VictorJuiz/thesis huggingface dataset:
Angiogenesis in Patches and Injectable Biomaterials for Cardiac Repair

Treatment of cardiac diseases involves transplantation of donor hearts, since the damaged heart has limited self-regeneration potential. An alternative treatment option has emerged as engineered cardiac tissues, grown in vitro by cultivation of cardiac cells on biomaterials, have comparable properties to native myocardium and can be implanted for cardiac repair. Major current limitations are a viable cell source and adequate vascularization to support cell survival. In this thesis, two proangiogenic biomaterials, a scaffold and a hydrogel, were developed to achieve vascularization in vitro and in vivo for cardiac repair. Scaffold patches are suitable for repairing congestive heart failure or congenital malformations, while injectable biomaterials allow minimally-invasive treatment post-myocardial infarction (MI). In the first aim, a collagen scaffold with covalently immobilized vascular endothelial growth factor (VEGF) was developed, and improved cell mobilization, survival and proliferation when used for free wall repair in adult rats. This increased angiogenesis, which aided in retaining the biomaterial size to allow tissue growth. In the second aim, a collagen-chitosan hydrogel with encapsulated thymosin β4 (Tβ4) was developed to 1) recruit cells from the heart epicardium for repair post-MI in vivo, and 2) guide capillary outgrowths from arteries and veins to form oriented capillary structure for in vitro cardiac tissue engineering. Results showed that the encapsulation of Tβ4 into collagen-chitosan hydrogels led to cell outgrowths from rat or mouse cardiac explants in vitro. A portion of the recruited cells were CD31-positive endothelial cells (ECs) that formed tubes. The hydrogel was injected in vivo to increase vascularization and number of cardiomyocytes within the infarct area post-MI, which improved left ventricular wall thickness. Tβ4-hydrogel also promoted the outgrowth of capillaries from vascular explants that followed the direction of the hydrogel-coated grooves of a micropatterned polydimethylsiloxane (PDMS) substrate. These capillary outgrowths eventually formed a vascular bed for engineering vascularized cardiac tissues. This thesis presents two bioinstructive biomaterials with sustained and localized delivery of angiogenic molecules to be used for in situ cardiac repair based on improved vascularization. The use of cell-free bioactive materials overcomes limitations of cell isolation and expansion as required for cell therapies or implantation of engineered tissues.

Keywords: angiogenesis
cardiac tissue engineering
biomaterials
Advisor: Radisic, Milica
Dropped Foot Impairment Post Stroke: Gait Deviations and the Immediate Effects of Ankle-foot Orthotics and Functional Electrical Stimulation

Individuals with stroke often demonstrate impaired ankle-foot function, commonly termed dropped foot that affects their ability to walk safely at home and within their community. While interventions are available to improve gait function, they have inconsistency demonstrated positive effects due to the lack of evidence-based practice guidelines and a limited understanding of the mechanisms leading to dropped foot. The aim of this dissertation was to 1) determine the relationship between dropped foot gait deviations and impaired sensorimotor control, 2) compare gait biomechanics between stroke survivors with and without dropped foot impairment, and 3) evaluate the immediate effects of an ankle-foot orthotic (AFO) and functional electrical stimulation (FES) device among stroke survivors with dropped foot impairment. Our evaluation combined standardized clinical measures of ankle-foot function (i.e. sensorimotor control, strength, spasticity and range of motion) and gait analysis using advanced laboratory techniques (i.e. electromyography and electrical goniometers) to quantify mechanisms of dropped foot impairment. Fifty-five stroke survivors completed the assessment prior to discharge from inpatient rehabilitation. Individuals with poor generation of isometric dorsiflexor force and reduced passive ankle range of motion were likely to demonstrate greater plantarflexion in swing and limited stance phase ankle joint excursion, respectively. Results from the gait analysis revealed a delayed onset and reduced activation time of the ankle dorsiflexors, and decreased co-activation time in the stance phase as possible mechanisms leading to dropped foot. A detailed case series was performed with four stroke survivors with dropped foot currently using an AFO. Application of an AFO immediately improved peak dorsiflexion in the swing phase and limited ankle range of motion during stance. When walking with the FES device, individuals with moderate dorsiflexor muscle weakness improved their ankle position at initial contact and increased peak dorsiflexion during stance, while no significant changes were observed among individuals with greater impairment. Overall, the results highlighted individual differences in response to interventions aimed at improving dropped foot gait deviations. These findings contribute to a greater understanding of gait dysfunction post stroke, and may lead to the development of a more effective clinical assessment and intervention strategies to improve dropped foot impairment.

