VictorJuiz/thesis huggingface dataset:
Improving Workflow and Accuracy in Craniofacial Reconstruction with Computer-assisted Surgical Planning

Trauma and pathological involvement can result in major disruption of the face and skull’s complex 3D bony and soft tissue structure. Accurate craniofacial reconstruction is challenging when there is insufficient patient-specific 3D face and skeletal shape information, especially for severe bilateral cases. The objective of the research in this thesis is to develop computer-assisted pre-operative planning and intra-operative workflow for ‘outside-in’ craniofacial reconstruction to restore pre-injury/pathology morphology, including improving accuracy in related nasal reconstruction, rhinoplasty and facial reanimation procedures. To estimate 3D facial morphology from 2D photos for bilateral cases, the accuracy of morphable models was investigated to quantify the spatial distribution of error by evaluating a database of 100 subjects’ 3D faces. To account for a patient’s smile and provide guidance to facial reanimation, a 3D analysis quantified lip and cheek movement at 4 increasing smile intensities, where small differences were found between sexes and races. Applying 3D pre-operative planning to surgical workflow, a newly developed CAD-CAM process was utilized in a case series of five patients undergoing nasal reconstruction. 3D digital noses were flattened to create 2D templates, printed 1:1 scale and successfully used as an intra-operative guide to shape forehead flaps for nasal reconstruction. With the aim of improving the assessment of nasal symmetry, a deviation measurement algorithm was developed and validated on a controlled asymmetrical nose model. The average maximum nasal deviation for 100 subjects was evaluated to provide context for clinical assessment. To infer the underlying 3D skull morphology from a 3D facial surface, a forensics tissue depth model was ‘reverse-engineered’ on 33 head CT images. A new algorithm was developed to improve measuring tissue depths perpendicular to the face and demonstrated that a 3D skull shape can be inferred with low error for the outermost craniofacial skeleton. Overall, this thesis presents the development and validation of new algorithms to improve pre-operative planning and intra-operative workflow in craniofacial reconstruction. This research leverages personal photos, repurposes non-clinical software and generates physical templates in order to improve the accuracy of surgeons to restore craniofacial soft tissue and skeletal structures to their pre-injury/ pathology state.

Advisor: Whyne, Cari
Fialkov, Jeffrey
The Least Prime whose Frobenius is an n-cycle

Let L/K be a Galois extension of number fields. We consider the problem of bounding the least prime ideal of K whose Frobenius lies in a fixed conjugacy class C. Under the assumption of Artin's conjecture we work with Artin L-functions directly to obtain an upper bound in terms of irreducible characters which are nonvanishing at C. As a consequence we obtain stronger upper bounds for the least prime in C when many irreducible characters vanish at C. We also prove a Deuring-Heilbronn phenomenon for Artin L-functions with nonnegative Dirichlet series coefficients as a key step. We apply our results to the case when Gal(L/K) is the symmetric group Sn. Using classical results on the representation theory of Sn we give an upper bound for the least prime whose Frobenius is an n-cycle which is stronger than known bounds when the characters which are nonvanishing at n-cycles are unramified, as well a similar result for (n-1)-cycles. We also give stronger bounds in the case of Sn-extensions over Q which are unramified over a quadratic field. We also consider other groups and conjugacy classes where unconditional improvements are obtained.

Keywords: Number theory
Advisor: Murty, Kumar
Mechanisms of Improved Renal Function Following Normothermic Ex-vivo Kidney Perfusion Preservation of Grafts Severely Damaged by Prolonged Warm Ischemia

Normothermic ex-vivo kidney perfusion (NEVKP) is an emerging technique for renal graft preservation. We investigated whether NEVKP could improve early function of severely injured donation-after-cardiovascular death (DCD) grafts to reduce the incidence of delayed graft function (DGF). First, we develop a large-animal model of significant renal dysfunction (SRD) that resembles clinical DGF following static cold storage (SCS). After comparing the function of these grafts following NEVKP-storage, we investigated potential mechanisms that may account for the observed outcomes by examining their gene expression pattern. To establish the SRD model, kidneys from 30kg-Yorkshire pigs were procured following increasing warm ischemic (WI) times of 0-120min (n=3-6/group) to mimic DCD. Following 8h of SCS and autotransplantation, animals were followed for 7-days. SRD was defined as oliguria

Keywords: Donation-after-cardiovascular death
Genomics
Ischemia Reperfusion Injury
Kidney Transplantation
Organ Procurement
Porcine models
Advisor: Selzner, Markus
Robinson, Lisa A
A Modeling Framework for Analyzing Process Architecture Transformations in the Software-enabled Enterprise

