VictorJuiz/thesis huggingface dataset:
A Mixed-method Study of Bariatric Patients’ Experiences in Integrated Care: Implications for Patient-centered Care
Keywords: Bariatric Surgery
Chronic Disease Management
Health Related Quality of life
Mental Health
Obesity
Patient-Centred Care

Patient-centered care is a hallmark of high-quality care. Despite the significant attention and quality improvement efforts that followed the 2001 ‘Crossing the Quality Chasm’ report by the Institute of Medicine, notable gaps in care delivery persist for patients with chronic diseases. A challenge to addressing these gaps is the ability of current patient experience measures to capture important aspects of care delivery, such as chronic disease self-management, from the patient’s perspective. Development of reliable measurement tools that truly assess patient-centered care is critical to bridging these care gaps. In this dissertation, I investigated the relationship between patient-centered care and patient outcomes in the context of the integrated care model for chronic disease management. The primary aim of this research was to determine the key aspects of integrated care delivery that promote patient-centered care from the patient’s perspective and improve health-related quality of life (HRQoL) outcomes in an integrated bariatric surgery program. Study 1 generated the “Caring About Me” framework, which defines patient-centered care from the patient’s perspective. Study II demonstrated distinct differences in bariatric patients physical and mental HRQoL following bariatric surgery. Study III examined bariatric patients’ personal care experiences to explain difference in HRQoL trajectories. Results from this mixed-methods research program revealed that integrated care can enable patient-centered care that impacts long-term clinical outcomes by enabling positive patient-care team interactions, promoting access to responsive treatment interventions and empowering patients through the development of long-term self-management skills. Overall, this dissertation illuminated the core care elements that promote patient-centered care and improve clinical outcomes in integrated care. This relationship reinforces the importance of integrated care pathways that address the personalized care needs of the target patient population.
Principal Practices of Authentic Parental an Community Engagement in Urban Schools
Keywords: parents
reflection
relationships
strengths

The notion of parents more engaged in their children’s education has been enthusiastically embraced during the last quarter of a century. The acknowledgement of the significance of conferring with parents about their opinions of school and learning has increased. Moreover, the Ontario Ministry of Education published its Parent Engagement Policy and enabling regulations in 2010. Parent engagement practices are delineated as procedures in which parents have chances to affect decisions that will influence their children’s learning. Research demonstrates how consulting parents benefit the parents as well as the schools. There is a gap in the research explicitly investigating the practices of school principals in engaging parents. This qualitative study investigated the practices of elementary principals who had keenly pursued parent engagement. Eleven administrators from three Ontario school boards were interviewed about their practices expediting parent engagement. It was found that these principals used comparable practices, and experienced similar supports and barriers. When exploring the data from the first set of interviews, it became clear that the conceptual framework needed to shift the focus to the practices of principals who strive to meet the needs and work with the strengths of the parents (Hornby, 2011). Also, six of the participants were found to be more reflective practitioners. They had previously published in the field of education or were profoundly influenced by their professional reading. The significance of more reflective practice on parent engagement is discussed. The importance of trusting relationships as the foundation of parent engagement is emphasized. Principals build relationships with and among staff, students and parents to engage parents. Suggestions are proposed for the roles that teachers, students and parents need to play to facilitate parent engagement. Recommendations have been made for professional development for staff, engaging parents, as well as suggestions for the ministry and school boards. Where participants have been able to develop trusting relations with parents, parents are more engaged in their child’s schooling. Keywords: parents, relationships, strengths, reflection
Insights into the Role of Meteorology on Improving Model-measurement Agreement of Oxidants in Forested Environments
Keywords: chemical fluctuations
column modeling
forests
oxidation chemistry
ozone deposition
turbulence

