VictorJuiz/thesis huggingface dataset:
Computational Modeling and Analysis of Complex Muscle Architecture

Muscle architecture is a primary determinant of the muscle function associated with body movement. An assessment of muscle architecture is therefore of great importance, not only for investigating anatomical aspects of muscle but also for predicting its functional capacity. Most muscles have a variable complexity in their architectures, making it challenging to accurately assess them. Previous cadaveric approaches only take into account limited portions of architecture. On the other hand, conventional radiological approaches, such as ultrasonography and MRI, examine two-dimensional projected images. Neither of these approaches provides a thorough understanding of the entire muscle architecture. This may lead to under- or overestimation of architectural parameters that are signicant for both clinical and computational studies. Therefore, the purpose of this thesis is to develop a computational modeling approach to facilitate quantication and reconstruction of complex muscle architecture. Cadaveric specimen data are used to investigate muscle architecture and to reconstruct accurate models. Associated geometric complexity and variation are carefully examined to yield consistent estimation of architectural parameters. This method demonstrates robustness against non-uniformity in the data and consistency over various types of muscle architecture; less than 10% error in PCSA estimation. By incorporating ultrasonographic assessment, this method is extended to approximate muscle architecture in living subjects, which enables estimation of PCSA for in vivo muscle in a more consistent manner. Validation experiments demonstrate 0:4 􀀀 8:4 % estimation errors between the original architecture and its approximation, depending on the anatomical complexity, which provides a practical insight into the quantication of PCSA for in vivo muscle.

Keywords: Cadaveric specimen
Digitization
Muscle architecture
PCSA
Skeletal muscle
Ultrasonography
Advisor: Jackson, Kenneth
Fiume, Eugene
Azure

Azure is a single-movement, through-composed work for large orchestra; its tense urgency nonetheless finds at its centre a stretch of utter calm. As I wrote Azure I wanted to explore what is vast. Its title refers to the blue of the sky, and also the sense of scale that “sky-blue” and “ocean-blue” evoke. Azure falls into four large sections followed by a dark coda. The opening gesture – repeating, monolithic tutti punches – gives way to an ostinato, around which the woodwinds, brass, and strings exchange small “call” figures, most importantly the recurring triplet-sixteenth motive, which carries through the entire work. Cross-fading major-minor triads become another important and recurring motive. Glissandi and other Doppler effects give a sense of vast space and then become siren-like, adding to the music’s martial atmosphere and growing urgency. The second large section is a slow waltz. After the towering chords return, the decay of the orchestra’s sound becomes an illustrated silence, time frozen as the players’ magnified breathing slowly gives way to a luminous C minor chord which hangs suspended as far as the ear can hear: music heard from a great height. Small, half-remembered gestures move glacially across this plane, and slowly the war-like atmosphere returns. But as the piece approaches its climax the opening chords do not reappear – instead, the tension evaporates into a coda much darker than anything that came before. Azure draws not only on many of the images and thematic interests that have come to govern my work, it also draws on my growing interest in time-distortion, pitch bending, Doppler effects, and the other features of a recognizable but disturbed tonal language that I find evocative. Azure may be sky-blue but this work is agitated and tense, offset by moments of gentle tranquility that are in themselves vast, timeless, and elemental.

Keywords: landscape
orchestra
programme music
symphony
tonal
tone poem
Advisor: Hatzis, Christos
Photonic Enhancement of Colloidal Quantum Dot Photovoltaics

Colloidal quantum dots, nanocrystal semiconductors that can be cross-linked and assembled into absorbing thin films, are an attractive material for third-generation photovoltaic applications due to low-cost fabrication and bandgap tunability. As a result of their limited charge transport, these solution-processed thin films suffer from a mismatch in absorption length and charge extraction length. Concepts based on the interdigitation of n- and p-doped layers, approaches that reduce the distance photogenerated carriers must travel before extraction, offer promise on overcoming this limitation. In this thesis, I explore and develop techniques to address the absorption-extraction compromise in CQD materials by implementing nano- and micro-structuring techniques to enhance light absorption in the active film. First, I focus on the development of nanomaterials for light guiding/scattering enhancement in CQD films. For this, I develop a nanostructured gold reflector that, when suitably designed, guides light and traps it within the active film. I show that this yields enhanced broadband absorption with more than 4-fold improvement at the most improved wavelength, which translated into a 34% improvement in photocurrent in a working solar cell. I also show that periodic nanostructures employed for absorption enhancement can lead to improvements in solar cell performance. Limitations in device architecture and film formation, however, prevented significant performance advances for these nano-scale approaches. Regardless, these early results pointed me to a new and more impactful strategy. I focus in on realizing micron-scale structured electrodes to enhance absorption, which I show to be considerably more useful in view of the need to extract charge carriers with high efficiency. I discover that conformal film formation atop these structured electrodes is an absolute prerequisite to enhancing performance. These devices, which I term micro-pyramid CQD cells, provide a 24% enhancement in current and a consequent 15% improvement in power conversion efficiency. Ultimately, this work offers a prescription for photonic enhancements of solar cells within this emerging class of photovoltaic materials.

