VictorJuiz/thesis huggingface dataset:
Strategies for Interfacing Digital Microfluidics with Nuclear Magnetic Resonance Spectroscopy
Keywords: Digital Microfluidics
Force Velocity
Nuclear Magnetic Resonance

Digital microfluidics (DMF) is a fluid handling paradigm wherein minute droplets (with volumes in the range of 100 nL - 1 mL) are actuated through electrostatic forces over an electrode array. The discrete nature of DMF makes it a perfect fit for delivery of samples and other reagents to microcoil sensors used for high field Nuclear Magnetic Resonance (NMR) spectroscopy. This thesis describes the outcome of several years of work towards the development of a DMF-NMR interface. Chapter 2 considers a one-plate DMF design with a 1 mm outer diameter (OD) planar microcoil and demonstrates how the system can be used to manipulate, mix, and sense droplets within the NMR spectrometer. Chapter 3 is motivated by the need to ensure reliable droplet movement in an NMR spectrometer (where there is no visualization of droplet movement). This section evaluates how to determine best practices for droplet manipulation on the basis of the relationship between applied force and droplet velocity. Chapter 4 describes a two-plate DMF device configuration, enabled by altering the microcoil substrate to include a copper grounding plate to serve as the DMF counter-electrode. The increased droplet control of this design allows for better spectral resolution and better time resolution when studying reacting droplets. Finally, chapter 5 proposes a method to overcome the space limitations within the NMR spectrometer that limit the DMF device size by mindfully engineering the electrodes to allow for continuous forward motion using only two electrical channels. I propose that these innovations establish DMF as a useful new tool sample handling in conjunction with micro-NMR detectors like the planar microcoils described here, with potential extension to microslots, microstriplines, and other geometries in the future.
Patient Readmissions After Hospital Discharge
Keywords: Health services research
Pharmacy services
Primary care
Readmissions
Transitional care

Many readmissions after hospital discharge may be preventable through improved transitional care. This thesis seeks to inform clinical practice and policy development to reduce avoidable readmissions. The three included projects use health administrative data to examine the post-discharge care processes and outcomes for patients hospitalized in Ontario, Canada. In the first study, we compared the outcomes for patients discharged during the extended December holiday to outcomes for patients discharged from hospital at other times, over a 14 year period. We found that December holiday-discharged patients were at greater risk of 30-day death or readmission, while also being less likely to have outpatient physician follow-up within 14 days of discharge. The second study evaluated the effects of a physician financial incentive (an additional billing code) on timely follow-up after discharge. Despite physician uptake of the incentive code, there was no change in 14-day follow-up rates after incentive introduction, suggesting that it was not effective in changing physician behavior. In our third study, we compared the outcomes of post-discharge patients receiving a community pharmacy-based medication review to those not receiving one. Among older adults filling a prescription in a community pharmacy, receipt of a medication review was associated with a reduced rate of 30-day death or readmission. These thesis findings provide evidence to support decision- and policymaking relating to the clinical care of patients transitioning home from hospital.
Dynamic Cross-Talk between Macrophages and Contractile Fibroblasts in Fibrosis
Keywords: Biomechanics
collagen
intracellular communication
macrophages
myofibroblast
wound repair

Accumulation and contraction of collagen extracellular matrix (ECM) by myofibroblasts (MFs) is a hallmark of fibrosis that can culminate in loss of organ function. In contrast to the sequential appearance and disappearance of macrophages (Mϕ) and MFs in normal tissue repair, Mϕ-MF pairs co-exist in excessive healing. Spatial proximity of Mϕ supports persistent activation of MFs. The Hinz lab has shown that Mϕ-MF contacts are mediated by strong homotypic cadherin 11 (Cad11) junctions. However, the initial guidance cues and mechanisms directing migratory Mϕ towards contracting MFs are not clear. We hypothesize that local remodelling of collagen ECM by contracting MFs provides mechanical and physical cues in the ECM that act as attraction signals for distant migratory Mϕ. To test this hypothesis, we used collagen type I ECM to investigate Mϕ adhesion and migratory mechanism in response to MF-induced deformation fields in in vitro co-cultures. My data show that MF-generated deformations in collagen ECM extended far beyond the cell diameter. When positioned within deformation fields, Mϕ sense and migrate towards mechanical forces exerted by contracting MFs and actuated microneedles. Mϕ chemotaxis is excluded as attraction mechanism by eliminating possible cytokines using fluid flow. Microneedle experiments identified the presence of a dynamic force source as the critical signal initiating and directing Mϕ migration in the ECM. In contrast, collagen fiber alignment resulting from MF remodelling activities is neither required nor sufficient to guide Mϕ migration. We show that Mϕ perceive changes in the displacement of their local fibrillar collagen substrate. The ability of Mϕ to follow actuated microneedles is impaired in the presence of α2β1 integrin antibodies and stretch-activated membrane channel blockers, suggesting the functional requirement of them in Mϕ force navigation in the ECM. We propose a novel mechanism of far-ranged Mϕ mechanosensing that integrates mechanical changes in the ECM to facilitate MF-Mϕ attraction and forming a pro-fibrotic niche. Our study identified stretch-activated ion membrane channels and fibrillar collagen receptors required for Mϕ mechanosensation as potential molecular targets for anti-fibrotic strategies.
The Design of Optogenetic Constructs for the Regulation of Translation Initiation
Keywords: AsLOV2
eIF4E
optogenetics
protein engineering
protein synthesis
translation

