VictorJuiz/thesis huggingface dataset:
The Importance of Thermal Preferences in Governing Fish Productivity, Foraging Behaviour, and Interactions in a Changing World

Fisheries are an important source of food, income, and recreation across the world, yet they are vulnerable to exploitation and environmental change. As ectotherms, a fish’s environment directly affects how it acquires and metabolizes energy. Energy acquisition and metabolism differ among fish species based on their unique diets, behaviours, and habitat preferences, resulting in differential (or asynchronous) responses to environmental change. Therefore, natural resource managers must learn these unique qualities and responses to create adaptive policies under changing conditions and protect fisheries into the future. However, research about the simultaneous effects of multiple interacting environmental factors on multiple interacting species is still at its infancy. My research seeks to understand the effects of environmental factors on the productivity of multiple fish species (referred to as fish productivity for the remainder of this thesis), as well as their behaviours, and interactions. First, I show that species-specific fish productivity (g·ha-1·yr-1) in inland lakes is differentially influenced by various abiotic (e.g. temperature, dissolved organic carbon, habitat area) and biotic (e.g. presence of predators and invasive species) factors. Second, I use stable isotopes to show that behavioural foraging (i.e., trophic position and habitat use) is mediated by local and broad-scale habitat conditions but does not necessarily reflect fish productivity. Third, I used a temperature-dependent food web model to study how thermal guild interactions are altered by changing environmental conditions, which may lead to unexpected outcomes of a species-removal management strategy. Together, my research suggests that fish species respond asynchronously to different environmental conditions. This means that some species may behave differently and be more or less productive than others when exposed to new conditions, which will manifest in unique species interactions and food web dynamics. Such information will be crucial for assessing the effectiveness of adaptive management policies in a changing climate.

Keywords: climate change
fisheries
freshwater
species interactions
Advisor: McMeans, Bailey C
Chu, Cindy
Ideological Intergroup Conflict and Cooperation

Ideological beliefs are strongly held, prescriptive beliefs about how a society should function. Differences in ideological beliefs can be a cause of intergroup conflict and a driver of polarization. This thesis explores how individuals react when encountering people and groups whose ideological beliefs conflict with their own. I find that across a range of ideological beliefs that span the political spectrum, people report similar experiences of ideological threat and intergroup perceptions and intentions. In each chapter, I explore ideological disagreement through the lens of different psychological phenomena. In Chapter 2, I use data-driven methods to build an evidence-based description of the attitudes and characteristics of political moderates. I show that moderates have more diverse and less extreme views than partisans, and confirm existing literature showing they are less prone to negative views and dogmatic ideological beliefs. However, I also show how the American culture war polarizes moderates' attitudes towards certain issues such that they resemble partisans' attitudes in their consistency and extremity. In Chapter 3, I investigate the relationship between perceptions of ideological threat and moral conviction. I find that perceptions of a preferred ideological policy as being under threat is related to higher moral conviction towards that policy. In Chapter 4, I develop a measure of ideological prejudice that captures negative attitudes towards both ideological outgroup members and their beliefs. I find that negative attitudes towards ideological outgroups largely centre around generalized dislike towards outgroup members and condemnation of ideologies that would restrict others' freedom of expression. Finally, in Chapter 5, I identify psychological mechanisms related to cooperative intentions towards ideological outgroup members. I design and test a series of wise interventions leveraging each mechanism. While I do not identify an effective intervention in this chapter, I discuss insight gained from these tests and the identified correlates of cooperation. In this thesis, I seek insight into ideological disagreement through the lens and tools of social psychology. Overall, I find evidence that individual ideological beliefs have great power over perceptions of the social world and engagement with it.

Keywords: Conflict Resolution
Cooperation
Ideology
Intergroup Relations
Political Attitudes
Threat
Advisor: Page-Gould, Elizabeth
Estimating the Functional Impact of Single Amino Acid Changes Using Machine Learning