Keywords: Colloidal Quantum Dots
Optoelectronics
Photonics
Photovoltaics
Advisor: Sargent, Edward H
How Does Ontario Primary Care Perform? Effectiveness, Costs and Efficiency

In 2001, Ontario began introducing new primary care models characterized by physician remuneration mechanisms, interdisciplinary teams, access requirements, and patient enrolment. The objectives of the primary care reform were to improve the quality of and access to primary care and to make primary care more attractive as a physician specialty. This thesis explores the performance of the new primary care models – enhanced fee-for-service (FFS), blended capitation, and interdisciplinary teams - compared to the traditional FFS model. The effectiveness, costs and efficiency are reviewed separately in three distinct studies. The study about effectiveness aims to measure the risk of having a hospitalization for an ambulatory care sensitive condition (ACSC). The risk of having an ACSC hospitalization was lower for patients whose physician practiced in an enhanced-FFS or in a capitation model compared to patients whose saw a FFS physician. It was higher for patients who saw physicians who worked in interdisciplinary teams. The second study examined primary care costs and total health care costs for a randomly selected 10% sample of the Ontario adult population. The costs were calculated at the individual level based on the prices of the services and the utilization. Compared to patients of FFS physicians, patients in capitation models had higher primary care costs but lower total health care costs. Enhanced-FFS patients had the lowest primary care costs and total health care costs. The third study employed a Stochastic Frontier Analysis (SFA) to assess the efficiency of physicians. The analyses were supported by survey data on a physician’s hours worked on direct patient care, duration of the visits and other characteristics of a physician’s practice and linked to administrative data on patient visits. After controlling for input and explanatory variables, efficiency scores were on average higher for physicians in blended capitation models and in interdisciplinary teams compared to physicians in FFS. The three studies show significant differences across models for each of the outcomes examined (ACSC hospitalization; primary care costs and total health care costs; efficiency). More research is needed to understand these variations and the causal relationships in these variations, in order to better inform policy.

Keywords: costs
efficiency
patient outcomes
performance measurement
primary care
Advisor: Wodchis, Walter P
Characterizing Structural Changes of the Magnesium channel, CorA: Implications for Gating

CorA is the primary magnesium channel in prokaryotes and the most extensively studied member of the CorA/Mrs2/Alr1 superfamily of magnesium channels that extends into eukaryotes. Existing crystallographic structures define the closed state of CorA and provide a structural basis for its structure-function relationships. However, detailed mechanisms of gating and ion permeation remain poorly understood. In this thesis, a combination of biochemical and biophysical methods were used to understand the molecular details involved in CorA gating. Specifically, dynamic structural elements involved in CorA gating were identified through limited proteolysis and mass spectrometry. Cysteine cross-linking along with mutagenesis assays show that the formation of an inter-protomer salt-bridge at the membrane-cytosol interface may be a key component of the activation mechanism. This ties in with the earlier limited proteolysis and mass spectrometry results indicating that the channel exposes its membrane-cytosol interface during gating. Finally, we report the first structural elucidation of the CorA soluble domain in a pentameric arrangement. The structure reveals significantly increased closure of the soluble domain funnel compared to the regular closed state, suggesting that the membrane domain can impose constraints on the soluble domain to resist the closing motion of the funnel triggered by Mg2+ binding. A model is proposed based on this observation, which may explain the mechanics underlying channel gating. Altogether, these studies have furthered the understanding of the molecular basis of CorA gating, particularly on the communication mechanism linking structural rearrangements in the soluble regulatory domain and the motion of the membrane domain. Furthermore, the results from this thesis agree with a sequential gating mechanism in which the channel undergoes asymmetric conformational changes.

