VictorJuiz/thesis huggingface dataset:
Evolutionary Population Genomics and Transcriptomics in Cancer
Keywords: Cancer
Evolution
Genomics
Recombination
Selection
Transcriptomics

Cancer progression is an evolutionary process: somatic mutations can confer selective advantages to certain cells, eventually causing them to abnormally proliferate. Parallels can be drawn between the evolution of organismal populations and cancer cell populations. In both, selective forces act on mutations to promote or obstruct the transmission of alleles to future generations. As an integral component in shaping the genomic landscapes of populations, recombination and selection have a high potential to contribute to cancer progression. Despite the clear similarities between evolutionary processes in populations and in cancer cell populations, many theoretical evolutionary concepts remain to be applied to a cancer context.This thesis characterizes processes known to drive the evolutionary trajectory of populations in a cancer context. I first uncover the role of the meiotic recombination factor PRDM9 in cancer. I identify the aberrant expression of PRDM9 in cancer and uncover the association between sites of somatic structural variant breakpoints and sites of PRDM9 binding and activity, reminiscent of the role of PRDM9 in recruiting the double stranded break machinery in meiosis. This study is the first to provide evidence of an association between the aberrant expression of the meiosis-specific gene PRDM9 with genomic instability in cancer. To further investigate the role of selection and linkage in cancer, I model the evolution of cancer cell populations to infer a comprehensive history of the evolution of beneficial, deleterious and neutral mutations within individual biopsies. In 172 Barrett’s esophagus samples, an esophageal adenocarcinoma cancer risk condition, and 47 samples from esophageal adenocarcinoma, sarcoma, prostate, and pancreatic cancer, I capture previously under-detected selective processes in tumors. Negatively selected mutations occur alongside positively selected mutations in many tumors where a signature of positive selection is observed. The accumulation of damaging mutations concurrently with beneficial mutations is associated with increasing the age of sub-clones harboring these mutations, slowing down tumor progression, implying that early detection diagnostics should be developed to screen individuals for tumor progression to improve survival outcomes. Overall, my research highlights the role of evolutionary processes in cancer which has important ramifications on personalized treatment opportunities, resistance and timing of diagnosis.
Structural Dynamic Analysis and Health Monitoring of Aeroengines: Nonlinear Modelling of Bolted Flange Connections and Transfer Path Analysis
Keywords: Aeroengine
Bolted flange connections
Finite element analysis
Nonlinear dynamic analysis
Structural health monitoring
Transfer path analysis

In this research, a full and comprehensive category of analysis techniques were proposed, developed, and implemented on aircrafts, specifically aeroengines. Initially, by proposing a novel nonlinear experimental protocol in conjunction with finite element modelling methodologies, the underlying nonlinear dynamic characteristics of the aeroengine casing assemblies were determined at a significantly reduced testing duration. Due to lack of a computationally efficient and accurate nonlinear bolted flange connection modelling methodology, a set of nonlinear analytical bolted flange connection models was developed and proposed. Using finite element techniques, the proposed nonlinear analytical model was incorporated in the finite element model of the aeroengine to capture the underlying nonlinearities. The proposed nonlinear analytical model illustrated a very good correlation compared to the experimental results. Moreover, the proposed nonlinear analytical model demonstrated outstanding computational efficiency. In the second stage, to address noise and vibration problems arising from the aeroengine, a novel bond graph transfer path analysis was implemented on a reduced aeroengine-wing assembly. Using this novel approach and process, vibration energy transmission paths and path contributions in the aeroengines were investigated and determined based on the bond graph transfer path analysis methodology. Moreover, vibration reduction strategies are proposed to minimize and attenuate vibration energy transfer in the aeroengine-wing assembly. The theoretical bond graph transfer path analysis methodology has proven to be extremely time efficient while reducing associated costs in performing conventional methodologies. The proposed bond graph transfer path analysis methodology was validated using finite element simulations. In the last stage, a novel theoretical approach was proposed using the bond graph methodology to perform structural health monitoring on the aeroengine-wing assembly. The proposed analytical structural health monitoring technique permits the rapid detection of damage in the structure while also allowing the determination of damage severity in the structure. The analytical findings of the proposed methodology can be used as a benchmark against experimental measurements to rapidly detect, localize, and analyze the severity of damage in the structure. Moreover, design guidelines and strategies were proposed to minimize damage and defect formation in the structure. The proposed structural health monitoring methodology was validated using finite element simulations.
E-Cigarettes: Biomarkers of Exposure and the Development and Validation of a Research Toolkit
Keywords: biomarkers
dependence
e-cigarette
nicotine
questionnaire
stimuli

