VictorJuiz/thesis huggingface dataset:
Posttraumatic Symptoms in Therapists Following the Suicide of a Client

Research has shown that client suicide can be an alienating, isolating and frightening experience for therapists, whether it occurs at the beginning of their career or well after they have established themselves as professionals. Previous research has failed to examine the therapistâ s experiencing of posttraumatic symptoms in response to client suicide and the factors that affect this, particularly the history of prior trauma, the presence of prior psychological problems, number of previous client suicides, gender, education, working alliance, and perceived support following the client suicide. Ninety-one clinicians who live in North America who experienced a client suicide in the past five years completed measures assessing trauma history (stressful life experiences), prior client suicide, demographics, working alliance, training preparedness, and posttraumatic adjustment. Furthermore, clinician survivors were given the opportunity to reflect on what they found most and least helpful following the suicide of a client, and what advice they would give to another clinician who is experiencing the suicide of a client for the first time. The results of this study indicate that overall clinicians experience posttraumatic distress following a client suicide and that this decreases for most clinicians over time. When a number of factors were examined (e.g., working alliance, setting, gender, multiple client suicides, prior graduate training in client suicide, prior stressful life events, and perceived social supports), it was found that previous graduate school training in client suicide and perceived social support were associated with lower levels of posttraumatic distress, both immediately and several months following a client suicide. In addition, multiple client suicides was associated with higher levels of distress immediately post suicide but prior stressful life events and gender (i.e., women) were associated with higher levels of impact six months following the suicide of a client The type of social support that was recommended to be most useful following the suicide of a client was collegial and supervisorial support. Furthermore, prior graduate training in client suicide was correlated with lower levels of distress, both at seven days and six months post client suicide.

Keywords: client suicide
postraumatic symptoms
relational cultural theory
Advisor: Stermac, Lana
Disability (and) Care in Late-Capitalist Struggle: A Dialectical Analysis of Toronto-based Disability (and) Care Activism

Disability organizing has proliferated across North America, particularly in the historic centres of disability organizing: San Francisco and Toronto. Similarly, attention to “care” in its multiple practices and formations has proliferated in community-based and radical activism. This proliferation is linked to the historical developments of austerity, neoliberalism, and imperialism as dominant material and ideological social relations. In this context, the meanings of disability (and) care are being reworked and reconceptualized by the state, grassroots organizers, and a variety of financial interests, proliferating disability identities. These social relations place care (and social reproduction) at the heart of radical and revolutionary organizing. Disability organizers and activists seeking to consciously intervene and change these conditions and social relations must grapple with the disability (and) care of the past as well as possibilities for the future in order to shape their projects from forms of resistance to prefigurative and strategic revolutionary struggle. Drawing on oral stories, zines and blogs of activists and organizers, I use a relational/reflexive method (Gorman 2005) to dialectically investigate how disability activists, anti-poverty organizers and political care workers develop “disability consciousness” as they mediate and politicize the contradictions of their disability care praxis. In my interviews with activists beyond the umbrella of disability politics proper, I broaden the historical and material dialectics of care to include disability consciousness around processes and stigmatized drug use in the context of gentrification and drug wars. By expanding these dialectics I can better attend to the social relations of race, imperialism and finance capitalism that remain marginal in disability politics. This thesis is an investigation of how disability activists, anti-poverty organizers and political care workers develop “revolutionary disability consciousness” through struggle. My analysis will develop dialectical methods for recognizing this struggle, while also charting a path towards a revolutionary future, which is not wistful, but realistic, necessary and already becoming.

Keywords: activism
care
community
disability
historical materialism
social movements
Advisor: Magnusson, Jamie
Comparative and Evolutionary Genomics of Pseudomonas syringae