Keywords: allosteric regulation
ion channel
Magnesium channel
pentameric protein
structural biology
X-ray crystallography
Advisor: Pai, Emil F
Bimanual Grasping: An In-depth Examination of the Visual, Neural, and Motor Mechanisms

Action coordination is one of the fundamental motor skills that humans need to acquire for their successful interaction with the environment. To study action coordination, one effective model is bimanual grasping, where the two hands reach-to-grasp a single object. Bimanual grasping is a particularly suitable model because it involves coordinating the two arms and hands in space and time, and hence, it relies on a delicate interplay between hemispheric coordination and specialization. Learning about the underlying mechanism can help us understand how the brain uses different strategies to integrate its action computations. The focus of my thesis is to investigate the underlying mechanisms of bimanual grasping, which to date has been largely ignored. The objective is to examine bimanual grasping from 3 perspectives: First, I will examine bimanual grasp at the visual input level, and specifically its performance across visual fields, which would give us insight into its hemispheric specialization (Experiments 1 and 2). Second, I will investigate the visuomotor neural mechanisms underlying bimanual grasping (Experiments 3 – 5). Third, I will examine the motor coordination mechanisms (Experiment 6). In general, the results show that bimanual grasping is predominantly controlled by the right hemisphere, specifically by brain areas typically involved in unimanual grasping. These findings have medical significance because they could help develop new rehabilitation programs for patients with motor deficits after cortical or hand/arm damage.

Keywords: action
bimanual
coordination
grasping
TMS
Advisor: Niemeier, Matthias
The Secondary Schooling Transnational Nexus: Student and Educator Reflections Beyond and Within the Nation

This dissertation qualitatively examines how Greater Toronto Area (GTA) secondary schools are responding to the ongoing ties (transnational connections) some students and their families maintain to their place(s) of origin. Interview participants comprised transnational recent graduates of GTA secondary schools and educators, encompassing both teachers and administrators. “Transnationalism” was defined in terms of both behavioural and attitudinal characteristics. Interviewees were located in the public and private school systems, and included migrants with and without papers. Social class was conceived of and explored as a critical and decisive mediating factor (as well as a lens for analysis) in experiences of transnationalism in the GTA. The data were organized to elucidate themes at the levels of individuals and families, schools and institutions, and in terms of policy implications. Key findings include: that when students travel to their sending societies for ongoing periods there are disconnections at school that some teachers consider a threat while others see as an opportunity; that as families are increasingly transnationally reconfigured and some students’ parents or family members travel continually to their home country there can be difficulties in supervision at home which have reverberations at school; and finally, that when there are ongoing direct contacts with the home country, including both travel and new modes of communication, this may create knowledge and vivid experiences for transnational youth, leading to more difficult adjustment problems in secondary schools than has been typical for immigrant youth in the past. As well, the data suggest that within the GTA, there is a tension between the extent to which schools can and should accommodate transnational students and their families, and the extent to which transnational students and families ought to assimilate to the pre-existing (but changeable) assumptions and requirements embedded within the secondary schooling system as it stands.

Keywords: Greater Toronto Area
Immigration
Integration
Secondary Schooling
Social Class
Transnationalism
Advisor: Troper, Harold
The Role of the Board of Trustees in Public Universities in China

Inherited from the American tradition of lay boards and first introduced into the public higher education system in the 1920s, the board of trustees in Chinese public universities has, over time, played a changing role, from being an autonomous top governing body, to being manipulated by government officials, to being completely removed from institutional governance structures. After China adopted reform policies in the late 1970s, boards of trustees were reintroduced in some public universities. However, higher education regulations and ideological influences have given the board an ambiguous and elusive role, little known to those both outside and inside the university sector. This thesis investigates the role, function and structure of boards of trustees in Chinese public universities. By examining the policies and operations of these boards, the study aimed to identify whether and how these boards facilitate interaction between universities and their external stakeholders in the overall national context of adaptive institutional change. Following a qualitative approach, the study gathered data from document analysis, a national survey of 40 board secretariats, and semi-structured interviews with secretariat staff of 37 institutions. The study found that boards of trustees can be found in 84 public institutions. Predominantly composed of members from industry and government, the boards mainly serve as a medium for fundraising and a conduit for university–industry collaboration in teaching and research. The relationship between an institution and its board members is ostensibly interest-oriented and can even involve economic and personal gain. The board is essentially an advisory body, albeit its role in giving advice is very limited. The many challenges associated with board operation and functioning suggest that adaptive governance, which is characteristic of the Chinese party-state, has had both positive and negative impacts on the board. This thesis advances our understanding of the Chinese board through interlocking political, social, and educational dimensions.

