VictorJuiz/thesis huggingface dataset:
Maltreatment in the Father-child Relationship: An Exploration of Problematic Relational Dynamics

Despite the high prevalence of father-perpetrated maltreatment, relatively little empirical attention has been given to men who abuse and neglect their children (Dubowitz, 2006, 2009; Haskett, Marziano, & Dover, 1996). To further our understanding, the current dissertation explored father-child relational dynamics that underlie risk for child maltreatment. In the first study, data from a sample of 121 maltreating fathers were used to discern differential patterns of parenting dynamics using both theoretical and statistical approaches to classification. It was hypothesized that fathers would show problems predominantly in one of five areas: emotional unavailability; negative attribution, harshness, and rejection; developmentally inappropriate interaction; poor psychological boundaries; and exposure of a child to hostile inter-parental relations. Contrary to expectation, little support was obtained for the predominant problem hypothesis. Although methodological limitations may play a role, results indicated that men were more clearly differentiated by the degree of severity evidenced across their problematic parent-child interactions, than by differences in the specific pattern of problems they experienced. An interesting finding from Study 1 was that increasingly severe relational problems were associated with a misprioritization of parent and child needs. Study 2 further explored this dynamic by revising and re-evaluating a self-report measure of men’s ability to balance needs in the father-child relationship. Data from two samples (93 community fathers and 85 maltreating fathers) provided mixed results: Support was obtained for the internal consistency and construct validity of the image-emotional needs subscale of the measure; however, minimal support was obtained for the personal needs subscale. Furthermore, in contrast to expectation, discriminant validity was not obtained for either subscale, as maltreating fathers reported a better ability to balance needs on both scales than fathers drawn from a community sample. Social desirability was one of several factors deemed to play a key role in this finding. Each study’s contribution to the field is reviewed, along with discussion of limitations and future directions.

Keywords: child maltreatment
domestic violence
fathers
Advisor: Scott, Katreena
Inter-professional Clinical Practice Guideline for Vocational Evaluation following Traumatic Brain Injury

Due to physical, cognitive and emotional impairments, many individuals are unemployed or under-employed following a traumatic brain injury. The research evidence links the rigour of a vocational evaluation to future employment outcomes. Despite this link, no specific guidelines exist for vocational evaluations. Using the research evidence and a diverse panel of clinical and academic experts, the primary objective of this doctoral research was to develop an inter-professional clinical practice guideline for vocational evaluation following traumatic brain injury. The objective of the guideline is to make explicit the processes and factors relevant to vocational evaluation, to assist evaluators (i.e. clients, health and vocational professionals, and employers) in collaboratively determining clients’ work abilities and developing recommendations for work entry, re-entry or vocational planning. The steps outlined in the Canadian Medical Association's Handbook on Clinical Practice Guidelines were utilized to develop the guideline and include the following: 1) identifying the guideline’s objective/questions; 2) performing a systematic literature review; 3) gathering a panel; 4) developing recommendations; 4) guideline writing; 5) pilot testing. The resulting guideline includes 17 key recommendations within the following seven domains: 1) evaluation purpose and rationale; 2) initial intake process; 3) assessment of the personal domain; 4) assessment of the environment; 5) assessment of occupational/job requirements; 6) analysis and synthesis of assessment results; and 7) development of evaluation recommendations. Results from an exploratory study of the guideline’s implementation by occupational therapists in their daily practices revealed that clinicians used the guideline to identify practice gaps, systematize their evaluation processes, enhance inter-professional and inter-stakeholder communication, and re-conceptualize their vocational evaluations across disability groups. Statistically significant improvements were also noted in clients’ participation scores on the Mayo-Portland Adaptability Inventory–4 following guideline use. This guideline may be applicable to individuals with TBI, clinicians, health and vocational professionals, employers, professional organizations, administrators, policy makers and insurers.

Keywords: clinical practice guidelines
vocational rehabilitation
traumatic brain injury
evidence-based practice
health plan implementation
return to work
employment
work capacity evaluation
brain injury
vocational evaluation
work assessment
job performance
work performance
employment status
re-employment
review
work integration
work re-integration
brain injuries
practice guideline
knowledge transfer
knowledge translation
implementation
occupational therapy
neurological rehabilitation
knowledge exchange
research utilization
continuing professional development
quality improvement
practice change
change management
health care technology
implementation research
Advisor: Rappolt, Susan
Dawson, Deirdre R.
Dissecting the Role of Morphogenesis in the Origins of the First Two Cell Lineages in the Mouse Embryo