The Pseudomonas syringae species complex comprises many genetically diverse strains ubiquitously found in both agricultural and non-agricultural environments. More popularly known as a plant pathogenic bacteria, P. syringae has a very broad host range. However, distinct strains show strong host specificity and are able to cause disease on limited crops. Multi-locus sequence typing studies have sub-divided the P. syringae complex into at least 13 different subgroups referred as phylogroups. Given such extensive genetic and ecological diversity within the species complex, there is an ongoing debate over the species definition of P. syringae strains. My research work investigated strains within the P. syringae species complex to determine if they belong to a single species population or if distinct phylogroups are in fact different species by performing whole-genome analysis of approximately 400 P. syringae strains using various comparative and evolutionary approaches. To overcome the computational challenges of large-scale comparative genome analysis, we designed a novel comparative genomic pipeline named DeNoGAP. The DeNoGAP pipeline provides a robust computational pipeline for performing various comparative genomics tasks, such as gene prediction, ortholog prediction, functional annotation, and analysis of a pan-genome. The comparative genome analysis of more than 400 strains shed insight into the P. syringae pan-genome. We found P. syringae pan-genome to be big and diverse, comprising of more than 77,000 gene families. Evolutionary analyses of gene families showed evidence of homologous recombination and positive selection across entire genomes of P. syringae strains. Although our analysis showed that phylogroups rarely exchange genes via homologous recombination, we found that inter-phylogroup homologous recombination occurs disproportinately among virulence-associated and positively-selected genes that are essential for ecological adaptation and evolution of P. syringae strains. Based on these findings, we hypothesized that P. syringae maintains genetic cohesion between its divergent strains due to an exchange of ecological and evolutionarily relevant genes. Together, my work provides a robust computational pipeline for large-scale comparative genomics projects and sheds insight into species definition of the P. syringae species complex based on strong evolutionary species concepts rather than molecular methods.

Keywords: Bioinformatics
Comparative genomics
Evolutionary genomics
Pathogens
Pseudomonas syringae
Recombination
Advisor: Guttman, David S
Improving the Estimation of Seasonal Leaf Area Index of Coniferous Forests for Better Carbon and Water Flux Estimation

The availability of global products of leaf area index (LAI) using remote sensing (RS) data makes it possible to model land surface processes at regional and global scales. Due to the lack of continuous observations of in-situ LAI, studies on the seasonal variability of RS LAI products are rare in the literature. Moreover, the application of existing global LAI products is largely restricted by the underestimation of winter LAI over high-latitude evergreen coniferous forests. Low winter LAI values, due to the influence of background, the presence of ice and snow on leaves and the seasonal variation of leaf pigments, exaggerate the LAI seasonality, possibly causing errors in land surface modeling. The aim of this thesis is to gain a better understanding of the quality of existing RS LAI products, to improve these products, and to further investigate the influence of the improvements on modeling carbon, water and energy fluxes. Frequent measurements of LAI in all seasons were conducted at two white pine sites near Turkey Point, Ontario, Canada, using direct and indirect methods. The in-situ LAI measurements were then used to validate the University of Toronto RS LAI product Version 2. Results show that RS LAI captures mostly canopy structural information from the onset of needleleaf growth to the seasonal peak, but captures both leaf chlorophyll and structural information from the seasonal peak to the completion of needleleaf fall. This finding has significant implications for the application of current RS LAI products to terrestrial productivity modeling and prompts the need for separating leaf structure and chlorophyll information. A simple scheme for correcting the distorted LAI seasonality of evergreen conifers is proposed in my research, through which an improved LAI product over conifers in Canada has been developed. It is demonstrated that the improved product greatly increases the accuracy of the simulation of land surface carbon, water and energy fluxes in coniferous forests in Canada.

Keywords: Coniferous forests
Land surface models
Leaf area index
Remote sensing
Surface energy budget
Advisor: Chen, Jing M.
Global Well-Posedness and Scattering of Besov Data for the Energy-Critical Nonlinear Schrödinger Equation

We examine the Defocusing Energy-Critical Nonlinear Schrödinger Equation in dimension 3. This equation has been studied extensively when the initial data is in the critical homogeneous Sobolev space $\dot{H}^1,$ and a satisfactory theory is given in the work of Colliander, Keel, Staffilani, Takaoka and Tao (2008). \bigskip We extend the analysis of this equation to include infinite energy data $u_0 \in \dot{B}^1_{2,q}$ ($2 \leq q \leq \infty$) that can be decomposed as the sum of a finite energy component in $\dot{H}^1$ and a small part in a Besov space, with the size of the Besov part small enough compared to the size of the energy part. The solution is shown to scatter for initial conditions $u_0 \in \dot{B}^1_{2,q}$, for $2 \leq q

Keywords: evolution equation
nonlinear
PDE
Schroedinger
Advisor: Sulem, Catherine
Colliander, Jim
Response Styles in Student Evaluation of Teaching