Keywords: Gait
Stroke
Dropped foot
Ankle-foot orthotic
Functional electrical stimulation
Advisor: Perry, Stephen Douglas
Transitioning to Agile: A Framework for Pre-adoption Analysis using Empirical Knowledge and Strategic Modeling

Transitioning to the Agile style of software development has become an increasing phenomenon among software companies. The commonly perceived advantages of Agile, such as shortened time to market, improved efficiency, and reduced development waste are among key driving motivations of organizations to Agile. Each year a considerable number of empirical studies are being published, reporting on successful or unfavorable outcomes of enacting Agile in various organizations. Reusing this body of knowledge, and turning it into a concise and reachable source of information on Agile practices, can help many software organizations which are at the edge of transition to Agile, dealing with the uncertainties of such a decision. One of the early steps of transitioning to Agile (or any other process model) is to confirm the adaptability of new process with the current organization. Various Agile adoption frameworks have proposed different checklists to test the readiness of an organization for becoming Agile, or to identify the required adaptation criteria. Transitioning to Agile, as a significant organizational initiative, is a strategic decision, which should be made with respect to key objectives of the target organization. Having a reliable anticipation of how a new process model will impact the strategic objectives helps organizational managers to choose a process model, which brings optimum advantage to the organization. This thesis introduces a framework for evaluating new Agile practices (compartments of Agile methods) prior to their adoption in an organization. The framework has two distinguishing characteristics: first, it acts strategically, as it puts the strategic model of organization at the center of many decision makings that should be performed during Agile adoption; and second, it is based on a repository of Agile practices that allows the framework to benefit from the empirical knowledge of Agile methods, in order to improve the reliability of its outcomes. This repository has been populated through an extensive literature review of empirical studies on Agile methods. The framework was put in practice in an industrial case, at one of the R&D units of Ericsson Company in Italy. The target R&D unit was proposed with a number of Agile practices. The application of framework helped R&D unit managers to strategically decide on the new process proposal, by having a better understanding of its strategic shortcomings and strengths. A key portion of framework’s analysis results were evaluated one year after the R&D unit made the transition to Agile, showing that over 75% of pre-adoption analysis results came to reality after the enactment of new process into the organization.

Keywords: Software Process
Agile
Advisor: Yu, Eric
Data Quality Through Active Constraint Discovery and Maintenance

Although integrity constraints are the primary means for enforcing data integrity, there are cases in which they are not defined or are not strictly enforced. This leads to inconsistencies in the data, causing poor data quality. In this thesis, we leverage the power of constraints to improve data quality. To ensure that the data conforms to the intended application domain semantics, we develop two algorithms focusing on constraint discovery. The first algorithm discovers a class of conditional constraints, which hold over a subset of the relation, under specific conditional values. The second algorithm discovers attribute domain constraints, which bind specific values to the attributes of a relation for a given domain. These two types of constraints have been shown to be useful for data cleaning. In practice, weak enforcement of constraints often occurs for performance reasons. This leads to inconsistencies between the data and the set of defined constraints. To resolve this inconsistency, we must determine whether it is the constraints or the data that is incorrect, and then make the necessary corrections. We develop a repair model that considers repairs to the data and repairs to the constraints on an equal footing. We present repair algorithms that find the necessary repairs to bring the data and the constraints back to a consistent state. Finally, we study the efficiency and quality of our techniques. We show that our constraint discovery algorithms find meaningful constraints with good precision and recall. We also show that our repair algorithms resolve many inconsistencies with high quality repairs, and propose repairs that previous algorithms did not consider.