Within forest canopies, biogenic emissions and anthropogenic pollutants interact through complex chemicalreactions, impacting atmospheric composition, climate, and ecosystem processes. The need to understand the biosphere-atmosphere exchange of heat, momentum, and chemical species has led to a significant body of work on the transport and fate of molecules within and above plant canopies. The impact of these canopies on the fast oxidation chemistry responsible for regulating the lifetime of greenhouse gases is still insufficiently understood. This is largely owing to the complexity of the chemical reactions involved and the lack of fully explicit physical descriptions of in-canopy turbulence and deposition. This thesis investigates the role that improved meteorological representation can play in reducing model error for simulated chemistry and improving our understanding of oxidation chemistry in forested environments. I examine long-term air quality monitoring data to show evidence that ozone mixing ratios in much of the United States are impacted by the presence of vegetation through the ability of plants to remove ozone from the atmosphere, and that this dry deposition sink is regulated by vapor pressure deficit. Examining the role of forest canopies in modulating chemistry further, I used the FORest Canopy Atmosphere Transfer (FORCAsT) model to simulate dynamics and reactions in a forest at the University of Michigan Biological Station (UMBS). I found that updating modeled meteorology by assimilating observations improves simulations of primary species, but key discrepancies in oxidation products exist, suggesting possible changes to branching ratios in the chemical mechanism may be needed. I use the micrometeorology measurements I made at the UMBS in conjunction with high resolution volatile organic compound (VOC) data to determine the impact of turbulence on VOCs, providing novel data for future model validation and parameterization. Further, I simulate the impact of turbulence on chemical reactions by incorporating the turbulence-induced covariance between chemical reactants in a box model and show that turbulent fluctuations strongly impact reactions involving short-lived radicals, leading to significant concentration changes, at canopy height. This work contributes to our understanding of the impact that meteorology plays on oxidation chemistry in and above forests.
Hypothesis-Driven Source Separation and Dimension Reduction of Neural Time Series Data
Keywords: data analysis
decision making
dimension reduction
EEG
eigendecomposition
spatial filtering

Neural dynamics spanning diverse spatial and temporal scales produce electrical fields that can be measured using non-invasive tools like electroencephalography (EEG), which records neural activity from multiple recording sites on the scalp of the head. However, most analytic approaches in EEG research do not fully exploit the rich, high-dimensional data to gain insights into how the brain processes information nor address the volume conduction problem. That is, EEG data contain a mixture of electric fields, produced by hundreds or thousands of neural sources, that propagate simultaneously to all recording sites on the scalp. Although this source mixing problem poses many analytic challenges, it also provides opportunities to develop better algorithms that can provide further theoretical and practical insights. Generalized eigendecomposition (GED) provides a multivariate framework for separating sources and reducing the dimensionality of EEG data while allowing for flexible hypothesis testing. I derived four analytic approaches from this framework and applied them to simulated and empirical data in four studies. Simulations in Study 1 showed that GED-based approaches were effective for separating sources, reducing data dimensionality, increasing signal-to-noise ratio, and testing hypotheses. Study 2 used GED to identify the determinants of cognitive control allocation and test the predictions of a theory of control allocation. Study 3 combined GED with time-frequency approaches to examine cognitive control processes during value-guided choice. Study 4 used GED to isolate sources whose activities reflected trial-varying decision attributes and showed that the timing of these activities was consistent with the predictions of decision models. In summary, my research provides evidence for the value of GED, a hypothesis-driven multivariate source separation and dimension reduction framework that can be used to improve our understanding of brain and cognitive function.
Quantitative Experimental and Mathematical Approaches to Extract Information about Transcription Factor Pulsing
Keywords: modeling
pulsatility
quantitative biology
short linear motif
signaling
stochastic dynamics

The picture of intracellular information processing is changing from a passive, predictable mechanism to an active, spontaneous dynamic system. Together with an increasing appreciation of the stochastic nature of signaling pathways and regulatory networks, a key discovery in this transition was that many transcription factors show stochastic pulsing: these transcription factors repetitively shuttle in and out of nuclei when cells are in a constant environment. Although functional explanations of stochastic pulsing have been proposed, many outstanding questions remained when I started my thesis research: What are the key regulators that lead to pulsing? Is the regulation encoded in the amino acid sequence of these transcription factors? Is stochastic pulsing beneficial to the organism or a byproduct of other biological functions? How does stochastic pulsing evolve? Two systems biology approaches have been widely applied to study stochastic single-cell dynamics: mathematical modeling, which helps us explain complex cellular phenomena, and quantitative experiments, which help us falsify model predictions. Hence, my thesis research aims to understand the mechanism underlying stochastic pulsing through quantitative, mathematical, and experimental approaches. I first characterized the mechanism at the level of the signaling pathway by using a stochastic pulsing transcription factor, Crz1, which is downstream of the calcium signaling pathway. I found that Crz1 shows damped oscillations after rapid fluctuations in cytosolic calcium concentration. Using a stochastic model, I found that the stochastic pulsing of Crz1 can be explained as a synchronous molecular movement with delay to upstream signals. I next characterized the mechanism at the level of peptide sequence by taking the advantage of wide sequence variation among Crz1 orthologues. By developing a reporter system for the calcium/Crz1 pathway, I found that the intrinsically disordered regions (IDRs) of the orthologous Crz1 show differences in their signaling dynamics. I also found that a few evolutionary changes in the IDRs are sufficient to introduce pulsing and improve fitness, supporting the hypothesis that pulsing is beneficial. Finally, I contributed to developing inference methods for quantitative studies on stochastic signaling pathways, which are known to include IDRs. Starting with the high osmolarity glycerol (HOG) pathway, I quantified the effects of conserved elements in IDRs of the HOG pathway. I developed a method to fit data with non-symmetrical errors and demonstrated the current limit of model interpretability. Overall, my thesis clarifies key challenges in systems biology and provides a promising direction to investigate the mechanism of stochastic signaling pathways.
OPEs, What Do We Do? Modeling Emissions, Fate, and Mitigation of Organophosphate Esters in Urban Systems
Keywords: multimedia modeling
OPEs
Persistent Organic Pollutants