Student Evaluation of Teaching (SET) typically refers to the use of summated rating scales to measure teaching quality base on studentsâ report. SET is widely used in post-secondary education institutions for informing teacher professional development, curriculum revision, personnel decisions, and for institutional accountability. The literature on SET validity is abundant but often atheoretical, the evidence inconclusive, and provides scarce attention to content and response process. Specifically, research examining whether students respond independently of content relying on response styles is rare. Types of response styles are acquiescence/disacquiescence (tendency to agree/disagree across items), extreme (tendency to endorse extreme response options across items), and midpoint response styles (tendency to use the midpoint option across items). Evidence of a substantial degree of response style would reduce the validity of SET scores as a measure of teaching quality and their utility for informing formative and summative decisions due to overestimation or underestimation of the actual level of teaching quality and artificial changes in the relationship to other variables. Three topics examined in the study are the degree to which SET scores are affected by response styles, differences in the extent to which SET scores are affected by response styles across measurement conditions, and the degree to which response styles moderate differences in SET scores between female and male teachers. Responses to a SET summated rating scale from N=5,921 education graduate students were analyzed. Student-level indexes of response styles suggest a high degree of acquiescence in the direction of teaching quality overestimation, and no disacquiescence, extreme, or midpoint response styles. A 2 (academic department) x 2 (program type) x 6 (academic session) ANOVAs on response styles indexes suggests no statistically significant differences across measurement conditions. Finally, multiple linear regression analysis indicates a statistically significant moderator effect of acquiescence on the difference in SET scores between female and male teachers. The discussion addresses implications of the findings for developers and users of SET summated rating scales, alternative interpretations of the observed pattern of responses, limitations, and suggestions for future research.

Keywords: bias
course evaluation
measurement
response styles
student evaluation of teaching
validity
Advisor: Lam, Tony C.M.
Genetic and environmental influences on neuroanatomy across the lifespan

After centuries of debate, it is acknowledged that the brain is not ﬁxed following development, but is rather a highly dynamic organ that continues to change in structure throughout the lifespan. This neuroanatomical plasticity is driven by the dynamic interplay between genetic and environmental forces that continuously shape the structure of the brain. When these forces are disrupted by genetic mutations or environmental insults, a range of behavioural and neuropsychiatric disorders arise. The aim of this thesis is to investigate the role genes and the environment play in shaping neuroanatomy across the lifespan and in the context of health and disease. In order to understand how these forces inﬂuence neuroanatomy, in-vivo and ex-vivo magnetic resonance imaging (MRI) techniques paired with deformation-based morphometry analytical methods were used to detect volumetric changes in the brain. Mice were used as experimental subjects due to the ability to generate inbred, transgenic animals with a level of control that can be used to speciﬁcally test genetic and environmental variables. Genetic inﬂuences on the brain were studied in the context of two neuropsychiatric disorders, Alzheimer's disease and Rett syndrome. The TgCRND8 mouse model of Alzheimer's disease was scanned longitudinally over the time course of pathological onset using a manganese-enhanced MRI sequence. An additional diﬀusion-weighted sequence was used to gain neuroanatomical images of the developing brain. Mouse models of Rett syndrome were studied using ex-vivo and in-vivo imaging techniques to determine whether neuroanatomical phenotypes that arise early in life could be rescued following the reactivation of Mecp2 in adulthood, the genetic determinant which drives this neurodevelopmental disorder. The eﬀects of the environment on the brain was investigated using in-vivo imaging to track the spatial and temporal changes that occur in the brain following exposure to an enriched housing environment. These studies demonstrate that the structure of the brain is inﬂuenced by genes that play important roles in development and maturation and is highly responsive to environmental challenges in adulthood.

Keywords: Alzheimer's disease
Environmental Enrichment
Magnetic Resonance Imaging
Mouse models
Neuroscience
Rett Syndrome
Advisor: Lerch, Jason P
Automation of Single Cell Manipulation for Embryo Biopsy

Assisted reproductive technologies (ART) are a host of technologies and procedures related to fertility and reproduction. Preimplantation genetic diagnosis (PGD), a procedure within ART, is a form of embryo biopsy in which a single cell, called a blastomere, is non-destructively extracted from the embryo for genetic analysis. PGD procedures are currently performed manually with low success rates, potentially caused by operator performance variability and contamination through handling, and are financially, physically, and psychologically taxing for the patient. The automation of PGD can increase the procedure repeatability and hence improve overall success rates. This thesis presents novel methods for the automation of certain PGD embryo biopsy procedures using robotic micromanipulators, computer vision and automation algorithms. This dissertation is separated into three main chapters, each pertaining to the automation of the three main phases of PGD biopsy: The first step in PGD biopsy automation is automated embryo position and orientation control using independently controlled parallel plates. Computer vision algorithms are used for tracking the embryo position and orientation. A novel 3D mapping technique for use with Hoffman modulation contrast microscopy is described and used for ablation zone optimization. Open and closed loop position and orientation control is demonstrated using the parallel plates. The second step of PGD biopsy automation performs a novel two-stage optimization for laser zona drilling to reduce embryo heating. The first stage uses computer vision algorithms to identify embryonic structures and determines the optimal ablation zone farthest away from critical structures such as blastomeres. The second stage combines a genetic optimization algorithm with a thermal model of LZD to optimize the combination of laser pulse locations and pulse durations. The third step of PGD biopsy automation involves blastomere extraction using the displacement method. A process flow for blastomere extraction automation is developed, and implemented using algorithms for non-vision-based feedback micropipette position control, and computer vision algorithms for blastomere extraction event detection and blastomere tracking during retrieval. For each PGD biopsy step, automation experiments were performed on mouse embryos. Successful demonstration of the above methods proves the feasibility of biopsy automation, and presents a step towards fully automated ART.

