VictorJuiz/thesis huggingface dataset:
Quantitative Ultrasound Characterization and Monitoring of Locally Advanced Breast Cancer

Traditional assessment of tumour response to cancer therapy is based on tumour size reduction, which takes several weeks to become clinically significant. In this thesis, novel ultrasound backscatter signal analysis and machine learning techniques were developed to characterize breast tumours and detect early changes correlated to response. In the first study, tumour cell death was induced in human breast cancer tumour-bearing mice, using human mimicking chemotherapy drugs. Treatment-related changes in quantitative ultrasound (QUS) parameters, including change in average acoustic concentration (AAC) and heterogeneity index, revealed a strong correlation to histologically determined cell death extent (r2=0.64). In the second study, radiofrequency (RF) ultrasound data were acquired from locally advanced breast cancer (LABC) patients prior to treatment. Results suggested that a multiparameter QUS model can sensitively (88%) and specifically (91%) differentiate breast tumours from surrounding normal tissue. Furthermore, a local texture - based QUS model was demonstrated as a promising tumour grade predictor (86% accuracy). In the final study, ultrasound RF data were acquired from LABC patients prior to treatment, at 3 times during the treatment (weeks 1, 4, 8), and prior to surgery. Tumour response classification analysis using a multiparameter QUS model of midband fit (MBF), spectral slope (SS), and spacing among scatterers (SAS) demonstrated desirable classification performance at 4 weeks into treatment (80 ± 5%). Secondly, the QUS classification model demonstrated a significant difference in survival rates of responding and nonresponding patients at weeks 1 and 4 (p=0.035, and 0.027, respectively). In summary, the incorporation of QUS assessment of the breast during or after an ultrasound-guided breast biopsy session may potentially permit cross-verification of the histopathological findings. Furthermore, patients undergoing neoadjuvant chemotherapy can potentially benefit from a weekly QUS assessment in order to evaluate their early tumour response so that the appropriate treatment intervention can be made if the patient was nonresponding.

Advisor: Czarnota, Gregory J
The Social Construction of Disability in Occupational Therapy: An Examination of Muriel Driver Lectureships (1975-2009)

Disability is a core concept in rehabilitation sciences, and specifically in occupational therapy. Critical disability theory challenges the ways that disability is understood, and disability scholars have challenged rehabilitation professionals to reconsider how they conceptualize disability. The way that disability is given meaning is central to the profession of occupational therapy because it can influence client-therapist interactions, treatment plans and interventions, research agendas, services offered, and the development of policy. In my research, I address the need to examine how disability has been given meaning in occupational therapy. I adopt an overarching critical theoretical approach informed by social constructionism to examine the meaning of disability in the profession of occupational therapy. The objectives of the research include examining: a) how disability is presented in occupational therapy literature; b) what this tells us about the ideological, political, and theoretical underpinnings of disability; and c) what the dominant discourses of disability are in occupational therapy literature. I draw on methods developed by Fairclough to conduct a critical discourse analysis of highly influential Canadian occupational therapy texts (Muriel Driver Memorial Lectureships). The analysis is presented in two parts, discussing: (1) how disability has been broadly defined or described in the texts through written language and visual images; and (2) the existential meaning of disability in the texts. The implications of text and dominant discursive practices related to disability on the professional practices of occupational therapy are discussed. Critical examination of how disability is conceptualized in occupational therapy allows for the consideration of alternative views of disability, which are likely to influence future occupational therapy theory, practice, and knowledge.

