VictorJuiz/thesis huggingface dataset:
Vertical Integration of Optical Waveguides in the AlGaAs/GaAs Semiconductors

The rapidly growing Internet services put a higher bandwidth requirement on datacenters. A lowpower and low-cost photonic integrated circuit (PIC), using wavelength division multiplexing (WDM), holds the promise to further scale the density, reach, and bandwidth needed for nextgeneration datacenter networks. Multi-guide vertical-integration (MGVI) scheme improves device yields, saves substantial fabrication costs and offers many other advantages. The AlxGa1-xAs semiconductors provide optical gain and allow for the monolithic integration of different active and passive components. In this thesis, we demonstrate the vertical integration of optical waveguides via the MGVI scheme in the AlxGa1-xAs semiconductors. First, we begin by developing wet chemical etching techniques and demonstrate sacrificial etching of AlxGa1-xAs layers with a low aluminum content against layers with a high aluminum content. We also demonstrate sacrificial etching of Al0.7Ga0.3As layers against AlxGa1-xAs layers with x

Keywords: Aluminum gallium arsenide
Monolithic integration
Multi-guide vertical-integration
Nanofabrication
Photonic integrated circuits
Waveguides
Advisor: Aitchison, J. Stewart
X-ray Spectroscopy and Scattering Studies on Thermoelectric Skutterudites

The interest in developing high performance thermoelectric materials has inspired a wide range of theoretical and experimental studies of their structural, electrical and lattice dynamical properties. In this dissertation, I have employed x-ray spectroscopy and scattering techniques to investigate the local structure and vibrational dynamics of various fillers and dopants in thermoelectric Co4Sb12-based skutterudites. X-ray absorption spectroscopy studies were carried out to elucidate the local structure of Ga and Yb dopants in a series of polycrystalline YbxGayCo4Sb12. EXAFS data at Ga K-edge provide direct experimental evidence that Ga dopants occupy two distinct crystallographic sites. The fraction of Ga occupying the 24g site increases gradually as a function of additional Yb, reaching 100% when x = 0.4. Combined with the Fermi level shift observed in the x-ray absorption near-edge structure (XANES) spectra, we find the charge-compensated defect model can explain the observed increase of Ga24 fraction very well. This study provides an important strategy to optimize the thermoelectric performance in partially filled skutterudites. Significant interaction between filler species was further investigated in the double- filled YbxInyCo4Sb12 samples. We found in both Yb-Ga and Yb-In double-filled skutterudites the local structure of Ga and In are subject to the lling concentration of the secondary filler, Yb. However, contrary to the Ga dopants which form dual-site defects in the absence of Yb fillers, the result shows that both Yb and In occupy the on-center 2a sites exclusively in their single-lled samples. The temperature dependent EXAFS results provide further evidence that the In2a, very similar to the normal filler Yb, is loosely bound inside the cage and vibrates as an Einstein oscillator. This is distinct from Ga2a which forms a stiff bond with the cage atoms at a rather high Debye temperature. The vibrational dynamics of Yb fillers has been studied in YbxCo4Sb12 compounds by performing both EXAFS and inelastic x-ray scattering (IXS) measurements. The low-energy vibrational mode introduced by the Yb fillers has been successfully detected. We further found that the cubic anharmonic interaction between Yb and Sb is well evident at high temperatures.

Keywords: Extended X-ray Absorption Fine Structure
Local structure
Skutterudite materials
thermoelectrics
Vibrational Properties
Advisor: Kim, Young-June
“The Metropolitan Moment: Municipal Boundaries, Segregation, and Civil Rights Possibilities in the American North”

