Graduate Theses & Dissertations

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Deep learning for removal of non-resonant background in CARS hyperspectroscopy
In this work, a deep learning approach proposed by Valensise et al. [3] for extracting Raman resonant spectra from measured broadband CARS spectra was explored to see how effective it is at removing NRB from our experimentally measured “spectral-focusing”-based approach to CARS. A large dataset of realistic simulated CARS spectra was used to train a model capable of performing this spectral retrieval task. The non-resonant background shape used in creating the simulated CARS spectra was altered, to mimic our experimentally measured NRB response. Two models were trained: one using the original approach (Specnet) and one using the updated NRB “Specnet Plus”, and then tested their ability to retrieve the vibrationally resonant spectrum from simulated and measured CARS spectra. An error analysis was performed to compare the model's retrieval performance on two simulated CARS spectra. The modified model's mean squared error value was five and two times lower for the first and second simulated CARS spectra, respectively. Specnet Plus was found to be more effective at extracting the resonant signals. Finally, the NRB extraction abilities of both models are tested on two experimentally measured CARS hyperspectroscopy samples (starch and chitin), with the updated NRB model (Specnet Plus) outperforming the original Specnet model. These results suggest that tailoring the approach to reflect what we observe experimentally will improve our spectral analysis workflow and increase our imaging potential. Author Keywords:
Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec
Genetic variation is the raw material and basis for evolutionary changes in nature. The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision making. Whole genome analysis can be an asset to conservation biology and the management of species through the generation of more precise and novel metrics. This thesis uses whole genome re-sequencing to characterize the demographic history and quantify genomic metrics relevant to conservation of caribou (Rangifer tarandus) in Québec, Canada. We calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. When compared to the census size, NC, the endangered Gaspésie Mountain caribou population had the highest ancestral Ne:NC ratio which is consistent with recent work suggesting high ancestral Ne:NC is of conservation concern. These ratios were highly correlated with genomic signatures (i.e. Tajima’s D) of recent population declines and explicit demographic model parameters. Values of contemporary Ne, estimated from linkage-disequilibrium showed Gaspêsie having among the highest contemporary Ne:NC ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based off this metric alone. Inbreeding measures suggested nuanced patterns of inbreeding and correlated to the demographic models. This study suggests that while the Québec populations are all under decline, they harbour enough ancestral genetic variation to replenish any lost diversity, if conservation decisions are made in favour of these populations, specifically supporting NC. Author Keywords:
Demography of a Breeding Population of Whimbrel (Numenius phaeopus) Near Churchill, Manitoba, Canada
I used a GIS raster layer of an area in the Churchill, Manitoba region to investigate the effect of breeding habitat on demography and density of Whimbrel from 2010 through 2013. Program MARK was used to quantify adult and daily nest survival. Apparent annual survival of 0.73 ± 0.06 SE (95% CI = 0.60-0.83) did not significantly differ between sexes or habitats and was lower than expected based on longevity records and estimates for other large-bodied shorebirds. Nest success, corrected for exposure days, was highly variable, ranging from a low of 3% (95% CI = 0-12%) in 2011 to a high of 71% (95% CI = 54-83%) in 2013. The highest rate of nest survival occurred in the spring with the warmest mean temperature. I developed a generalized linear model (GLM) with a negative-binomial distribution from random plots that were surveyed for abundance to extrapolate a local breeding population size of 410 ± 230 SE and density of 3.2 birds per square km ± 1.8 SE. The result of my study suggests that other aspects of habitat not captured by the land cover categories may be more important to population dynamics. Author Keywords: abundance, apparent survival, curlew, land cover map, nest-site fidelity, nest success
Detectability and its role in understanding upland sandpiper (Bartramia longicauda) occurence in the fragmented landscape of southern Ontario
Upland Sandpipers (Bartramia longicauda), like many grassland birds, are undergoing population decline in parts of their range. Habitat fragmentation and change have been hypothesized as potential causes of decline. I used citizen-science occurrence data from Wildlife Preservation Canada’s Adopt-A-Shrike Loggerhead Shrike (Lanius ludovicianus) program in conjunction with validation surveys, using similar point-count methods, to examine detectability and determine if landscape level habitat features could predict occupancy of Upland Sandpipers in Southern Ontario. In a single season detectability study, I used Wildlife Preservation Canada’s survey protocol to determine detectability in sites that were known to be occupied. Detectability was low, with six surveys necessary to ensure detection using a duration of at least 18 minutes early in the breeding season. The proportion of open habitat did not affect detection on the landscape. Using a larger spatial and temporal scale, with five years of citizen-science data, I showed that Annual Crop Inventory data could not effectively predict Upland Sandpiper occupancy. Model uncertainty could be attributed to survey protocol and life history traits of the Upland Sandpiper, suggesting that appropriate survey methods be derived a priori for maximizing the potential of citizen-science data for robust analyses. Author Keywords: Bartramia longicauda, citizen-science, detection, landscape, occupancy, Ontario
