VictorJuiz/thesis huggingface dataset:
Transcriptome Assembly and Molecular Evolutionary Analysis of Sex-biased Genes in Caenorhabditis Species 9 and Caenorhabditis Species 5

Differential gene expression between sexes is the main contributor of the morphological and behavioral differences observed between them. Studying the signatures of these differences at the genetic level will help us understand the forces acting on them. The existence of androdioecious and gonochoristic species in the genus Caenorhabditis makes it suitable for sex-biased gene expression studies. In this thesis, I have assembled the transcriptome of C. sp. 9 and C. sp. 5 using de novo and reference-based techniques. Evolutionary analysis of the assembled contigs showed that genes with male-biased expression evolve faster than those with a female bias, as observed in other taxa. Furthermore, I found a positive correlation between gene expression and codon usage bias.

Keywords: Molecular evolution
Bioinformatics
Advisor: Cutter, Asher
Ultrasonographic Investigation of Cleft-type Compensatory Articulations

Cleft lip and/or palate is a craniofacial condition that can lead to complex speech disorders. In particular, the auditory-perceptual speech assessments of individuals with cleft palate can be difficult because cleft-type compensatory articulations may be outside of English phonology. Therefore, it is desirable to supplement auditory-perceptual assessments with instrumental measurements. In the first study, thirteen participants with cleft-type compensatory articulations completed ultrasound speech exams. The stimuli were repeated VCV combinations (target consonants: [t], [k], [s], [sh], [n], [ng]; vowel contexts: [a], [i], [u]). Ultrasound imaging confirmed auditory-perceptual impressions and revealed covert articulatory movements. In the second study, six participants were assessed after a course of speech therapy. Outcomes were recorded on a severity metric with categories describing auditory-perceptual and motor aspects of speech errors. The severity metric quantified the incremental changes in both dimensions. Based on the research presented, further investigations of cleft palate speech using ultrasound are warranted.

Keywords: cleft palate
ultrasound
biofeedback
Advisor: Bressmann, Tim
High Temperature Gas to Liquid Metal Foam and Wire Mesh Heat Exchangers

Metal foams and wire meshes are open cell structures with low weight and density, high permeability and high thermal conductivity which make them attractive for a wide range of industrial applications involving fluid flow and heat transfer. In this study, the effect of natural convection, radiation and heat transfer enhancement of metal foams and wire meshes of 10 and 40 PPI (pores per inch) heat exchangers were examined and compared for different heat exchanger orientation, coolant flow rate and atmosphere temperature. Thermal spray coating processes were also used in development of a new class of high temperature stainless steel heat exchangers. Stainless steel wire mesh heat exchangers were prototyped by connecting the tube to the wire mesh using wire arc thermal spray coating. Thermal spray coating provided efficient connections between the wire mesh and the tubes’ outer surface, and has potential to replace expensive brazing or other metal connection techniques.

Keywords: Metal Foam
Wire Mesh
Heat Transfer
Heat Exchangers
Wire Arc Thermal Spray
Advisor: Chandra, Sanjeev
Non-invasive 3D Visualization and Thickness Analysis of the Human Insula

Anatomical variability of the human insula has not been well studied because the structure of the insula is difficult to image. Thus, the aim of this study was to apply a novel method to reconstruct insular topology in order to assess the anatomic variation within a population. An analysis of 60 healthy male and female subjects revealed a significant amount of anatomic variation. Some structures, such as the central sulcus were extremely stable and showed little inter-individual variability, while other structures such as the middle short gyrus were highly variable, being more conspicuous in the left hemisphere and in males. Grey matter in the cortex was found to be thinner in the left posterior and dorsal insular subregions in older female subjects but not males. This work shows that the insula is an anatomically complex and variable structure and that some of the variability is related to sex and laterality.