The precise spatiotemporal regulation of protein synthesis (translation) is essential for many complex biological processes such as memory formation, embryonic development and tumor formation. Current methods for studying protein synthesis offer a limited degree of spatiotemporal control. Optogenetic methods, in contrast, offer the prospect of controlling protein synthesis non-invasively within minutes and with a spatial scale as small as a single synapse. This thesis presents several novel optogenetic constructs designed to control protein synthesis via well-known binding interactions of the translation initiation machinery. Chapter 2 presents a yeast system capable of screening optogenetic designs for the light-dependent down-regulation of protein synthesis. Using this system, we discovered cLIPS1 (circularly permuted LOV inhibitor of protein synthesis 1), a fusion of the LOV2 domain from Avena sativa (AsLOV2) and 4EBP2 (eukaryotic initiation factor 4E binding protein 2), a native inhibitor of translation initiation. This construct was improved, producing cLIPS2. We show that these constructs can inhibit translation in yeast harboring human eIF4E and bind human eIF4E in vitro in a light-dependent manner. Chapter 3 presents the characterization of LITRs (LOV2 insertion in Translational Regulators), a group of constructs where AsLOV2 is inserted into flexible loops of eIF4E (eukaryotic initiation factor 4E). With a different yeast-based screen, we discovered LITUP1, a light-dependent up-regulator of protein synthesis. We showed that the linker sequences between AsLOV2 and eIF4E were coupled to the activity of LITUP1. This led to the discovery of LITUP2, an improved version, and LITDOWN1 a light-dependent down-regulator of protein synthesis. Chapter 4 presents two photocaging strategies using Dronpa and RsLOV. These were initial attempts at designing optogenetic 4EBP2 and eIF4E constructs, which encountered difficulties with in vitro characterization. Altogether, the constructs presented in this work expand the current optogenetic toolbox and will hopefully allow researchers to dissect the dynamic molecular events underlying translation.
Stubborn Subject: The Persistence of Self in Dramatic Acting
Keywords: acting
character
drama
mirror
self
subjectivity

Dramatic acting, as a theatrical event that mysteriously fuses actor with character, is also a process that is deeply invested in the idea of Self. From Diderot’s early paradox through Stanislavski’s highly influential psychotechnique and into the present day, notions of who actors are – and how they precisely feel – when portraying characters have remained at the centre of Euroamerican discussions about dramatic performance. Conversely, for most of the twentieth and into the twenty-first century, the concept of the Self as an organic, reflexive, self-directed and differentiated human being in the world has been not only “deconstructed” within every dominant critical and artistic discourse but has also – until recently – been pretty much left for dead. Yet within the realm of acting in the traditional theatre’s models, the tenacity of the Self’s hold as the centrepiece of both pedagogy and methodology appears to be the hallmark of a concept that, if somewhat bruised and battered, is still very much alive. Is there something inherent – or at least necessary – within the study and practice of dramatic acting that perpetually reconstitutes the stubborn idea of an autonomous and cohesive subjectivity within the actor? Through a freewheeling, and sometimes unorthodox, methodology of interrogation, this dissertation asserts that, for the modern dramatic actor, a demonstrable sense of self is an inescapable vocational reality. This position is argumentatively framed through a valorization of the actor’s phenomenological and psychological experience as fundamental to assessing how the Actor and the Self creatively collide. Though drawing from a broad range of interdisciplinary discourses, the author’s subjective and self-historicizing experience as someone who has worked as a professional actor in the Canadian theatre and other media since childhood, for over forty years, is everywhere implicit in this analysis.
Investigating the Role of microRNAs in Cell Fate Determination
Keywords: Embryo
Embryonic Stem Cells
Genetics
microRNA
Trophoblast

