VictorJuiz/thesis huggingface dataset:
The Evolution of Sexual Dimorphism: Resource Investment in Anura and a Case of Sexual Selection in a Scramble Breeder (Lithobates sylvaticus)

While empirical studies suggest that sexually dimorphic traits are characterized by positive allometry, theoretical work suggests that this pattern may be restricted to exceptionally extravagant traits. I examine fourteen diverse traits to test this hypothesis. While I find a positive relationship between trait sexual dimorphism and allometric slope in L. clamitans, L. sylvaticus shows no relationship. I also find an overarching effect of sex on allometry, with more positive allometry than expected by theory in all four species. Secondly, I test for strength of sexual selection in the explosive breeding L. sylvaticus. I find sexual selection on forearm, body size, and hind limb shapes, with males possessing wider forearm shapes tending to mate with larger females. A preliminary literature review of sexual selection estimates reveals comparable estimates between lekking and scramble mating systems, challenging the view that sexual selection is particularly week in explosive breeders with apparent scramble competition.

Keywords: allometry
anura
evolution
resource investment
sexual dimorphism
sexual selection
Advisor: Rowe, Locke
Proteomic Analysis of PP2A Mutants and PP2A-related Tumor Virus Proteins

Protein phosphatase 2A (PP2A) is a tumor suppressor, whose function and activity is influenced by mutations of PP2A subunits and PP2A-related tumor virus proteins. In this work, protein-protein interaction changes in the normal PP2A interaction network caused by mutations of PP2A scaffolding A (PPP2R1A) and catalytic C (PPP2CA) subunits have been characterized by AP-SWATH. The results show that the normal function and activity of PP2A holoenzyme may be significantly altered and influenced by these mutations. This study also characterizes the interactomes of several PP2A-related tumor viral oncoproteins, including E4orf4. It is revealed for the first time that ASPP-PP1 complex subunits are among the major interactors of E4orf4, suggesting the involvement of E4orf4 in the regulation of Hippo signaling pathway. The results gained in my M.Sc. work provide a deeper understanding of the consequences of PP2A subunits mutations and the PP2A-dependent and PP2A-independent functions of the PP2A-related tumor virus proteins.

Keywords: mass spectromestry
PP2A mutations
Protein phosphatase 2A (PP2A)
tumor virus proteins
Advisor: Gingras, Anne-Claude
Analysis of Alpha-catenin Mediated Intercellular Adhesion in Drosophila

Dynamic linkage between the cadherin-catenin complex (CCC) and the actin cytoskeleton at Adherens Junctions is essential for cell-cell adhesion in epithelial cells. Alpha-catenin is a core component of the CCC that is responsible for maintaining the linkage between the actin cytoskeleton and the CCC. As part of my project, I generated an alpha-Catenin (alpha-Cat) RNAi line that was used to knockdown maternal alpha-Cat in Drosophila embryos. Knockdown of alpha-Cat in the female germline produced embryonic lethality that was characterized by severe defects throughout the embryo which suggests that the maternal contribution of alpha-Cat is indispensable for embryonic development. I also investigated if alpha-catenin function is conserved among metazoans and Dictyostelium discoideum. I generated rescue constructs using mouse, zebrafish, worm and slime mold alpha-catenin proteins and attempted to rescue alpha-Cat1 mutant embryos. The results of my analysis suggest that alpha-catenin function is conserved among metazoans but not between Dictyostelium and metazoans.

Keywords: alpha-catenin
Beta-catenin
catenin
cell adhesion
Drosophila
E-Cadherin
Advisor: Tepass, Ulrich
On Cryoloading: A Novel Technique used for the Functional Analysis of CAV2.2 - Synaptic Vesicle Tethering

Temporal synchronization between quantal release and Ca2+ influx through single CaVs led to the prediction that SVs are attached by a molecular tether to channels. It has been proposed that tethering is mediated by RIM binding to channels via the C-terminal tip PDZ-ligand domain, and indirectly via a proximal SH3 domain. We hypothesized that if SV binding to the channel C-terminal was blocked by competing peptides then SV recycling should be compromised. We developed a novel method, termed cryoloading, to introduce alien compounds into synaptosomes and assayed SV recycling by a standard styryl dye uptake and release method. Neither mimetic peptide blocker, cryoloaded alone or in combination, had any effect on SV turnover. Lack of functional deficit together with complementary biochemical SV binding studies led us to conclude that SVs tether to CaV C-terminals by an alternative mechanism. Here, we propose the novel HQARRVPNGY region as a candidate tethering site.

