6) with lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (Poly IC) during mid-gestation to mimic a bacterial or viral infection, respectively. We also performed the same Poly IC treatment on a mouse model of Fragile X syndrome (i.e. Fmr1 knockout), a genetic disease with high incidences of ASD. We found modest female-specific impairments in social interaction and striking male-specific increases in repetitive behavior in adult MIA offspring. Moreover, prenatal Poly IC treatment caused genotype-specific deficits in sociability in addition to reduced body weight and rearing in Fmr1 knockout mice only. Therefore, ASD-related behaviors caused by MIA may be sex, treatment, and/or genotype-dependent.

Keywords: Autism Spectrum Disorder
Fragile X Syndrome
Advisor: Hampson, David R.
Development of Lightweight, Biodegradable Plastic Foam Fibres with Poly (Lactic) Acid-clay Nanocomposites

Polymeric fibres influence our everyday life in numerous aspects; the area of applications ranges from industrial to everyday commodities, textile and non-textile. As the global demand for the polymeric fibres increases rapidly, new innovative classes of fibres and the manufacturing processes are sought after. This thesis develops an approach to produce fine cell structure and low void fraction foams, which is then used in the manufacturing of lightweight, biodegradable foam fibres. Poly (lactic) acid-clay nanocomposite have been foamed with nitrogen and drawn to different melt draw ratio to produce foam fibres. The foam fibres are then characterized for crystallinity, Young’s modulus and the yield stress. While the drawability of foam has been demonstrated, the crystallinity as well as the mechanical properties of the foam fibres are not drastically enhanced by drawing, as would be expected. Further drawing processes of the as-spun foam fibres are recommended.

Keywords: Plastic foam manufacturing
Fibre spinning
Foam fibre
PLA
Nanoclay
Biodegradable
Foam drawability
Advisor: Park, Chul B.
Partial Nephrectomy for the Treatment of Renal Cell Carcinoma and the Risk of End Stage Renal Disease

The surgical management of renal masses involves either radical nephrectomy (RN) or partial nephrectomy (PN). The relationship between treatment choice and definitive outcomes of CKD are lacking. Our aim was to examine whether PN is associated with a lower risk of end-stage renal disease (ESRD) requiring renal replacement therapy (RRT). We performed a population-based, retrospective cohort study with data from administrative databases in the province of Ontario, Canada. We included individuals with renal cell carcinoma diagnosed between 1995 and 2010. Cox proportional hazards, propensity score, and competing risks models were used to assess the impact of treatment. PN compared to RN reduces the risk of ESRD in a modern cohort of patients (2003-2010). PN is associated with a lower risk of CKD, reduced cardiac morbidity, and improved overall survival. We provide further evidence for the benefit of PN compared to RN, particularly related to definitive outcomes of renal failure.

Keywords: kidney
cancer
dialysis
surgery
Advisor: Alibhai, Shabbir Muhammad Husayn
Characterizing the Impact of Helicobacter pylori Infection on the Host Exosome Pathway

Helicobacter pylori is a gram-negative bacterium that infects half the world population and is the etiological cause of numerous gastric pathologies. H. pylori possess numerous mechanisms to promote its survival and modulate host immunity. We propose that H. pylori can modulate intercellular communication by manipulating the host exosome pathway. Exosomes are secreted nanovesicles that contain different proteins and microRNAs that can be transferred between cells to alter cell signaling and gene expression. We demonstrate that H. pylori infection increases host exosome secretion. Furthermore, infection can alter exosome composition as VacA, a bacterial virulence factor, can be exported in exosomes and Argonaute 5, a miRNA effector protein, is upregulated in exosomes during infection. Lastly, we show preliminary evidence that infection-modulated exosomes can modulate immune-regulatory signaling in dendritic cells by activating STAT3. Together, these studies elucidate a novel mechanism by which H. pylori can modulate the host environment and promote its continued survival.