Keywords: Neuroscience
Neuroimaging
Insula
Anatomy
Advisor: Hodaie, Mojgan
Examining a Role for Planar Cell Polarity Signaling in Endothelial Cell Alignment and Organization

Endothelial cells (ECs) respond to flow but the exact mechanism producing alignment is not completely understood. We characterized EC alignment in microfluidic channels, 4 mm wide by 350 um high, to generate shear of 20 dynes / cm2 across the cell surface. In microchannels, ECs aligned perpendicular under flow. Analytical tools were developed to quantify nuclear alignment at 67% for human umbilical vein endothelial cells (HUVECs); cell elongation under shear flow shifted aspect ratio from 2.41 to 2.86. We next sought to probe the mechanism through which ECs communicate during realignment. The planar cell polarity (PCP) signaling pathway is involved in cell organization and coordination during development. A number of genes are known to affect the formation and organization of cellular structures through PCP signaling in human ECs. Higher expression of Vangl1 and Dvl1 proteins did not alter cell reorganization; knockdown of Vangl1 expression decreased EC alignment.

Keywords: planar cell polarity (PCP)
endothelial cells
shear flow
microfluidic
Advisor: McGuigan, Alison P.
Numerical Modeling of Self-heating in MOSFET and FinFET Basic Logic Gates Using Effective Thermal Conductivity

Recent trend of minimization in microprocessors has introduced increasing self-heating effects in FinFET and MOSFET transistors. To study these self-heating effects, we developed self-consistent 3D models of FinFET and MOSFET basic logic gates, and simulated steady-state thermal transport for the worst heating case scenario. Incorporating size-dependent effective thermal conductivity of thin films instead of bulk values, these simulations provide a more accurate prediction of temperature rise in the logic gates. Results of our simulations predict higher temperature rise in FinFETs, compared to MOSFETs. Existence of buried oxide layer and confined geometry of FinFET structure are determined to be the most contributing to this higher temperature rise. To connect the results of our simulations to higher scale simulations, we proposed an equivalent thermal conductivity for each basic logic gate. These values were tested and found to be independent of the magnitude of chosen boundary conditions, as well as heat generation rate.

Keywords: Self-heating
MOSFET
FinFET
Basic Logic Gates
Effective Thermal Conductivity
Advisor: Amon, Cristina
Simulation of Perfusion Flow Dynamics for Contrast Enhanced Imaging

Dynamic Contrast Enhanced Computed Tomography is an imaging tool that aids in evaluating functional characteristics in different stages of disease assessment: diagnostic, treatment effectiveness and monitoring. At the present time, following all the technological advances, there remains no universally validated method of quantitative, non-invasive, perfusion imaging. In order to address this challenge, certain quality assurance flow phantoms have been developed. This work presents the first step in the prospective framework of phantom simulations with the goal of enhancing the understanding of contrast agent kinetics. Existing knowledge about a two-compartmental fluid exchange phantom was used to validate the constructed computational fluid dynamics (CFD) simulation model. The sensitivity of various parameters, both in the geometric and computational domains, was determined. Finally, the model was employed to evaluate current perfusion parameter estimation models. This provides the groundwork for future phantom developments within the framework.

Keywords: CT
DCE-CT
Perfusion
Advisor: Coolens, Catherine
Roles for the Cohibin Complex and its Associated Factors in the Maintenance of Several Silent Chromatin Domains in S. cerevisiae

In Saccharomyces cerevisiae, the telomeres and rDNA repeats are repetitive silent chromatin domains that are tightly regulated to maintain silencing and genome stability. Disruption of the Cohibin complex, which maintains rDNA silencing and stability, also abrogates telomere localization and silencing. Cohibin-deficient cells have decreased Sir2 localization at telomeres, and restoring telomeric Sir2 concentrations rescues the telomeric defects observed in Cohibin-deficient cells. Genetic and molecular interactions suggest that Cohibin clusters telomeres to the nuclear envelope by binding inner nuclear membrane proteins. Futhermore, telomeric and rDNA sequences can form G-quadruplex structures. G-quadruplexes are non-canonical DNA structures that have been linked to processes affecting chromosome stability. Disruption of the G-quadruplex stabilizing protein Stm1, which also interacts with Cohibin, increases rDNA stability without affecting silent chromatin formation. In all, our findings have led to the discovery of new processes involved in the maintenance of repetitive silent chromatin domains that may be conserved across eukaryotes.