Keywords: Critical Discourse Analysis
Disability
Social Constructionism
Advisor: Iwama, Michael
A Hybrid Bayesian and Data-envelopment-analysis-based Approach to Measure the Short-term Risk of Initial Public Offerings

Initial public offerings (IPOs) are perhaps the most exhilarating events on stock exchanges. Yet, the ‘ambiguity’ of the risk of IPOs overshadows the thrill and deters many investors from possibly considering the IPOs. It is the insufficient accounting and market history at the IPO stage that burdens their proper risk quantification. The main objective pursued by this thesis is to offer a methodology for measuring the short-term risk of IPOs which conforms to the mathematical principles of market risk analysis employed in the case of public companies. Here, short-term risk is defined as the uncertainty associated with the stock price of the IPO of interest (IPOI) 90 days subsequent to the issuing day and is quantified as a value-at-risk (VaR) inferred from the probability density function of price on day 90 (i.e., PDF_90^IPOI). This thesis develops a Bayesian framework where PDF_90^IPOI can be estimated in a recursive and iterative process. In most IPO cases, there exist limited hard data, yet, strong ‘prior’ belief (soft data). The Bayesian setting offers a unique risk quantification approach which befits and serves these two characteristics of IPOs. To obtain the data required for carrying out the risk analysis, this research relies upon the ‘closest comparable’ of IPOI. The ‘closest comparable’ would be a public firm whose pre-IPO idiosyncratic financial data most resemble those of IPOI. Furthermore, it is expected to have gone public in similar macro-economic and sector conditions. Concisely, the risk quantification process involves two phases: In Phase I, a Data Envelopment Analysis-based multi-dimensional similarity metric is developed to select the closest comparable. Phase I indeed identifies the most suitable source of ‘prior’ knowledge and passes the output to Phase II which encompasses the Bayesian process. Phase II is designed to formulate and refine the ‘prior’ evidence and then employ the achieved ‘posterior’ knowledge towards estimating PDF_90^IPOI. This PDF_90^IPOI subsequently acts as the basis for VaR inferences. In the last stage of the research, the proposed Bayesian VaR methodology is examined (backtested) using the following two tests: test of uniform cumulative probability values and test of VaR break frequency.

Keywords: Backtesting
Bayesian
Initial Public Offerings (IPO)
Short-Term Risk
Value at Risk (VaR)
Advisor: Paradi, Joseph C.
Run Like a Girl? That's So Gay: Exploring Homophobic and Sexist Language among Grade 7 and 8 Students in the Toronto District School Board

Homophobic name-calling abounds in schools, especially at the high school level. Driving much of this research is the negative impact of anti-gay language and epithets on lesbian, gay, bisexual and trans (LGBT) identified students, students with LGBT parents and guardians, and students overall. Studies in the US, UK, and Canada report regular use of phrases such as ‘that’s so gay’, ‘faggot’, and the word “gay” itself to denote something or someone with little to no value. However, a dearth of research looking at the prevalence of homophobic language at the middle school level exists. Furthermore, there is even less research looking at the relationship between homophobic and sexist language use. Using a mixed methods explanatory sequential design, this three-paper dissertation explored homophobic and sexist language use in middle school, specifically investigating, among other things, how often and under what conditions grade seven and eight students use these types of language. A stratified random sample of middle school students (n=488) completed a survey that included the Homophobic Content Agent Target Scale (HCAT). The newly developed Sexist Content Agent Target Scale (S-CAT) explored sexist language. Students reported their frequency of homophobic and sexist language use in five relationship domains including friends, strangers, and antagonists. As well, five focus groups explored more deeply students’ perceptions and understandings of homophobic and sexist language use at school. A number of important findings were produced including the prevalence of homophobic name-calling prior to high schools as well as the strong association between homophobic and sexist language use. These empirical findings join the literature that has long conceptually linked sexism and homophobia, whereby their interlocking nature manifests in name-calling experiences of middle school students. Students (boys in particular) as either agents or targets of sexist language had increased likelihood of being agents or targets of homophobic language. Given the often contentious nature of anti-homophobia education, the hesitancy of school staff to intervene regularly (even in the presence of this language), the findings presented here suggest anti-sexist education as another means to address homophobic language, thereby contributing to creating and maintaining more positive learning environment for all students.