One of the great challenges in genetics is to accurately separate functional from neutral variation in human genome sequence. Towards more accurate pathogenicity prediction of human genetic variants, it has become possible to experimentally map the fitness landscape of missense mutations for specific targeted human disease-associated proteins. Coupling exhaustive mutagenesis with a deep sequencing read-out of multiplexed yeast functional complementation assays can yield a “variant effect map” covering most of possible amino acid changes in these proteins. The first challenge I wished to address is that for each variant effect map, a substantial minority of missense mutations remain unmeasured. The second challenge is that variant effect maps are available for less than 1% of disease-associated proteins, with a high-quality fully comprehensive experimental atlas of functional missense variation being likely decades in the future. Towards the first challenge, I imputed the functional effect of unmeasured variants using machine learning model trained on variants with experimental measurement, each of which is represented by a list of features including conservation scores, chemical physical proprieties of the residues, and engineered feature derived from the functional effect of similar amino acid substitutions in the same map. Towards the second challenge, I built a computational model VARITY to predict the pathogenicity of all possible missense variants for ~18,000 human proteins. I exploited a larger reservoir of training examples with uncertain accuracy and representativity, each assigned with a differential weight determined via hyperparameter tunning that optimizes predictive performance on a small high-quality set of annotated variants. Performance of the final model (VARITY) exceeds that of all analyzed previously described computational methods.

Keywords: Balanced Precision
Data quality and quantity
Variants Pathogenicity
Weighted training examples
Advisor: Roth, Frederick P
Digitisation, Dissemintation, and Reception of Percussion Performance: Evaluating YouTube Videos of John Cage's Third Construction Through Analysis and Case Studies

This dissertation investigates the digitisation, dissemination, and reception of percussion performance on YouTube. It examines three questions: 1) How has YouTube impacted the percussion field? 2) What are the available audiovisual recordings of John Cage’s Third Construction (1941) on YouTube and would analysing them illustrate consistencies and divergences in the performance practice of the work? 3) How would undergraduate percussionists who have never performed Third Construction evaluate selected performance videos of the work? Would their opinions on performance quality or accuracy of interpretation change if they watched these videos under differing conditions (e.g., with and without the musical score)? Chapter 2 describes academic research on the topic of YouTube, and summarizes the current video content pertinent to percussionists. Despite a well-established and thriving percussive subculture on the site, discussing YouTube as educational resource has not been substantially addressed within music performance scholarship. Chapter 3 presents a corpus study on performance videos of John Cage’s Third Construction (1941). In addition to outlining the processes of navigating, collecting, and analyzing data on a dynamic, digital environment, this corpus study presents qualitative and quantitative data on how percussionists have chosen to interpret Cage’s quartet. Chapter 4 presents the findings from a case study conducted on nine undergraduate percussionists. The participants were first asked questions about their uses of YouTube in a precursory survey. Participants then examined five excerpts of YouTube videos of Third Construction under two differing conditions: first, by simply watching them and; second, by following along with the musical score. Each viewing condition included questionnaires that solicited their opinions of the video excerpts. Chapter 5 summarizes the research findings. Despite the wealth of concerns to be had about the world’s largest tech corporations (e.g., data privacy, cyber security, censorship, anti-trust/monopolization), online videos of music performance present opportunities for future generations of scholars, educators, and students. Rather than seeking to reconcile the concerns with and benefits of these digital experiences, the author advocates that they should become a greater part of the discussions held within academic environments.

Keywords: audiovisual recordings
music education
music performance
percussion performance
performance analysis
YouTube
Advisor: Huang, Aiyun
Focusing Ultrasound to the Vertebral Canal

The blood spinal cord barrier (BSCB) and blood brain barrier (BBB) are semi-permeable barriers separating the spinal cord and brain vasculature from the parenchyma. Focused ultrasound can transiently open the BBB to improve therapeutic agent delivery to the brain. The extension of this technique to the human BSCB may similarly improve targeted therapies to the spinal cord. However, focusing ultrasound to the spinal cord is difficult because it is encased in the spine, which consists of stacked, irregularly shaped vertebrae that distort the intended foci. This thesis aimed to develop a spine-specific ultrasound array and simulation-based aberration correction method to generate a controlled focus in the intact vertebral canal. A spine-specific formulation of a multi-layered ray acoustics model was developed, and its accuracy characterized through comparison with set of 90 field measurements produced with a spherically focused 514kHz transducer. This model predicted maximum pressure locations and weighted focal volume locations with an accuracy of 2.3mm and 1.5mm respectively. The ray acoustics model was then used to optimize a vertebra-specific density (rho) - speed of sound (cL) function to maximize the model accuracy in calculating vertebra-induced time delays. A linear model was optimized in this work, cL(rho) = 0.35(rho - rho_w) + cL_w (w denotes water), which was able to reproduce the vertebra-induced delays with an accuracy of lambda/16, where lambda is the wavelength. The ray acoustics model was used to optimize the design of a spine-specific ultrasound phased array for maximum efficiency in focusing ultrasound through the posterior elements of the spine. The optimized array had four quadrants, two 64-element arrays for focusing ultrasound through the vertebra laminae, and two 64-element arrays for focusing ultrasound through the paravertebral spaces. One array quadrant was built and used to demonstrate transspine beamforming with geometric delays, hydrophone-based delays, and delays calculated with the ray acoustics model. The ray acoustics delays outperformed the geometric delays, but not the hydrophone-based delays. Demonstrating the feasibility of ultrasound array-based focusing through the spine is a critical step to advancing ultrasound treatments of the spinal cord.