miRNAs are key regulators of a myriad of cellular processes, including proliferation, differentiation, and signaling. These developmentally regulated and abundantly expressed RNA species elicit their effects by controlling the expression of multiple genes in a spatial and temporal manner. microRNAs are differentially expressed in the extra-embryonic trophoblast and embryonic inner cell mass of the preimplantation embryo and their stem cell models, but while they are required for trophoblast development, it is unknown whether they have the capacity to specify or determine trophoblast fate in the preimplantation embryo. Knockout phenotypes of microRNA processor genes have not identified a role for microRNAs in this early cell fate choice, and expression of microRNAs in embryonic stem cells (ESCs) has not yet induced a trophoblast cell state. In this thesis I have identified miRNAs with trophoblast function and interrogated their role in cell fate specification. First, I employed stem cell models of the early embryo and confirm that overexpression of these miRNAs in ESCs induces a trophoblast phenotype, resulting in the derivation of a novel mural trophectoderm-like cell (mTELC) type. Second, by ectopically expressing these miRNAs in the preimplantation embryo ex vivo, I provide evidence that miRNAs may be involved in trophoblast fate specification by modulating components of the Hippo signaling pathway. Finally, I elaborate on the role of these miRNAs in trophoblast development and reveal that they could be driving a state of dormancy in this lineage by impinging on mTOR signaling. Together, these studied reveal a role for miRNAs in modulating embryo developmental transitions and specification of cell lineages.
School Travel for Families Living with Childhood Disability
Keywords: childhood disability
critical ableist studies
inclusive design
photovoice
pilot study
school transport

The rise of automobility during the past century has contributed to children becoming more sedentary and isolated from public life and, correspondingly, exhibiting reduced independent mobility and a troubling range of chronic health problems. Concern over these issues has led to an increase in attention to school transportation among planning scholars and practitioners. School transportation has come to be regarded as an opportunity for creating change since converting sedentary trips to and from school into trips involving active modes could help to mitigate the children’s health issues. Unfortunately, the increased attention to school transportation has come to pass with little regard for childhood disability. This dissertation engages school transportation’s childhood disability gap. Using a critical ableist studies perspective, attention is given to questioning and unsettling the ableist normative ordering of childhood disability as excludable within the planning and design of school transportation and school sites. A systematic review of disability’s treatment in the active school travel and children’s independent mobility literatures demonstrates and offers insight into the childhood disability gap. Following this is a presentation of an ethnographic research design that used photovoice, institutional ethnographic conceptual tools, and numerous inclusive measures to study how families living with childhood disability experience everyday school travel across Ontario, Canada’s Greater Toronto and Hamilton Area. Pilot study findings are then presented and discussed to demonstrate the value of piloting qualitative research designs involving disabled children. Lastly, findings about how families of disabled children experience parking at school are considered. The findings show how the families are expected and relied on to take on various types of inequitable work (e.g., work that is social, physical, and temporal in nature) to overcome normalized, ableist school site designs.
Inpatient Rehabilitation for Patients with Traumatic Brain Injury: Process and Content
Keywords: Inpatient Rehabilitation
Outcome
Post-discharge
Therapeutic Activities
Traumatic Brain Injury

The goals of this thesis were to a) compare the content and process of inpatient rehabilitation (IR) between patients with Traumatic Brain Injury (TBI) who were treated in one Canadian and nine US facilities, b) investigate the association of therapeutic factors with short-term functional outcomes, and c) describe the functional recovery from admission to nine months post-discharge at 4 time points as well as explore the predictive value of therapeutic and post-discharge determinants to explain the variation in long-term outcomes in patients with TBI who were admitted to a Canadian facility. This thesis was based on three studies. The results of the first study showed that there are significant differences between components of IR for patients with TBI who were treated in Canadian versus US facilities. These findings provide informative data for practitioners and researchers about variations in service provision for patients with similar profiles. The findings of the second study revealed that level of effort was associated with higher discharge cognitive scores. Additionally, more intensity of time spent in complex occupational and physical therapy activities were significant predictors of better discharge motor scores. These findings provide evidence to consider patient level of effort and intensity of specific activities in the process of goal setting. The results of the third study demonstrated that after three months post-discharge, patients did not show significant variations in functional outcomes. Also, the number of post-discharge health issues was negatively associated with both cognitive and motor scores at nine months post-discharge, and a greater intensity of time spent in complex occupational therapy activities was a predictor of better motor scores at nine months follow-up. These findings inform health care providers about the temporal influence of IR and the necessity of investigating the association of continuous treatments with long-term outcomes after IR discharge. In summary, this thesis provides valuable information for stakeholders to consider the effect of variations of pattern and content of care on short and long-term outcomes following IR and to direct the resources for providing adequate and appropriate level of care.
Development of a 3 French Dual Frequency IVUS Catheter
Keywords: Atherosclerosis
Dual frequency
High frequency
Intravascular imaging
Intravascular ultrasound
Transducers