Keywords: Cohibin
G-quadruplex
telomere
ribosomal DNA
silent chromatin
genome stability
Advisor: Mekhail, Karim
Structural and Functional Characterization of Clp Chaperones and Proteases in the Human Malaria Parasite Plasmodium falciparum

The Clp chaperones and proteases play a pivotal role in maintaining cellular homeostasis. They are highly conserved across prokaryotes and can also be found in the mitochondria of eukaryotes and chloroplast of plants. For my thesis, I provide an analysis of the Clp chaperones and protease in the human malaria parasite Plasmodium falciparum. The parasite contains four Clp ATPases, which I term PfClpB1, PfClpB2, PfClpC, and PfClpM. One PfClpP, the proteolytic protomer, and one PfClpR, an inactive isoform, were also identified. All proteins, with the exception of PfClpB2, were found to be localized to the apicoplast, a non-photosynthetic relic plastid in P. falciparum. Both PfClpP and PfClpR form mostly homoheptameric rings as observed by various techniques. Through X-ray crystallography, PfClpP assumed a compacted tetradecamer structure similar to that observed for other ClpPs. My data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.

Keywords: Clp
protease
chaperone
apicoplast
Plasmodium falciparum
PfClp
ATPases
PfClpP
PfClpR
Advisor: Houry, Walid A.
High Folate, but not High Multivitamin Gestational Diets, Affect the Serotonergic Regulation of Food Intake in Female Wistar Offspring

The hypothesis that high multivitamin gestational (HV) diets affect the development of central serotonergic regulatory systems in female offspring, and that this is due to its high folic acid content, was investigated. Dams were fed the AIN-93G diet containing the recommended multivitamin mix (RV), 10-fold the RV amount (HV), or the RV diet with 10-fold the folic acid (Hfol). Serotonergic control of food intake and macronutrient selection was assessed by measuring long-term intake and selection, short-term intake and selection following injections of serotonin receptor agonists, and hypothalamic serotonin receptor expression. Offspring from Hfol dams selected more protein and were less responsive to agonist injections, but showed no altered serotonin receptor expression. In contrast, those born to HV fed dams were not different from the RV controls in any measure. In conclusion, the Hfol, but not HV gestational diet affects serotonergic regulation of food intake in female rat offspring.

Keywords: folate
nutritional programming
gestational diet
multivitamin
serotonin
food intake regulation
Advisor: Anderson, G. Harvey
Efficacy of Bacteriophage Treatment on Pseudomonas aeruginosa Biofilms

This study examined the use of phage therapy against Pseudomonas aeruginosa strain PA14 biofilms. Part 1: 24 and 96h PA14 biofilms grown in microplates were phage treated and bacterial biomass was quantified using crystal violet staining. Part 2: 24 and 96h PA14 biofilms grown in prepared root canals of human mandibular incisors were treated with phages and intra-canal samples using paper points and round burs were taken to assess phage and bacterial counts. Part 1: Two phages (JBD4 and JBD44a) were used. Treatment with phages produced significant reduction in the mean percentage of biomass in 24h (p<0.05) and 96h (p=0.08) biofilms. Part 2: In 24 and 96h biofilms in a root canal model, no significant difference was found in colony forming units after phage treatment (p>0.05). Phage application significantly reduced the biomass of 24 and 96h PA14 biofilms grown on microplates, but did not in the extracted tooth models.

Keywords: Pseudomonas aeruginosa
bacteriophage therapy
apical periodontitis
root canal
Advisor: Basrani, Bettina
The Role of Endoglin in the Resolution of Inflammation

Endoglin, a co-receptor of the TGF-β superfamily, is predominantly expressed in endothelial cells and in some myeloid cells and implicated as a potential modulator of immune responses. We previously demonstrated that Endoglin heterozygous (Eng+/-) mice subjected to the dextran sulfate sodium colitis model developed persistent inflammation and epithelial ulceration, while Eng+/+ mice recovered following the acute phase of disease. Our aim was to assess potential alterations in distribution and number of immune cells, expression of inflammatory mediators and mechanisms of oxidative burst in Eng+/- mice. While the number of overall T, B and myeloid cells was unaltered between the genotypes, changes in neutrophil regulating cytokines and angiogenesis mediating factors were observed in Eng+/- mice. In addition, downregulation of phagocyte oxidative burst enzymes point to potential defects in microbial clearance in Eng+/- mice. These findings suggest a role for endoglin in regulating immune and vascular functions during inflammation.

