Changes in the Ecology and Abundance of Smallmouth Bass in Lake Ontario: 1958-2014

Understanding the reasons for long-term population change in a species requires an evaluation of ecological variables that may account for the observed dynamics. In this study, long-term changes in indices of Smallmouth Bass condition and population levels were examined for eastern Lake Ontario and the Bay of Quinte. Smallmouth Bass are an extremely important recreational fish species native to Lake Ontario. They have experienced numerous changes in their environment through direct human impacts, climate change, predation, and habitat sharing with non-native species. Smallmouth Bass have experienced an increase in body length and weight likely due to a diet shift from crayfish to predominantly Round Gobies which has allowed them to increase their growth rate. According to existing assessment data however, this increase in body size has not been associated with an increase in abundance. Long-term data from gill net sampling shows that Smallmouth Bass populations have been declining since the late 1980s with no indication of recovery. This could be due to a variety of factors, but it is most likely due to a change in the selectivity of gill nets because of the change in body size as well as a habitat shift away from gill net sampling sites. Adjusting for gill net selectivity has revealed that sub-adult bass abundance is currently greater than it was historically, and that very large bass are likely not being retained within the gill nets that are currently used. The use of a long-term data set in this study has led to a much better understanding of Smallmouth Bass abundance and ecology.

ENVIRONMENTAL INFLUENCES AND EPIGENETIC MECHANISMS IN RISK FOR DEPRESSION

Genetic and environmental factors interact to influence vulnerability for internalizing psychopathology, including Major Depressive Disorder (MDD). The mechanisms that account for how environmental stress can alter biological systems are not yet well understood yet are critical to develop more accurate models of vulnerability and targeted interventions. Epigenetic influences, and more specifically, DNA methylation, may provide a mechanism by which stress could program gene expression, thereby altering key systems implicated in depression, such as frontal-limbic circuitry and its critical role in emotion regulation. This thesis investigated the role of environmental factors from infancy and throughout the lifespan affecting the serotonergic (5-HT) system in the vulnerability to and treatment of depression and anxiety and potential underlying DNA methylation processes. First, we investigated the contributions of additive genetic vs. environmental factors on an early trait phenotype for depression (negative emotionality) in infants and their stability over time in the first 2 years of life. We provided evidence of the substantial contributions of both genetic and shared environmental factors to this trait, as well as genetically- and environmentally- mediated stability and innovation. Second, we studied how childhood environmental stress is associated with peripheral DNA methylation of the serotonin transporter gene, SLC6A4, as well as long-term trajectories of internalizing behaviours. There was a relationship between childhood psychosocial adversity and SLC6A4 methylation in males, as well as between SLC6A4 methylation and internalizing trajectory in both sexes. Third, we investigated changes in emotion processing and epigenetic modification of the SLC6A4 gene in depressed adolescents before and after Mindfulness-Based Cognitive Therapy (MBCT). The alterations from pre- to post-treatment in connectivity between the ACC and other network regions and SLC6A4 methylation suggested that MBCT may work to optimize the connectivity of brain networks involved in cognitive control of emotion as well as also normalize the relationship between SLC6A4 methylation and activation patterns in frontal-limbic circuitry. Our results from these three studies strengthen the theory that environmental influences are critical in establishing early vulnerability factors for MDD, driving epigenetic processes, and altering brain processes as an individual undergoes treatment, or experiences relapse.

Towards Mapping of Rock Walls Using a UAV-Mounted 2D Laser Scanner in GPS Denied Environments