Electronic nicotine delivery systems (ENDS) have gained worldwide popularity. Even so, there is limited research on the potential effects of regular ENDS use on health. Moreover, little is known about ENDS dependence and studies are often limited by a lack of validated research tools. Current measures of ENDS dependence are adapted from cigarette dependence questionnaires and do not consider concepts unique to ENDS vaping. Similarly, there are currently no validated ENDS-related stimuli for use in the research of drug reward and addictive behaviors. This thesis therefore directly compared the urinary cotinine levels, a biomarker of nicotine exposure, in individuals who use ENDS exclusively, use ENDS in conjunction with smoking tobacco cigarettes (dual users), and smoke cigarettes exclusively. We found no significant differences in cotinine levels between genders [F(2,84)=0.46, p=0.636], and between participant groups [F(2,84)=0.12, p=0.892]. In exclusive ENDS users, individuals with higher levels of cotinine also reported shorter times before vaping after waking [r(21)=-0.46, p=0.028]. Additionally, this thesis developed and validated a questionnaire to assess ENDS dependence and a database of 120 ENDS-related image cues. Exploratory factors analysis reduced an initial pool of 28 ENDS dependence items to 15 that were included in the final ENDS Nicotine Dependence Questionnaire (ENDS-DQ). Further analyses found that the ENDS DQ has high internal consistency (Cronbach α=0.84), external validity, and test-retest reliability (ICC=0.87). Regarding the development of an ENDS-related cue database, findings from our preliminary and follow-up validation studies were consistent with one another and with literature. Desire-to-vape ratings of ENDS-related images were correlated with valence (r=0.55, p
Learning Conflict in the Midst of Violence. Urban Youth and School Life in Colombia’s (Post)Conflict Transition
Keywords: Colombia
Peace
Pedagogy
School
Violence
Youth

This thesis explores the (dis)encounters between youths’ lived experiences and understandings of conflict and violence and the curricular intentions and practices in their schools. Participating youth attend two schools in marginalized urban areas of Colombia that are differently affected by violence and the armed conflict. One school is located in a municipality directly affected by armed conflict violence. The other is in a traditional neighborhood in a large city, affected by insecurity and urban criminality but located away from the direct effects of the armed conflict. Soon after the 2016 peace agreement between the Colombian state and the largest guerrilla organization, I conducted three months of participant observations, focus groups with youth from grades 8 to 10, interviews with teachers, and follow-up visits in each field site. I show that, despite young people’s different locations in relation to war, intimate expressions of direct violence—interpersonal, criminal, domestic, and drug-related—were prominent in students’ narratives about the social conflicts affecting their lives in both field sites. These concerns overrode both the visibility of armed conflict and indirect socio-cultural and structural forms of violence in their understandings of social conflict. I also show how the prevalent practices embedded in these schools’ curriculum, based on convivencia [peaceful coexistence] and (global) citizenship education discourses and guidelines, emphasized a similarly individualized, depoliticized, and ahistorical framing of violence and conflict. I argue that school life is a symbolic device that contributes to the normalization of violence in the everyday life of these (school) communities. While it provides a space for stability, inclusion, and young people’s personal visions of their future paths, it also undermines their ability to understand the Colombian conflict as a social process, with causes, actors, and a history. By contrasting youths’ and schools’ conceptions and practices of conflict and violence in two different geographies, this dissertation shows how predominant approaches to convivencia as securitization and order, conceptions of citizenship that blame others for violence, and skepticism towards peace (building) and collective action hinder youth-oriented peacebuilding pedagogies efforts for conflict transformation and reconciliation during Colombia’s transition from war to post-conflict.
Structures Strike Back: Their Significance for Our Models of Opinion Formation
Keywords: Hierarchical/Multilevel Models
Middle Eastern North African Politics
Opinion Formation
Public Opinion
Quantitative Methods
Survey Data

Why do our models of opinion formation work in some situations but fail in others? In this dissertation, I explain that our models of opinion formation work in some cases but fail in others because of the structural level variations that are not accounted for when these models are designed only with individual level variables in mind. By structural level variations, I mean the societal conditions that affect everyone in a given society and which are typically measured by societal level variables. These variables, I argue, are as fundamental to the process of opinion formation as the individual level variations scholars focus on by default. In Chapter 1, I elaborate on the theoretical foundations of this argument and set the tone for the three empirical chapters that test my argument. In Chapter 2, I start testing my argument by engaging with the structural impact of socioeconomic development on elite directed opinion formation at the individual level in MENA countries. I use survey data collected by three waves of the Arab barometer between 2010 and 2016 to show that socioeconomic development reverses the correlation between political awareness and the adoption/rejection of party cues in Islamist publics. In Chapter 3, I address the structural impact of colonization on the model of secularization postulated by modernization theories based on individual material conditions in MENA countries. Based on 42 surveys delivered between 2000 and 2014, my findings suggest that postcolonial MENA societies do indeed break with the pattern predicted by modernization theorists. In Chapter 4, the last empirical chapter of this dissertation, I discuss the structural impact of different immigration systems on patterns of xenophobia predicted by the economic competition theory based on individual social class in MENA countries. Using data from 14 MENA countries gathered between 2000 and 2011, it argues that where immigration systems prevent the social mobility of migrants, as in the case of the kafala system, xenophobic attitudes develop among those with a higher as opposed to a lower socio-economic status. Chapter 5 concludes by outlining some of the key theoretical and methodological implications of these empirical findings.
Measuring Balance Confidence in Youth with Cerebral Palsy: Measure Development, Sensibility, Content Validity, and Initial Psychometric Evaluation
Keywords: balance
balance confidence
cerebral palsy
measurement
participation
self-efficacy