Exploring battles over school desegregation in metropolitan Boston, Detroit, and Philadelphia in the 1960s and 1970s, “The Metropolitan Moment” examines how black and white city dwellers at odds over integration within the city pursued – and sometimes allied over – efforts that crossed municipal lines to incorporate the suburbs in desegregation remedies. Though possessing divergent motivations, such as the white tactical aim of ensuring white majorities in all area schools by enlarging the desegregation area and the black desire for improved educational opportunities, both groups sought access to white suburban schools and at times acted together in court in an attempt to implement metropolitan desegregation. The search for such solutions opened a “metropolitan moment” across the urban North in the late 1960s and early 1970s when proposed regional remedies offered real possibilities of heading off white flight, fostering interracial coalitions, and substantively combatting segregation. Though this moment was foreclosed by the U.S. Supreme Court’s 1974 decision in Milliken v. Bradley – a case prompted in part by just such a surprising urban black-white alliance in Detroit – its legacies, including suburban anti-busing movements that helped fuel the rise of the New Right and the transformation of the Democratic Party, and the larger retreat from metropolitan solutions to metropolitan dilemmas of race, schooling, services, and inequality, echo down to today. The findings complicate several historiographies pertaining to the long civil rights movement, post-World War II urban and suburban history, the rise of the right, and representations of the “busing” controversy. Throughout, “The Metropolitan Moment” broadens the conception of the municipal reformer to include both ordinary black parents and white reactionaries.

Keywords: Boston
busing
Detroit
metropolitanism
Philadelphia
suburbs/suburban
Advisor: Kazal, Russell A
A Genome-Scale Analysis of Alternative Splicing Regulation by Splicing Factors in C. elegans

Alternative splicing (AS) is a key mechanism that contributes to the high level of complexity present within metazoan proteomes. This process is highly regulated and important for the development for any animal. With advances in high-throughput technologies, our knowledge of the many AS events that occur in the cell has rapidly increased. However, for many of these events, it is still not known which splicing factors (SF) are involved, and how they regulate splicing outcomes. Here, I use a genomic approach in the nematode C. elegans to study how SFs govern AS events during development. Specifically, for this thesis, I focus on four SFs – ASD-1, FOX-1, EXC-7 and MEC-8. In the first data chapter, I use RNA sequencing, RNA-binding preferences and conservation information to identify likely direct targets of these SFs. I find that AS regulation by these SFs is often combinatorial and converges upon genes with neuronal and cytoskeletal functions. I further show that loss of these SFs can lead to synergistic defects in the neuromuscular system. Many of these co-regulated AS events are also developmentally regulated, suggesting a crucial role in development. In the second data chapter, I then focus on a subset of MEC-8 targets to provide a more detailed view of splicing regulation. I find that MEC-8 regulates the developmental AS transitions in multiple transcripts encoding components of the fibrous organelle – a complex crucial for maintaining structural integrity in the worm. Differential mec-8 expression during development likely contributes to the dynamic regulation of these AS events in a cell- and developmental-stage specific manner. Finally, I find that these AS patterns can vary among C. elegans natural isolates and differential splicing is associated with differences in mec-8 expression. These data suggest that the study of natural variation in AS regulation can provide insight into the regulation of splicing regulatory pathways.

Keywords: Alternative splicing
C. elegans
Genetics
Genomics
Advisor: Fraser, Andrew G
Student Development of Team-effectiveness Behaviours in Engineering Teams

The Canadian Engineering Accreditation Board requires all graduating engineering students to demonstrate the ability to work effectively in teams. This thesis provides a response to this requirement through the development and testing of an on-line team-effectiveness learning system (TELS) for use in large 250-900 student classes. Based on Kolb’s Experiential Learning Theory and Hewson and Little’s feedback model, TELS provides students an opportunity to develop their team-member effectiveness through: i) guiding intra-team self and peer assessments of teamwork using an inventory of behaviours customised for engineering students; ii) providing students self and peer feedback to identify opportunities for improvement, and iii) providing online, integrated lessons and exercises on how to improve each behaviour within the system. The Team-Effectiveness Learning System (TELS) was developed and tested in a multi-year study of two first-year engineering design courses. A mixed-methods approach was taken to assess the efficacy of the system, combining an analysis of students’ self and peer assessments, their use of the online learning system and students’ self-reported assessments of the system’s utility. Findings from three-years of testing and revision indicate that TELS guided students to provide feedback for improvement that was reliable and that the behavioural inventory used to provide feedback expanded student discussion of relational and communication behaviours. A statistically significant improvement in students’ self and peer assessed weaknesses was seen between mid-term and end-of-term feedback. Student improvement was predominantly motivated by the feedback a student received; students who received feedback that had a greater focus on strengths and weaknesses reported being more motivated to improve their behaviour and did improve their behaviour more than those whose feedback discussed few strengths and weaknesses. Student improvement methods focused on reviewing their feedback and reflecting on how to improve their weaknesses – only 13% of students used the online lessons as scaffolding to support development. Integration of the Team-Effectiveness Learning System (TELS) into team projects in engineering education affords instructors in large classes a way to provide personalised feedback to individual students. In first-year engineering design classes it has been found to improve students’ team behaviour and expand students’ understanding of effective teamwork.

