VictorJuiz/thesis huggingface dataset:
Cache Coherence for Approximate Computing

Coherence induced cache misses are an important aspect limiting the scalability of shared memory parallel programs. Many coherence misses are avoidable, namely misses due to false sharing – when different threads write to different memory addresses that are contained within the same cache block causing unnecessary invalidations. Our work leverages the domain of approximate computing and the value similarity within store values present in multi-threaded error-tolerant applications. We introduce a novel cache coherence protocol for approximate computing which implements an approximate store instruction and coherence states to allow some incoherence within approximatable shared data to mitigate both coherence misses and coherence traffic within various sharing patterns. For applications within multi-threaded Phoenix and AxBench suites, we see dynamic energy improvements within the NoC and memory hierarchy up to 50.1% and speedup up to 37.3% with low output error for approximate applications that exhibit false sharing.

Keywords: Approximate Computing
Cache Coherence
Computer Architecture
Advisor: Enright Jerger, Natalie
Numerical Study of the Transition from Regular to Mach Reflection on a Wedge and Semicylinder

The transition from regular (RR) to Mach reflection (MR) on wedges and semicylinders in inviscid, diatomic gases is examined herein via numerical methods. The objective of this work is to develop and demonstrate a systematic numerical post-processing methodology that can accurately determine the RR-MR transition for the oblique shock reflection problem on the semicylinder. In the case of a semicylinder, oblique shock reflection is a fully unsteady flow process. The proposed methodology exploits the continuous nature of the transition on the semicylinder and avoids the limitations present in standard image processing techniques commonly used in experimental approaches for determining the RR-MR transition. The numerical results obtained for the RR-MR transition on the semicylinder are compared to existing theoretical and numerically-determined boundaries for the transition on wedges. It is observed that the numerically-determined RR-MR transition on the semicylinder occurs at a slightly lower equivalent wedge angle than that of the wedge.

Keywords: Mach Reflection
Oblique Shock Interaction
Regular Reflection
Shock Reflection
Shock Reflection Transition
Shock waves
Advisor: Groth, Clinton P. T.
Gottlieb, James J.
Mitigating Mortality of Wildlife in Rouge National Urban Park

Rouge National Urban Park is one of the largest urban parks in North America, encompassing natural and developed areas, resulting in high numbers of wildlife road mortalities. Ecopassages are a common method to mitigate wildlife road mortality to provide safe crossing. To determine the placement of an ecopassage in the park, six kilometers of road was surveyed for five field seasons to record wildlife road-kill. Landscape features, traffic volume, distance to railway, seasonal movement, and weather were shown to be related to wildlife road mortality. After the installation of an ecopassage, a common tool used to assess its efficacy is PIT-tagging freshwater turtles, and strategically placing antennae at the entrances of an ecopassage. By completing arena experiments, this study investigated how PIT-tag placement, antenna type, environmental conditions, turtle orientation, and tag orientation influenced detection success. Overall, pass-over antenna, external placements, and vertical tag orientation had significantly higher detection.

Keywords: Antenna
Ecopassage
PIT-tag
Road mortality
Wildlife
Advisor: Mandrak, Nicholas
Cadotte, Marc
Social Capital as a Determinant of Microfinance Clients' Outcomes

In this paper, I examine the role of social capital as a determinant of microfinance clients’ ability to leverage microloans to improve key socioeconomic metrics. Social capital theories are deployed in an attempt to account for differentials in these metrics among a unique sample of borrowers. Microfinance emerges prominently in the literature on poverty reduction. While it is important to remain critical of policy agendas that emphasize solutions such as microfinance, it is also necessary to understand how disadvantaged groups can effectively negotiate the system. A deeper understanding of how and whether social capital plays a role in microfinance borrowers’ success may allow us to assess what types of supports will increase the likelihood of success for clients in these programs. Based on survey data collected for this thesis, I was unable to demonstrate a trend between social capital and changes in socioeconomic metrics, but did discover other interesting trends.