Keywords: Inflammation
Inflammatory bowel disease
Endoglin
Transforming growth factor beta superfamily
Angiogenesis
Neutrophil
Advisor: Letarte, Michelle
Characterizing the Biological Functions of Five Shikimate Dehydrogenase Homologs Enzymes in Pseudomonas putida KT2440

The shikimate pathway links carbohydrate metabolism to biosynthesis of the aromatic amino acids in plants, fungi, bacteria and apicomplexan parasites. The pathway has seven enzymatic steps which convert erythrose-4-phosphate and phosphoenolpyruvate to chorismate, the precursor of tyrosine, tryptophan and phenylalanine. Due to the absence of the pathway in mammalian species, the enzymes are attractive targets for herbicides and antimicrobials. Shikimate dehydrogenase (SDH) catalyses the fourth step, the NADP-dependent reversible reduction of 3-dehydroshikimate to shikimate. Five SDH homologs – AroE, Ael1, YdiB, RifI and SdhL – have been identified through kinetic analysis and phylogenetic studies in the bacterium Pseudomonas putida. SDH homolog gene knockouts (KO) were used to characterize their functions. The AroE KO and Ael1 KO were successfully constructed via gene SOEing of the SDH homolog with a gentamycin antibiotic cassette and homologous recombination via electroporation into WT P. putida KT2440. Preliminary characterization tested KO growth, auxotroph recovery and fluorescent activity.

Keywords: Shikimate pathway
Shikimate dehydrogenase
Pseudomonas putida
Gene knockouts
Advisor: Christendat, Dinesh
The Political Ecology of Community Conservation in northern Kenya: A Case Study of the Meibae Community Wildlife Conservancy

The majority of Kenya’s wildlife exists outside the network of national parks and reserves, predominantly in private and community-owned lands. Although works must be acknowledged for having explored the community conservation approach, the body of research examining how Kenya’s wildlife conservation approach is being negotiated by local stakeholders and incorporated into local livelihood strategies is limited. Based on a case study of the Meibae Community Wildlife Conservancy in northern Kenya, this study examines the motivations of local and non-local groups to pursue wildlife conservation. Viewed through a political ecology lens, this paper analyzes how local people moderate the influence of external conservation values and interests. Findings suggest that local people adopt wildlife conservation projects to access better systems of rangeland management, pursue strategic linkages with external stakeholders and develop basic industries. I conclude that this process represents how Samburu pastoralists strategically embrace externally driven wildlife conservation efforts in self-defining ways.

Keywords: political ecology
community conservation
Kenya
Advisor: Kepe, Thembela
Improving the Effectiveness of In-suite Ventilation Systems with Respect to Cross Contamination and Odour Transmission in MURBs

As in-suite heat recovery ventilator (HRV) use increases, cases of cross-contamination and odour transmission in MURBs are beginning to appear. To mitigate these issues and maximize HRV benefits, a better design and construction methodology specific to MURBs is required. Previously conducted condition surveys suggest the possibility of the fresh air supply becoming contaminated by the exhaust air stream from adjacent units. It is suggested that the intake and exhaust configuration has a significant influence on the potential for cross contamination. The results show cross contamination is an issue in high-rise condominiums. With a low exhaust vent angle and the right wind direction and speed, contaminants can travel from an exhaust source to a fresh air supply in a significant quantity. The potential impact here is to protect the health and safety of all home owners living in high-rise condominiums that utilize in-suite ventilation systems.

Keywords: Building Science
Improving In-Suite Ventilation Systems
Cross Contamination
Odour Transmission
Advisor: Pressnail, Kim D.
Generalized Degrees of Freedom for Gaussian Interference Channel with Discrete Constellations

In wireless channels and many other channels, interference is a central phenomenon. Mitigating interference is a key to improving system performance. To find the limit of the achievable rates for these channels in the presence of interference, the two-user Gaussian interference channel has been the subject of intensive study in network information theory. However, most current results have been obtained by assuming Gaussian input distributions. While optimal in single-user Gaussian channels, the issue with this assumption is that the Gaussian noise becomes the worst noise when the input distribution is also Gaussian. In this thesis, we propose a class of discrete constellations. We show that this class of constellations can automatically achieve the same sum rates as schemes that treat interference as noise or perform time sharing.

