VictorJuiz/thesis huggingface dataset:
Understanding and Mitigating the Interruptions Experienced by Intensive Care Unit Nurses

Intensive Care Unit (ICU) nurses get interrupted frequently. Although interruptions take cognitive resources from a primary task and may hinder performance, they may also convey critical information. Effective management of interruptions in ICUs requires the understanding of interruption characteristics, the context in which interruption happens, and interruption content (3 Cs of interruption). Using this proposed framework, two observational studies were conducted in a cardiovascular ICU (CVICU) at a Canadian teaching hospital. The focus of the first study was to understand the anatomy of interruptions, whereas the second one evaluated an awareness-display designed to help minimize interruptions that occur at inopportune times. Finally, a laboratory study was conducted to study a phenomenon that was observed during the observational studies, namely, nested interruptions. The first observational study revealed that the rate of interruptions with personal content observed during low-severity tasks (outcome if an error occurs) was significantly higher compared to medium- and high-severity tasks. This finding suggested that other personnel may tend to regulate their interruptions based on nurses’ tasks. However, given that nurses’ tasks are not always immediately visible to an interrupter, a task-severity awareness tool (TAT) was designed and installed in a CVICU room for the second observational study. When a nurse engaged the tool within the room, a “Do Not Disturb Please!” message was displayed outside the room. It was found that the interruption rate during high-severity tasks in the TAT room was significantly lower than in other rooms. In addition, in the TAT room, interruptions with personal content were entirely mitigated during high-severity tasks. In these two studies, it was also observed that not only do nurses receive frequent interruptions resulting in a switch to a secondary task, these secondary tasks also get interrupted; a phenomenon defined here as nested interruptions. It was hypothesized that nested interruptions would tax working memory even further compared to performing serial secondary tasks or no secondary tasks as the nurses would have to resume both the secondary and the primary tasks. Thirty nurses from the same CVICU participated in a simulated ICU study where they were interrupted during an electronic order entry task (primary task). Three conditions were tested during the interruption period: no secondary task; a serial condition where participants performed two secondary tasks back-to-back; and a nested condition where participants performed a secondary task that itself got interrupted. Compared to the other two conditions, nested interruptions resulted in significantly longer resumption lags and less accurate task resumption. Overall, this dissertation contributes to our understanding of ICU interruptions and ways to mitigate them and also expands the theory of interruptions through experimental findings.

Keywords: Error
ICU
Interruptions
Nursing
Advisor: Donmez, Birsen
Trbovich, Patricia
Hybrid Deformable Image Registration for Advanced Applications in Image-guided Interventions

Accounting for tissue deformation in medical imaging through Deformable Image Registration (DIR) is of significant clinical importance in diagnostic and therapeutic applications. Recent advancements in Magnetic Resonance Imaging (MRI) have enabled better diagnosis of cancerous lesions in soft tissue organs such the prostate. However, correlative pathology is needed to validate the precise boundaries of MRI diagnostic findings. Correlation of histopathology with in vivo imaging involves several mechanical deformations to the prostate tissue, demanding the use of a DIR. At the therapy level, tissue deformations and physiological motion can lead to significant differences between the planned and the delivered radiation dose in radiotherapy treatments such as the lung. Deformable dose reconstruction using an accurate DIR is essential in better estimation of the delivered dose at the time of planning. A hybrid biomechanical intensity-based technique was developed and validated using 4-dimensional Computed Tomography (4DCT) of lung cancer patients. The hybrid method was designed to take advantage of the benefits of the intensity-based algorithms (i.e. use of high contrast structures for accurate alignment) without losing the physical plausibility of complex physiological deformations obtained through the biomechanical modeling process. The combination of biomechanical and intensity-based registrations enabled a significantly more accurate registration with an average of 1.5 mm compared to 3.1 mm and 2.6 mm using each of the methods alone, respectively. The method was further tested using prostate MRI with average improvements of 0.7 mm compared to the biomechanical DIR. The biomechanical model based DIR was adapted for the correlation of histopathology with MRI showing the limited (53%) sensitivity of MR imaging in detecting the true cancerous regions in the prostate. This result is fundamental to the delivery of various treatments for locally recurrent prostate cancer where accurate definition of tumor burden is required. The impact of the hybrid method in radiation therapy was assessed in a retrospective lung dose calculation study. The results revealed that 1.6 mm reductions of average registration error using the hybrid method translates to over 1 Gy dose difference in up to 50% of a lung radiation therapy patient population, which may be clinically significant. In summary, the work in this thesis resulted in the development of a highly accurate hybrid DIR technique with substantial effects on understanding the prostate cancer diagnosis sensitivity, and the dosimetric calculations for lung radiotherapy.