Keywords: data management
data quality
Advisor: Miller, Renee J.
Commercialization of Higher Education: MBA Students' Experience and Expectations

This study begins by discussing the commercialization of higher education. The commercialization of higher education is the transformation of public goods and services into products that are privately owned by individuals or corporations and sold for profit. Higher education is increasingly being treated by providers and consumers as a commercial product that can be bought and sold like any other commodity. The purpose of this study was to better understand how students perceive commercial behaviors in their institutions, the degree to which students perceive identified commercial behaviors as influencing their experience of teaching and learning, and how they experience the commercial conduct within commercialized educational environments. This study also aimed to explore how commercial behaviors influence students’ expectations for their higher education studies. Selecting the Rotman School of Management at the University of Toronto and the Schulich School of Business at York University and their MBA students as the research population, this study revealed MBA students’ experiences and program expectations in a commercialized academic setting by employing a combination of quantitative and qualitative research methods, coupled with the framework of Chickering and Gamson’s Seven Principles of Good Practice in Higher Education as well as Gould’s Corporate Ethos. Data was collected by means of an on-line survey questionnaire and in-person interviews. The two case study business schools shared similar major quantitative findings that indicated that the studied commercial practices carried slim influence on the studied students’ experiences of teaching and learning. In addition, the practices of marketing strategies and customer service were evidenced to have more than somewhat of an influence on intensifying participants’ expectations of program characteristics, obtaining better professional skills and getting better knowledge in areas of expertise. The qualitative findings illustrated that commercial practices exerted different levels of influence on MBA students’ experiences of teaching and learning as well as their expectations for their MBA. Qualitative findings in many cases also revealed that MBA students care more about future rewards and career advancement than learning.

Keywords: Higher Education
Commercialization
Student Experience
MBA
Advisor: Chambers, Anthony
Negotiating Two Worlds: A Cross-cultural Narrative of Chinese Immigrant Parents' Encounter with Canadian Schooling

From 1998- 2009, mainland China has been the number one source of immigrants in Canada (Citizenship and Immigration Canada, 2011). For newcomer families, adjusting to the local school is a major concern, since their children’s education is a crucial factor in families’ immigration decision. In my research, I examined Chinese immigrant parents’ experience with Canadian schooling. The study focuses on four families living in the Greater Toronto area, who have immigrated from mainland China. I employed narrative inquiry to tell the stories of the lived experience of the four families in my study. The data for these stories are mainly drawn from field notes of each of my home visits and my interviews with the family members over a six month period. I found that the challenges and difficulties the immigrant parents face are deeply rooted in the differences between Chinese and Canadian cultures and social systems. The discussion on the features of Chinese culture in its comparison with Western culture provides a reference point for understanding the Chinese immigrant parents’ values and opinions on such matters as schooling, moral education, and parenting practice. Parental involvement in schools is different between China and Canada, and the parents, and school teachers and administrators have different understanding on this issue. What’s more, the language barrier impeded the parents’ involvement in their children’s school life. The acculturation gap between the parents and their children is another major reason for miscommunication over such issues as extracurricular activities, choice of university major, and future career. The less heard voice of immigrant parents will open new venues for the understanding of cross-cultural experiences of immigrant students. I find that instead of mainly using the traditional Chinese practice and Chinese educational values in approaching their children’s education, it is important for Chinese immigrant parents to make efforts to familiarize themselves with the ideas and values that their children are exposed to in the new environment.