Keywords: engineering
first year design
online learning
students
team-effectiveness behaviours
teams
Advisor: Evans, Greg J
Reeve, Doug W
Modeling the Development of Human Atrial and Ventricular Cardiomyocyte Lineages from Human Pluripotent Stem Cells

The ability to direct the differentiation of human pluripotent stem cells (hPSCs) to the different cardiovascular lineages is a prerequisite to modeling specific forms of cardiovascular disease in vitro and for developing novel therapies to treat them. Here we have investigated the development of human atrial and ventricular lineages and demonstrated that retinoic acid (RA) signaling is critical for the atrial fate specification. Insights into the origin of RA signaling has led us to identify that the atrial and ventricular cardiomyocyte lineages develop from distinct mesoderm populations that are marked by the expression of RALDH2 and CD235a, respectively. The RALDH2+ cells give rise to highly enriched atrial cardiomyocytes in the presence of retinol, suggesting that these progenitors can both produce and respond to RA in an autocrine fashion. Analyses of derivative cardiomyocyte populations have demonstrated that the generation of highly enriched, functional cardiomyocyte subtypes depend on the appropriate patterning of early progenitor populations. Based on these findings, we have initiated two independent analytical approaches, the CD-antibody library screen and single cell RNA-seq (scRNA-seq) analyses, to gain better insights into these progenitor populations. Analyses from the antibody screen has identified a new cell surface marker CD324 that has uniquely marked the transition from CD235a+ mesoderm to the early NKX2-5+ cardiomyocyte progenitor stage. We hypothesize that CD324 expression marks the formation of the cardiac crescent-like population from hPSCs. From the same study, we have identified that NOTCH2 and -3 receptors are expressed on the ventricular but not atrial mesoderm populations, suggesting a lineage-specific role of this signaling pathway. Preliminary analyses of scRNA-seq study has also demonstrated heterogeneity within the ventricular progenitor population. Together, these findings provide novel insights into the earliest stage of human heart development that enable the generation of highly enriched cardiomyocyte subtypes for future therapeutic applications.

Keywords: atrial cardiomyocyte
heart
Human pluripotent stem cell
regenerative medicine
ventricular cardiomyocyte
Advisor: Keller, Gordon M
An Examination of the role of MicroRNA-21 in the Pathobiology of Degenerative Cervical Myelopathy Using Human and Animal Data