Keywords: Deformation
Histology
Image Registration
Lung Cancer
Prostate Cancer
Radiation Therapy
Advisor: Brock, Kristy
Intestinal Cholecystokinin and Leptin Signaling and the Regulation of Glucose Production

The number of individuals affected by diabetes is on the rise due in part to lifestyle and/or genetic factors. Diabetes and obesity are characterized by a disruption in glucose homeostasis due in part to an elevation in glucose production (GP). It is of utmost importance to understand the regulation of GP in normal, obese and diabetic settings in hopes to unveil therapeutic targets that lower blood glucose concentrations in diabetes and obesity. The small intestine has also been documented to regulate glucose homeostasis independent of changes in food intake although the intestinal signaling mechanism(s) remain largely unknown. Specifically, the duodenum senses an increase in lipids and triggers release of CCK and activates the CCK1 receptor in the duodenum to lower GP via a gut-brain-liver axis. However, the downstream intestinal CCK1 receptor signaling effectors remain unknown. In study 1 of this thesis, the signaling molecule PKA was shown, for the first time to our knowledge, to lie downstream of the duodenal CCK1 receptor to trigger vagal afferent firing and a gut-brain-liver axis to lower GP. Importantly, direct activation of duodenal PKA lowered GP and bypassed duodenal CCK resistance in high fat fed rats. Like the duodenum, the distal part of the small intestine, the jejunum, also senses lipids to lower GP via a gut-brain-liver axis, but whether hormonal action mediates this GP-lowering effect of the jejunum remains unknown. In study 2 of this thesis, a novel GP-lowering effect of leptin in the jejunum was described. Specifically, jejunal leptin activated the long form leptin receptor and PI3K to lower GP in normal, high fat fed or uncontrolled diabetic rodents via a neuronal network, and contributed to the early anti-diabetic effect of bariatric surgery. In conclusion, this doctoral thesis demonstrates that independent activation of duodenal CCK-PKA and jejunal leptin-PI3K signaling potently lowers GP in normal, high-fat fed and diabetic rodents via a gut-brain-liver neuronal axis. Thus, targeting hormonal (i.e., CCK and leptin) signaling in the small intestine represents a potential therapeutic strategy to lower GP and restore glucose homeostasis in diabetes and obesity, and may mimic the anti-diabetic effect of bariatric surgery.

Keywords: Bypass Surgery
Cholecystokinin
Diabetes
Glucose production
Leptin
Obesity
Advisor: Lam, Tony KT
High Performance Spatial and Spatio-temporal Data Processing

The rapid growth of spatial data volume and technological trends in storage capacity and processing power are fueling many emerging spatial and spatio-temporal applications from a wide range of domains. Spatial join is at the heart of many of the emerging spatial data analysis applications. However, spatial join processing on even a moderate sized dataset is very time consuming. At the same time, there is a rapid expansion in available processing cores, through multicore machines and Cloud computing. The confluence of these trends points to a need for effective parallelization of spatial query processing. Unfortunately, traditional parallel spatial databases are ill-equipped to deal with the performance heterogeneity that is common in the Cloud. We introduce a parallel spatial data analysis infrastructure that exploits all available cores in a heterogeneous cluster. We also present an approach to parallelize spatial join queries in a large main memory multicore machine. Among the emerging spatio-temporal applications Location Based Services (LBS) are the most prominent. These applications are characterized by high rate of updates and many concurrent short running range queries. We present a parallel in-memory spatio-temporal indexing technique to support the demands of LBS workloads. Our system achieves significantly better performance than existing approaches to indexing spatio-temporal data. We also introduce a parallel in-memory spatio-temporal topological join approach.

Keywords: Indexing
LBS
Moving object trajectory
Spatial
Spatial join
Spatio-temporal
Advisor: Demke Brown, Angela
Metabolic Reprogramming by Hexosamine Biosynthetic and Golgi N-Glycan Branching Pathways