Detecting anti-estrogens and anti-androgens in surface waters impacted by municipal wastewater discharges and agricultural runoff
This study focused on detecting 22 target anti-estrogenic and anti-androgenic compounds in surface waters influenced by both discharges of municipal wastewater and agricultural runoff in Canada and Argentina. Polar organic chemical integrative samplers (POCIS) were used to monitor the target compounds in surface waters. The removals of the target compounds in a municipal wastewater treatment plant (WWTP) in Canada were also evaluated. In both Canada and Argentina pesticides with potential anti-estrogenic and anti-androgenic activities were detected in the surface waters. The highest concentrations were found in Argentina (up to 1010 ng L-1) in areas impacted by heavy agricultural practices. Cyproterone acetate and bicalutamide were the only two anti-cancer drugs detected only at the Canadian study site, the Speed River, ON. In the Guelph WWTP, that discharges into the Speed River, these target compounds were not all efficiently removed (>70%) during treatment. Overall, this study provides insight to possible anti-estrogenic and anti-androgenic compounds that may be contributing to endocrine disrupting activities in surface waters. Author Keywords: Anti-androgens, Anti-estrogens, Cancer Therapy Drugs, Current use pesticides, Pharmaceuticals and Personal Care Products, Polar Organic Chemical Integrative Samplers
Detection of four at-risk freshwater pearly mussel species (Bivalvia
Environmental DNA (eDNA) detection uses species-specific markers to screen DNA from bulk samples, such as water, to infer species presence. This study involved the development and testing of species-specific markers for four freshwater pearly mussels (Unionidae). The markers were applied to water samples from intensively sampled mussel monitoring sites to compare species detections from eDNA with established sampling method detections. Target species were detected using eDNA at all sites where they had previously been detected by quadrat sampling. This paired design demonstrated that eDNA detection was at least as sensitive as quadrat sampling and that high species specificity can be achieved even when designing against many sympatric unionids. Detection failures can impede species conservation efforts and occupancy estimates; eDNA sampling could improve our knowledge of species distributions and site occupancy through increased sampling sensitivity and coverage. Author Keywords: conservation genetics, cytochrome oxidase subunit I (COI), environmental DNA (eDNA), quantitative PCR (qPCR), species at risk (SAR)
Determinants of Breeding Bird Diversity in Ontario's Far North
190 species of birds are known to breed in Ontario’s far north making the region an important nursery for boreal birds. Digital point count data were collected using two different autonomous recording units (ARUs): one model with two standard microphones to detect birds and anurans, and one model with one standard microphone and one ultrasonic microphone for detecting bats. ARUs were deployed either in short or long-term plots, which were four to six days or approximately 10 weeks, respectively. I assessed differences in breeding bird richness detections between ARU and plot types. I also tested the relative impact of the habitat heterogeneity and species-energy hypotheses in relation to breeding birds and created predictive maps of breeding bird diversity for Ontario’s far north. I found no difference in species richness estimates between the two ARU models but found that long-term plots detected about 7 more bird species and 1.5 more anuran species than short-term plots. I found support for both the species-energy and habitat heterogeneity hypotheses, but support for each hypothesis varied with the resolution of the analysis. Species-energy models were better predictors of breeding bird diversity at coarser resolutions and habitat heterogeneity models were better predictors at finer resolutions. Breeding bird diversity was highest in the Ontario Shield Ecozone compared with the Hudson Bay Lowlands Ecozone, but concentrated areas of higher diversity found in the Lowlands were associated with large rivers and the associated coastlines. Author Keywords: boreal birds, breeding birds, habitat heterogeneity, Hill diversity, Ontario, species-energy hypothesis
Determinants of Deviance
Background: Researchers have provided evidence that attachment may be independently linked to early adversity and criminal behaviour. In this study, I examined the combined associations among these variables in a student and community sample. Method: The first study consisted of undergraduate students (n = 590) who completed surveys to assess early adversity (Felitti, et al., 1988), attachment (Scharfe, 2016), and criminal behaviours. Participants were grouped based on their reports of adverse experiences and engagement in criminal behaviour. The second study was a replication of the first using a community sample (n = 294). Results: My hypotheses were partially supported, and my findings were consistent across Study 1 and Study 2. As I expected, there was a significant main effect for adversity when examining the mean scores of the attachment representations for attachment to mothers (Study 1 F (16, 1763.402) = 3.61, p < .001; Study 2 (F (16, 849.942) = 2.377, p = .002) and attachment to fathers (Study 1 F (16, 1763.402) = 4. 349, p < .001; Study 2 (F (16, 840.776) = 3.067 p < .001)). From examining the means, I concluded that participants who reported greater adversity reported higher insecure-avoidant and lower secure attachment to mothers and fathers. There were no significant main effects for criminal behaviour or significant interaction effects. Impact: To date, no study has explored all three variables explicitly. My findings are able to highlight the critical importance of secure attachment relationships and add further comprehension to exploring factors associated to criminal behaviour. Author Keywords: Attachment, Criminal Behaviour, Early Adversity
