VictorJuiz/thesis huggingface dataset:
Landscape Influences on Hydrological Transit Times in Precambrian Shield Catchments

The estimation of mean transit times (MTTs) is regarded as a powerful descriptor of catchment systems since it provides broad information about hydrological mixing and storage processes in a single encompassing measurement. In this study, convolution lumped modeling was incorporated into the R programming language. Approximately 3.5 years of precipitation and streamflow water isotope signatures were used to estimate transit times across six Precambrian Shield catchments in the Muskoka-Haliburton region of south-central Ontario. The main objective of this study was to explore the main physical controls governing catchment-scale transit times by investigating relationships with light detection and ranging (LiDAR)-based landscape metrics. The MTTs were best correlated to topographic metrics such as flow path gradient and the ratio of flow path length to gradient (i.e. L/G index). These findings support the notion that within shallow-soil catchments in the Precambrian Shield region, it is topography, especially gradient-driven metrics, which is most meaningful in dictating catchment-scale water storage and movement.

Keywords: catchment modelling
hydrology
isotope tracers
mean transit time
water management
watersheds
Advisor: Mitchell, Carl P.J
A High-throughput Screen for Novel Genes Involved in Maintaining Genome Stability and the DNA Damage Response Pathway in Saccharomyces cerevisiae

Oncogenesis is frequently accompanied by rampant genome instability, which fuels genetic heterogeneity and resistance to targeted cancer therapy. I have developed an approach that allows precise, quantitative measurement of genome instability in a high-throughput format in Saccharomyces cerevisiae. My approach takes advantage of the strongly DNA damage-inducible gene RNR3, in conjunction with the Reporter Synthetic Genetic Array methodology, to infer mutants exhibiting genome instability by assaying for increased Rnr3 abundance. We screen for genome instability across ~4200 non-essential mutant yeast alleles in untreated conditions and in the presence of the DNA damaging agent MMS. Our results provide broad insights into the cellular processes and pathways required for genome maintenance. Preliminary follow-up work suggests that several genes have bona fide roles in the maintenance of genome stability. In addition, I conducted both screens in their entirety on two, highly orthogonal fluorescence imaging platforms and compared their reproducibility and sensitivity.

Keywords: Cancer
DNA damage
Genome Instability
Ribonucleotide reductase
Advisor: Brown, Grant W
Using Tendon Vibration between Trials to Alter Proprioceptive Sensitivity and its Influence on Upper-limb Control during Voluntary Reaching

The current study investigated the effects of a novel tendon vibration method on upper-limb position sense and upper-limb rapid movement control. The relative contributions of proprioception and vision during action were assessed. Vibration of elbow extension muscles was applied between trials to avoid reflexive activations that typically occur with vibration during movement. In the position-sense task, participants were asked to move the non-vibrated arm to match the position of the vibrated arm. In the action task, participants were asked to perform a discrete reaching movement. Vibration was found to decrease position sense precision and yielded increased trajectory variability towards the end of the movement. Notably, the influence of vibration on trajectory variability was also observed for reaches made in the presence of vision. Tendon vibration presented between trials likely perturbs proprioceptive feedback during trials. Also, it is concluded that proprioceptive information contributes significantly to the control of visually guided movements.

Keywords: multisensory integration
online control
proprioception
tendon vibration
Advisor: Tremblay, Luc
Development of a General Dynamic Multimedia Indoor Model for SVOCs: Applications to PBDEs

An unsteady-state, fugacity-based, indoor chemical fate model was developed to explore kinetic resistance of multilayer of polyurethane foam (PUF) commonly found in upholstered furniture. The Dynamic Layered PUF Simplified Multimedia Indoor Model (DLP-sMIM) was based on the Multimedia Indoor Model created by Zhang et al. (Zhang, Diamond et al. 2009). DLP-sMIM was applied to real and hypothetical scenarios indoor environments consisting of air, carpet, PUF furniture and the surface film on walls. The model showed good agreement with reported concentrations from a study of indoor polybrominated diphenyl ethers (PBDE) air concentrations over nine months. The PUF compartment was predicted to experience long PBDE residence time. It is suggested that steady-state models and using the well-mixed assumption for a single PUF compartment causes an orders-of-magnitude overestimation of the mass of chemicals in PUF. Rather, two vertical layers of PUF need to be considered in a time-dependent model of indoor chemical fate.