Software is becoming a fundamental enabler of all kinds of evolving enterprise capabilities and opportunities. For the enterprise to take advantage of software-based technologies, there will be redesigns of processes that are responsible for the development of software, and the business processes where these software are used. There exists extensive work on business process modeling and analysis however, it is not adequate to study and optimize processes in isolation as enterprise objectives are attained by multiple interrelated processes as a collection. We refer to a collection of processes and their interrelationships as a process architecture. By repositioning decision points within a process architecture, an enterprise can take better advantage of software flexibility and data-driven capabilities. In this thesis research, we model and analyze process architecture reconfigurations and study possible alternative configurations of these process architectures, with emphasis on adaptability and flexibility. Through reconfigurable and flexible process architectures, enterprises can respond to changing situations by selecting suitable process architecture alternatives that best meets enterprise business objectives. We introduce the hiBPM framework to support the study of process architecture reconfigurations. A hiBPM model describes processes, and their relationships and interactions needed to accomplishenterprise objectives. hiBPM emphasizes the existence of various decision-making points and offers expressiveness to allow relevant architectural properties to be analyzed, and to contrast amongst alternative process architecture configuration options. Through hiBPM, enterprise architects can explore alternatives to come up with process architecture that enable enterprise flexibility while factoring in other non-functional criteria, such as the time or cost involved. This thesis research used design science research to determine hiBPM framework design artifacts, and case study research for the evaluation and validation of the developed conceptual modeling framework. The case studies performed contributed to the validation of the hiBPM framework by highlighting the varying degrees of plan and design completeness suitable to different contexts and situations within the enterprise under uncertain conditions, elaborating on the different types of processes in the process architecture and their relationships, and determining additional processes that were necessary for meeting of enterprise functional and non-functional requirements.

Advisor: Yu, Eric
Longitudinal Analysis of Out-of-home Activity Generation in the Greater Toronto and Hamilton Area

“Activity generation” is a critical component of any agent-based, activity-based travel demand model since it determines the overall activity/travel levels, which are then utilized for answering various transportation-, land use- and environment-related research/policy questions. This thesis reports on significant progress in three research areas regarding activity generation modelling with a focus on activity participation/frequency and timing (start time/duration) decisions. The analyses cover investigating the behaviour associated mainly with work- and school-related activities, in addition to shopping and other activities, in the Greater Toronto and Hamilton Area over a 20-year period between 1996 and 2016. First, cross-sectional models and four types of “joint/pooled” models of activity/trip generation are estimated for various activity purposes to examine changes in behaviour over time. Strong temporal stability is observed in utility-based econometric model parameters when the parameter estimates of cross-sectional and joint models are statistically compared. This major contribution supports the development and use of robust parametric joint models for forecasting applications in the region utilizing full information accrued over the years. Second, to explore the interpretability of machine learning models and to inspect how these powerful tools can be leveraged within a microsimulation framework, longitudinal models of work and school activity participation are developed using a diverse set of algorithms, which are compared to microeconomic models. Remarkable parallelism is detected between microeconomic models and machine learning algorithms in terms of activity frequency model specifications. This notable finding encourages researchers to benefit from both modelling domains, integrating their strengths. Third, joint models of activity start time and duration are built adopting a copula approach for work and school activities of agents/individuals from mutually exclusive population subsamples: “worker”, “student”, and “both worker and student”. Simultaneous activity episode start time and duration simulation models show that complex timing behaviour can be captured with relatively parsimonious models. Each of these three modelling applications additionally demonstrates the significance of establishing a comprehensive disaggregation structure for the analyses, since considerable differences have been observed across distinct agent classes and activity types.

Keywords: Activity Generation
Activity Participation/Frequency
Activity Timing (Start Time and Duration)
Greater Toronto and Hamilton Area
Longitudinal Analysis
Advisor: Miller, Eric J.
A Class of Mixture of Experts Models for General Insurance Ratemaking and Reserving