In geotechnical engineering, the stability of rock excavations and walls is estimated by using tools that include a map of the orientations of exposed rock faces. However, measuring these orientations by using conventional methods can be time consuming, sometimes dangerous, and is limited to regions of the exposed rock that are reachable by a human. This thesis introduces a 2D, simulated, quadcopter-based rock wall mapping algorithm for GPS denied environments such as underground mines or near high walls on surface. The proposed algorithm employs techniques from the field of robotics known as simultaneous localization and mapping (SLAM) and is a step towards 3D rock wall mapping. Not only are quadcopters agile, but they can hover. This is very useful for confined spaces such as underground or near rock walls. The quadcopter requires sensors to enable self localization and mapping in dark, confined and GPS denied environments. However, these sensors are limited by the quadcopter payload and power restrictions. Because of these restrictions, a light weight 2D laser scanner is proposed. As a first step towards a 3D mapping algorithm, this thesis proposes a simplified scenario in which a simulated 1D laser range finder and 2D IMU are mounted on a quadcopter that is moving on a plane. Because the 1D laser does not provide enough information to map the 2D world from a single measurement, many measurements are combined over the trajectory of the quadcopter. Least Squares Optimization (LSO) is used to optimize the estimated trajectory and rock face for all data collected over the length of a light. Simulation results show that the mapping algorithm developed is a good first step. It shows that by combining measurements over a trajectory, the scanned rock face can be estimated using a lower-dimensional range sensor. A swathing manoeuvre is introduced as a way to promote loop closures within a short time period, thus reducing accumulated error. Some suggestions on how to improve the algorithm are also provided.

The application of PCA as a movement pattern recognition technique: A proof of principle

Quantitative methods can help us understand how underlying attributes contribute to movement patterns. Applying principal components analysis (PCA) to whole-body motion data may provide an objective data-driven method to identify unique and statistically important movement patterns. Therefore, the primary purpose of this study was to determine if athletes’ movement patterns can be differentiated based on skill level or sport played using PCA. Motion capture data from 542 athletes performing three sport-screening movements (i.e. bird-dog, drop jump, T-balance) were analyzed. A PCA-based pattern recognition technique was used to analyze the data. Prior to analyzing the effects of skill level or sport on movement patterns, methodological considerations related to motion analysis reference coordinate system were assessed. All analyses were addressed as case-studies. For the first case study, referencing motion data to a global (lab-based) coordinate system compared to a local (segment-based) coordinate system affected the ability to interpret important movement features. Furthermore, for the second case study, where the interpretability of PCs was assessed when data were referenced to a stationary versus a moving segment-based coordinate system, PCs were more interpretable when data were referenced to a stationary coordinate system for both the bird-dog and T-balance task. As a result of the findings from case study 1 and 2, only stationary segment-based coordinate systems were used in cases 3 and 4. During the bird-dog task, elite athletes had significantly lower scores compared to recreational athletes for principal component (PC) 1. For the T-balance movement, elite athletes had significantly lower scores compared to recreational athletes for PC 2. In both analyses the lower scores in elite athletes represented a greater range of motion. Finally, case study 4 reported differences in athletes’ movement patterns who competed in different sports, and significant differences in technique were detected during the bird-dog task. Through these case studies, this thesis highlights the feasibility of applying PCA as a movement pattern recognition technique in athletes. Future research can build on this proof-of-principle work to develop robust quantitative methods to help us better understand how underlying attributes (e.g. height, sex, ability, injury history, training type) contribute to performance.

Provenance of Holocene Calcareous Aeolianites, Eastern South Australia

The southeastern coast of South Australia contains a spectacular and world-renown suite of Quaternary calcareous aeolianites. This study is focused on the provenance of components in the Holocene sector of this carbonate breach-dune succession. Research was carried out along seven transects from ~30 meters water depth offshore across the beach and into the dunes. Offshore sediments were acquired via grab sampling and SCUBA. Results indicate that dunes of the southern Lacepede and Otway coasts in particular are mostly composed of modern invertebrate and calcareous algal allochems. The most numerous grains are from molluscs, benthic foraminifera, coralline algae, echinoids, and bryozoans. These particles originate in carbonate factories such as macroalgal forests, rocky reefs, seagrass meadows, and low-relief seafloor rockgrounds. The incorporation of carbonate skeletons into coastal dunes, however, depends on a combination of; 1) the infauna within intertidal and nearshore environments, 2) the physical characteristics of different allochems and their ability to withstand fragmentation and abrasion, 3) the wave and swell climate, and 4) the nature of aeolian transport. Most aeolian dune sediment is derived from nearshore and intertidal carbonate factories. This is particularly well illustrated by the abundance of robust infaunal bivalves that inhabit the nearshore sands and virtual absence of bryozoans that are common as sediment particles in water depths > 10mwd. Thus, the calcareous aeolianites in this cool-water carbonate region are not a reflection of the offshore marine shelf factories, but more a product of shallow nearshore-intertidal biomes.