Keywords: Fugacity model
Indoor environment
Multimedia model
Polybrominated diphenyl ethers
Polyurethane foam
Unsteady-state model
Advisor: Diamond, Miriam L
Robust Control of Active Ankle Torque during Quiet Stance: a Servomechanism Problem

Treatment and restoration of motor abilities to individuals with spinal cord injury (SCI) is possible with neuro-rehabilitative systems for unsupported upright stance, also known as quiet stance. The aim of this research project is to develop a controller that will regulate active ankle torque during electrical stimulation for quiet stance. This study uses a novel technique of applying an optimal robust servomechanism controller to bring the human's centre of mass (COM) to a specified reference position independent of external disturbances. The robust controller obtained was able to track quiet stance within 1 second, and highly attenuate both constant and Gaussian noise disturbances intensity. The robust controller presented can be considered as a step forward in neuro-rehabilitative systems for quiet stance, as previous controllers have not considered dealing with the servomechanism control problem in the regulation of ankle torque.

Keywords: Quiet Stance
Robust Control
Servomechanism
Advisor: Davison, Edward J
Popovic, Milos R
Mothers' Explicit and Implicit Moral Identity, Parenting and Adolescent Moral Development

Grusec and Goodnow (1994) proposed a framework wherein children's internalization of values depends upon the accurate perception and acceptance of parents' values. The present research attempted to demonstrate the utility of the proposed framework. Using a longitudinal approach with measures taken at two time points, reasoning, directiveness and ignoring misbehaviour were examined as potential moderators of the relation between maternal moral identity, explicit and implicit, and adolescents' internalization of moral values. Two measures of adolescent internalization were used: mother-adolescent value congruency and adolescent relative autonomy. The results indicated that higher levels of reasoning moderated the relation between maternal implicit moral identity and adolescent moral values, lower levels of directiveness moderated the relation between maternal explicit moral identity and adolescent moral values, and lower levels of ignoring misbehaviour moderated the relation between maternal explicit moral identity and adolescent relative autonomy. The theoretical and practical implications are discussed.

Keywords: Moral Development
Moral Identity
Moral Values
Parenting
Socialization
Advisor: Grusec, Joan
Preparation of Polypropylene Foams with Micro/Nanocellular Morphology using a Sorbitol-based Nucleating Agent

The effect of a sorbitol-based nucleating agent on expanded polypropylene (EPP) bead foaming and extrusion foaming was investigated. The main purpose of this study was to study and develop a fundamental processing baseline for the production of nanocellular foams.During the EPP bead foaming experiments using different concentrations of a sorbitol-based nucleating agent, NX8000, foams having a sub-micron sized cells (

Keywords: Bead foaming
Extrusion fomaing
Microcellular
Nanocellular
Polypropylene foam
Sorbitol
Advisor: Park, Chul B
Cyclosporin A Promotes Neural Precursor Cell Survival to Enhance Neurogenesis in the Hippocampus

Neural precursor cells (NPCs) in the adult mammalian brain show potential in applications of regenerative repair in the CNS. Recent work has shown that Cyclosporin A (CsA), a commonly used immunosuppressive drug, expands the size of the NPC pool in the lateral ventricle subependyma by promoting cell survival, with no concomitant effect on proliferation kinetics. We asked if CsA had similar effects on neural precursors in the neurogenic dentate gyrus within the hippocampus. In vitro, we found that CsA increases the size of the NPC pool. Our in vivo studies reveal an increase in proliferating immature neurons in mice subcutaneously infused with CsA for seven days. A time course study reveals that CsA promotes the survival of newly born NPCs, which can then go on to form new neurons in the DG. Together these findings support the hypothesis that CsA administration promotes neurogenesis and may have implications for tissue repair following injury.