MicroRNA-21 (miR-21) is upregulated in multiple models of traumatic and neuroinflammatory CNS injury. Here, we sought to evaluate the role of miR-21 in the most common form of adult spinal cord dysfunction, degenerative cervical myelopathy (DCM). Using a mouse model of DCM where the spinal cord is progressively compressed over multiple weeks, we found elevated expression of miR-21 in both spinal cord and plasma at 6 weeks and 12 weeks after onset. Deletion of miR-21 in a null mutant mouse strain significantly preserved locomotor function on the rotarod and forced swim tests, but at the cost of increased neuropathic pain. Preservation of motor function was attributed to reduced inflammation, denoted by the approximately 50% reduction in stereological counts of Iba1-positive activated microglia in miR-21 knockout spinal cord sections. In vitro experiments using primary microglia found that miR-21 is induced under pro- or anti-inflammatory conditions, but that miR-21 deletion did not affect the cells natural reaction to these stimuli. Target prediction algorithms identified the IL-6/STAT3 pathway as a potential downstream target of miR-21, and subsequent in vitro testing found that components of the IL-6 receptor complex, IL-6ra, and IL-6st were significantly higher in miR-21 knockout microglia. Finally, to determine whether miR-21 and other microRNAs related to human DCM could be used as biomarkers, we examined plasma microRNA expression in a human DCM cohort. Expression of miR-21 and other microRNAs were found to be correlated to current patient symptoms. In the surgical cohort, baseline levels of miR-132-3p and miR-34a were found to predict surgical outcome, while miR-21 approached a statistically significant correlation with post-operative lower motor function (p=0.05). In aggregate, we find that miR-21 may have a pro-inflammatory role in the DCM microglial response, and that miR-21 expression may be related to the manifestation of motor deficits.

Keywords: Biomarkers
Cervical Myelopathy
Inflammation
Microglia
MicroRNA-21
Advisor: Fehlings, Michael G
ESSENTIAL COFACTORS IN ANAEROBIC MICROBIAL CONSORTIA USED FOR BIOREMEDIATION: BIOSYNTHESIS, FUNCTION AND REGENERATION

Most microorganisms in nature live in communities and have developed tightly coordinated metabolism via metabolite exchanges. Cofactors are “helper molecules” in all cells, modulating the activity of many enzymes or serving as the electron shuttle. However, biosynthesis of cofactors, such as cobamides, is sometimes accomplished by only one specific phylogenetic group of microorganisms. Therefore, cofactors and their producers play pivotal roles in the functionality, metabolic rates, and population structure of a microbial community. This thesis focuses on three types of cofactors: (i) cobamides, (ii) NADPH, and (iii) prenylated flavin mononucleotide (prFMN) that are involved in anaerobic bioremediation of chlorinated solvents and aromatic pollutants. Cobamides are a family of cobalt-containing tetrapyrroles involved in biochemical reactions including methyltransfer reactions, isomerizations, and reductive dehalogenation. This thesis reports the identification of a functional cobamide prosthetic group in tetrachloroethene dehalogenases (PceA) of Desulfitobacterium hafniense and Geobacter lovleyi using a tiered blue-native polyacrylamide gel electrophoresis (BN-PAGE) and liquid chromatography-mass spectroscopy (LC-MS) method. The metabolic annotations of Dehalobacter restrictus (Dhb), a model organism for bioremediation of chlorinated solvents, were experimentally verified. The verified annotations were written into a constraint-based metabolic model, which identified that NADPH regeneration and de novo serine biosynthesis could be bottlenecks in Dhb metabolism. Using an integrated computational/experimental approach, the stringent nutrient requirements of Dhb were characterized. Further experimental analysis on the Dhb-enriched ACT-3 consortium has revealed an interspecies malate-pyruvate shuttle system between Dhb and its syntrophic partner. prFMN is a newly identified cofactor of UbiD reversible aromatic decarboxylases that are involved in ubiquinone biosynthesis, biological decomposition of lignin monomers, and anaerobic biodegradation of aromatic pollutants. We discovered that in Escherichia coli, dimethylallyl-monophosphate (DMAP), the prenyl donor of prFMN, can be produced from either prenol phosphorylation or from dimethylallyl-pyrophosphate dephosphorylation. In conclusion, this thesis reports biosynthesis and function of new cofactors as well as new mechanisms for reconciling cofactor regeneration in anaerobic microbial communities. Realizing these metabolic interdependencies generates opportunities to manipulate the microbiomes for better outcomes in bioremediation and industrial biotechnology. Interestingly, the identified interspecies cofactor exchange mechanism also provides insights into how life gradually evolved into complexity.