Keywords: Assay
Calcium channel
Cryoloading
Functional
Synaptic vesicle
Tether
Advisor: Stanley, Elise F
E3 Ubiquitin Ligase Huwe1/Mule Regulates Oocyte Survival through p63 Activity

Objective: To determine the role of Mule in early oocyte development and explore ovarian phenotypes of Mule deficient mice. Methods: Ovaries from floxed wildtype (Mule fl/fl), conditional knockout (Mule-cKO), and Mule+/+ wildtype (ICR) mice were collected for follicle counts, immunocytochemistry, real time PCR, western blotting, and co-immunoprecipitation. Results: Oocyte specific disruption of Mule causes lack of ovulation by 7 weeks of age with severely compromised ovarian reserve. Conditional knockout mice show decreased numbers of follicles at all stages of development compared to Mulefl/fl animals, particularly at the primordial stage. Mule interacts with the transcription factor p63, causing its mono-ubiquitination, and lack of Mule results in increased expression of the p63 target Noxa, but not Puma. Conclusion: lack of Mule results in the inappropriate activation of p63 in oocytes, leading to the accumulation of downstream pro-apoptotic factors such as Noxa, and premature depletion of the ovarian reserve.

Keywords: Apoptosis
infertility
Mule/Huwe1
Oocyte
p63
Premature Ovarian Failure
Advisor: Jurisicova, Andrea
Stromal Lysyl Oxidase-Like 1 Increases Extracellular Matrix Stiffness and Enhances Collagen Fibre Alignment in Non-Small Cell Lung Cancer

Cancer associated fibroblasts (CAFs) represent a large portion of non-small cell lung cancer (NSCLC) stroma where they mediate extracellular matrix (ECM) remodelling and its interactions with neoplastic cells. A recognized NSCLC CAF marker, fibrillar collagen-binding receptor integrin alpha11 (11), known to promote lung tumour growth and metastasis, was highly correlated with stromal lysyl oxidase-like 1 (LOXL1) in two NSCLC patient cohorts. Both genes were up-regulated in tumour stroma compared to normal lung tissue and were associated with desmoplasia status in patient tumour samples. Over-expression of 11 resulted in up-regulation of LOXL1 in three in vitro models. When cultured within three-dimensional collagen matrices, cells with over-expressed 11 caused linearization, alignment and contraction of collagen fibres. In the absence of 11 expression, over-expression of LOXL1 rescued this phenotype. LOXL1 expression was directly proportional to tissue stiffness; degree of gel contraction; and collagen fibre linearization in in vitro and xenograft tumour models.

Keywords: Cancer associated fibroblasts
Collagen
Integrin alpha 11
Lysyl oxidase-like 1
Non-small cell lung cancer
Stroma
Advisor: Tsao, Ming S
Development and Calibration of a 3-component Force Sensor for Meso-milling

In the Autonomous Systems and Biomechatronics Laboratory (ASBLab), a concept of a novel three-component piezoelectric force sensor has been designed in order to achieve the requirements for meso-milling applications. The sensor is designed to have a minimum resolution of 10 mN, an operational frequency bandwidth of 8.3 kHz and a measuring range of up to 10-15 N. This thesis focuses on the development of a prototype of the force sensor design, including the design for physical development of the force sensor, the development of its amplification system and its calibration methodology. The result from the calibration test demonstrates that the prototype sensor developed has the required specifications for the meso-milling applications.