Keywords: Beamforming
Focused Ultrasound
Phased Array
Simulation
Spine
Vertebrae
Advisor: O'Reilly, Meaghan A.
Three Essays in Labour Economics and Applied Econometrics

The dissertation is comprised of three chapters. Chapter 1 investigates the marital behaviour of veterans.I first examine the extent to which military service makes men more marriageable using the NLSY97. I present evidence that non-college blacks enjoy the greatest return to military service in both the labour and marriage market. Second, to explain the relatively high intermarriage rates among veterans, I apply a local log odds framework to Census data to examine the social exchange hypothesis. Consistent with this hypothesis, I find both white and black women demand compensation to intermarry. Third, I present evidence in favour of the contact hypothesis. Chapter 2 evaluates the effects of racial integration during the Korean War (1950-1953). First, I evaluate whether the Army achieved its goal of improving efficiency as measured by the survival rates of wounded soldiers. Using casualty data, I develop a novel wartime integration measure to quantify exogenous changes in racial integration over time and across regiments. Based on a two-way fixed effects model, I find that a one standard deviation increase in integration improved overall casualty survival rates by 3%. Second, I explore the effects of wartime racial integration on the prejudicial attitudes of veterans after the war. To do so, I link individual soldiers to post-war social security and cemetery data using the expectation maximization algorithm. With these linked samples, I show that a one standard deviation increase in wartime racial integration caused white veterans to live in more racially diverse neighborhoods and marry spouses with less distinctively white names. Chapter 3 addresses the misuse of out-of-sample predictive performance tests for model selection. I compare in-sample alternatives for non-nested hypothesis testing of two possibly misspecified models developed by Vuong (1989), and compare those to the out-of-sample tests developed by Clark and McCracken (2014). Using Monte Carlo simulations, I demonstrate that the out-of-sample procedure indeed exhibits markedly worse statistical size and power. I then reproduce an applied example on GDP growth where the conclusions are found to be sensitive to the choice of out-of-sample versus full sample procedure.

Advisor: Siow, Aloysius
Eli, Shari
Nursing Students’ Self-efficacy to Care for Older Adults in Acute Care Settings in Ghana: A Mixed Method Study

Self-efficacy has been reported to serve as a motivator for goal achievement and to impact care quality and career development choices. Understanding nursing students’ self-efficacy to care for older adults can provide an opportunity to identify gaps and develop strategies to shape nursing students’ interest in caring for older adults. This study sought to identify the relationship between nursing students’ knowledge about, attitudes towards, and self-efficacy to care for older adults and explored nursing students’ understanding of their self-efficacy to care for older adults. The study also examined stakeholders’ perceptions about nursing students’ self-efficacy to care for older adults and how these views shape gerontological nursing education and practice in Ghana. Bandura’s self-efficacy theory guided this study. Results of this sequential explanatory mixed-method study showed that nursing students’ age and attitudes towards older adults were associated with their self-efficacy to care for older adults. Content knowledge about gerontology was not associated with self-efficacy. Nursing students suggested their self-efficacy to care for older adults was based on their perceived competency in routine procedural nursing care, the impact of the general nursing education program, and the sociocultural norms of caring for older adults in Ghana. Stakeholders indicated that nursing students were well prepared and confident to care for older adults and that the general nursing education program and sociocultural norms of caring for older adults enhanced nursing students’ self-efficacy to care for older adults; however, they also acknowledged the need for gerontological clinical placements for nursing students and the challenges of the gerontology curriculum in the general nursing program. Findings suggest a need for a larger study encompassing different nursing training institutions to determine the extent of revisions needed in gerontological nursing curricula. Findings also indicate a need for gerontological nursing clinical placements to enhance students’ gerontological skills development, for capacity building of faculty, and for the government’s commitment to invest in gerontology education and practice.

