VictorJuiz/thesis huggingface dataset:
The Genetic Architecture of Pigmentation Traits in Modern Human Populations

Pigmentation traits, here defined as hair, eye and constitutive skin pigmentation are some the most variable phenotypes among human populations. They have a complex genetic basis, in which interactions among genes and pleiotropy are common. Several genes involved in the pigmentation pathway have been described across mammalian species, which explain a significant proportion of the normal pigmentation variation in humans. However, the full understanding of the genetic architecture of pigmentation in human populations has not yet been achieved. Major effect genes are known to explain a relatively high proportion of the variance for each pigmentation trait at a population-basis level, but a substantial number of genetic loci modulating pigmentation in several populations have small effects and remain unknown. The objective of my thesis was to contribute to and improve the state of knowledge of the genetic architecture of pigmentation traits in modern humans. To achieve this, I have taken advantage of novel approaches at different stages of the research program, such as the use of large sample sizes and different cohorts, the application of diverse statistical approaches, and the use of genomic and epigenomic databases and computational advances to follow-up putative causal loci. I have identified a complex genetic architecture across known pigmentation regions such as TYR and OCA2, in which a combination of missense and non-coding SNPs are independently associated with pigmentation traits. These associations seem to vary among populations and among pigmentation traits to certain extent, as evidenced by fine-mapping and genetic correlations in a Canadian cohort of European ancestry. Finally, I explored the putative regulatory role of pigmentation loci. I have identified shared causal signals between hair or eye colour and quantitative trait loci (i.e. methylation and expression), and I have identified significant associations between hair or eye colour and the expression of pigmentation genes such as OCA2 and SLC24A4. Overall, my research has nominated several candidate causal variants across loci, and has provided insights to further explore the biological role of these SNPs in human pigmentation.

Keywords: eye colour
GWAS
hair colour
human evolution
pigmentation
skin pigmentation
Advisor: Parra, Esteban
eHealth Antenatal Coparenting Intervention to Prevent Postpartum Depression among Primiparous Women, Karachi, Pakistan: A Pilot Randomized Controlled Trial

Background: Postpartum depression is highly prevalent among women and a lack of partner support is a strong risk factor for PPD. Partner support has been shown to decline significantly during the transition to parenthood. The primary objective of this pilot randomized controlled trial was to examine the feasibility and acceptability of an eHealth antenatal coparenting intervention called eACoP and obtain preliminary estimates on clinical outcomes for a future larger trial. Methodology: 212 primiparous couples were recruited from the Aga Khan University Hospital and randomly allocated into the intervention group or the control group using sequentially numbered opaque sealed envelopes. Couples in the intervention group received the eACoP intervention during pregnancy which consists of eight 45-minute online videos. Primary outcomes were feasibility and acceptability measured through enrollment rates, intervention adherence rates, follow-up rates, and intervention satisfaction. Secondary outcomes were depressive symptomatology, anxiety, postpartum partner support, coparenting relationship, relationship satisfaction, postpartum childcare stress, child development, extrafamilial support, and healthcare services utilization. Results: Primary outcomes: The enrollment rate of eligible participants in this pilot study was 83.5%. One in five couples completed the minimum intervention dosage of watching at least five videos. Complete follow-up data was collected from 66.5 (n=137) of women and 56.7% of partners (n=117) at 4-6-weeks, decreasing slightly to 60.7% (n=124) of women and 50.4% of (n=104) partners at 12-weeks postpartum. The 24 couples who watched at least five videos and completed the satisfaction forms felt that the content of the videos was helpful and provided appropriate strategies for managing situations or problems. Participants provided important recommendations, including the inclusion of Pakistani cultural and religious aspects in the videos and making the videos shorter. Secondary Outcomes: At 4-6-weeks postpartum, 22.1% of women and 3.5% of partners in the intervention group showed depressive symptomatology while 32.8% of women and 7% of partners had anxiety symptoms. At 12-week postpartum, 14.1% of women and 5.7% of partners had depressive symptoms while 21.9% of women and 11.3% of partners had anxiety symptoms. Similarly, 13.11% of women and 9.6% of partners reported relationship dissatisfaction. There was no difference found between the intervention group and control group with respect to other secondary outcomes. Conclusion: This pilot trial found that a future randomized controlled trial of eACoP intervention is not feasible nor acceptable in the Pakistani context without modifications. .