Although the mechanisms underlying the divergence of the first cell types in the mouse, the trophectoderm (TE) and the inner cell mass (ICM) have received considerable attention, the upstream signals stimulating their divergence are not well understood. The work presented here examines the roles that morphogenetic factors such as cell adhesion and polarization play in the development of these cell types. I show here that in embryos completely lacking both maternal and zygotic E-cadherin, the normal epithelial morphology of outer cells is disrupted but individual cells still initiate TE and ICM-like fates. A larger proportion of cells than normal expressed TE markers like Cdx2 (a homeodomain containing transcription factor), suggesting that formation of an organized epithelium is not necessary for TE-specific gene expression. Individual cells in such embryos still generate an apical-like domain that correlates with elevated Cdx2 expression. I also show that repolarization can occur in isolated early ICMs from both wild type and Cdx2 mutant embryos, indicating that Cdx2 is not required to initiate polarity. Importantly, I demonstrate a critical role for the Rho-associated kinase ROCK in apical-basal polarization of preimplantation blastomeres. Loss of apical-basal polarization leads to a reduction of Cdx2 expression in outer blastomeres due to activation of Lats1/2 kinase and reduced nuclear Yap1. The influence of polarization upon Lats1/2 kinase is stage-dependent however, as apolar 8-cell blastomeres retain nuclear Yap1. Cell position appears to serve as an additional cue for nuclear localization of Yap and Cdx2 expression from the 8-cell stage to E3.5. Cell polarization plays an additional role in the embryo of maintaining cells in consistently outer or inner positions, thus ensuring that Cdx2 is expressed exclusively in the developing TE. The results of this work demonstrate important links between morphogenesis, cell fate and patterning in the preimplantation embryo. Both cell polarization and cell position act as critical cues to determine gene expression and to pattern this expression within the embryo.

Keywords: mouse
epithelium
polarity
polarization
blastocyst
cell adhesion
E-cadherin
Cdx2
aPKC
ROCK
Yap
embryo
PKC zeta
Lats
Oct4
Advisor: Rossant, Janet
Lie 2-algebras as Homotopy Algebras Over a Quadratic Operad

We begin by discussing motivation for our consideration of a structure called a Lie 2-algebra, in particular an important class of Lie 2-algebras are the Courant Algebroids introduced in 1990 by Courant. We wish to attach some natural definitions from operad theory, mainly the notion of a module over an algebra, to Lie 2-algebras and hence to Courant algebroids. To this end our goal is to show that Lie 2-algebras can be described as what are called \emph{homotopy algebras over an operad}. Describing Lie 2-algebras using operads also solves the problem of showing that the equations defining a Lie 2-algebra are consistent. Our technical discussion begins by introducing some notions from operad theory, which is a generalization of the theory of operations on a set and their compositions. We define the idea of a quadratic operad and a homotopy algebra over a quadratic operad. We then proceed to describe Lie 2-algebras as homotopy algebras over a given quadratic operad using a theorem of Ginzburg and Kapranov. Next we briefly discuss the structure of a braided monoidal category. Following this, motivated by our discussion of braided monoidal categories, a new structure is introduced, which we call a commutative 2-algebra. As with the Lie 2-algebra case we show how a commutative 2-algebra can be seen as a homotopy algebra over a particular quadratic operad. Finally some technical results used in previous theorems are mentioned. In discussing these technical results we apply some ideas about distributive laws and Koszul operads.

Keywords: Operads
Categorification
Advisor: Arkhipov, Sergey
Understanding and Addressing Barriers: Engaging Adolescents in Mental Health Services

This randomized-controlled pilot study explored the impact of a pretreatment, telephone engagement intervention on adolescents’ (ages 13-19) initial mental health service attendance (i.e., the first 3 counseling sessions) and four secondary outcome variables (i.e., autonomous/ controlled treatment motivation, self-efficacy, and working alliance). Twenty-seven adolescents received the engagement intervention and completed assessments and 24 adolescents completed assessments only. Both groups completed follow-up assessments 6 weeks after study enrollment. Associations between the outcome variables and initial treatment attendance were explored. The extent to which demographic variables (i.e., age, gender, race, immigration status, and residence in low income neighbourhoods), psychological distress, and self-reported barriers (i.e., mismatched treatment expectations and external demands) were associated with treatment attendance was also explored. The primary findings from this pilot study indicated that adolescents who received the engagement intervention had greater initial treatment attendance (M=2.11, SD=1.01) than the assessment only group (M=1.54, SD=1.22), but the difference only approached significance. Moreover, no significant between-group differences in the secondary outcome variables were found. Paired samples t-tests were used to examine changes in autonomous/controlled treatment motivation and self-efficacy within groups between baseline and follow-up. The results of the paired samples t-tests indicated that that the experimental and control groups both demonstrated a significant decrease in controlled motivation at follow-up. In addition, the control group demonstrated a significant decrease in autonomous treatment motivation at follow-up. Post hoc analyses, using correlation and linear regression analyses, explored the associations between initial attendance and the secondary outcome variables, psychological distress, self-reported barriers, and demographic variables. A negative association between age, self-reported barriers and initial attendance was found. A positive association was found between working alliance and initial attendance. While the majority of adolescents who participated in this research lived in low income neighbourhoods and nearly half were second generation immigrants, these demographic variables were not associated with initial treatment attendance. Although the engagement intervention had a medium effect on initial treatment attendance, this difference was not statistically significant. Future research with a larger sample size and longer follow-up is needed to determine the effectiveness of the engagement intervention.