Keywords: Anaerobic bioremediation
Biosynthesis
Cofactors
Cross-feedings
Environmental microbiology
Organohalide respiration
Advisor: Edwards, Elizabeth A
A Mixed Method Exploration of Suicidality in Clients with Intellectual Disability

The goal of this dissertation was to investigate suicidality in individuals with intellectual disability (ID). Study 1 reviewed files of adolescent clients at an agency that serves individuals with ID to estimate the prevalence of suicidality, identify factors associated with suicidality, and describe clinical practices regarding suicidality. Study 2 used in-depth interviews with clinicians, which were analyzed qualitatively, to explore their experiences with suicidality in their clients with ID and their practices to address clients’ suicidality. The results of both studies were integrated using a mixed-methods approach. In study 1, 192 case files of adolescent clients aged 12 to 17 were systematically reviewed using a researcher-generated coding scheme. Data was collected on variables that spanned demographic information, mental and physical health, personal characteristics and experiences, family stressors, and suicidality domains. Adequate inter-rater reliability of data collection was achieved. The estimated suicidality prevalence was 13.0%. Factors associated with suicidality included abuse history, trauma history, psychopathology in the family, and higher functioning (i.e., borderline intelligence and mild ID). These factors provided some support for diathesis-stress models of suicide in youth with ID. Files infrequently documented clinical practices addressing client suicidality. In study 2, semi-structured interviews with 10 clinicians were analyzed using Grounded Theory to create an explanatory framework for understanding clinicians’ experiences with suicidality in their child, adolescent, and adult clients with ID. Although aspects of responding to suicidality in clients with ID were similar to that of clients without ID, the process was more complex due to the inadequacy of the mental health system to address clients’ needs, and clients’ cognitive and communication difficulties made it more difficult to assess suicidality and implement interventions. Suicidality in clients also put an inordinate burden on their caregivers, and the clinicians felt that they were facing the unknown when they worked with these clients.

Keywords: Developmental disability
Intellectual disability
Suicide
Suicide assessment
Suicide prevention
Suicide screening
Advisor: Greenbaum, Rachel
Wiener, Judith
Negotiating the Zone of Proximal Development in a Pre-University Advanced Academic Writing Classroom

Grounded in sociocultural theory (SCT) of mind and a social-constructivist view of learning, the present study analyzed in depth the construction of Zones of Proximal Development (ZPD) among an experienced teacher and her students over the duration of a pre-university academic English writing course. The research (a) investigated the teacher’s perceptions of the factors that facilitated the creation of opportunities for learning, (b) analyzed classroom dynamics, participation, and interaction patterns over time to identify the instructional choices most conducive to learning, and (c) examined the factors that facilitated or hindered 3 focal students’ take up of opportunities for learning. Multiple sources of data included in-depth teacher interviews, observation and coding of 70 hours of classroom instruction, the teacher’s and students’ stimulated recalls on selected episodes of classroom interactions, and documents such as handouts, students’ assignments, and the teacher’s feedback on students’ writing. The teacher’s interviews revealed a dialectic relationship between two types of facilitative factors she implemented: (a) emotional sustenance, achieved by building rapport with students, maintaining dependable codes of academic behavior, and balancing senses of challenge and attainment in students and (b) four instructional design and pedagogical choices: establishing continuity between course components, monitoring students’ progress, providing several types of assistance, and then later withholding assistance to encourage students’ self-regulation. A microgenetic analysis of two instructional units showed how continuity was established through the use of advanced organizers and clear intertextual links. The gradual decrease of teacher talk over the units gave room for active student participation and engagement. Case studies of 3 focal students revealed that these students valued different mediational tools according to their individual developmental histories and goals. They all showed evidence of investment and intentionality with stronger students commanding a larger repertoire of strategies and showing more understanding of the course design and the teacher’s goals. In sum, the findings indicate that opportunities for learning within the ZPD were constructed through the overlap of multiple interacting factors including emotional sustenance, effective instructional practices, individualized support, and students’ self-regulation and investment. Implications are suggested for deconstructing the ZPD, understanding academic writing teaching and learning, and further research.

Keywords: English as a Second Language
English for Academic Purposes
Second Language Writing
Socio-cultural Theory
Zone of proximal development
Advisor: Cumming, Alister