Keywords: Canada
homophobia
middle school
sexism
Advisor: Mishna, Faye
Polarimetry from the Stratosphere with Spider and BLASTPol

This thesis presents the hardware development and flight performance of two balloon-borne experiments. The Spider experiment is a millimetre-wavelength polarimeter designed to measure B-mode polarization in the Cosmic Microwave Background at degree scales. This pattern is the imprint of the primordial gravitational waves predicted to have been produced by inflation. The BLASTPol experiment is a submillimetre-wavelength polarimeter designed to measure the linearly-polarized emission from aligned dust grains in Galactic molecular clouds, inferring the directions of the magnetic fields there. One goal of this measurement is to understand the role of magnetic fields in the earliest stages of star formation. Spider had a Long-Duration Balloon flight around Antarctica in January 2015. BLASTPol had two such flights, in December 2010 and 2012. Analysis of Spider data is underway. Results of BLASTPol 2012 data analysis are presented herein. The design and performance of the Spider pointing control system is presented. A new pivot motor control mode was developed, in which the servo drive controlled motor velocity, not current. This mode enabled sinusoidal azimuth scans at a peak speed of 5 deg/s, with a peak acceleration of 0.5 (deg/s)/s, in flight. The pointing stability in flight was 1'' to 2'' RMS. A new elevation drive system was designed and built for Spider. The Spider observing strategy is presented. It enabled observation of a 10% patch of sky, avoiding the sun and Galactic plane, with uniform coverage in declination, and good cross-linking. A model of the BLASTPol 2012 PSF was developed, allowing centroiding, flat-fielding, and map deconvolution. The latter was attempted in Fourier space, and using the Lucy-Richardson method. A net linear polarization of the dust emission in the Carina Nebula was measured by BLASTPol. The mean fractional polarization is 6.75% +/- 0.015%, 6.84% +/- 0.016% and 7.06% +/- 0.019%, at 250, 350, and 500 μm respectively. A falling polarization spectrum was found, in contrast with the V-shaped spectrum measured in other molecular clouds. The median ratios of the fractional polarization between bands have been measured to be 1.0155 +/- 0.00035 between 250 and 350 μm, and 0.9376 +/- 0.00056 between 500 and 350 μm.

Keywords: Cosmic Microwave Background
Inflation
Instrumentation
Molecular Clouds
Polarization
Scientific Ballooning
Advisor: Netterfield, Calvin B
Ready Schools in Pakistan: School and Classroom Factors Associated with Children's Success in Early Primary

The school system in Pakistan seems to be failing children from the very start – with low levels of enrolment, retention (staying in school), and learning, especially in early primary. What makes a ready school in Pakistan, a school that is ready to support children they first transition into early primary? This study used mixed methods to investigate school and classroom factors associated with children’s transition outcomes: entry, adjustment, and learning in early primary. Quantitative methods examined relationships between school factors and transition outcomes at 35 schools. Grade 1 enrolment was higher at schools in urban areas, with better toilet and water facilities, with higher levels of intervention in the Grade 1 classroom, and with pre-primary programmes, particularly better quality pre-primary classrooms. Grade 1 attendance rates were also higher at schools with pre-primary programmes. Grade 1 learning achievement scores were associated with levels of intervention in the Grade 1 classroom, as well as with Grade 1 and pre-primary classroom quality. Qualitative interviews and focus group discussions were conducted at four of the schools. Grade 1 teachers and parents were asked about their perspectives on school factors affecting children’s transition outcomes. Respondents highlighted the affordability of government schools as important for children’s enrolment. The teacher’s attention towards children was described as affecting children’s attendance and retention. For children’s adjustment to school, respondents emphasized the teacher’s approach and interactions towards children, peer interactions, and pre-primary programmes easing the transition. For children's learning, respondents gave importance to the teacher’s instructional effectiveness, in addition to her/his attention and approach towards children. In addition, Grade 1 children’s perspectives on their school were gathered through drawings and interviews. In their drawings, children focused on peers, particularly siblings and close cousins, as well as elements of the school’s physical environment (e.g., furniture). These findings indicate that education reforms in Pakistan should focus on improving access and quality in government-provided education, developing teachers’ relational skills as well as instructional skills, and providing pre-primary education.