Keywords: Autophagy
Helicobacter pylori
Exosomes
microRNAs
Advisor: Jones, Nicola L.
The Role of Ubiquitin on Yeast Proteasome Dynamics in Quiescence

The ubiquitin-proteasome system regulates protein degradation. Although proteasomes localize in the nucleus of proliferating Saccharomyces cerevisiae, they are sequestered into cytoplasmic proteasome storage granules (PSG) in quiescence. Although important for cell cycle regulation and mediating external stressors, the content and structure of these membraneless PSGs remain unknown. Yeast deletion genetic screens identified several ubiquitin-related genes involved in proteasome sequestration into PSGs. This study aims to determine whether changes in free ubiquitin levels or ubiquitin post-translational modifications affect proteasome dynamics in quiescence. Unlike the wild-type, PSGs were not seen in catalytically inactive Ubp6 mutant strains in quiescence and proteasomes failed to be imported into the nucleus upon the resumption of cell growth. Although no significant differences in proteasome configurations were observed, Western blot analysis of these mutants suggests the presence of post-translationally modified monoubiquitinated proteasomes in quiescence. Ubiquitin modification may target proteasomes towards lysozomal degradation rather than into PSGs for storage.

Keywords: proteasome
ubiquitin
quiescence
Advisor: Enenkel, Cordula
Effect of Alpha-linolenic Acid on Growth of Breast Cancer Cells with Varying Receptor Expression and Estrogen Environments

Breast cancer molecular subtypes, based on expression of estrogen, progesterone and human epidermal growth factor 2 receptors, alter prognosis and treatment options. &alpha;-linolenic acid (ALA) is a complementary therapy, however its effectiveness across breast cancer types and estrogen environments is unclear. This research determined the effect of ALA on growth, apoptosis, fatty acid profile, and gene changes in four breast cancer cell lines with varying receptor expression with or without (&plusmn;) estradiol (E2). ALA (50-200uM) &plusmn; E2 reduced growth in all cell lines. 75&mu;M ALA +E2 increased phospholipid % ALA in all cell lines and induced apoptosis in cell lines lacking the three receptors. Cellular % ALA was positively associated with apoptosis and inversely associated with cell growth. ALA altered expression of cell cycle, apoptosis and signal transduction genes. In conclusion, ALA incorporates into breast cancer cells, reduces growth and induces apoptosis regardless of receptor status or E2 level.

Keywords: breast cancer
nutrition
n-3 PUFA
flaxseed oil
alpha-linolenic acid
estrogen
Advisor: Thompson, Lilian
Transmembrane Helix-Helix Interactions in a Bacterial Small Multidrug Transport Protein

EmrE from Escherichia coli is a member of the small multidrug resistance protein family that oligomerizes to export hydrophobic cationic antimicrobials by utilizing the proton motive force. We studied the helix-helix interactions of the four transmembrane (TM) segments of EmrE to determine how this protein might assemble into its oligomeric forms. Using a combination of biochemical and biophysical techniques, we assessed the oligomerization propensities of Lys-tagged EmrE TM peptides in membrane-mimetic environments. Our results established that each of the TMs of EmrE display detergent-sensitive self-association, but in particular, TM2 had the greatest dimerization capability that was not completely abolished even by scrambling the native sequence. Mutations made to TM2 in full-length EmrE also revealed that efflux-defective mutations are located on one face of the helix. These findings reveal another potential oligomerization site for EmrE - and perhaps SMRs - and may provide a target for development of novel efflux-inhibitors.

Keywords: Membrane protein
Peptide
Advisor: Deber, Charles M.
Spatially Enhanced Local Binary Patterns for Face Detection and Recognition in Mobile Device Applications

Face detection and recognition has been very popular topics. Recently, its applications for mobile devices have gained tremendous attention due to the rapid expansion of the market. Although numerous techniques exist for face detection and recognition, only a few solve realistic challenges under the mobile device application environment. In this thesis, we propose an automatic face authentication system including both face detection and recognition components for mobile device applications by using spatially enhanced Local Binary Patterns (LBP) feature extraction. The first contribution is to propose a fast and accurate face detector by using LBP features and its spatially enhanced variant. The simplicity of LBP ensures low computational complexity and spatially enhanced LBP achieves high accuracy. The second contribution is to propose color based spatially enhanced LBP features for face recognition. The proposed features achieve high accuracy by extracting complementary information from color channels and spatial correlations between LBP features.