Advisor: Ryan, Sherida
Vieta, Marcelo
Ultrafine Particulate Pollution Exposure during the School Commute: GIS-based Modelling techniques for Estimating Dosage and Examining Environmental Inequality

This research is broadly divided into experiments focusing on two primary objectives: (1) To develop modelling techniques for examining ultrafine particulate (UFP) dosage in the walk-to-school commute, and (2) use these models to examine spatial patterns in dosage from an environmental inequality perspective. The first objective was met through development of a GIS-based modelling workflow which yielded estimates of commute dosage that account for variations in ambient concentration, walking speed, and ventilation rate within a single commute route. The second objective was met by applying these models to estimate commute related UFP dosage across an entire population and conducting analysis within a standard environmental inequality framework combining spatial regression and cluster mapping. We identified associations and patterns of exposure-burdening on vulnerable population groups, which indicate evidence of UFP dosage disparities. However, a divergence from those found in the literature suggests a need for further research to validate these outcomes.

Keywords: Air Pollution Exposure
Children
Commute
GIS
Modelling
Ultrafine Particulate Matter
Advisor: Adams, Matthew D
Heterologous Expression and Characterization of the Antibacterial Lasso Peptide LP2006

The lasso peptides are a class of ribosomally synthesized peptide natural products with diverse bioactivities and structures resembling a lasso. Although the targets of several antibacterial lasso peptides have been investigated to date, the majority remain uncharacterized. Among those that have been characterized, the antibacterial lasso peptides have diverse targets and unique mechanisms of action. One antibacterial lasso peptide with a unique structure, LP2006, is the only member of the class IV peptides. Currently the target and mechanism of action of LP2006 remains unknown. The aim of this study is to develop a system for the heterologous expression of LP2006 to allow for the study of its target and mode of action. I demonstrate that LP2006 can be heterologously expressed using Streptomyces coelicolor M1146, and that purified LP2006 does not appear to activate the cell wall stress response gene liaI.

Advisor: Nodwell, Justin
Continuous-time Pipelined Binary-search Flash ADC

A novel ADC architecture is introduced with a sampling rate comparable to flash converters, but with reduced input capacitance, power consumption and kickback. Broadband active delay circuits pass the input along with a clock through a continuous-time pipeline. The 5-bit prototype has a 2.5-bit first stage, 1.5-bit second stage, and 2-bit final stage allowing for digital correction of interstage errors. Consuming 47mW at 7GS/s in 28nm CMOS, the converter has 15fF differential input capacitance

Keywords: ADC
Binary
Continuous
Delay
Flash
Pipeline
Advisor: Chan Carusone, Anthony
Current and Emergent Suicidal Ideation in Schizophrenia: Effect of Stressful Life Events and Genome-Wide Methylation

Suicide is a serious problem, especially in patients with schizophrenia. In order to prevent suicide, it is imperative to identify those with suicidal ideation and emergent suicidal ideation. We tested the effect of childhood trauma and recent stress on current and emergent suicidal ideation. Furthermore, we identified differentially methylated probes and regions associated with current suicidal ideation, as well as methylation changes in individual sites associated with emergent suicidal ideation. We found that an increase in total stress and health-related stress were significant predictors of emergent suicidal ideation. We also report the most significant positions and regions associated with current and emergent suicidal ideation. The anticipated outcomes of these studies were to improve the understanding about risk factors for suicidal ideation, and the identification of methylation markers to monitor for suicidal ideation in psychosis.

Keywords: Epigenetics
Schizophrenia
Stress
Suicidal Ideation
Advisor: De Luca, Vincenzo
Zen as a Creative Agency: Picturing Landscape in China and Japan from the Twelfth to Sixteenth Centuries

This essay explores the impact of Chan/Zen on the art of landscape painting in China and Japan via literary/visual materials from the twelfth to sixteenth centuries. By rethinking the aesthetic significance of “Zen painting” beyond the art and literary genres, this essay investigates how the Chan/Zen culture transformed the aesthetic attitudes and technical manifestations of picturing the landscapes, which are related to the philosophical thinking in mind. Furthermore, this essay emphasizes the problems of the “pattern” in Muromachi landscape painting to criticize the arguments made by D.T. Suzuki and his colleagues in the field of Zen and Japanese art culture. Finally, this essay studies the cultural interaction of Zen painting between China and Japan, taking the traveling landscape images of Eight Views of Xiaoxiang by Muqi and Yujian from China to Japan as a case. By comparing the different opinions about the artists in the two regions, this essay decodes the universality and localizations of the images of Chan/Zen.