There is a need for imaging modalities capable of more fully visualizing the features of atherosclerotic plaque and monitoring treatments. Currently, only invasive modalities are able to precisely assess fibrous cap thickness, plaque size, the extent of positive remodelling, and the correct expansion of stents. No individual modality can visualize all of these features at the present time, and considerable effort has been made to develop hybrid imaging catheters for broader capabilities. In line with that goal, this thesis describes the development of a dual frequency intravascular ultrasound (DF IVUS) catheter incorporating a bidirectional transducer stack with centre frequencies of 30 and 80 MHz. 30 MHz is within the range of currently available clinical IVUS, and 80 MHz was chosen to provide the desired superficial resolution. The prototype was designed to have a clinically-relevant size and form factor to ensure its applicability for this purpose. The design and fabrication process are explained in detail, and the characterization results show the successful performance of the prototype with respect to the design criteria. Imaging of phantoms, in vitro human atherosclerotic coronary arteries and in vivo healthy porcine coronary arteries demonstrate that the prototype is able to provide complementary, coplanar images; with superficial axial resolution as low as 16 μm, lower-resolution depth penetration up to 6 mm, penetration through blood at both 30 and 80 MHz, and improved visualization of a stent relative to the vessel wall. Features of plaque and the vessel wall were well-visualized compared with conventional IVUS (30 MHz). These results suggest that DF IVUS is technologically and clinical feasible as a technique for improved coronary imaging. Other design approaches to DF IVUS may provide additional benefits, including contrast-enhanced imaging, and the procedures described here may be relevant to the development of these and other sub-millimetre ultrasound devices.
Stratospheric Ballooning With SPIDER and BIT
Keywords: B Modes
CMB
Star Cameras
Stratospheric Ballooning
Weak Lensing

Stratospheric ballooning is an important platform for astrophysics and cosmology. This work presents the development of Spider, a CMB polarimeter, and BIT, a visible light and near-UV imager, both of which are balloon experiments. Both experiments require gondolas and pointing systems to track or scan on the sky, and their development is an important area of research in the field. Spider aims to observe the relics of inflation by constraining the tensor to scalar ratio, r. It flew an initial flight in 2014-15 and the data analysis is presented here. This work includes the development of the Spider noise model which is an important component of any CMB analysis. Development work on the second Spider gondola is also presented, preparing it for a second Antarctic campaign in the near future. BIT is attempting to constrain Ω_m , the energy density of matter and σ_8 , the scale size of early universe fluctuations, through the use of weak lensing. Although no weak lensing data has been obtained yet, this thesis presents the development of the instrument from its earliest stages through its two successful test flights. Specific emphasis is given to the development of the star camera subsystem, which was integral to the success of the project.
Functional Neural Correlates of Cognitive Impairment and Neural Compensation in Mild to Moderate Cerebral Small Vessel Disease
Keywords: Attention
Cerebral Small Vessel Disease
Cognitive Reserve
Executive Function
Vascular Cognitive Impairment
White Matter Hyperintensities

Rationale: Aging is associated with both structural and functional changes along with decline in certain cognitive domains. Reduced white matter integrity is a common age-related structural change that is accelerated in those cerebral small vessel disease (CSVD), a disease characterized by white matter hyperintensities and subcortical lesions. To what extent these lesions contribute to age-related cognitive decline is unclear as there is considerable heterogeneity in the cognitive abilities of those with similar amounts of vascular lesion burden. Research Aims: The aim of this dissertation is to use a combination of neuropsychological testing, structural brain imaging and multimodal functional neuroimaging to investigate individual differences in cognitive function among older adults with CSVD. Hypothesis: I hypothesize that poor executive function in those with CSVD will relate to deficits in top-down attentional control as indexed by electrophysiological markers of attention as well as changes in functional brain activity. Results: In chapter 3, six trends within the CSVD functional imaging literature are identified and summarized within a proposed “distributed network disruption and interference model”. This model proposes that cognitive impairment in CSVD results from diffuse disruption of fronto-subcortical circuits. This in turn contributes to DMN hyperactivation and compensatory frontal activation. Subsequent chapters build upon this model with chapter 4 confirming the presence of high cognitive heterogeneity in CSVD and identifying distinct behavioural subgroups within the CSVD population. Whereas Chapter 5 presents evidence that poor attentional control in CSVD is related to a specific deficit in suppression of irrelevant stimuli as indexed by an attenuated selection negativity. Chapter 6 relates individual differences in executive dysfunction and the suppression deficit to differences in task-related brain activation. Interpretation: Cumulatively these results point to a mechanism for understanding cognitive impairment and compensation in CSVD which is rooted in the ability to suppress irrelevant stimuli and promote greater involvement of the frontoparietal control network. This may have implications for guiding the development and assessment of cognitive interventions for this growing patient population.