Keywords: Gaussian Interference Channel
Generalized Degrees of Freedom
Discrete Constellations
Advisor: Kschischang, Frank R.
Yu, Wei
Evaluation of the Effectiveness of Inpatient Rehabilitation for Mild Stroke Patients - A Functional Recovery Analysis of Inpatient Rehabilitation for Mild Stroke Patients

The recommendations for stroke best practice suggest that mild stroke patients could receive their therapy within an ambulatory environment. However, a significant number of mild stroke patients continue to be admitted to inpatient rehabilitation. A retrospective chart audit was conducted for acute stroke discharges from two centres in Ontario. Stroke cases with a Projected Full FIM® > 80, we're stratified into two groups: discharged home - discharged to inpatient rehabilitation. There were 813 patients eligible for inclusion. Overall, 33% of mild stroke patients were admitted to inpatient rehabilitation. The results did not explain why so many mild stroke patients are admitted to inpatient rehabilitation. The two groups did not differ in rates of recurrent stroke or re-admission to hospital at follow-up. According to the results, milder stroke patients may effectively be managed in the community where rehabilitation services are available.

Keywords: Stroke, Mild Rehabilitation
Advisor: Lindsay, Patrice
Evanescent Photosynthesis: A New Approach to Sustainable Biofuel Production

Immobilization of photosynthetic cultures has been used to generate biofuels and high value compounds through direct conversion of CO2 and water using sunlight. Compared with suspended cultures, immobilized bacteria can achieve much higher densities resulting in greater areal productivity. Limitations exist however, on the density that can be reached without compromising access to light and other nutrients. In this thesis an optofluidic approach to overcoming the challenge of light delivery to high density cultures of cyanobacteria is described and proof of concept experiments presented. This approach uses optical waveguides to deliver light to cells through bacterial interaction with the evanescent field and is tailored to meet each cell's need for light and nutrients. Experiments presented here demonstrate biofilm proliferation in the presence of evanescent fields. Illumination of surfaces by surface plasmon enhanced evanescent fields is also shown to be an effective and potentially useful technique to grow biofilms within optofluidic architectures.

Keywords: optofluidics
bioenergy
optofluidic
biofuel
cyanobacteria
microalgae
alternative energy
solar fuel
evanescent
microfluidics
Advisor: Sinton, David
Receptivity of Laminar Boundary Layers to Spanwise-periodic Forcing by an Array of Plasma Actuators

This work is concerned with the response of a Blasius boundary layer to dielectric-barrier-discharge (DBD) plasma actuators for the purpose of using these devices in bypass transition control. The plasma actuators consist of a spanwise-periodic array of high voltage electrodes, which are oriented to produce streamwise vortex pairs. The structure of actuator-induced streaks is measured using hot-wire anemometry over a streamwise distance of approximately 100 boundary layer thicknesses, and is decomposed into 4 spanwise Fourier modes. The modal content and corresponding streamwise growth characteristics are discussed for ten plasma actuator geometries over multiple excitation voltages and freestream velocities. Actuator power consumption was found to control the streak amplitude, whereas freestream velocity affected both amplitude and streamwise extent of the streaks. A common relationship between disturbance energy and power consumption was found among actuators of different dielectric thickness and similar electrode geometry.

Keywords: plasma actuator
transition
transient growth
laminar
boundary layer
streaks
power consumption
wind tunnel
turbulence
hot-wire
anemometry
disturbance velocity
power spectrum
nanofabrication
data collapse
electrode geometry
Advisor: Lavoie, Philippe
What’s Stopping Us? Identifying Barriers to the Local Food Movement Using Ontario, Canada as a Case Study

The local food movement has been offered as an alternative to the conventional food system. This thesis identifies the barriers that are constraining the local food movement using the case study of Ontario, Canada, by performing qualitative analysis of informal interview responses. In addition to generating a comprehensive account of the barriers constraining local food, barriers to local food procurement in the institutional context are also identified. Findings suggest that the barriers to the local food movement can be related to a lack of access, lack of resources, poor governance structures, poor information sharing and uncooperative relationships between local food actors. I argue that these barriers are reflective of the broader challenges associated with attempting to create food systems change from within the dominant system. Daunting as they may be, they can be overcome in an incremental, pragmatic way. Nineteen recommendations are made to this end.

Keywords: local food
barriers
food systems
Advisor: Wakefield, Sarah