Advisor: Liu, Johanna
Agricultural Technology in the Developing World: A Solar Udraft Aerator for Aquaculture and a Meta-analysis of the Adoption Literature

Agricultural technology can play an important role in the effort to eliminate food insecurity and global poverty. This thesis presents an evaluation of a technology at the design stage, and a meta-analysis of the factors that influence adoption of technologies at the dissemination stage. First, a case study of a project to design an aerator for aquaculture ponds in Bangladesh is discussed. The project is not found to be successful, but the evaluation methodology employed may be generalized to other agricultural technologies. The case study also yields observations about the value and role of laboratory, research station, and on-farm trials in agricultural technology development. Next, some considerations for the dissemination phase are discerned through a meta-analysis of 218 adoption studies. Barriers to adoption of various types of technology are identified and recommendations are made for adoption researchers and policy makers.

Keywords: Adoption
Agriculture
Aquaculture
Development
Evaluation
Technology
Advisor: Bilton, Amy M
The Development of a Microsimulation Model to Evaluate the Cost-utility of Telemonitoring for Patients with Heart Failure in Ontario, Canada

Objective: To assess the cost-utility of telemonitoring compared to the current standard of care in the management of patients with heart failure over a 25-year time horizon from a public payer perspective. Methods: A microsimulation model was developed to analyze telemonitoring’s cost-utility by using data from the Medly Program Evaluation and literature. Scenario analyses were conducted in relation to HF severity and TM deployment models. A probabilistic sensitivity analysis (PSA) and one-way analyses were performed. Results: TM had an incremental cost of $16,478 and incremental Quality-Adjusted Life Year (QALY) of 0.671 resulting in ICER of $24,553/QALY. PSA showed 84.4% likelihood of cost-effectiveness under $50,000/QALY willingness-to-pay. Scenario analyses did not show significant changes to ICERs. Results were sensitive to the reduction of hospitalizations by TM. Conclusion: The model demonstrates that TM is cost-effective compared to current standard of care. This study could be repeated when more follow up data becomes available.

Keywords: cost-effectiveness
cost-utility
heart failure
telemonitoring
Advisor: Seto, Emily
Laporte, Audrey
Targeting Casein Kinases in the Fungal Pathogen Candida albicans

Fungal pathogens are a major public health burden. We previously screened a library of over 700 protein kinase inhibitors and identified compounds with potent antifungal activity in combination with the echinocandin antifungal drug caspofungin, against an echinocandin-resistant isolate of Candida albicans. My thesis aimed to validate the interaction of two of the top compounds, GW416484 and SB-400868, with their putative casein kinase targets, Yck2 and Hrr25. Genetic analysis suggested that GW461484 and related molecules targeted both Yck2 and Hrr25, whereas the SB-400868 scaffold specifically engaged with Yck2. Through use of in vitro kinase assays I confirmed that Yck2 activity is inhibited by both GW461484 and SB-400868 suggesting an important role of this family of kinases in governing echinocandin resistance. In collaboration with the Savchenko Lab, we solved the structure of C. albicans Yck2. Overall, this work reveals that targeting casein kinases may be an effective strategy to cripple drug-resistant C. albicans.

Keywords: Candida albicans
Genetics
Kinase
Microbiology
Yck2
Advisor: Cowen, Leah E
The Role of Macrophage Receptor with a Collegenous Structure (MARCO) in Atherosclerosis