Keywords: curriculum studies and teacher development
cross-cultural studies
Advisor: Wallace, John
A Ribosome-inactivating Protein Toxin as a Template for Cancer Drug Discovery

Cancer cells display aberrant receptors on their surface that can serve as targets for the development of directed drug therapies. As such, our group has utilized two parallel approaches to redirect the cytotoxic properties of a ribosome-inactivating protein (RIP), Shiga-Like Toxin 1 (SLT 1), by altering its receptor specificity to target and kill cancer cells. The first combinatorial protein library was constructed such that a randomized 7 AA long peptide was inserted within the cytotoxic domain (A chain) of SLT-1. A high-throughput protein-based screening campaign identified a novel A chain toxin variant (named SLT 1AIYSNKLM) capable of targeting and killing human melanoma cells. This variant harbours a peptide insert (IYSNKLM) that directs the A chain to kill human melanoma cell lines. Equilibrium binding studies using 125I-radiolabeled SLT-1AIYSNKLM were conducted to determine the equilibrium binding constant and receptor density on 518-A2 human melanoma cells. When injected into SCID mice bearing a human melanoma xenograft, nanoSPECT/CT imaging as well as the biodistribution profile showed marked tumour uptake and retention of the radiolabeled toxin variant. Furthermore, preliminary experiments have shown that the SLT-1AIYSNKLM receptor is a protein, highlighting the potential for this method to be used in the discovery of novel biomarkers. A second approach was employed to demonstrate that our toxin-based combinatorial library system can be adapted to target known cancer biomarkers. Specifically, SLT-1 A chain variants harbouring 12-residue inserts were expressed in a phage display library. The library was screened against cell lines expressing the human colon cancer marker carcinoembryonic antigen (CEA; CD66e; CEACAM-5) to identify candidates that not only targeted, but internalized into cancer cells within a 1 h period. Variant, CSTA-10, was found to kill CEA-expressing BxPC-3 cells. Overall, the directed evolution of an RIP template such as SLT-1 represents a novel and powerful strategy for the identification of tumour-targeted toxin variants.

Keywords: Biomarker
Cancer
Toxin
Targeted-Therapy
Shiga-like Toxin 1
Combinatorial Library
Advisor: Gariepy, Jean
Jet Definitions in Effective Field Theory and Decaying Dark Matter

In this thesis jet production and cosmological constraints on decaying dark matter are studied. The powerful framework of effective field theory is applied in both cases to further our knowledge of particle physics. We first discuss how to apply the Soft Collinear Effective Theory (SCET) for calculating hadronic jet production rate. By applying SCET power counting, we develop a consistent approach to perform phase space integrations. This approach is then successfully applied to one-loop calculations with regard to a variety of jet algorithms. This allows us to study if the soft contribution can be factorized from the collinear ones. In particular we point out the connection between such factorization and the choice of ultraviolet regulator. We then further our study of the (exclusive) kt and C/A jet algorithms in SCET with the introduction of an additional regulator. Regularizing the virtualities and rapidities of graphs in SCET, we are able to write the next-to-leading-order dijet cross section as the product of separate hard, jet, and soft contributions. We show how to reproduce the Sudakov form factor to next-to-leading logarithmic accuracy previously calculated by the coherent branching formalism. Our resummed expression only depends on the renormalization group evolution of the hard function, rather than on that of the hard and jet functions as is usual in SCET. Finally we present a complete analysis of the cosmological constraints on decaying dark matter. For this, we have updated and extended previous analyses to include Lyman-alpha forest, large scale structure, and weak lensing observations. Astrophysical constraints are not considered in this thesis. The bounds on the lifetime of decaying dark matter are dominated by either the late-time integrated Sachs-Wolfe effect for the scenario with weak reionization, or CMB polarisation observations when there is significant reionization. For the respective scenarios, the lifetimes for decaying dark matter are constrained by Gamma^{-1} > 100 Gyr and (f*Gamma)^{-1} > 5.3 x 10^8 Gyr (at 95.4% confidence level), where the phenomenological parameter f is the fraction of decay energy deposited into the baryonic gas. This allows us to constrain particle physics models with dark matter candidates, by analyzing effective operators responsible for the dark matter decays into Standard Model particles.