Keywords: Gerontological nursing
Instrument adaptation
Knowledge
Nursing students
Older adults
Self-efficacy
Advisor: Cranley, Lisa
Puts, Martine
Three Papers in Game Theory and Organizational Economics

This thesis includes three chapters. The common theme among the chapters is the application of game theory to gain insights in organizational economics. In Chapter 1, titled "Customizability in Negotiations", I propose a model where the buyer and seller can trade a customizable product where some attributes are optional and can be removed. The buyer privately knows his type. The buyer and seller play a one shot bargaining game where the player chosen can make a menu of offers. I show that as customizability increases it becomes easier for the seller to screen the buyer which increases the probability of agreement. Lastly I show that customizability will always benefit the seller, however it can make the buyer worse off. In Chapter 2, titled "Cheap Talk in Win-Win Negotiations", I propose a model where the buyer and seller can trade a customizable product just like in Chapter 1. In this Chapter though, I make several key changes. All attributes can now be kept or removed. The buyer can report his privately known type to the seller at the beginning of the game and it is the seller's responsibility to design the product. I show that in a one-shot offer game the buyer will always disclose truthfully. I then extend these results to the alternating offer framework. This suggests a mechanism for why credible talk can exist in a bargaining game. In Chapter 3, titled "Disclosure in Agency Problems", I propose a two sided moral hazard model where on the agent's side is a traditional unobservable effort problem while on the principal's side is a disclosure problem. The principal might have private information about the potential output that he can disclose to an agent. His disclosure decision is not contractible but if he discloses, the information is verifiable. I show that in such an environment, the principal will not disclose private information that reflects the potential of a low outcome. I then show that if the disclosure decision is contractible, the principal will write a contract that allows him to commit to full-disclosure.

Keywords: Game Theory
Negotiations
Organizational Economics
Advisor: Deb, Rahul
The Design and Development of Organotellurium Scaffolds for Mass Cytometry

Fluorescence-based Cytometry (FC) is an essential technique in investigating heterogeneous cell populations. FC uses tagged antibodies to detect biomarkers on individual cells. However, the inherent spectral overlap between fluorophores limits the use of the methodology in highly multiparametric assays. In recent years, mass cytometry (MC) has emerged as an effective alternative technique to study heterogenous cell populations in highly parameterized assays. MC utilizes bio-orthogonal heavy isotope (> 100 Da) tags, rather than fluorophores, to read out the biomarkers on a cell. Here, we investigate three classes of organotelluriums as a mass cytometry compatible isotope tag: methyl tellurides, trifluoromethyl tellurides and 2-alkyl-tellurophenes. Stability and toxicity assays showed that the 2-alkyl-tellurophene containing scaffold was the most reliable isotope tag for mass cytometry. As a result, we investigated the use of tellurophenes in the development of a MC barcoding reagent, an antibody-conjugated MC polymer reagent and a potential activity-based MC probe to study protease activity (Cathepsin S).

Keywords: Mass Cytometry
Mass tags
Molecular probes
Organotellurium
Single cell
Tellurium
Advisor: Nitz, Mark
Developing Leadership in the Decanal Role in Ontario Institutes of Technology and Advanced Learning (ITALS): A Case Study of Humber College ITAL

There is growing need for ongoing leadership development in the Ontario college system with very little research and literature on how to achieve this. This case-study explored the pathways to decanal leadership at Humber College Institution of Technology and Advanced Learning (ITAL). This was done by examining theparticipants’ perceptions of the challenges of the decanal role, alongside the competencies or leadership frameworks that are required. This study also examined how those in the role were supported in their professional development. This was an exploratory descriptive case study that used both document analysisof job descriptions, advertisement and LinkedIn profiles, alongside semi-structured interviews with 12 current and previous deans who have held the role since Humber became an ITAL in 2003. Semi-structured interviews were also conducted with the Senior Vice-President Academic and the current President. Key findings of this study include a profile of the ideal candidate for these dean positions, including the ideal pathway. The key challenges included defining and defending the ITAL status, alongside the complexities brought about by this focus. The role of collaboration and conflict was also noted, along with isolation and limited resources. The American Association of Community Colleges (AACC) competencies were examined alongside Bolman and Deal’s framework for leadership. Supports for professional development were identified, including the role of mentorship, external Professional Development, graduate studies and inhouse training which can all be used pre-service or in-service with a Dean group. The implications for policy and practice include the need to develop intentional training structures that move away from a reliance on informal mentoring, while investing in the development of in-house training. There is also a clear need to develop multi-framework leadership to address the broad range of challenges faced at the decanal position, acknowledging that one approach to leadership does not fit in a position that is meant to deal with a broad range of issues. While this study addresses a gap in the literature, there is a need to expand future research across the Ontario college sector, while addressing the emerging challenges arising from the impact that COVID will have on our industry.

Keywords: administration
college
dean
higher education
leadership
Ontario
Advisor: Janzen, Katharine