Keywords: early primary
ready schools
school readiness
transition
Advisor: Corter, Carl
Characterization of a Copper Resistance and Transport System in Streptococcus Mutans

Proteins and enzymes require metal ions as enzymatic cofactors for optimal biological activities. Copper metal ion is utilized by various bacterial systems in trace amounts; however, it can be extremely toxic at higher concentrations. The copYABZ operon, involved in copper homeostasis, has been extensively studied and characterized in several Gram positive bacteria. CopA and CopB encode for P-type ATPases, involved in copper translocation, whereas, CopY and CopZ regulate the expression of the cop operon. In Streptococcus mutans, the primary etiological agent of dental caries, copYAZ has been partially investigated for its role in copper transport and resistance. In this study, we demonstrated the probable mechanisms by which copper induces toxicity in S. mutans; and elucidated the role of copYAZ operon in modulating copper transport and resistance, as well as other physiological processes of this oral pathogen. Copper induces toxicity by generating oxidative stress and dissipating membrane potential in S. mutans. During biofilm growth, copper impaired S. mutans ability to adhere to a surface and produce biofilm biomass; while significantly repressing the expression of genes involved in maintaining the functional and structural integrity of biofilm matrix. Results from copper transport studies validated the role of copYAZ in copper efflux in S. mutans. The knock-out strain in copYAZ (∆copYAZ) was more sensitive to copper, oxidative and acid stress relative to its wild type. Loss of copYAZ resulted in prolonged membrane depolarization in S. mutans. The presence of copper and/or the absence of copYAZ significantly impaired S. mutans ability to acquire foreign DNA from the surrounding environments; while repressing the transcription of genes involved in competence development. The copYAZ-associated phenotypes were further validated via genetic complementation studies. Taken collectively, we illustrated the implications of copper-induced toxicity in S. mutans; and have provided evidence describing the importance of copYAZ operon in copper resistance and transport, biofilm formation, acid and oxidative stress tolerance, maintenance of membrane potential, and genetic transformation in S. mutans.

Keywords: biofilm
copper transport
genetic competence
Streptococcus mutans
Advisor: Cvitkovitch, Dennis G
Levesque, Celine M
Machiavelli's Republicanisms: Society, Discord and the Politics of Equilibrium in the Florentine Histories

The purpose of this project is to show that Niccolò Machiavelli’s Florentine Histories (1520-24), represents a departure from earlier Machiavellian conceptions of liberty, power and authority toward an attraction to Venice, collective structures of power and constitutional mechanisms to create stability. In this later writing, which Anglo-American scholarship has largely overlooked, we see a republicanism built on different conceptual and theoretical foundations than the Roman model introduced in Machiavelli’s most famous republican treatise, the Discourses on Livy (1513-17). This transformation indicates Machiavelli’s rejection of the assumptions of classical republicanism and marks a crucial transition in his own analysis of power and authority. Contrary to received wisdom, I demonstrate that in the Histories and other key post-1520 works, we can observe Machiavelli's rapprochement to the Venetian style of “institutional virtù” and his consequent éloignement from the Roman model of civil discord and popular “guardianship of liberty.” In a word, while the Florentine Histories confirms that Machiavelli was a devoted republican thinker, it also shows that his preference for a collective form of self-government underwent some integral alterations from the earlier political works – with the late Machiavelli coming increasingly closer to the Venetian form of republicanism advocated by his intellectual contemporaries.

Keywords: Citizenship
Florentine Histories
Machiavelli
Renaissance
Republicanism
Venice
Advisor: Balot, Ryan K
Investigating the Function and Regulation of Two CRISPR Systems of Streptococcus mutans