Organophosphate esters (OPEs) are high production volume chemicals that span a broad range of physicochemical properties. Their global distribution raises concern that they could be classified as Persistent Mobile Organic Compounds (PMOCs) for which assessment tools and mitigation measures are required. This thesis has advanced the development of such tools and measures for PMOCs, using OPEs as a case study. By developing a novel workflow including a novel Bayesian model, I generated final adjusted values (FAVs) for 12 physicochemical properties of 74 compounds across nine compound classes, including OPEs, filling an important data gap. This work also found that different in silico estimation methods used to predict physicochemical properties varied widely, underlining the continued importance of measuring these properties for use both in understanding compounds fate and in further improving the in silico estimations. I developed and applied an updated polyparameter linear free energy relationships multimedia urban model (ppLFER-MUM) to better model PMOC fate and emissions in cities. Application of the model to OPEs in Toronto, Canada, I identified that chlorinated-OPEs acted as PMOCs with atmospheric deposition driven by efficient scavenging from air to receiving waters by precipitation while non-chlorinated-OPEs acted as Persistent, Bioaccumulative and Toxic (PBTs) compounds. Stormwater and treated wastewater discharges were important pathways of OPEs from Toronto air emissions to receiving waters. Using bioretention cells as an example stormwater management technology, I undertook a scoping review of bioretention research. This review found that uptake by vegetation was a potentially important pathway for the fate of PMOCs, requiring further study. I then developed a multimedia, activity-based chemical transport model called “SubsurfaceSinks” and a submodel called “BioretentionBlues” for bioretention cells. Fate in a bioretention cell was determined first by hydrology, then by sorption to soil, and finally transformation of compounds that were captured; vegetation played a minor role. Persistent compounds with soil-organic carbon distribution coefficients (log10 DOC) ≤ 2.7 were not captured and so are likely PMOCs transmitted to the environment through stormwater. Compounds with 2.7 ≤ log10 DOC ≤ 3.8 may be PMOCs transmitted to the environment through stormwater, depending on chemical- and location- specific factors.
Multi-Physics Simulation of Foaming Phenomena
Keywords: CFD
Computational Fluid Mechanics
Fluid-Solid Interaction
Foam composites
Foaming
Lattice Boltzmann Method

Polymer foams are usually produced by injecting gas at high pressure into a molten polymer, and then reducing the pressure suddenly to nucleate gas bubbles. The nucleated bubbles grow and form a low density cellular structure that has many applications. This thesis focuses on the development of numerical models for the simulation of foaming phenomena. Different simulation techniques, including the lattice Boltzmann method, molecular dynamics, and the immerse boundary method, are explored to develop a an improved 1D Cell Model, as well as a comprehensive 2D/3D numerical model that accounts for all physical aspects of foaming, and can be used for modeling of the foaming process and polymer foam composites. An improved 1D Cell Model is presented where the effect of the local variation of viscosity around growing bubbles is investigated. Due to the diffusion of gas from the polymer melt into growing bubbles, the viscosity at the bubble-melt interface can be significantly larger than further from the bubble. This effect of the viscosity profile on bubble growth and deformation is numerically investigated. We show that the viscosity variation slows the bubble growth rate at the early stages, and increases the resistance of bubbles to deformation. Next, a 2D/3D free surface lattice Boltzmann method simulation package called LBfoam for the simulation of foaming processes is presented. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated bubbles, bubble dynamics and coalescence, surface tension, the stabilizing disjoining pressure between bubbles, and Newtonian and non-Newtonian rheological models. Finally, a hybrid lattice Boltzmann method-molecular dynamics-immersed boundary method model is presented for simulating the foaming process of polymer composites. The LBfoam solver is used to resolve the foaming process, and the MD model accounts for filler dynamics. These two solvers are coupled by a direct forcing IBM. This solver can simulate composite foaming processes involving many bubbles and filler particles, including rigid, deformable, and fragile fillers. The solver relaxes most simplifying assumptions of earlier polymer composite models, allowing for a better understanding of filler motion and interaction with growing bubbles, to produce composite foams with improved mechanical, electrical, and electromagnetic properties.
Applied Mindfulness for Physicians: A Prospective Qualitative Study
Keywords: Burnout
Empirical
Intervention
Mindfulness
Qualitative
Wellbeing