Understanding the effect of policyholders' risk profile on the number and the amount of claims, as well as the dependence among different types of claims, are critical to insurance ratemaking and IBNR-type reserving. To accurately quantify such features, it is essential to develop a regression model which is flexible, interpretable and statistically tractable. In this thesis, we first propose a highly flexible nonlinear regression model, namely the logit-weighted reduced mixture of experts (LRMoE) models, for multivariate claim frequencies or severities distributions. The LRMoE model is interpretable as it has two components: Gating functions to classify policyholders into various latent sub-classes and Expert functions to govern the distributional properties of the claims. The model is also flexible to fit any types of claim data accurately and hence minimize the issue of model selection. Model implementation is then illustrated in two ways using a real automobile insurance dataset from a major European insurance company. We first fit the multivariate claim frequencies using an Erlang count expert function. Apart from showing excellent fitting results, we can interpret the fitted model in an insurance perspective and visualize the relationship between policyholders' information and their risk level. We further demonstrate how the fitted model may be useful for insurance ratemaking. The second illustration deals with insurance loss severity data that often exhibits heavy-tail behavior. Using a Transformed Gamma expert function, our model is applicable to fit the severity and reporting delay components of the dataset, which is ultimately shown to be useful and crucial for an adequate prediction of IBNR reserve. After that, we further extend the fitting algorithm to efficiently fit the LRMoE to random censored and truncated regression data. Such an extended algorithm is then found useful and important for broader actuarial applications such as unbiased claim reporting delay modeling and deductible ratemaking.

Keywords: Claim frequency and severity modeling
Denseness theory
Mixture of Experts Models
Multivariate regression analysis
Property and Casualty Insurance
Advisor: Lin, X. Sheldon
Badescu, Andrei L.
Brain Networks Involved in Higher Cognitive Functions in Adults with Autism Spectrum Disorder

People with autism spectrum disorder (ASD) experience difficulties with higher cognitive functions, including executive functions and theory of mind (ToM). They show atypical recruitment of brain regions involved in these functions, but functional connectivity among these areas within particular frequency bands has been less well characterized in ASD. Examining these factors is crucial to elucidating the neural mechanisms by which long-range underconnectivity and short-range overconnectivity reported in ASD influences their cognitive abilities. Therefore, this thesis used magnetoencephalography to explore the frequency-specific functional networks subserving executive functions and ToM in three studies of overlapping groups of 39 control adults and 40 adults with ASD aged 18–40 years old. Study 1 demonstrated that during inhibitory control, lower alpha-band synchrony between the right inferior frontal gyrus (IFG) and areas not typically linked to inhibition was found in adults with ASD compared to controls and was associated with everyday inhibition, suggesting weaker suppression by the right IFG of extraneous brain activity. Study 2 revealed that while connectivity did not differ between groups when maintaining stimuli in working memory, adults with ASD showed reduced theta-band network synchrony involving the right IFG and left inferior parietal lobule when recognizing previously presented stimuli. Therefore, despite intact maintenance, recognition in adults with ASD may be affected by diminished inhibition of irrelevant stimulus representations. Study 3 determined that during a ToM false-belief task, adults with ASD had lower theta-band synchrony among brain regions implicated in ToM and the right IFG, suggesting reduced inhibition of their own belief when inferring another’s false belief. Adults with ASD reported difficulties in all three functions assessed by these three studies. Together, this work suggests that reduced connectivity impacts higher cognitive functions in ASD, and that atypical inhibitory control may be a common, key contributor to cognitive difficulties in adults with ASD.

Advisor: Taylor, Margot J.
Black Howler Monkey (Alouatta pigra) Demography and Behaviour in Unprotected Forest Fragments around Palenque National Park, Chiapas, Mexico

Habitat loss and fragmentation are urgent threats to primate species worldwide. Species’ responses to these threats are mediated by many factors, and there remains an urgent need to generate species- and habitat-specific knowledge to better understand their effects. I examined how living in unprotected forest fragments shapes Endangered black howler monkey (Alouatta pigra) demography and behaviour in a single fragmented landscape around Palenque National Park (PNP) in Chiapas, Mexico. I surveyed 34 fragments and collected demographic and behavioural data on the black howlers inhabiting them (62 groups, 407 individuals). I collected data on fragment size, shape, isolation, and forest composition. I found that the demographic population structure of the black howler population in the fragmented landscape has been stable over the last 17 years, while patch occupancy and ecological density have increased. Compared to the PNP black howler population, the study population was denser, and differed mainly in a lower proportion of adult males and fewer adult males per group. I then examined how variation in fragment isolation and habitat characteristics affected the population composition of black howler monkeys within fragments, and whether this variation differentially affected adult males and females. My results showed a significant effect of fragment variables on population demography in fragments. Population size increased with fragment area while density decreased, and the proportion of adult males and females, and their average number per group, were differentially affected by variation in fragment characteristics: there were more females in larger, less isolated fragments, and more males in more isolated, secondary-growth fragments. Lastly, I analyzed how variation in fragment habitat shaped time budgets and group movements of black howler monkeys in the study fragments. Fragment habitat variables significantly explained over half of the variation in these behaviours. Results showed that black howlers employed variable strategies (energy-minimizing or energy-maximizing) in response to variation in fragment habitat quality. Taken together, my results indicate that habitat loss and fragmentation are affecting the study population via demographic and behavioural changes simultaneously, with implications for the likelihood of long-term persistence of black howlers in unprotected forest fragments around PNP.