CRISPR-Cas (clustered, regularly interspaced short palindromic repeats–CRISPR-associated proteins) provide adaptive microbial immunity systems against invading viruses and natural transformation via plasmids. Naturally competent Streptococcus mutans UA159 harbors two CRISPR-Cas systems: type II-A system (CRISPR1) and type I-C system (CRISPR2) and several spacers matching sequences of phage M102 or genomic sequences of other S. mutans strains. In addition, previous transcriptome studies in S. mutans linked CRISPR/Cas systems to stress response and virulence. The goal of this work was to determine the role of CRISPR/Cas systems in phage defense and natural transformation in S. mutans, and also to investigate if they play additional functions in the cell physiology. Deletion of CRISPR1 and/or CRISPR2 cas genes or removal of the spacers in S. mutans UA159 did not affect its M102 phage resistant phenotype, suggesting that CRISPR-independent mechanisms contribute to the phage resistance. Using a plasmid-based interference assay, we identified DNA interference activity in S. mutans UA159, which is mediated by its type II-A CRISPR/Cas system (CRISPR1). Spacers 2 and 3 from type II-A, both matching sequences from phage M102, were found to be essential for CRISPR interference against engineered plasmids containing matching proto-spacer sequences. Functional analysis of the cas deletion mutants revealed that CRISPR1-Cas system modulates stress tolerance induced by low pH, high temperature, oxidative and cell membrane stress, as well as DNA damaging conditions, whereas the CRISPR2-Cas participates in the tolerance associated with heat shock. Transcriptional analysis identified that VicR/K two-component signal transduction system differentially regulates the expression of cas genes for both systems in S. mutans. Further, structural, biochemical and functional studies found that the Cas5d protein SMU.1763c, a putative endoribonuclease associated with the CRISPR system I-C, acts on structured RNA substrates that is likely to be involved in CRISPR RNA processing but not in sensing cell envelope stress or preserving cell integrity in S. mutans. Together our data provide in vivo evidence that the CRISPR-Cas systems of S. mutans play novel roles in resistance against incoming plasmids that carry matching protospacer sequences and stress response.

Keywords: cell physiology
CRISPR
phage infection
Streptococcus mutans
Advisor: Cvitkovitch, Dennis G
Significant Predictors of Functional Status and Complications in Patients Ungergoing Surgery for the Treatment of Cervical Spondylotic Myelopathy

Introduction: Cervical spondylotic myelopathy (CSM) is a degenerative spine disease and the most common cause of spinal cord dysfunction in adults worldwide. Surgery is increasingly recommended as the preferred management strategy for these patients as it can effectively halt neurological progression and improve functional status. In this field, there is an increasing need to manage patients’ expectations of outcomes and inform them of relative risks and benefits of their surgical procedure. Objectives: This thesis aims to identify important predictors of functional outcomes and perioperative complications in patients undergoing surgery for the treatment of CSM. Methods: Three systematic reviews of the literature were performed to identify 1) important clinical predictors of surgical outcome; 2) important imaging predictors of surgical outcome; and 3) significant clinical and surgical predictors of complications. Two surveys were also conducted to evaluate what spine professionals believed were the most critical predictors of functional outcomes and complications. Finally, using prospectively-collected data, we developed a clinical and a complications prediction rule to predict functional status at 1-year follow-up and a patient’s risk of complications. Results: Patients were more likely to achieve an “optimal outcome” if they were younger; had milder myelopathy and a shorter duration of symptoms preoperatively; did not smoke; had fewer and less severe co-morbidities; and did not present with gait dysfunction. Patients were at a higher risk of perioperative complications if they had a greater number of co-morbidities, co-existing diabetes, a diagnosis of myelopathy secondary to ossification of a posterior longitudinal ligament and a longer operative duration. Conclusions: Our outcomes prediction study provides information that can be used by clinicians to manage patients’ expectations and counsel concerned patients as to potential treatment options. Furthermore, the results from this study emphasize the importance of accurately detecting CSM at a mild disease state and referring these patients for early surgical consultation. The knowledge gained from our complications study can be used by surgeons to objectively quantify a patient’s risk of complications and discuss this risk during the surgical consent process. Furthermore, surgeons should use this information to institute case-specific preventative plans and to strategize appropriate postoperative care.

Keywords: cervical spondylotic myelopathy
neurosurgery
outcomes
prediction
spine
validation
Advisor: Fehlings, Michael G