Cardiovascular diseases account for a quarter of all deaths in Canada. A main contributor towards vascular disease is atherosclerosis, or a build-up of plaque in the arteries. During the inflammatory atherogenic response, macrophages can perpetuate inflammation through lipid accumulation. Macrophages ingest lipids through scavenger receptors (SRs) which have functions that potentially affect atherogenesis. Nevertheless, SRs remains controversial in atherosclerosis. My project assesses Macrophage Receptor with Collagenous Structure (MARCO) in experimental atherosclerosis. Consistent with our MARCO expression data, MARCO deficiency did not affect lipid uptake in bone marrow derived macrophages but was impaired in peritoneal macrophages. To assess how MARCO shapes disease, we used a Marco-/- Ldlr -/- and an AAV-PCSK9 injected Marco-/- mice. Both atherosclerosis models developed similar lesion sizes compared to controls. Inflammatory profiles also were similar while bone marrow transplant experiments suggest hematopoietic MARCO does not impact atherosclerosis. Despite binding lipids, MARCO seems to have no influence in atherosclerosis.

Keywords: Atherosclerosis
Hypercholesterolemia
Lipid Uptake
Macrophage
Scavenger Receptor
Advisor: Robbins, Clinton
Using Milk-derived Exosomes To Repair Malnutrition-induced Gut Barrier Dysfunction In Mice

Malnutrition is linked to 45% of death below the age of 5 and intestinal dysfunction, including intestinal barrier breakdown and mucosal atrophy. Exosomes are minute extracellular vesicles that were shown to influence intestinal stem cell function, which could stimulate intestinal repair. This study aimed to investigate the effect of exosomes in malnutrition-induced mucosal atrophy and barrier dysfunction. C57BL/6J mice received a control or isocaloric protein deficient diet for 14 days to induce malnutrition. From day 10 to 14 they received daily oral gavage of milk-derived exosomes or PBS control. Malnourished mice demonstrated villus blunting, increased permeability as evidenced by significantly increased FITC levels and loss of Claudin-3 which were improved with exosomes. Small intestinal cellular proliferation was increased with exosomes (Ki67 staining) and associated with signs of increased leucine-rich repeat-containing G-protein coupled receptor 5 stem cell activity. Exosomes could be an attractive therapy to restore intestinal function in malnourished children.

Keywords: Barrier
Exosomes
Intestine
Malnutrition
Mice
Milk
Advisor: Bandsma, Robert HJ
Virtual Constraint Generation

This thesis examines the problem of systematically generating virtual holonomic constraints. A virtual holonomic constraint is a relation between the generalized coordinates of a mechanical control system which can be enforced through feedback. Virtual holonomic constraints have become popular in recent years as a powerful method in the control of biped robots, and the framework has been extended to solve many problems in the control of underactuated mechanical systems, though systematic design procedures have been lacking. This thesis present the virtual constraint generator, a control system whose orbits are regular virtual holonomic constraints, to address this gap. This thesis begins an exploration of transforming constraint design problems into control specifications for this virtual constraint generator. Using this approach, several basic motion control problems for an underactuated mechanical system are posed and solved.

Advisor: Maggiore, Manfredi
Reconfigurable Dual-band and Wide-band Spatially-fed Array Antennas

This thesis presents the designs of two reconfigurable spatially-fed antenna arrays with the potential to be applied in satellite communications. The first design is a dual-band circularly-polarized reflectarray antenna (RA). The RA unit cell is comprised of two concentric microstrip rings, one for each operation frequency. Each ring is loaded with four varactor diodes to achieve CP response through concurrent manipulation of both vertically and horizontally polarized waves. Experimental characterization of the unit cell showed sufficient phase-shifting capability covering the two frequency bands of interest. The second design is a reconfigurable Huygens’ metasurfaces (HMS) that have the potential of obtaining wideband tunable responses by incorporating tunable elements into the surface. This is possible since the HMS implements both the electric and magnetic responses. An equivalent circuit model for the HMS is presented, followed by a low-complexity reconfigurable HMS unit cell design.

Advisor: Hum, Sean V
Sharing Psychosocial Risk Assessment Information with Paediatric Oncology Healthcare Providers: Service Utilization and Related Factors

The increased risk for psychosocial morbidity in paediatric oncology patients and their families is widely recognized. Although routine screening has been proposed as an important standard of care, systematic screening is limited. Additional research is required to provide evidence for greater integration of risk screening into clinical practice. The present study investigated whether healthcare providers’ (HCPs) knowledge of family psychosocial risk translates to increased rates of psychosocial intervention. The number of psychosocial services documented when HCPs provide care as usual or are informed of risk as measured by the Psychosocial Assessment Tool was compared. Results showed no significant difference in the number of services received by families when HCPs were aware of risk or not, indicating that knowledge of high-risk families is not sufficient to impact rates of intervention. The intensity of the child’s cancer treatment was found to be the strongest predictor of the amount of psychosocial care provided.