Keywords: animal behaviour
conservation biology
demography
endangered species
habitat loss and fragmentation
primates
Advisor: Lehman, Shawn M
Teichroeb, Julie A
Child Care Utilization and Stability of Quality: Implications for System Management and Oversight

Child care can be a public service tool capable of supporting multiple social and economic goals including improving gender equity and reducing inter-generational transfer of poverty through high quality early learning and care for all children, but especially those in low income families. Recent estimates indicate that almost 60% of preschool-aged children regularly spend time in non-parental care (Statistics Canada, 2019b). Yet, Canadian families also rank very low on the OECD’s measures of child care affordability and access to licensed care. This means that families must use unlicensed care which receives virtually no government oversight. Current government statistics provide accurate counts of child care centre capacities. However, little is known about licensed home child care (HCC). Even less is known about the families who utilize unlicensed care, or do without any non-parental care. Beyond access, with very few exceptions, little is known about quality of care most families can access. Such data must form the basis for a social investment strategy that reduces existing inequalities. The dissertation consists of three papers that address gaps in our knowledge of child care in Canada. The first study, used data from the 2011 General Social Survey of Canada. Study findings show substantial heterogeneity in usage rates across the country as well as inequality whereby the families with the fewest resources are more likely to use unlicensed care or to have no care at all. The second study outlines a model for individually licensing and ensuring quality in HCC providers, including requirements for annual health and safety inspections, independent quality assessment and a wide-ranging system of quality supports and enhancements. Cost estimates are provided which are substantially lower on a per provider basis than the current agency-based licensing approach to HCC used in a number of provinces. Using administrative data from the City of Toronto the third study investigated the stability of quality ratings of 1,019 preschool classrooms over a three year period. The results show significant levels of instability suggesting that the frequency of ratings cannot be reduced. Implications for service oversight, system management and further research are discussed.

Keywords: Child care
Early childhood education and care
HCC licensing
Quality assessment
Advisor: Perlman, Michal
Phase-amplitude Coupling and Neuroglial Networks of the Brain: Big Role for a Small Cell

Epilepsy affects over 45 million people worldwide and while treatment options exist, antiepileptic drugs don't work in up to 50% of the cases; furthermore, poorly-treated epilepsy may cause complications such as sudden unexpected death in epilepsy (SUDEP) and status epilepticus. Brain rhythms can characterize both normal and pathologic brain states and the coupling between these rhythms, namely between low frequency oscillations (LFOs,

Advisor: Bardakjian, Berj L
Ricardo Viñes’s Pianistic Legacy: An Evaluation of his Articles, Recordings, Compositions, and Pedagogy

Ricardo Viñes (1875-1943) was a Catalan pianist who spent most of his career based in Paris. He premiered many of the major piano works by Debussy, Ravel, and other French, Spanish and Latin American composers of the early twentieth century. He had a reputation among his peers as a pianist who possessed an extraordinary technique, who was selflessly committed to the integrity of his musical performances, and who sacrificed further career success to promote the music of lesser-known composers. His legacy is that of a contemporary music specialist. Literature on Viñes is based mostly on his diary, which he kept between 1885 and about 1914, testimony by his students, press reviews and homages by his peers. The English literature on Viñes is lacking a study of his published articles, compositions and recordings, and has not convincingly challenged Elaine Brody’s assertion that Viñes was essentially a self-taught pianist. This dissertation examines that material and finds that Viñes’s articles indicate his preference for romantic musical ideals, his compositions belie his purported technical prowess, his recordings reveal some technical limitations, and his training and teaching methods are rooted in the French piano school tradition. This dissertation also adds new information on Viñes to the English literature from French and Catalan sources, including the only French biography of the pianist by Mildred Clary. Viñes’s legacy of disseminating contemporary music over the course of his career was well earned, but not selflessly. The research in this dissertation demonstrates that Viñes capitalized on his association with contemporary composers to cultivate a reputation as a new music specialist, which was a career direction that played to his strengths.

Keywords: Debussy
Paris Conservatoire
Piano
Ravel
Recital
Ricardo Viñes
Advisor: McClelland, Ryan