‘Black Settlers’: Hybridity, Neoliberalism and Ecosystemic Change Among Tonga Farmers of Southern Zambia, 1964-2008

This dissertation examines a process of indigenous accumulation among Tonga farmers in Zambia’s Southern Province. In the 1970s multiple authors concluded that capitalist farmers had emerged among Tonga agro-pastoralists, predominantly within private titled holdings. Relying on archival research, newspapers, secondary sources and extensive oral testimony this thesis fills a 35-year gap on the topic, providing insights into the social and environmental impacts of neoliberal policy among African peasants and capitalist farmers. In contrast to dominant narratives of the post-independence period, this study argues that Zambia did experience a developmental process post-independence, which saw significant achievements made in the agricultural sector, including the doubling of national cattle stocks. The data reveals a painful process of disarticulation beginning in the late 1980s. Following neoliberal adjustment, we observe significant heterogeneity in production systems, some regional specialization, and processes of migration. Most importantly, the thesis uncovers processes of overwhelming ecosystemic change that contributed to livestock epidemics of severe scale and scope. Amazingly, this went largely undocumented because of the simultaneous crisis of the state, which left the national statistics office and other state bodies incapable of functioning from the late 1980s into the 2000s. In response, the Zambian state has introduced a number of neodevelopmental initiatives in the sector, yet the lack of animal traction remained up to 2008 and agricultural production declined, while more capitalized farmers (largely white, and/or with foreign direct investment) have become more significant players in the country. This thesis provides compelling evidence to challenge dominant economic thinking of the Washington institutions as well as many of the common Marxian formulations.

EXAMINING HOW SAME-GENDER AND MIXED-GENDER COUPLES NAVIGATE SEXUAL ISSUES IN THEIR RELATIONSHIPS

Sexual scripts—the definitions and expectations that individuals hold for sexual interactions—are thought to play an important role in the maintenance of sexual well-being. Sexual scripts can be rigid or flexible, and they can be concordant or discordant between members of a couple. Sex therapists support sexual script flexibility for maintaining sexual and relationship satisfaction when couples are navigating sexual issues. However, empirical research examining the role of sexual script flexibility and the degree of script concordance/discordance in couples’ sexual well-being has been limited, due in part to the limited measures available. Furthermore, within the existing research, there has been an unfortunate tendency to exclude individuals in same-gender relationships – perpetuating the long-standing knowledge gap in the literature on positive sexuality in diverse relationships. To address these gaps in the literature, we conducted a series of online studies that recruited individuals in diverse relationships. A measure of individual sexual script flexibility in response to sexual issues was developed (Chapter 2); in addition, the structure of an existing measure assessing couple sexual scripts in response to a sexual issue was evaluated (Chapter 3). Chapter 4 examined how individuals in diverse relationships compared on measures of individual sexual script flexibility and on couple sexual scripts. Findings suggest that there are more similarities than differences across diverse couples. Chapter 5 explored how flexibility in an individual’s approach to sexual issues relates to sexual well-being, specifically by assessing sexual communication and partner responses as mediators. Results suggest that individual sexual script flexibility relates to sexual well-being through reciprocal partner processes. Collectively, this research program suggests that more similarities than differences exist between individuals in same- and mixed-gender relationships, and that partners are important to consider in the relationship between individual sexual script flexibility and sexual well-being. These findings have implications for sex and couple therapy; these results emphasize the importance of interventions that target both members of the couple, and further our understanding of sexuality in same- and mixed-gender relationships.