Keywords: Knowledge translation
Paediatric
Psychosocial intervention
Psychosocial screening
Psycyho-oncology
Advisor: Barrera, Maru
Beyond Yield Alone: Functional Traits of Regionally Adapted Daucus carota (carrot) Varieties on Organic Farms

While agronomic traits have been widely studied, crop functional trait expression and variation among regionally and broadly adapted seeds have not. I measured 14 above- and below-ground functional traits in six varieties of Daucus carota (carrot) grown at ten organic farms across Canada to test whether seed regionality corresponds to differential expression of functional traits. Environmental conditions at the farm level over varietal difference explained variation in trait expression. Leaf traits trade off in patterns predicted by the Leaf Economics Spectrum. Environmentally-patterned variation in trait expression differed between varieties. Regionally adapted varieties expressed higher resource acquisitive traits when grown outside their local region, and while hybrid varieties performed more consistently between sites, hybrids expressed higher resource acquisitive traits when grown in western regions. By testing trait tradeoffs between varieties, this research addresses a knowledge gap regarding the ecological consequences of crop functional trait expression, with implications for multiple end users.

Keywords: Canada
Daucus carota (carrot)
functional traits
intraspecific
organic crops
phenotypic plasticity
Advisor: Isaac, Marney
Analysis of Protein Expression Differences in Cardiac Fibroblasts Isolated from 7-day Sham-operated and Infarcted Murine Hearts

Myocardial infarction (MI) induces cardiac remodeling, activation of cardiac fibroblasts (CFs), reduced tissue compliance, and heart failure progression. To identify novel mediators of cardiac fibrosis, we conducted mass spectrometry on CFs isolated by pre-plating or fluorescence activated cell sorting (FACs) from 7-day sham and infarcted mouse hearts. Pre-plated CFs from infarcted and remote regions showed that CFs were enriched similarly in proteins associated with myofibroblast activation and profibrotic signaling, including cell-cell/matrix adhesion, protein folding, and collagen organization. Thus, MI causes more global effects on CF activation than were previously understood. Using a fibroblast reporter mouse (Col1α1-GFP/αSMA-dsRED), αSMA- and αSMA+ CFs were isolated by FACs from 7-day sham and infarcted hearts to examine potential differences in the response of these two CF populations to ischemic injury. Surprisingly, greater differences were observed in sham compared to infarcted hearts, suggesting that cardiac injury induced convergence of all CFs towards a more profibrotic phenotype.

Keywords: cardiac fibroblasts
cardiac fibrosis
cardiovascular
heart failure
proteomics
Advisor: Heximer, Scott
To Sedum or Not to Sedum: Improving Extensive Green Roof Functioning Using Invasion Theory as a Management Tool

Green roofs have become increasingly popular to mitigate the negative impacts of urbanization and to restore key ecosystem functions in cities. In this thesis, I evaluate green roof functioning in two ways, using a meta-analysis of existing literature and a field-based manipulation experiment. The meta-analysis showed that Sedum survived better than non-Sedum, but there was no pattern of roof cooling and stormwater management. In the field, I conducted a factorial experiment using invasion theory as a management tool to increase native species diversity on extensive green roofs and evaluate green roof functioning. I hypothesized that resource addition via irrigation and disturbance treatments will enhance native species success and increase roof cooling and stormwater management. Results show plants aid in roof cooling and increase moisture retention, however evidence supporting diversity enhancing green roof functioning is lacking. Diversity effects on function theoretically require co-existence mechanisms, thus requiring observation over longer temporal scale.

Keywords: Ecosystem function
Extensive green roofs
Invasion biology
Native plants
Roof cooling
Stormwater management
Advisor: MacIvor, J Scott
Cadotte, Marc W