Developing Social-Emotional Competencies in Youth
Trait Emotional Intelligence (TEI) plays an important role in the health and wellness of children and adolescents. Not surprisingly, the literature on TEI and youth has expanded dramatically. Although the quality of this work continues to be uneven due to the continued proliferation of TEI-related measures with questionable psychometric features. One over-looked TEI measure in the field is the short form developed for the Emotional Quotient Inventory Youth Version (EQ-i:YV-S). The core goal of Study 1 was to examine the overall reliability and validity of the EQ-i:YV-S. The aim of Study 2 was to evaluate the utility of the EQ-i:YV-S as a measure of the effectiveness of a new school-based social and emotional learning program for elementary school students. Results from Study 1 demonstrated that the EQ-i:YV-S had good internal reliability, 6-month test-retest reliability, and convergent validity. Study 2 found that Total EI and most key EI-related dimensions had significant improvement from pretest to post test on the EQ-i:YV-S. These findings have important implications for TEI measurement in youth and the effectiveness of school-based psychoeducational programming for TEI, with the EQ-i:YV-S as a viable option for research in this area. Author Keywords: emotional intelligence, psychoeducational programming, social-emotional competencies
Developing social skills
Guidelines regarding social skills interventions for children with ASD suggest incorporating a holistic approach. This includes increasing the family’s understanding of deficits associated with ASD, integrations of natural environments, and parents as active agents while supporting their well-being. The current availability of holistic parent-mediated interventions for children with ASD is limited, with no qualitative understanding of its potential benefits for either the parent or child. The current study examined qualitative parent reports on a parent-mediated social skills intervention for children with ASD (TalkAbilityTM) incorporating a longitudinal approach (i.e., 6-month follow-up). Following Braun and Clarke’s model of thematic analysis, data was coded into four themes: 1) communication difficulties, frustrations and progress, 2) social relationships and concerns, 3) communication strategies, and 4) thoughts and emotions surrounding TalkAbilityTM. Results highlight the importance of considering parent experiences regarding interventions for their child’s social communication skills through a qualitative viewpoint. Author Keywords: autism spectrum disorder, parent-mediated intervention, qualitative review
Development and Use of Passive Samplers for Monitoring Dissolved and Nanoparticulate Silver in the Aquatic Environment
Silver nanoparticles (nAg) are the largest and fastest growing class of nanomaterials, and are a concern when released into aquatic environments even at low μg L-1+). Diffusive gradient in thin films (DGT) with a thiol-modified resin were used to detect labile silver and carbon nanotubes (CNT-sampler) were used to measure nAg. Laboratory uptake experiments in lake water provided an Ag+ DGT diffusion coefficient of 3.09 x 10 -7 cm2s-1 and CNT sampling rates of 24.73, 5.63, 7.31 mL day-1, for Ag+, citrate-nAg and PVP-nAg, respectively. The optimized passive samplers were deployed in mesocosms dosed with nAg. DGT samplers provided estimated Ag+ concentrations ranging from 0.15 to 0.98 μg L-1 and CNT-samplers provided nAg concentrations that closely matched measured concentrations in water filtered at 0.22 μm. Author Keywords: ICP-MS, mesocosms, nanoparticles, nanosilver, passive sampling
Development of a Cross-Platform Solution for Calculating Certified Emission Reduction Credits in Forestry Projects under the Kyoto Protocol of the UNFCCC
This thesis presents an exploration of the requirements for and development of a software tool to calculate Certified Emission Reduction (CERs) credits for afforestation and reforestation projects conducted under the Clean Development Mechanism (CDM). We examine the relevant methodologies and tools to determine what is required to create a software package that can support a wide variety of projects involving a large variety of data and computations. During the requirements gathering, it was determined that the software package developed would need to support the ability to enter and edit equations at runtime. To create the software we used Java for the programming language, an H2 database to store our data, and an XML file to store our configuration settings. Through these choices, we can build a cross-platform software solution for the purpose outlined above. The end result is a versatile software tool through which users can create and customize projects to meet their unique needs as well as utilize the features provided to streamline the management of their CDM projects. Author Keywords: Carbon Emissions, Climate Change, Forests, Java, UNFCCC, XML

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