Investigating the Role of PDE4D1/2 in Vascular Smooth Muscle Cell Desensitization

Vascular smooth muscle cell (VSMC) behaviour and phenotypic modulation is critical to vessel repair following damage, and the progression of various cardiovascular diseases. The second messenger cyclic adenosine monophosphosphate (cAMP) plays a key role in VSMC function under the synthetic/activated phenotype, which is typically associated with unhealthy cell behaviour. Consequently, cAMP signaling is often targeted in attempts to impact several pathological diseases, including atherosclerosis, restenosis, and pulmonary arterial hypertension (PAH). The cyclic nucleotide phosphodiesterases (PDEs) catalyze hydrolysis of cAMP to an inactive form, and therefore directly regulate cAMP signaling. The PDE4D family dominates in synthetic VSMCs, and there is considerable interest in determining how distinct PDE4D isoforms affect cell function. Specifically, we are interested in the potential link between short isoforms of PDE4D and VSMC desensitization to pharmacological agents that impact cardiovascular disease via cAMP signaling. This study extends on previous work that assessed the expression of PDE4D splice variants in rat aortic VSMCs following prolonged challenge with cAMP-elevating agents. It was determined that PDE4D1 and PDE4D2 were uniquely expressed in synthetic VSMCs incubated with these agents, and that this upregulation impacted PDE activity and cAMP accumulation in these cells. Here, we report that PDE4D1 and PDE4D2 are markedly upregulated in synthetic human aortic smooth muscle cells (HASMCs) following prolonged challenge with cAMP-elevating agents. Using a combination of RNAi-based and pharmacological approaches, we establish that this upregulation is reflected in levels of cAMP PDE activity, and restricted to the cytosolic sub-cellular compartment. Our results suggest a role for localized PDE4D1 and PDE4D2 activity in regulating cAMP-mediated desensitization in HASMCs, and highlight their therapeutic potential in treating various cardiovascular diseases.

If People Were Kaleidoscopes: Sharpening the Resolution on Patient Engagement in Safety

Healthcare is unacceptably error prone. The question remains why, with 20 years of evidence, is error and harm reduction not being effective? While precise numbers may be debated, all stakeholders recognize the frequency of healthcare errors is unacceptable, and greater efforts to ensure safety must occur. In recent years, one of these strategies has been the inclusion of the patient and their family as partners in safety, and has been a required organizational practice of Accreditation Canada in many of their standard sets. Existing patient advisories created to encourage engagement, have typically not included patient perspectives in their development or been comprehensively evaluated. There are no existing tools to determine if and how a patient wants to be involved in safety engagement. As such, a multi-phased study was undertaken to advance our knowledge about the client’s and family’s role in promoting safety. Phase 1 of the study was a scoping review to methodically review the existing literature about patients’ and families’ attitudes, beliefs and behaviours about their involvement in healthcare safety. Phase 2 was designed to inductively explore how a group of patients in an Ontario, Canada, community hospital, describe healthcare safety and see their role in preventing error. The study findings, which include the narratives of 30 patients and 4 family members, indicate that although there are shared themes that influence a patient’s engagement in patient safety, every individual has unique, changing beliefs, experiences and reasons for involvement. Five conceptual themes emerged from their narratives: Personal Capacity, Experiential Knowledge, Personal Character, Relationships, and Meaning of Safety. These study results will be used to develop and test a pragmatic, accessible tool to enable providers a way to collaborate with patients for determining their personal level and type of safety involvement. The most ethical and responsible approach to healthcare safety is to consider every facet and potential way for improvement. This exploratory study provides fundamental insights into the complexity of patient engagement in safety, and evidence for future steps.

A Restorative Theory of Criminal Justice

In this project, I defend a restorative theory of criminal justice. I argue that the response to criminal wrongdoing in a just society should take the form of an attempt to heal the damage done to the community resulting from crime. I argue that the moral responsibilities of wrongdoers as wrongdoers ought to provide the framework for how a just society should respond to crime. Following the work of R.A. Duff, I argue that wrongdoers incur second-order duties of moral recognition. Wrongdoers owe it to others to recognize their wrongdoing for what it is, i.e. wrongdoing, and to shoulder certain burdens in order to express their repentant recognition to others via a meaningful apology. In short, wrongdoers owe it to their victims and others in the community to make amends. What I will deny, however, is the now familiar claim in the restorative justice literature that restoring the normative relationships in the community damaged by criminal forms of wrongdoing requires retributive punishment. In my view, how we choose to express the judgement that wrongdoers are blameworthy should flow from an all things considered judgment that is neither reducible to the judgement that the wrongdoer is culpably responsible for wronging others, nor the judgement that the wrongdoer in some basic sense “deserves to suffer” (or “deserves punishment,” etc.).