Most mammalian growth factor receptors and solute transporters are co-translationally N-glycosylated. N-glycans are branched and elongated in the Golgi, and their interaction with lectins regulates cell surface residency and activity of transmembrane glycoproteins. The Golgi branching N-acetylglucosaminyltransferases, Mgat1, 2, 4, 5 and 6, require a common donor substrate uridine-diphosphate-N-acetylglucosamine (UDP-GlcNAc) generated de novo by the hexosamine biosynthetic pathway (HBP) from glucose, glutamine and acetyl-CoA, as well as from GlcNAc salvage pathway. In this thesis I describe evidence for cell-autonomous regulation of cellular metabolism by the Golgi N-glycan branching pathway. Induced expression of Mgat1, Mgat5 or Mgat6, and GlcNAc supplementation to the HBP, increased central metabolites in an additive manner. I show that UDP-GlcNAc levels are also sensitive to dietary GlcNAc supplementation in vivo, increasing nutrient uptake and promoting anabolic metabolism via the Golgi N-glycan branching pathway. Chronic oral GlcNAc supplementation in C57BL/6 mice increased hepatic UDP-GlcNAc and N-glycan branching on liver glycoproteins. Furthermore, GlcNAc supplementation altered levels of numerous hepatic metabolites, insulin and glucagon balance, and promoted excess lipid storage, as well as body-weight increase, without affecting food intake or energy expenditure. In cultured cells, GlcNAc enhanced uptake of glucose, glutamine and fatty acids, and elevated fatty acid synthesis and storage in an N-glycan-dependent manner. Mgat5-/- mice exhibit a lean phenotype, and oral GlcNAc rescued fat accumulation, consistent with functional redundancy of N-glycan branches. However, fat accumulation in this context was rescued at the expense of lean mass, suggesting that Mgat5 plays a role in lean to fat body composition. These results suggest that GlcNAc reprograms cellular metabolism by enhancing nutrient uptake and lipid storage through the HBP and UDP-GlcNAc supply to the Golgi N-glycan branching pathway.

Keywords: body-weight
GlcNAc
Hexosamine
metabolism
Mgat5
N-glycan branching
Advisor: Dennis, James W
Making a Scene: Producing Media Literacy Narratives in Canada

In a highly mediated world, understanding how we communicate becomes an essential skill of citizenship. In Canadian secondary schools this is often taught as media literacy, either as a new stand-alone subject or integrated within the existing curriculum. As a school subject media literacy is particularly difficult to define and document because it continually changes to keep pace with technological innovation. Combining aspects of genealogy and scene-based analysis helps attend to the spatial and temporal formations of media literacy, thus bringing principles of circulation, exchange, and ephemerality into view. The first part of this dissertation considers the construction of media literacy as a secondary school subject in Canada. I problematize the dominance of a single historical narrative, where Ontario has come to stand in for the rest of the country, by tracing that narrative’s genealogical threads any by considering how it has travelled both nationally and internationally. I argue that a multitude of narratives have been obscured by this singular version of events. In the second part of the dissertation I study one such alternative narrative in British Columbia, using the sensitizing concept of “scene” to better understand how school subjects are produced. The various places, actors, organizations and activities producing a media literacy scene in BC do not neatly fit into the dominant national narrative. I discuss some of the ways in which school subjects have been studies, and then advance a model of scene-based analysis as a more flexible, generative research framework for studying social phenomena. I argue that media literacy is more than just a collection of canonical theories and methods. Its specific formation is contingent upon and shaped by forces both inside and outside of institutional learning, influenced by national and transnational trends, as well as locally specific conditions and relations.

Keywords: Media Education
Media Literacy
Media Studies
Scenes
School Subjects
Advisor: Dehli, Kari
Nonlinear Polarimetric Microscopy for Biomedical Imaging

A framework for the nonlinear optical polarimetry and polarimetric microscopy is developed. Mathematical equations are derived in terms of linear and nonlinear Stokes Mueller formalism, which comprehensively characterize the polarization properties of the incoming and outgoing radiations, and provide structural information about the organization of the investigated materials. The algebraic formalism developed in this thesis simplifies many predictions for a nonlinear polarimetry study and provides an intuitive understanding of various polarization properties for radiations and the intervening medium. For polarimetric microscopy experiments, a custom fast-scanning differential polarization microscope is developed, which is also capable of real-time three-dimensional imaging. The setup is equipped with a pair of high-speed resonant and galvanometric scanning mirrors, and supplemented by advanced adaptive optics and data acquisition modules. The scanning mirrors when combined with the adaptive optics deformable mirror enable fast 3D imaging. Deformable membrane mirrors and genetic algorithm optimization routines are employed to improve the imaging conditions including correcting the optical aberrations, maximizing signal intensities, and minimizing point-spread-functions of the focal volume. A field-programmable-gate array (FPGA) chip is exploited to rapidly acquire and process the multidimensional data. Using the nonlinear optical polarimetry framework and the home-built polarization microscope, a few biologically important tissues are measured and analyzed to gain insight as to their structure and dynamics. The structure and distribution of muscle sarcomere myosins, connective tissue collagen, carbohydrate-rich starch, and fruit fly eye retinal molecules are characterized with revealing polarization studies. In each case, using the theoretical framework, polarization sensitive data are analyzed to decipher the molecular orientations and nonlinear optical susceptibilities. The developed nonlinear optical polarimetric microscopy is applicable to a wide variety of structural studies on ordered materials, and provides a non-invasive possibility to study the structural organization and dynamics within biological samples. For example, the technique is well suited for studies of a muscle contraction, histopathology of collagen structure for cancer tissue diagnostics, investigations of the polysacharide structural organization within a starch granule of a plant, or developmental study of the retina in an eye, among other applications.