Background: Physician burnout is increasingly recognized as having adverse impacts on the wellbeing of individual physicians, and by extension the healthcare delivery systems of which they are part. Amidst growing evidence showing increased physician burnout, mindfulness has been recommended as one potential approach for addressing physician burnout and enhancing physician wellbeing. Few empirical studies have been published on Mindfulness-Based Interventions (MBIs) adapted for physicians, and none based on the foundational teachings of internationally renowned scholar, Zen Master and Noble Peace Prize Nominee Thích Nhất Hạnh. Moreover, the majority of these studies have been quantitative, leaving a gap in understanding the lived experience and practical application of mindfulness in the context of physicians’ daily lives. Methods: Through a prospective qualitative study, forty-five physicians participated in a five-week Applied Mindfulness Program for Medical Personnel (AMP-MP) on-site at a tertiary care hospital in Toronto, Canada. The program content, based on the teachings of Thích Nhất Hạnh, was tailored to meet the interests and needs specific to the population of physicians. To inform this innovative and novel approach, an iterative reciprocal relationship was established with Thích Nhất Hạnh’s international Plum Village community. Following participation in AMP-MP, semi-structured interviews were completed with twenty-eight program participants. Interviews were transcribed and then analyzed using thematic analysis. To develop rigorous high-quality qualitative research, the study was theoretically grounded in the interpretive paradigm and utilized the middle range theory the Mechanisms of Mindfulness for analysis and interpretation. Results: Based on participants’ accounts, a thematic map was developed that illustrates a learning pathway for developing mindfulness in five phases: 1) Initial intention; 2) Establishing a mindful environment; 3) Development and application of practices concepts; 4) Broadening the conceptualization of mindfulness; and 5) Mindfulness becomes “a way of life”. The data indicates that participants developed a foundational competency in Applied Mindfulness that benefitted their personal sense of wellbeing, along with enhancing their interactions with their patients, colleagues and administrators. While these findings are encouraging, further research is needed to identify necessary systems-level changes to support broader implementation and long-term maintenance of mindfulness.
Emphasizing the Vectors in Vector-borne Disease Transmission and Evolution
Keywords: disease ecology
life-history evolution
malaria
mosquitoes
parasite
vector ecology

Disease transmission is a product of mechanisms and interactions at multiple levels of biological organization, and a comprehensive understanding of these processes is essential to disease control. Malaria parasites, for example, can infect dozens of vector species and undergo complex, density-dependent developmental transitions within those vectors, but the consequences of vector diversity on disease transmission, or vector-parasite interactions on parasite trait evolution, have rarely been explored. My research fills these gaps by investigating the myriad and nuanced roles that vectors play in disease ecology and evolution beyond simply carrying parasites. First, I examine the impact of vector diversity on malaria transmission. I curated a unique, multi-scale dataset of global mosquito distribution and malaria burden, and synthesized disparate theory for vector community ecology, linking principles of community assembly to disease risk. Using structural equation models, I provide the first empirical evidence that mosquito diversity amplifies malaria prevalence at both global and local scales, and demonstrate that this relationship is sensitive to a multitude of abiotic factors. Second, I investigate the evolutionary consequences of vector-parasite interactions. For malaria parasites, relative investment in transmission versus proliferative (i.e., host cell-infecting) stages is a key trait determining infectiousness, infection severity, and ultimately parasite fitness. To study how developmental processes and trade-offs that occur in the vector interact with the host half of the parasite life cycle to influence investment strategies in the host, I developed a mechanistic, mathematical model that links parasite development dynamics within-hosts and within-vectors. This model generates predictions for optimal transmission investment under a variety of scenarios, and provides refined proxies of parasite fitness by including transmission potential after passage through the vector, a major advancement over classic models of parasite evolution. Together, my research elevates vectors to their rightful place as crucial drivers of disease ecology and evolution.