Keywords: Communications
Signal Processing
Image Processing
Machine Learning
Pattern Recognition
Face Detection
Face Recognition
Local Binary Patterns
Advisor: Plataniotis, Konstantinos N.
Harmonic Oscillations in Optical Waveguide Arrays

The analogy of optical system to other physical systems has been attracting much attention over the past decades. In coupled optical lattices, phenomena originated from electronic systems, such as Bloch oscillations, Dynamic localization and Zener tunneling, have been extensively investigated and led to novel research directions and applications. Following this idea, harmonic oscillations are spatially mimicked by the propagation of supermodes in quadratically-coupled waveguide arrays. By analyzing the field envelope with the propagation constants and the superposition of the supermodes, we achieve conjugate-imaging at the half-period plane and self-imaging at the full-period plane, which give rise to the linear switching. Combining the linear switching and the nonlinear light propagation triggered at high power level, we demonstrate the superior performances of nonlinear power switching compared with traditional nonlinear directional couplers. Through the linear and nonlinear observation on AlGaAs waveguide array, we present the first experimental proof of the harmonic oscillations in optical waveguide arrays.

Keywords: Harmonic Oscillations
Optical Waveguide
AlGaAs
Nonlinear Switching
Linear Switching
Advisor: Aitchison, J. Stewart
Left Atrial Phasic Function during Exercise: The Role of Atrioventricular Coupling

Left ventricular (LV) filling increases during exercise, but left atrial (LA) phasic function and its contribution to LV filling is poorly understood. Sixteen endurance-trained middle-aged males were studied at rest and during light (LE) and moderate (ME) intensity cycle-ergometry. Atrioventricular-plane displacement (AVPD) increased from rest to LE (from 14±2 mm to 18±2 mm, p<0.01), but did not increase further at ME. LA reservoir volume increased from rest to LE (from 32±8 mL to 40±10 mL, p<0.01). LA passive contribution increased at LE (from 21±5 mL to 27±8 mL, p<0.01), while LA active contribution increased from rest only at ME (from 12±5 mL to 23±9 mL, p<0.01). AVPD, and thus the longitudinal shortening of LV systole, contributes to LA filling primarily during LE, but is a limited mechanism beyond LE. These data suggest that LV filling appears to shift to a reliance on conduit function to increase LV filling at ME.

Keywords: cardiovascular
cardiac function
exercise
aging
Advisor: Goodman, Jack
Modelling Intercity Travel Demand in the Quebec City – Windsor Corridor: A Study on the Effects of Local Accessibility Utilizing a Geographically Disaggregated Web-based Approach

This thesis presents a novel approach to evaluating intercity travel demand given the introduction of a new travel mode. A joint RP-SP survey is designed to collect both experienced and hypothetical travel decisions. The stated preference aspect of the survey evaluates the level-of-service attributes that influence intercity mode choice. Emphasis is placed on the effects of local accessibility by adapting a geographical disaggregation at the Forward Sortation Area (FSA). Survey distribution collected data primarily through the use of online social networks such as Facebook and Reddit in addition to an online marketing research survey panel. Intercity mode choice was modeled with Random Utility Maximizing (RUM) discrete choice models and is represented by Multinomial Logit (MNL) and Nested Logit (NL) choice structures. Key finding is that access to transit stations significantly influences intercity mode choices.

Keywords: survey
travel demand
transportation
Advisor: Habib, Khandker
The Role of NSAIDs in Impaired Osseointegration in Dental Implant Prosthodontics

Objective: To appraise whether adverse events following oral implant placement may be associated with peri-operative use of non-steroidal anti-inflammatory drugs (NSAIDs). Methods: All patients with recorded implant failures between 1979 and 2012 in the Implant Prosthodontics Unit were contacted to solicit additional information about potential peri-operative use of NSAIDs. Results: From a total of 168 patients with 292 implant failures between 1979 and 2012, 122 consented to participate and had intact records. Just over half (56.6%) reported no peri-operative NSAID usage. However, compared to patients who did not use peri-operative NSAIDs, four times as many had complicated medical histories and twice as many patients taking NSAIDs suffered multiple implant failures. Conclusions: Patients with a variety of systemic diseases may be adversely affected by the inhibitory effect of NSAIDs on bone healing. Further prospective clinical studies are warranted to clarify this potential causative relationship in humans.

Keywords: Dental Implants
Anti-Inflammatory Agents, Non-Steroidal
Dental Restoration Failure
Cyclooxygenase 1
Cyclooxygenase 2
Osseointegration
Advisor: Jokstad, Asbjorn