Paternalism and Competent Patient Choice in the Standards of Care for the Health of Transsexual, Transgender, and Gender-Nonconforming People

In 2016 physicians in Ontario will be granted the authority to refer patients with gender dysphoria for sex reassignment surgery. In order to be granted this authority physicians must be trained in the World Professional Association for Transgender Health’s Standards of Care, which outlines healthcare procedures for the treatment of gender dysphoria and provides background information concerning transgender health. The Standards of Care require that patients undergo a process of 12 months of continuous living in a gender role that is congruent with their gender identity prior to being given access to sex reassignment surgery. While this requirement can sometimes be helpful it can also cause more harm than benefit. This paper argues that the requirement is strongly paternalistic in its current form and should no longer be mandatory in most cases.

Communication-efficient decentralized sequential detection

The problem of decentralized sequential detection is studied in this thesis, where local sensors are memoryless, receive independent observations, and no feedback from the fusion center. In addition to traditional criteria of detection delay and error probability, we introduce a new constraint: the number of communications between local sensors and the fusion center. This metric is able to reflect both the cost of establishing communication links as well as overall energy consumption over time. A new formulation for communication-efficient decentralized sequential detection is proposed where the overall detection delay is minimized with constraints on both error probabilities and the communication cost. Two types of problems are investigated based on the communication-efficient formulation: decentralized hypothesis testing and decentralized change detection. In the former case, an asymptotically person-by-person optimum detection framework is developed, where the fusion center performs a sequential probability ratio test based on dependent observations. The proposed algorithm utilizes not only reported statistics from local sensors, but also the reporting times. The asymptotically relative efficiency of proposed algorithm with respect to the centralized strategy is expressed in closed form. When the probabilities of false alarm and missed detection are close to one another, a reduced-complexity algorithm is proposed based on a Poisson arrival approximation. In addition, decentralized change detection with a communication cost constraint is also investigated. A person-by-person optimum change detection algorithm is proposed, where transmissions of sensing reports are modeled as a Poisson process. The optimum threshold value is obtained through dynamic programming. An alternative method with a simpler fusion rule is also proposed, where the threshold values in the algorithm are determined by a combination of sequential detection analysis and constrained optimization. In both decentralized hypothesis testing and change detection problems, tradeoffs in parameter choices are investigated through Monte Carlo simulations.

The effects of the non-native invertebrate predator Bythotrephes longimanus and declining aqueous calcium on crustacean zooplankton communities in Canadian Shield lakes

Over the last several decades, human activities have resulted in environmental changes that have increased the number of stressors that can act on a single environment. In Canadian Shield lakes, two recent stressors, the invasion of Bythotrephes longimanus and calcium decline, have been documented. Widespread acidification of hundreds of North American lakes has resulted in the precipitous decline of lake water calcium concentration. Crustacean zooplankton with high calcium demands are likely to be vulnerable to calcium decline, especially <1.5 mg Ca/L, where survival and reproduction rates are reduced. These taxa are also vulnerable to predation by Bythotrephes that has been implicated in the loss of pelagic biodiversity in soft water lakes. Despite laboratory and field studies aimed at understanding the independent impact of these stressors, it is unclear how their co-occurrence will influence community response. Using a combination of data from a large regional lake survey and field experiments, I examined the individual and joint effects of Bythotrephes and calcium decline on native zooplankton community structure. Results demonstrated that much is known about Bythotrephes and our findings of reduced total zooplankton and species richness, due to the loss of Cladocera, are consistent with field surveys and other experimental studies. While we did not detect strong evidence for an effect of calcium on zooplankton using the lowest calcium concentration among invaded lakes (1.2 mg Ca/L), there is evidence that, as lake water calcium concentrations fall <1 mg Ca/L, per capita growth rates of a broad variety of taxa are expected to decline. At the regional scale, negative effects of Bythotrephes and calcium on abundances of small cladocerans and Daphnia pulicaria, respectively, were in agreement with my experimental observations. We also observed significant interactions between Bythotrephes and calcium for a broad variety of taxa. As Bythotrephes continues to spread and invade lakes that are also declining in aqueous calcium, both stressors are likely to amplify negative effects on Cladocera that appear the most vulnerable. Loss of these important zooplankton in response to both Bythotrephes and calcium decline, is likely to lower zooplankton productivity, with potential effects on phytoplankton and higher trophic levels.