Background: Youth with cerebral palsy (CP) generally participate in less physical activity than typically developing youth. In adults with physical disabilities, balance confidence is a strong predictor of participation. However, balance confidence has not been studied in youth with CP. Research objectives: (1) To explore whether concerns about balance influence physical activity participation of ambulatory youth with CP; (2) to determine how youth with CP feel when they lose their balance; (3) to build a balance confidence measure for this population; (4) to examine the sensibility and content validity of the measure; and (5) to evaluate test-retest reliability and construct validity of the measure. Participants: Eighty-one participants were involved in one or more stages of this measurement study (25 youth with CP, eight parents of youth with CP, 17 typically developing youth, and 31 health care professionals). Methods: Qualitative descriptive methodology with 16 interviews was used to explore balance confidence with ambulatory youth with CP and parents. A multi-step process was used to create the Feelings About Balance–Cerebral Palsy (FAB-CP) youth-report questionnaire and evaluate sensibility, content validity, test-retest reliability, and convergent and discriminant validity. Results: Qualitative analysis demonstrated that ambulatory youth with CP, especially those who do not use gait aids for ambulation, are often concerned about losing their balance during physical activities, which may lead to avoiding physical activities. The FAB-CP, an 11-item computer-based measure was created to investigate balance confidence of this population. Test-retest reliability was excellent (n=21; one-to-four week interval; ICC 0.97 [95% CI 0.93, 0.99]). Convergent validity was good when evaluated against measures of balance capacity (rho=0.74), advanced motor skills (rho=0.83), physical activity enjoyment (rho=-0.61) and participation (rho=0.77). The FAB-CP discriminated among participants of different levels of gross motor function (maximum p
Electrorefining and Electrochemistry of Molten Iron and Iron-Carbon Electrodes in Slag
Keywords: Decarburization
Electrochemistry
Electrorefining
Impedance
Slag
Steelmaking

Despite a perpetual societal need for steel, the industry is facing critical challenges as more steel must be continually recycled to improve sustainability and close material loops in circular economies. A major issue here is producing high-value products and controlling elements like carbon in the face of stringent consumer requirements, volatile markets, low profit margins, and scrap irregularity. In this dissertation, a new electrorefining process was developed where molten iron is decarburized by imposing an electromotive force between it and a slag electrolyte at 1600–1700 °C. Upon anodic polarization, oxygen-containing anions react with carbon dissolved in molten iron, evolving gaseous carbon monoxide. As carbon is oxidized from the iron anode, valuable metallurgical-grade silicon is recovered as a by-product on counter electrodes. Electrorefining trials were conducted over the entire compositional range from 4.5 to 0.005 wt% C and shown capable of producing high-value ultra-low carbon steel containing
Development of New Methods to Control Redox Conditions in High-pressure Experiments and their Application to Study Ore Metal Solubilities in Sulfur-bearing Magmatic Fluids
Keywords: magmatic fluids
MHC alloy
porphyry
Pressure vessels
redox
sulfur