Keywords: evidence-based practice
treatment engagement
adolescents
Mental Health Services Research
Advisor: Mishna, Faye
Development and Application of Hidden Markov Models in the Bayesian Framework

This thesis develops new hidden Markov models and applies them to financial market and macroeconomic time series. Chapter 1 proposes a probabilistic model of the return distribution with rich and heterogeneous intra-regime dynamics. It focuses on the characteristics and dynamics of bear market rallies and bull market corrections, including, for example, the probability of transition from a bear market rally into a bull market versus back to the primary bear state. A Bayesian estimation approach accounts for parameter and regime uncertainty and provides probability statements regarding future regimes and returns. A Value-at-Risk example illustrates the economic value of our approach. Chapter 2 develops a new efficient approach to model and forecast time series data with an unknown number of change-points. The key is assuming a conjugate prior for the time-varying parameters which characterize each regime and treating the regime duration as a state variable. Conditional on this prior and the time-invariant parameters, the predictive density and the posterior of the change-points have closed forms. The conjugate prior is further modeled as hierarchical to exploit the information across regimes. This framework allows breaks in the variance, the regression coefficients or both. In addition to the time-invariant structural change probability, one extension assumes the regime duration has a Poisson distribution. A new Markov Chain Monte Carlo sampler draws the parameters from the posterior distribution efficiently. The model is applied to Canadian inflation time series. Chapter 3 proposes an infinite dimension Markov switching model to accommodate regime switching and structural break dynamics or a combination of both in a Bayesian framework. Two parallel hierarchical structures, one governing the transition probabilities and another governing the parameters of the conditional data density, keep the model parsimonious and improve forecasts. This nonparametric approach allows for regime persistence and estimates the number of states automatically. A global identification algorithm for structural changes versus regime switching is presented. Applications to U.S. real interest rates and inflation compare the new model to existing parametric alternatives. Besides identifying episodes of regime switching and structural breaks, the hierarchical distribution governing the parameters of the conditional data density provides significant gains to forecasting precision.

Keywords: Hidden Markov model
Advisor: Maheu, John
Preparing Teacher Candidates for the Present: Exploring the Praxis of Mindfulness Training in Teacher Education

The fields of medicine and health care continue to demonstrate the benefits of mindfulness-based practice for stress reduction and well-being. Research is also beginning to reveal the professional benefits of mindfulness training with human service professionals, as well as the impact with children and youth, and more broadly within the field of education and human development. This qualitative action research study uses a grounded theory approach to elucidate the added value of the Mindfulness-Based Wellness Education (MBWE) program within three main areas of teacher education: dispositional development, content knowledge, and instructional repertoire. Two years being engaged in the iterative process of teaching, interviewing teacher candidates, and program development brought forth five main themes: (1) Personal and Professional Identity, Reflective Practitioner, (3) Constructivist Learning & Holistic Vision of Teaching, (4) Social and Emotional Competence on Practicum, and (5) Engagement in Teacher Education. Additional findings outline key curricular and pedagogical components of the MBWE program that facilitate teacher candidate learning. Finally, a holistic model of pedagogical well-being presents an avenue for understanding the integration of mindful wellness into teacher education, and the K-12 classroom.

Keywords: mindfulness
teacher education
teacher disposition
holistic education
Advisor: Miller, Jack
Error-correcting Codes for Fibre-optic Communication Systems