Keywords: cyclosporin A
hippocampus
neural stem cells
neurogenesis
Advisor: Morshead, Cindi
Low Power Circuit Topologies for Digital-to-analog Converters with a Mm-wave Sampling Clock

This thesis describes the design of an 8-bit, 75GS/s, full-rate, low-power DAC in 55nm SiGe BiCMOS process. This is the highest sampling frequency (75GHz) broadband DAC to the best of the author's knowledge. It has an output swing of 1.2Vppd, which is sufficient to directly drive high performance VCSELs for short-reach data center communication links. The low power circuit topologies minimize the power consumption of the DAC to

Keywords: DAC
Advisor: Voinigescu, Sorin
Value Impacts of Energy Efficiency Retrofits on Commercial Office Buildings in Toronto, Canada

The intent of this thesis is to strengthen the business case for sustainable building in Canada by studying the relationship between building energy efficiency and value. This is accomplished through detailed examination of four Toronto commercial office building retrofit case studies with quantitative pre- and post-retrofit energy and financial data. The income capitalization approach to building appraisal is adopted as a model for linking sustainability to value through net operating income. The results suggest that retrofitting buildings can decrease operating costs, increase occupancy rates, and increase effective rent (rental revenue), thereby increasing net operating income. These benefits are not necessarily achieved in every retrofit; however where these benefits do occur, they have positive effects on value.

Keywords: Buildings
Commercial
Energy
Retrofit
Sustainability
Value
Advisor: Pressnail, Kim
Diffusion of Methodological Innovation in Pharmacoepidemiology: Self-controlled Study Designs

Self-controlled designs are methodological innovations that complement traditional observational studies and are useful to control for time-invariant confounders. The use and diffusion of self-controlled case-control and cohort designs in pharmacoepidemiology was examined over time, and described using Rogers' Diffusion of Innovations Theory and co-authorship network analysis (visualized in a supplementary graphics interchange format (GIF) image). Studies experienced a lag in diffusion, followed by a rapid uptake in use since 2000. Overall, the co-authorship network was comprised of 176 papers, 763 authors and 46 components; 31 components contained one paper (61% self-controlled case-control). The largest component of the network was interconnected and was comprised of 69% self-controlled cohort studies. Future work to develop and disseminate standardized language could target seminal authors and key opinion leaders identified in the network. Formal reporting guidelines are also encouraged, as the majority of applications did not follow recommendations on reporting, such as raw data display.

Keywords: innovation
pharmacoepidemiology
research methods
self-controlled
Advisor: Cadarette, Suzanne M
The Role of DNA Damage Sensing Genes in Genetic Instability and Radioresponse in Prostate Cancer

Prostate cancer (PCa) is the second cancer-related mortality cause in North American men. Despite the use of clinical prognostic factors, 20-60% of localized PCa fail primary local treatment. There is need for biomarkers that can guide primary treatment decisions or identify patients that need treatment intensifications. I have hypothesized that localized PCa is associated with an altered DNA damage response (DDR), which in turn can lead to genomic instability and affect the response to radiotherapy. Using array comparative genomic hybridization I have determined the frequency and prognostic importance of copy-number alterations (CNAs) in the main sensors of the DDR. I have shown that CNAs in these loci correlate with tumour genomic instability. The main finding is that Nibrin gains are a significant predictor of outcome following treatment with radiotherapy, but not surgery. NBN gains may be the first PCa predictive biomarker to facilitate local treatment decisions using precision medicine approaches.

Keywords: Copy-number alterations
DNA Damage Response
DNA Repair
Genomics
Prostate Cancer
Radiation Therapy
Advisor: Bristow, Robert G
Social Participation, Self-Perception, and Social Support in Boys Living with Hemophilia

Social integration is a critical component of quality of life and understanding how persons with hemophilia interact socially with their peers may inform healthcare providers.A random sample of 50 boys with hemophilia from The Hospital of Sick Children completed measures of social participation, self-perception, and social support. Participants' parents completed a measure assessing the impact of chronic illness on the family.The majority of boys reported no significant participation restrictions. Social participation was strongly correlated with self-perception subscales Social Acceptance and Global Self-Worth. The Athletic Competence subscale was strongly correlated for adolescents only. There were strong correlations between social participation and social support from parents, teachers, and classmates and moderate correlations for support from close friends. There was minimal impact on the family and weak correlations between social participation and impact on the family.Boys with hemophilia have minimal social participation restrictions and are on par with their peers.