Keywords: Biomedical Imaging
Nonlinear Optics
Polarization
Stokes Mueller Polarimetry
Advisor: Barzda, Virginijus
Adiposity and Brain Health: A Study of Adolescents and Middle-aged Adults

Obesity, the excess accumulation of adipose tissue, presents a substantial public health burden. Research emerging over the past decade has shown that midlife obesity is associated with altered brain structure and increased risk of developing dementia. Prior research examining obesity-brain health relationships have utilized anthropometric measures of obesity (such as body mass index) and focused on adult populations. The current research aims to build on our understanding of obesity-brain health relationships by a) moving beyond the limitation of body mass index to examine the unique contributions of visceral vs. peripheral adiposity and b) examining two populations: adolescents and middle-aged adults to gain a clearer understanding of how these relationships progress across the lifespan. To this end, four investigations of obesity-brain health relationships were conducted. First, the relationship between adiposity and cognitive performance was examined in adolescents, and revealed a negative association between visceral fat and executive functioning that was more pronounced in females than in males. Second, the relationships between adiposity and two measures of structural brain integrity, signal intensity and magnetization transfer ratio, were assessed in adolescents. Robust relationships were found, possibly indicating variations in membrane phospholipid composition. Third, the relationship between adiposity and cortical thickness was examined in adolescents, revealing age-moderated relationships between adiposity and cortical thickness in males. Fourth, the relationships between adiposity and brain volumes, white matter integrity and cognition were examined in middle-aged adults, demonstrating a negative relationship between adiposity and brain volumes, as well as measures of white matter integrity. Overall these results suggest that high adiposity in adolescents is associated with altered brain structure and cognition, while in middle-aged adults, high adiposity is associated with altered brain structure. Given the rising rates of obesity worldwide, this research has implications for brain health throughout the lifespan.

Keywords: adolescence
brain
cognition
fat mass
obesity
visceral fat
Advisor: Paus, Tomas
Coverage Analysis and Resource Allocation in Heterogeneous Networks

The focus of this thesis is the analysis and design of multi-tier heterogenous networks (HetNets) with large density of access points (APs) located without a deterministic structure. We use stochastic geometry, specifically Poisson point processes (PPPs), to capture the randomness in AP locations. To differentiate their structural characteristics, APs are categorized into different tiers, each modeled by a PPP. The problem of cell association and resource allocation in a HetNet is considered from two different points of view: when the user is i) mobile and ii) stationary. To incorporate mobility in coverage analysis for mobile users, we derive the probability of handoff in an irregular multi-tier HetNet. To account for the service degradation due to handoffs, we propose a linear cost function, and use this to associate high speed users to upper tiers (e.g., macrocells) with a lower AP density. For stationary users, we first derive the statistical distribution of the load, and the minimum bandwidth required to meet an outage constraint in a multi-tier HetNet. This result is most useful for system design by relating the required spectrum to choices of network parameters. We then consider the dual problem with the objective of maximizing the overall rate coverage with orthogonal spectrum allocation across tiers given a total available bandwidth. We tackle this problem in two different phases: 1) load distribution and spectrum partitioning across tiers; 2) resource allocation across the APs and users within one tier. For analytical tractability in the former, we approximate the load of each AP by its mean, and derive the optimum tier association and fraction of spectrum to be allocated to each tier. In the latter, to account for different loads at each AP, we develop a hierarchical algorithm to allocate the available spectrum across the APs according to their load and to users according to their data rate demand. The latter benefits from adaptive power allocation and dynamic spectrum allocation across APs.

Keywords: Coverage Analysis
Heterogeneous Networks
Poisson Point Process
Resource Allocation
Stochastic Geometry
Wireless Communications
Advisor: Adve, Raviraj S.