Keywords: Cutting forces
Meso-milling applications
Piezoelectric force sensor
Prototype development
Sensor calibration
Sensor design
Advisor: Nejat, Goldie
Novel Framework for Reduced Order Modeling of Aero-engine Components

The present study focuses on the popular dynamic reduction methods used in design of complex assemblies (millions of Degrees of Freedom) where numerous iterations are involved to achieve the final design. Aerospace manufacturers such as Rolls Royce and Pratt Whitney are actively seeking techniques that reduce computational time while maintaining accuracy of the models. This involves modal analysis of components with complex geometries to determine the dynamic behavior due to non-linearity and complicated loading conditions. In such a case the sub-structuring and dynamic reduction techniques prove to be an efficient tool to reduce design cycle time. The components whose designs are finalized can be dynamically reduced to mass and stiffness matrices at the boundary nodes in the assembly. These matrices conserve the dynamics of the component in the assembly, and thus avoid repeated calculations during the analysis runs for design modification of other components. This thesis presents a novel framework in terms of modeling and meshing of any complex structure, in this case an aero-engine casing. In this study the affect of meshing techniques on the run time are highlighted. The modal analysis is carried out using an extremely fine mesh to ensure all minor details in the structure are captured correctly in the Finite Element (FE) model. This is used as the reference model, to compare against the results of the reduced model. The study also shows the conditions/criteria under which dynamic reduction can be implemented effectively, proving the accuracy of Criag-Bampton (C.B.) method and limitations of Static Condensation. The study highlights the longer runtime needed to produce the reduced matrices of components compared to the overall runtime of the complete unreduced model. Although once the components are reduced, the assembly run is significantly. Hence the decision to use Component Mode Synthesis (CMS) is to be taken judiciously considering the number of iterations that may be required during the design cycle.

Keywords: Finite Element Analysis
Mesh Convergence
Modal Analysis
Model Reduction
Advisor: Behdinan, Kamran
Polarization Dependence of Stimulated Brillouin Gain in a Spun Fiber

Stimulated Brillouin Scattering (SBS) in an optical fiber is dependent on the polarization of the counter-propagating pump and probe waves. This polarization dependence changes for different types of optical fibers. In this thesis, we show the study of the SBS behaviour in a Spun fiber, which is a fiber with elliptical core whose preform has been twisted during drawing. We report here, the first time observation of polarization-dependent spectral dip within the Brillouin gain, when spun fiber is used. Through experiments and simulations, we prove that this dip is caused by a filtering effect of the Spun fiber, similar to that of a solc filter, due to a twisted elliptical core fiber being combined with the polarizing effect of SBS.

Keywords: Brillouin Gain
Spectral Dip
Spun Fiber
Advisor: Qian, Li
Structure and Role of Chromatin Architecture in the Inactive X Chromosome

The significant impact of three-dimensional organization of chromatin on gene regulation is well known. Since silencing of the inactive X chromosome (Xi) provides a unique opportunity to explore structural components of the silent chromatin, the ultrastructure of the inactive X chromosome is evaluated in this study. Structure of the Xi is still unknown even after 50 years of research on the inactive X due to technical limitations. Therefore, superior imaging capabilities of electron spectroscopic imaging in correlation with fluorescence microscopy and nanogold labeling was chosen as my approach. I have shown that chromatin within the Xi, despite the fact that it is silenced, is not nearly as compact as constitutive heterochromatin. Nevertheless, the Xi adapts a more condense structure than euchromatin. My data also indicate that the Xi is enriched in ribonucleoproteins (RNPs) and a significant contribution of 10 nm fibers are found within the territory. I also demonstrate that there are channels within the Xi territory that run between fibers with RNP structures found in these channels. Further, my results revealed that Xist does not coat the periphery of the Xi chromosome. Finally, an interesting finding was that H3K27me3 is not uniformly distributed throughout the chromosome, but displays a configuration indicative of possible subdomains. Together, these results show that silencing does not necessarily imply high levels of chromatin compaction, the typical and generally accepted view. Importantly, this knowledge of the Xi structure will shed light on the structural requirements for the function of other facultative heterochromatin domains in the nucleus.

Advisor: Bazett-Jones, David P
The Role of Cognitive Functions and Language Proficiency in Arithmetic Achievement: Does L1/L2 Status Matter?