Electronic signal processing techniques have assumed a prominent role in the design of fibre-optic communication systems. However, state-of-the-art systems operate at per-channel data rates of 100 Gb/s, which constrains the class of communication algorithms that can be practically implemented. Relative to LDPC-like codes, product-like codes with syndrome-based decoding have decoder dataflow requirements that are smaller by more than two orders of magnitude, which strongly motivates the search for powerful product-like codes. This thesis presents a new class of high-rate binary error-correcting codes, staircase codes, whose construction combines ideas from convolutional and block coding. A G.709-compliant staircase code is proposed, and FPGA-based simulation results show that performance within 0.5 dB of the Shannon Limit is attained for bit-error-rates below 1E-15. An error-floor analysis technique is presented, and the G.709-compliant staircase code is shown to have an error floor below 1E-20. Using staircase codes, a pragmatic approach for coded modulation in fibre-optic communication systems is presented that provides reliable communications to within 1 bit/s/Hz of the capacity of a QAM-modulated system modeled via the generalized non-linear Schrodinger equation. A system model for a real-world DQPSK receiver with correlated bit-errors is presented, along with an analysis technique to estimate the resulting error floor for the G.709- compliant staircase code. By applying a time-varying pseudorandom interleaver of size 2040 to the output of the encoder, the error floor of the resulting system is shown to be less than 1E-20.

Keywords: optical communications
coding theory
staircase codes
coded modulation
Advisor: Kschischang, Frank R.
Technology Development for Next Generation Functional Analysis of Bioactive Molecules

The genome-wide HaploInsufficieny Profiling (HIPHOP) technique has been validated as a method to quantify the relative abundance of uniquely tagged yeast deletion strains using a microarray readout. The massive throughput of next generation sequencing presents a new technology for assessing HIPHOP profiles. I developed a new method called Barcode analysis by Sequencing (Bar-seq) that applies deep sequencing to genome-scale fitness. I show that Bar-seq outperforms the current benchmark barcode microarray assay in terms of both dynamic range and throughput. When applied to a complex genome-scale fitness assay, Bar-seq quantitatively identifies drug-targets, exceeding the performance of the microarray assay. I also established that Bar-seq is well suited to a multiplex format and provides a dramatic increase in throughput. I used the genome-wide HIPHOP assay and other functional genomics tools to explore the mechanisms underlying drug-drug synergies. Drug combination therapy, and synergistic combinations in particular, have several advantages over monotherapies. Synergistic drug combinations allow the dose of each agent to be reduced, often with the benefit of diminishing side effects while maintaining efficacy and decreasing the chances of drug resistance. I used my yeast model to identify synergistic drug combinations and found that inhibitors of ergosterol biosynthesis are highly synergistic with several agents, including those targeting other points within the same pathway. I also devised a method that enriches for synergistic interactions during screening of compound combinations. This new synergy prediction method can aid in the rapid identification of anti-proliferative combinations and can be readily applied to other organisms for further characterization and/or confirmation. Finally, I examined synergistic combination HIPHOP profiles and identified Gene Ontology enrichments that are combination-specific.

Keywords: Yeast
Sequencing
Technology Development
Chemical Biology
Chemical Genetics
Drug Discovery
Advisor: Giaever, Guri
Boone, Charles
Contributions of Epstein-Barr Nuclear Antigen 1 (EBNA1) to Epithelial Cell Infections

Epstein-Barr virus (EBV) latent infection is associated with lymphoid and epithelial tumours, including nasopharyngeal carcinoma (NPC) and gastric carcinoma (GC). Since EBNA1 protein is expressed in all EBV tumours, I explored whether EBNA1 alters the cellular environment in ways that would contribute to the development of these epithelial tumours. I have shown that EBNA1 disrupts nuclear bodies (NBs) formed by the PML tumor suppressor and degrades PML proteins in a proteasome dependent manner in NPC and GC cell lines. I have verified the role of EBNA1 in disrupting PML NBs through overexpression and silencing of EBNA1 and shown that EBNA1 alone is sufficient to mediate these effects. Using EBNA1 mutants I found that USP7 and protein kinase CK2 (two enzymes that negatively regulate PML NBs) are important for EBNA1-mediated disruption of PML NBs. Furthermore, I have shown that EBNA1 localizes to PML NBs, and interacts with PML IV, which mediates the enrichment of USP7 and CK2β with PML NBs and increases CK2 phosphorylation of PML proteins, a known prerequisite for PML degradation. Consequently, functions downstream of PML were impaired in the presence of EBNA1. In particular, cells expressing EBNA1 had decreased levels of p53acetylation, p21 and apoptosis in response to DNA damage. Furthermore, DNA repair was markedly impaired in these cells, despite the fact that they survived better after induction of DNA damage than cells lacking EBNA1. In keeping with these observations, immunohistochemistry staining of GC biopsies showed that EBV-positive GC biopsies had lower PML staining compared to EBV-negative samples. These results show that EBNA1 directly affects host cell processes that would be expected to promote malignant transformation. Additionally, I have shown that EBNA1's ability to disrupt PML NBs is important for reactivation of EBV from latency; hence, is required for efficient spread of EBV from host to host.

Keywords: Epstein-Barr Virus
EBNA1
PML nuclear bodies
p53
EBV reactivation
Advisor: Frappier, Lori