Keywords: adaptive governance
board of trustees
Chinese higher education
civil society
stakeholder society
university governance
Advisor: Jones, Glen A.
Development of Animal Models to Study Idiosyncratic Drug-induced Liver Injury

Idiosyncratic drug reactions (IDRs) represent a special problem because of their unpredictable nature and are a major reason for drug withdrawal. The objective of this research was to study the mechanism of DILI caused be amodiaquine (AQ) and D-penicillamine (D-pen). Amodiaquine (AQ) is associated with a relatively high incidence of idiosyncratic drug-induced liver injury (IDILI) and agranulocytosis. In this study, treatment of rats with AQ resulted in a mild delayed-onset liver injury that resolved despite continued treatment with the drug. Immunohistochemistry indicated the presence of Kupffer cell activation, apoptosis, and hepatocyte proliferation in the liver. There was also an increase in serum IL-2, IL-5, IL-9, IL-12, MCP-1, and TGF-β, but a decrease in leptin. Co-treatment with cyclosporin prevented AQ-induced liver injury, while Poly I:C co-treatment caused an earlier increase in alanine aminotransferase (ALT), which suggested that AQ-induced liver injury is immune-mediated. Coincident with the elevated serum ALT, liver CD4+ T cells, IL-17 secreting cells, and Th17/Treg cells were increased at week 3 and decreased during continued treatment. An increase in CD161+ cells and activated M2 macrophages were also observed during the liver injury. These results suggest that the outcome of the liver injury is determined by a balance between effector cells and regulatory cells. Similar results were also observed in AQ-treated C57BL/6 mice. Covalent binding of AQ was detected in the liver, and although AQ forms a glutathione conjugate, depletion of glutathione did not increase covalent binding and paradoxically prevented AQ-induced liver injury. Retinoic acid (RA), which has been reported to enhance natural killer (NK) cell activity, exacerbated AQ-induced liver injury. These characteristics indicate that we have established a rat model of AQ-induced liver injury that mimics mild AQ-induced liver injury in humans. The results suggest that AQ-induced IDILI is immune mediated, and the subsequent adaptation appears to represent immune-tolerance.

Keywords: amodiaquine
drug-induced liver injury
idiosyncratic drug reaction
penicillamine
Advisor: Uetrecht, Jack
Rethinking Disarmament: The Role of Weapons in the Resolution of Internal Armed Conflicts

Since the end of Cold War there has been an increase in the number internal conflicts and with it a corresponding rise in the number of third party interventions. Third parties, motivated by humanitarian concerns and spillover effects, have sought to create stable conditions for the termination of internal conflicts and the reconstruction of shattered societies. The disarmament of combatants has emerged as a leading practice. Disarmament is based on the arrestingly simple logic that the elimination of weapons removes the means by which combatants fight, thereby forcing them to commit to peace. Despite this emergent practice, however, belligerents consistently retain, and, in some cases, acquire weapons, even after signing peace agreements. Proponents of disarmament tend to view the retention of weapons as evidence of spoiling, yet disarmament leaves actors with little recourse in the likely event that a peace process collapses and conflict resumes. I argue that actors often retain weapons because the risk of violent reversal remains high even after the signing of a peace agreement. In the likely event of the breakdown of peace, weapons can be used to help ensure survival of those who retain them. This research explores the role of weapons and disarmament in internal conflicts with reference to both historical (the American War of Independence) and contemporary examples (Israel-Palestine and El Salvador). Though not all are examples of successful peacemaking, weapons played a productive role not only securing combatants, but also by allowing them to make more credible commitments and take greater risks associated with peace. This research reveals a paradox: while weapons provide belligerents with much-needed insurance, allowing them to take risks associated with peacemaking, retaining weapons appears to magnify the likelihood that an agreement will fail. Nevertheless, belligerents have at their disposal various ways to overcome this problem. I conclude by discussing the ways in which third parties may better support such initiatives.

Keywords: credible committments
disarmament
domestic security dilemma
peacekeeping
spoilers
Advisor: Kopstein, Jeffrey