Keywords: Health-related Quality of Life
Hemophilia
ICF
Self-Perception
Social Participation
Social Support
Advisor: Feldman, Brian
Dissecting the Roles of Anillin's Interaction with Importin Beta 2 and mDia2

Successful completion of cytokinesis, the final step of cell division, is required to prevent aneuploidy. A vital step in cytokinesis is the formation of an actomyosin ring. Actin filament formation and contraction is key to the ingression of the ring, but the mechanism still remains unclear. Anillin is a scaffolding protein able to cross-link actin with other cytoskeletal elements and regulatory factors of the ring. I sought to examine the roles of the interactions mediated by anillin in cytokinesis. I identified a novel anillin-importin beta 2 interaction which targets anillin to the nucleus and regulates cell shape in interphase. More importantly, I identified a mechanism by which anillin enhances RhoA dependent activation of formin mDia2. My data suggest a new model whereby anillin acts as an enhancer to help RhoA to fully activate mDia to effectively function in regulating actin organization during ring ingression.

Keywords: Actin cytoskeleton
Anillin
Cell division
Cytokinesis
importin beta 2
mDia2
Advisor: Wilde, Andrew
Pedagogical Progressivism and Science, Technology, Engineering, and Math Education: A Shared Historical Landscape, 1870-1970

This thesis is part of a larger project to sketch a history of how the science, technology, engineering, and math (STEM) subjects were structured in Ontario public schools. The thesis begins by studying the longstanding forces that have demarcated science from other subjects from the 1870s to the 1960s. It then examines the 1960s as a pivotal decade when the effects of school guidance counsellors, economic imperatives, and the preoccupation with human selection accentuated those longstanding divisive forces in public education. These developments culminated in an institutional entrenchment of disciplinary gulfs within the schooling system, opened the door to a constructed embodiment of subject-specific talents inside the child, and alienated math-related subjects from pedagogically progressive visions of education. The guidance movement and the reforms in mathematics during the 1960s were scrutinized in detail. The role of progressive education in its own marginalization from STEM subjects is also examined.

Keywords: career counseling
child-centred pedagogy
history of education
military-industrial complex
progressive education
science education
Advisor: Sandwell, Ruth
Examining the Role of Jagn1 in Pancreatic β-Cells

Endoplasmic Reticulum (ER) stress and activation of the Unfolded Protein Response (UPR) has been implicated in causing pancreatic beta cell dysfunction leading to the development of Type II diabetes. Jagn1 was identified in a proteomic screen as an upregulated protein in response to ER stress caused by mutant proinsulin production. Jagn1 is an ER membrane protein with an unknown function in mammalian cells. This thesis examined the role of Jagn1 in pancreatic beta cells. Jagn1 mRNA was detected in insulinoma cell lines and rodent islets and its levels were increased in response to ER stress. Knock-down of Jagn1 in INS-1 832/13 insulinoma cells resulted in an increase in insulin secretion, proinsulin biosynthesis and ER content compared to control cells. Conversely, overexpression of myc-Jagn1 decreased insulin protein levels, whereas overexpression of mutant Jagn1 had no effect. Overall, these results suggest that Jagn1 may regulate insulin biosynthesis in pancreatic beta cells undergoing ER stress.

Advisor: Volchuk, Allen
Closed-loop Control of Ankle Plantarflexors and Dorsiflexors using an Inverted Pendulum Apparatus

In the past, it has been shown that functional electrical stimulation (FES), when applied to lower limbs, can facilitate quiet stance in patients with various neurological disorders. Furthermore, the literature suggests that able-bodied individuals regulate balance during quiet stance using a control strategy that is similar to proportional-integral-derivative (PID) control. The purpose of this study was to test if a PID control strategy is capable of effectively regulating an FES system at the ankle joints during quiet stance. Specifically, we tested whether able-bodied individuals with compromised visual, vestibular and proprioceptive senses, would exhibit improved ankle joint control if FES was applied to contract the ankle muscles using a closed-loop, PID control strategy. In what follows we show that the proposed PID control strategy was able to outperform voluntary control of the ankle joint, indicating that the controller could be considered for use in neurological patients, including spinal cord injured individuals.