Keywords: Jet Definition
Effective Field Theory
Soft Collinear Effective Theory
Decaying Dark Matter
Advisor: Luke, Michael E.
Visuospatial Control of Perturbation-evoked Reach-to-grasp Reactions in Young and Older Adults

Rapid compensatory reach-to-grasp reactions are prevalent and functionally important responses to instability. The need to react very rapidly (to prevent falling) imposes temporal constraints on acquisition and processing of the visuospatial information (VSI) needed to guide the reaching movement. Previous results suggested that the CNS may deal with these constraints by using VSI stored in memory proactively, prior to perturbation-onset; however, the extent to which online visual control is necessary or sufficient to guide these reactions has not been established. Furthermore, the influence of memory-decay and concurrent cognitive-task on the performance of these reactions has not been examined. This Thesis employed a novel paradigm wherein the participant is stationary and a motor-driven handhold is positioned unpredictably in front of the participant for each trial. Reach-to-grasp reactions were evoked in healthy young and older adults by sudden unpredictable antero-posterior platform translation (barriers deterred stepping reactions). Liquid-crystal goggles were used to occlude vision either before (recall-delay time=0s/2s/5s/10s) or after perturbation-onset to force reliance on either stored- or online-VSI, respectively. Participants performed a spatial- or non-spatial-memory task during the delay-time in a subset of trials. When forced to rely on stored-VSI, all participants showed reduction in reach accuracy; however, a tendency to undershoot the handhold was exacerbated in the older adults. Forced-reliance on online-VSI led to similar delays in all participants; however, the older adults were more likely to reach with the “wrong” arm or raise both arms. Comparison with normal-VSI trials suggests that both sources of VSI are utilized when grasping the movable handhold for support, with stored-VSI predominating during initiation/transport and online-VSI contributing primarily to final target acquisition/prehension. In terms of recall-delay, both age groups showed comparable reduction in medio-lateral endpoint accuracy when delay-time was longest. Moreover, both cognitive tasks had similar (slowing) effects in both age-groups, suggesting these effects were related to generic attentional demands. However, the older-adults also showed a dual-task interference effect (poorer cognitive-task performance) that was specific to the spatial-memory-task. Further research is needed to establish whether interventions aimed to improve visual/cognitive processing speed, visuospatial memory, and/or attention capacity can reduce risk of falling among senior populations.

Keywords: postural balance
aging
Advisor: Maki, Brian Edward
The Effect of Subconscious Learning vs. Performance Goals on Performance on a Complex Task

This dissertation examined the effect of subconscious goals on performance of tasks that people must acquire knowledge or skill to perform them effectively. Two laboratory experiments were conducted to examine the effect of priming (1) a performance goal, (2) a learning goal, and (3) both a performance and learning goal on performance. In Experiment 1 (n =167), a 2 (primed performance goal vs. control) x 2 (primed learning goal vs. control) factorial design revealed a significant main effect for priming a learning goal on generating ideas for a complex brainstorming task. In Experiment 2 (n = 61), a 2 (primed performance goal vs. control) x 2 (primed learning goal vs. control) x 3 (trials) repeated measures factorial design showed a significant main effect for priming a learning goal on performance on a complex scheduling task. On the third trial, there was a significant interaction effect between a primed learning and a performance goal on performance. In both experiments, priming a performance goal significantly increased the implicit motive of need for achievement measured by a projective test. No mediating effects were obtained for a primed learning or performance goal with task performance. The results are interpreted within three theoretical frameworks: goal setting, automaticity, and goal systems.

Keywords: Subconscious goals
Advisor: Latham, Gary