This thesis perfected the method of admixing calculated amounts of H2 gas to the argon pressure medium to impose desired fO2 values in hydrous experiments. Using CoPd alloy redox sensors, the method was shown to be accurate within 0.3 log units for the P-T range of 960 – 2060 bar and 800 – 1100⁰C. The rate of progressive oxidation caused by diffusive H2 loss through the Molybdenum Hafnium Carbide (MHC) pressure vessel walls was determined experimentally and the hydrogen permeability constants of the MHC alloy were calculated. At T = 1000⁰C, fO2 at water saturation increased about 0.36 log units/day, and this value approximately doubled for every 100oC increase in T. A prototype MHC pressure vessel apparatus was developed that can be used with a modified Shaw membrane to impose fO2 precisely and accurately while maintaining rapid quench capability. It was shown that 95% of the imposed hydrogen pressure is attained inside the pressure vessel within 2 hours from the start of the experiment at 800 – 1000⁰C, after which a steady state equilibrium is established. Experiments comparing redox-dependent Cu solubilities in silicate melts at fO2 imposed by redox buffers and identical target fO2 imposed by the hydrogen membrane confirmed consistency between the two methods within 0.3 log units fO2 deviation at T=1000⁰C and P=2000 bar. Experiments using Fe(II)-Mg exchange between olivine and water-saturated melt to constrain Fe3+/Fetotal ratios in the silicate melt yielded results mostly consistent within 1σ error with those predicted by the equation of Kress and Carmichael (1991). The relationship between exchange coefficient of Fe-Ti between magnetite and silicate melt (K_(d,Fe-Ti)^(magnetite/melt)) and fO2 in hydrous mafic magmas was also constrained. Using the new experimental apparatus, the solubilities of Cu, Ag and Au in S-rich Cl-bearing magmatic fluids were determined at T = 900 ⁰C and P = 2000 bar covering a wide range of fO2 from NNO – 0.5 to NNO + 2.5 with 7 steps in-between. Thermodynamic model calculations were performed using the HCh software to determine the dominant species of the metals in the fluids.
An Aware and Strongly-coordinated Multi-robot System for Finding Multiple Dynamic Users in Human-centered Environments
Keywords: Human-Centered Environments
Min-Max Multi-Traveling Salesperson Problem
Multi-Period Multi-Knapsack Problem
Multi-Robot Coordination
Multiple Dynamic People
Search Within a Deadline

Socially assistive robotics considers robots helping people via social interactions. With technological advancements over the past few decades, there has been an increase in the number and types of socially assistive robotic applications. However, these applications have focussed on scenarios in which people begin collocated with the robot. Yet, in real-world environments, people go about their day-to-day lives and robots must first find users prior to assisting. To address this limitation, this thesis considers the multi-robot person search problem, defined herein as the person search team orienteering problem (PSTOP). The PSTOP considers dynamic users with changing locations during the search, a team of robots that may need to search a region multiple times, and a specified search time frame. User locations are modelled by novel activity probability density functions (APDFs) using past location data. The APDF is the only existing model which can determine the probability of a user occupying a region by considering when the region was previously searched. A two-stage multi-robot person search system (2-MRPSS) is introduced to generate team plans specifying when and for how long to search regions. The 2-MRPSS is the only planner which can consider user location data when determining repeated searches of a region. The 2-MRPSS is also the only existing planner which reasons about past user location data, while being both aware and strongly-coordinated. Moreover, this thesis is the first to deploy a multi-robot multi-user person search in a real-world human-centered environment by using a novel centralized architecture to oversee the generation, execution, and monitoring of the team plan. Within the architecture, this thesis introduces a novel low-cost information gathering technique and a navigation technique that adheres to human-etiquette. Simulations have been conducted to evaluate the theoretical contributions of the thesis and experiments have been conducted to evaluate the practical contributions of the thesis. The simulations show that the proposed approach finds more target users than existing state-of-the-art techniques. The experiments show that the architecture, information gathering, navigation, and 2-MRPSS can be used to successfully perform the multi-robot person search in a real-world human-centered environment.
The Effect of Vegetation on Student Achievement in the Toronto District School Board
Keywords: Achievement
Fixed Effects
NDVI
Vegetation

This dissertation builds on past research that has demonstrated positive and significant correlations between student achievement and vegetation. My research extends The Biophillia Hypothesis, which posits that humans receive psychological benefits from being near vegetation, by hypothesizing that schools with greater amounts of nearby vegetation will have better academic outcomes than schools with lesser amounts of vegetation, controlling for key confounders. Data come from student standardized test scores and demographic, obtained from the Toronto District School Board (TDSB) and from measures of satellite images of vegetation surrounding each school, obtained from the Canadian Urban Environmental Health Research Consortium (CANUE). Initial analyses using Pearson’s correlations and OLS regression show positive relationships between vegetation and achievement similar to those found in previous research. However, this dissertation also engages in a unique attempt to investigate whether vegetation has causal effects on school achievement, exploiting a natural experiment made possible by a large ice storm that hit Toronto in 2013 and destroyed approximately 20% of the city’s tree canopy. Several spatial and descriptive statistics were carried out, including Moran’s I, and long-term vegetation change measurements, to examine whether the ice storm was a significant and random event. Fixed Effects (FE) regression models were run to investigate whether proportions of students who met provincial standards in standardized tests dropped due to vegetation loss after the ice storm. These models test for causal impacts of vegetation by comparing levels of achievement before and after the ice storm while controlling for measured confounders such as school-level SES, as well as unmeasured and time-invariant confounders like school climate and culture. Descriptive statistics and OLS regression reveal mixed associations between vegetation and school achievement, while FE regression models did not yield consistent or significant results in support of the initial hypothesis. Implications of these findings for future research are discussed.