Keywords: Functional Electrical Stimulation
Inverted Pendulum Standing Apparatus
Plantarflexors/Dorsiflexors
Proportional-Integral-Derivative (PID) Control
Quiet Standing
Spinal Cord Injury
Advisor: Popovic, Milos R
To Heed the Lessons of Failure: Individual Differences in Cognitive, Affective and Behavioural Responses to Failure

Experiences with failure, while painful and ubiquitous, provide opportunities for learning and growth. But what is the range of reaction to failure, and what determines the sorts of reactions people will have? A sample of 143 participants recalled failure experiences, through autobiographical narratives and responding to questionnaires. Exploratory factor analyses of questionnaire items revealed six factors, specifying divergent reactions to failure: Self Criticism, Autonomous Preventability, Concern for Others, Transformational Analysis, Global Negative Self-Attribution, and Frustrated Anger. Each factor included a mixture of cognitive, affective, and behavioural responses, and suggested a strong potential for the derivation of a questionnaire assessing failure reactions. Multiple regression analyses were conducted to establish divergence between the extracted factors. Personality traits were found to be strong predictors of most reactions. Refining the measurement structure suggested by the factor analysis will broaden our understanding of failure and its consequences as they help or hinder survival and future success.

Keywords: autobiographical narrative
cognitive appraisal
exploratory factor analysis
failure
personality
questionnaire
Advisor: Peterson, Jordan B
Rat Cytomegalovirus Evasion of Innate Immunity via Modulation of NKR-P1:Clr Interactions

NK cells are innate lymphocytes that provide a crucial first line of defense against malignancies and infections. Pathological or infected target cells can send danger signals to activate NK cells by modulating their cell surface ligand expression, resulting in imbalanced self-nonself discrimination, to which NK cells respond by exerting cytotoxicity or secreting cytokines and chemokines.This thesis focuses on interactions between the NKR-P1 family of NK cell receptors and their cognate C-type lectin-related (Clr) ligands. Earlier studies in our laboratory identified an RCMV (rat cytomegalovirus) -encoded decoy ligand, RCTL (RCMV C-type lectin), which binds to the inhibitory rat NKR-P1B receptor to inhibit NK cell activation. In this thesis, we investigated the expression and function of two other putative immunoevasins encoded by distinct RCMV isolates, RCTL2 and r153, which are homologous to RCTL yet potentially serve distinct immunoevasive functions.

Keywords: Cytomegalovirus
Infection
Innate immunity
Natural Killer cell
Advisor: Carlyle, James R
The Multiplication Table and its Generalizations

Motivated by an old question investigated by Erd\H{o}s (colloquially referred to as the ''Multiplication Table'' problem) and recent developments in its study by Ford and Tenenbaum, we investigate the fundamental problem of locating the divisors of ''most'' integers in certain intervals. We generalize Erd\H{o}s' problem to a certain class of Arithmetical Semigroups using Ford's techniques. We generalize this problem in a different direction by providing explicit estimates of "restricted multiplication tables" in various interesting cases.

Keywords: Algebraic Number Fields
Arithmetical Semigroups
Arithmetic Functions
Distribution of Divisors
Advisor: John, Friedlander B
Indenpendent Transcription of a Functional Lucerne Transient Streak Virus Satellite RNA and its Packaging Requirement(s)

The satellite RNA of Lucerne Transient Streak Virus (LTSV) is a 322-nucleotide, single-stranded circular RNA. To investigate whether interactions between genomic and satellite RNA are important for satellite packaging into the helper virus capsid protein, transgenic plants were generated which contained turnip rosette virus capsid protein gene and LTSV satellite dimer sequence in tandem. Results of the RT-PCR and western blotting revealed that the ribozyme was functional in vivo and generated the unit length of monomeric LTSV circular RNA. This was confirmed by an infectivity assay results showing that the LTSV circular RNA was infectious when inoculated into plants with the turnip rosette helper virus. However, the TRoV capsid protein (CP) failed to be expressed in transgenic plants. Lack of TRoV mRNA for capsid protein in transgenic plants is probably due to the presence of the ribozyme which resulted in the destabilization and consequent degradation of CP TRoV mRNA.

Keywords: functional
packaging
sat RNA
Advisor: AbouHaidar, Mounir G