Polymer Light-Emitting Electrochemical Cells with Embedded Bipolar Electrodes: Visualizing Bipolar Electrochemistry in Solid State

The work presented in this thesis examines the properties of BPEs of various configurations and under different operating conditions in a large planar LEC system. Detailed analysis of time-lapsed fluorescence images allows us to calculate the doping propagation speed from the BPEs. By introducing a linear array of BPEs or dispersed ITO particles, multiple light-emitting junctions or a bulk homojunction have been demonstrated. In conclusion, it has been observed that both applied bias voltages and sizes of BPEs affected the electrochemical doping from the BPE. If the applied bias voltage was initially not sufficiently high enough, a delay in appearance of doping from the BPE would take place. Experiments of parallel BPEs with different sizes (large, medium, small) demonstrate that the potential difference across the BPEs has played a vital role in doping initiation. Also, the p-doping propagation distance from medium-sized BPE has displayed an exponential growth over the time-span of 70 seconds. Experiments with a linear array of BPEs with the same size demonstrate that the doping propagation speed of each floating BPE was the same regardless of its position between the driving electrodes. Probing experiments under high driving voltages further demonstrated the potential of having a much more efficient light emission from an LEC with multiple BPEs.

Alteration mineralogy and pathfinder element inventory of the McArthur River unconformity-related uranium deposit, Canada

The chemical compositions, modal mineralogy, and textural variability of interstitial minerals in sandstones of the Athabasca Group strata in the vicinity of the McArthur River unconformity-related uranium deposit were characterized using a combination of short wave infrared spectroscopy (SWIR), lithogeochemistry, scanning electron microscopy (SEM), electron probe microanalysis (EPMA) and laser ablation mass spectrometry (LA-ICP-MS) to determine the residence sites of pathfinder trace elements. The importance of integrating in-situ mineral chemistry with whole-rock analyses resides in the possibility to establish the mineralogical and paragenetic context of geochemical signatures in defining the footprint of the deposit. Located in the Athabasca Basin, Saskatchewan, Canada, the deposit is situated below ~550 m of quartz arenitic sandstones that are strongly silicified between depths of approximately 200-400 m. The silicified layer exhibits significant control on the distribution of alteration minerals, and appears to have restricted both the primary and secondary dispersion of pathfinder trace elements, which include U, radiogenic Pb isotopes, V, Ni, Co, Cu, Mo, As, Zn, and REEs. Diagenetic background sandstones contain assemblages of illite, dickite, aluminum-phosphate-sulfate (APS) minerals, apatite, and Fe-Ti oxide minerals. Altered sandstones contain assemblages of Al-Mg chlorite (sudoite), alkali-deficient dravite, APS minerals, kaolinite, illite, and oxide minerals. Throughout the sandstones, APS minerals account for the majority of the Sr and LREE concentrations, whereas late pre-ore chlorite, containing up to 0.1 wt.% Ni, accounts for the majority of Ni concentrations. Cobalt, Cu, Mo, and Zn occur predominantly in cryptic sub-micron sulfide and sulfarsenide inclusions in clay mineral aggregates and in association with paragenetically-late Fe-Ti oxides. Uranium occurs predominantly in cryptic micro-inclusions associated with pyrite in late-stage quartz overgrowths, and with paragenetically late Fe-Ti oxide micro-inclusions in kaolinite. Additionally, up to 0.2 wt.% U is cryptically distributed in post-ore Fe-oxide veins. Early diagenetic apatite, monazite and apatite inclusions in detrital quartz, and detrital zircon also contribute significant U and HREE to samples analyzed with an aggressive leach such as Aqua Regia. Detailed LA-ICP-MS chemical mapping of interstitial assemblages, detrital grains, and cements provides new insights into the distribution and inventory of pathfinder elements in the footprint of the McArthur River uranium deposit.