The current research examined the role of different cognitive functions as well as the role of English language proficiency in the arithmetic performance of 91 Grade 5 Native English Speakers (EL1) and 172 Grade 5 English Language Learners (ELL). Cognitive profiles of normally achieving (NA) children and children at-risk (AR) for a mathematics learning disability (MLD) were examined in each language group. Findings revealed that nonverbal reasoning, working memory, and processing speed significantly predict Grade 5 arithmetic performance, regardless of language background. English language proficiency did not predict arithmetic performance in either language group. Children at-risk for MLD exhibited similar cognitive profiles and processing deficits regardless of language group. Results suggest that English language proficiency does not place ELL children at a greater risk for poor achievement in arithmetic. Implications for the assessment and diagnosis of MLD in children who are learning English as a second language are discussed.

Advisor: Geva, Esther
A CMOS Multi-modal Contact-imaging Scanning Microscope

This thesis presents the design, implementation and partial experimental characterization of a multi-modality scanning-contact microscope (SCM) with application in biomedical imaging. Bench-top light microscopes are bulky and expensive and provide only one imaging modality. The resolution of most conventional lens-less (contact) microscopes is limited by their pixel size which renders them unsuitable for applications demanding high resolution such as cell imaging. The SCM's imaging component is a custom-made CMOS imager in the AMS0.35m imaging process. Six pixel types are integrated into the imager, which enable the SCM to support six imaging modalities. For sub-pixel resolution imaging, a specialized pixel layout is used which allows the system to support a super-resolution algorithm which takes multiple images with sub-pixel shifts as its input and generates a single high-resolution image. Each pixel type may generate an output voltage or current, depending on whether it is active or passive. A low-power dual-input 2nd order ADC with an SNR of 78dB is implemented to accommodate both current and voltage inputs while preserving noise-shaping characteristics for both inputs.

Keywords: Biomedical Imaging
CMOS active pixel
Delta Sigma
Image Sensor
Microscope
Pixel
Advisor: Genov, Roman
Gulak, Glenn
Design and Construction of a Commercial Aftermarket Automotive Head-Up Display

The contents of this report provides a comprehensive look at the details involved in the design and development of an automotive head-up display (HUD). By examining the product's complete assembly, including its optics, mechanical assembly, and embedded system, a portable aftermarket automotive HUD was successfully constructed. The resulting product addresses issues and criticisms present in commercially available HUDs, such as display clutter, placement, price, and versatility, giving it a strong competitive advantage within its target market. A brief overview on some performance improvements is also included, followed by recommendations for future actions to advance the developed product closer to commercialization.

Advisor: Ben Mrad, Ridha
Development of Coupling Partners for Bioorthogonal Reactions with N-Hydroxylamines

Bioorthogonal chemistry enables biological chemists to study the dynamics of complex biological systems. Bioorthogonal chemistry allows the selective reaction of an orthogonal tag, which is incorporated on the molecule of interest via biosynthetic or biochemical pathway, and its reactive partner without interfering with native biochemical processes. A number of reactions have been developed in the past two decades. However, there is still a need to develop new chemistries to widen the scope and power of these chemistries to elucidate the biological systems. Therefore, we developed a metal-free bioorthogonal reaction between N-hydroxylamine (orthogonal tag) and a bifunctional probe with aldehyde and alkene (reactive partner) to form a stable isoxazolidine cycloadduct. We showed that glucose could be modified with N-hydroxylamine in four steps. In addition, we designed and synthesized probes that condense then cyclize at 37 °C within 24 hours to yield the cycloadduct, thus making this reaction a viable chemistry to use in biological systems.

Keywords: bioorthogonal chemistry
hydroxylamine
Advisor: Nitz, Mark
Respiratory Syncytial Virus Fusion Protein Interaction with its Cellular Receptor, Nucleolin

Respiratory Syncytial virus (RSV) fusion protein (F) interacts with nucleolin during viral fusion. RNA binding domains 1 and 2 (RBDs) of nucleolin, when expressed as a complex, inhibits RSV infection in vitro. We examined the interaction between pre- vs. post-fusion F, and whole virus, with the RBDs complexed and individually. Both RSV Fs co-precipitated RBD1,2. Immobilized RBD1,2 precipitated both RSV Fs and whole viral particles. Immobilized RBD1 precipitated post-fusion but not pre-fusion RSV F. RBD1,2 inhibited infection at 20nM when co-incubated with the virus and the cells for 24 hours. RBD1 inhibited infection to a lesser extent with the same conditions. RBDs were not able to inhibit infection with coincubation with virus prior to infection. RBD1,2 interacts with RSV F, showing different preferential binding for one conformation over another depending on assay conditions, while inhibiting infection at 20nM with 24 hours of coincubation.