Keywords: Automation
Blastomere biopsy
Embryo biopsy
In vitro fertilization
Preimplantation genetic diagnosis
Single cell surgery
Advisor: Mills, James K
Doing Uncertain Time: Understanding the Experiences of Punishment in Pre-trial Custody

On any given day in Ontarioâ s provincial prisons, there are more legally innocent people in prison than there are sentenced prisoners. Yet, little is known about the experiences of these prisoners and the challenges they pose for correctional institutions. I seek to fill this gap by drawing on in-depth interviews with 120 pre-trial detainees (60 men and 60 women) and 40 staff at four maximum-security facilities in Ontario. My analysis focuses on the three temporal dimensions distinctive to what is known as pre-trial custody or â remand imprisonmentâ that have been neglected by prior research: experiences of arrest and police custody, making bail and court appearances, and daily life on remand. My findings indicate that this process inflicts a series of state-sanctioned harms on legally innocent prisoners. Much of the harm of this experience can be traced back to the fact that the criminal justice system is ignorant of or unconcerned with the human costs of this process. Police, acting under their authority to arrest, can apprehend and hold an individual, and have no legal obligation to allow a personal phone call so that arrangements about their lives can be made. Court appearances typically require some advance preparation; yet remand prisoners in Ontario must grapple with an outdated phone system that permits collect-calls to landlines but not cellular devices, leaving many unable to contact lawyers or loved ones, and seriously limiting their ability to prepare for court. Daily life in these facilities is characterized by uncertainty for both prisoners and staff, who must grapple with whatever challenges come their way in the form of an unpredictable flow of new admissions. In this thesis, I argue that disruption and uncertainty are unique features of pre-trial imprisonment and I examine the costs of these on the individuals confined to and working inside these facilities.

Keywords: Correctional staff
Courts
Male and female prisoners
Police custody
Pre-trial custody
Remand imprisonment
Advisor: Gartner, Rosemary I
Hybrid Steel Fibre Reinforced Concrete in Shear: From the Material to the Structural Level

High-performance fibre-reinforced cementitious composites (HPFRCC) are cementitious materials with improved mechanical characteristics and enhanced durability properties relative to conventional concrete. Most contain only one type of fibre that benefits performance within a limited range of deformation. Hybrid steel fibre-reinforced concrete (HySFRC) attempts to take advantage of different fibres by combining them. This dissertation examines the synergistic effects between steel fibres of different geometries, from the material to the structural level under shear-dominated conditions, by examining mixtures with the same total fibre volumetric ratio. At the material level, tests on cubes, cylinders, dogbones and prisms under bending were performed. A novel dogbone configuration suitable for FRC was also developed. The benefits of fibre hybridization on the shear behaviour and cracking properties of HySFRC with conventional steel reinforcement were evaluated using fourteen panel specimens. The test results showed that fibre hybridization benefited performance both at the serviceability limit state (SLS) and at the ultimate limit state (ULS) relative to the monofibre counterparts. These benefits in the mechanical performance may help reduce congestion of conventional reinforcement. Moreover, hybridization offers flexibility in the constitutive characteristics of the basic mechanical properties of concrete, which is useful for targeted concrete designs. An investigation on modelling HySFRC in shear was also conducted. Analysis identified the need for the development of a model that accurately captures the enhanced tensile post-cracking behaviour due to fibre bridging within the framework of the Disturbed Stress Field Model (Vecchio, 2000). The proposed formulations build on the Simplified Diverse Embedment Model (SDEM) developed by Lee, Cho and Vecchio (2013). Advancements include the consideration of interaction between fibres that are pulled-out simultaneously, the synergistic influence of short fibres on the pull-out behaviour of the longer fibres, and the fibre-matrix interactions that influence the bond-slip behaviour of a single fibre. Verification studies on structural elements were performed using the finite element analysis program VecTor2.

Advisor: Vecchio, Frank J.