Keywords: fusion
nucleolin
respiratory
RSV
syncytial
Advisor: Hegele, Richard
Non-intrusive, Automated Log Discovery and Parsing

Todayâ s distributed systems generate log data for tasks such as debugging failures. When aggregated into a log analytics tool, this data can be queried to perform anomaly detection and failure diagnosis at a scale that is infeasible otherwise. However, before analysis, this data must be discovered and parsed. harvester is a tool capable of automatically finding and parsing logs for indexing. harvester â s approach is novel in that it generates regular expressions for parsing using the constants of the executables that authored the messages. This allows harvester to parse logs for any software, without source code, so long as constants can be extracted from the softwareâ s binary. In our evaluation of two distributed systems written in Java and C, we are able to achieve an accuracy of 67.7% for the generated expressions. Our inaccuracies are remediable with slightly improved logging practices without having to overhaul existing logging.

Keywords: distributed systems
failure diagnosis
logging
Advisor: Yuan, Ding
Comparing Prediction Methods for Early Warning Systems

In this study, we investigate the use of prediction modeling to build an early warning system to identify students who are at risk of interacting with the criminal justice system in the future. First, we review algorithms for supervised learning and formulate the problem in a precise modeling framework. In the data cleaning phase, we match between the two datasets for an 86% match-rate. We then apply different supervised learning methods and identify the best model for our problem. Using detailed variables, temporal cross validation and our final prediction method of Random Forests, we achieved a precision of 0.3 at 1% of the student population. This greatly out-performs the current threshold-based system that flags a larger percentage of the student body while correctly identifying fewer at-risk students. We also describe the results of a similar approach to developing an early warning system for public safety.

Advisor: Stinchcombe, Adam
Burn-Induced Muscle Wasting: Changes in Muscle Progenitor Cells

Severe burn results in a prolonged hypermetabolic response that leads to significant muscle wasting. This rapid loss in muscle mass occurs due to increased protein degradation and alterations in protein synthesis. The objective of our study was to examine the mechanisms of burn-induced muscle wasting. Using a mouse full-thickness scald burn model we show that muscle wasting after burn injury is associated with increased inflammation and a significant reduction in muscle progenitors. A reduction in this inflammatory cascade and a restoration of muscle progenitors leads to recovery of muscle size. We next examined whether we could attenuate burn-induced muscle wasting pharmacologically. Metformin treatment attenuated muscle wasting in part due to increasing the number of muscle progenitors and increasing their proliferation. Metformin treatment also reduced fat infiltration, a significant source of muscle damage after burn injury. Treating severe burn injury with metformin may mitigate muscle wasting in addition to managing hyperglycemia.

Keywords: burn
metformin
muscle
Pax7
satellite cells
wasting
Advisor: Jeschke, Marc G
Mental Health Service Utilization in Women with Human Immunodeficiency Virus (HIV) during the Postpartum Period: A Population-Based Study

Purpose: The purpose of this study was to characterize postpartum mental health service utilization in HIV-positive women. Methods: We identified 861 365 women who had a live birth delivery in Ontario, Canada and described their use of mental health services. Adjusted odds ratios (aORs) and 95% confidence intervals (CIs) were reported to compare service use in HIV-positive and HIV-negative groups. Results: HIV-positive women (n=530) were more likely to access outpatient mental health services (aOR, 1.26; 95% CI, 1.03 to 1.55). Among those who accessed outpatient services, HIV-positive and HIV-negative women were equally likely to remain engaged in care (aOR, 1.24; 95% CI, .88 to 1.75). HIV-positive women were more likely to require a psychiatric ED visit or hospitalization (aOR, 2.74; 95% CI, 1.72 to 4.12). Conclusion: HIV-positive women were more likely to require a postpartum psychiatric ED visit or hospitalization despite using all outpatient mental health services in greater proportions.

Keywords: Health Services Research
Human Immunodeficiency Virus (HIV)
Postpartum Depression
Pregnancy
Reproductive health
Women's mental health
Advisor: Loutfy, Mona R.
Vigod, Simone N.