Keywords: co-parenting
Coparenting
Intervention
partner support
Pilot Randomized Controlled Trial
postpartum depression
Advisor: Dennis, Cindy-Lee CL
Tools to Live by: Starch Grain Analysis on Jomon Period Ground Stone from Southern Hokkaido, Japan

Over the past few decades of research on Jomon Period (ca. 16,500 – 2,300 BP) subsistence, many have come to accept that various edible tree nuts were central to everyday practices and foodways throughout this period. Despite palaeoethnobotanical research from southern Hokkaido challenging this generalization, studies continue to assume the importance of nuts based on macrobotanical remains, site features, and artifactual proxies. Ground stone technology is one artifact class that is consistently associated with nut processing, but research programs designed to explicitly evaluate this relationship have been relatively few for Jomon sites. In this dissertation, I examined the larger interaction between starchy plant species and grinding implements from Jomon sites across southern Hokkaido through the application of starch grain analysis on extracted residues. The ground stone implements sampled here did not yield clear evidence for nut species considered important to Jomon peoples in this region, such as Castanea crenata and Juglans ailanthifolia, and many artifacts had no visible starch to report. These results challenge the suggestion that handstones and netherstones, such as suri-ishi and ishizara respectively, were primarily for processing plant foods, and are particularly indicative of cracking and grinding nuts in Jomon communities. This leads to further questions about the potential of ground stone to be used beyond subsistence studies, turning the focus to discussions of foodways, resource processing, and the intersections of different activities within daily life at Jomon sites in Hokkaido.

Keywords: Foodways
Ground stone
Hokkaido
Jomon Period
Residue analysis
Starch
Advisor: Crawford, Gary W
Drivers of Holocene Carbon Uptake and Release in Peatlands of the Hudson Bay Lowlands, Canada

Northern peatlands are a key component of the terrestrial carbon cycle, acting as both a source and sink of carbon. Therefore, to predict impacts from anthropogenic climate change and create effective land management policies, constraining how environmental factors impact peatland carbon fluxes is critical, especially in peatland-rich regions such as the Hudson Bay Lowlands (HBL), Canada. This thesis aims to understand how local-scale factors impacted Holocene carbon uptake and release in the HBL using paleoecological and geochemical analyses of radiocarbon-dated peat cores. Paleoecological analyses of a site on the southern HBL margin demonstrate that landscape position controls local hydrology and can subsequently limit Holocene carbon accumulation rates (CARs). This record also demonstrates a summer bias in temperature and validates pH reconstructions from lipid biomarker proxies. Paired treed fen and bog sites from the western HBL margin show markedly high carbon masses owing to deep peat accumulation with old initiation ages. Mean testate amoeba trait values reflect hydrology and food web structure and are also influenced by vegetation shifts and peatland type. Further, mixotrophic taxa are not related to higher millennial-scale CARs, suggesting a minor role for their primary production in long-term carbon storage. The above records were synthesized with other hydrological records derived from testate amoebae across the HBL to reconstruct paleo-methane fluxes via a linear regression model developed from modern relationships between methane fluxes and water table depths. Land availability controlled by glacial isostatic adjustment was an important control on Holocene emissions when fluxes were scaled to regional emissions. The combined hydrological reconstructions also suggest that peatlands were drier under warmer Middle Holocene conditions. A charcoal record collected from the western HBL margin supports drier conditions, as warmer Middle Holocene conditions were related to higher fire frequency. Although higher fire frequency did not have a significant impact on millennial-scale CARs, carbon loss from combustion was potentially doubled, which has implications for atmospheric carbon budgets. Overall, this thesis advances our understanding of the complex interplay between climate and local processes in long-term carbon dynamics that is of fundamental importance for conservation priorities and constraining future carbon emissions.

Keywords: carbon
Holocene
Hudson Bay Lowlands
methane
peatlands
testate amoebae
Advisor: Finkelstein, Sarah
A Narrative Study About Teacher Knowledge and How It is Reflected in Pedagogical Choices, Practices, and Views When teaching Emergent Writing

AbstractThis research investigated how teachers’ various forms of knowledge are reflected in their pedagogical views, practices, and choices when teaching emergent writing. Emergent writing is one of the most understudied areas of literacy with limited research regarding primary writing instruction. Prior to attending school, most young children demonstrate emergent writing skills that include marks, scribbles, drawings, letters and words. Development of emergent writing abilities contribute to student self-regulation, higher order thinking skills, and concept formation. Additionally, these skills are good predictors of later school success in reading and writing, as well as better opportunities in the workplace. This research embraced a wholistic perspective to honour teachers’ lived experiences and stories. A narrative approach was used. Data collection consisted of narrative interviews with four kindergarten teachers who taught in Ontario, Canada. Teachers were encouraged to share their stories and experiences when teaching emergent writing. Narratives were analyzed inductively to develop a better understanding about teacher knowledge and how it is reflected in daily practices when teaching emergent writing. In alignment with a social constructivism perspective, teacher narratives described a play-based classroom where daily peer interaction, rich multimodal and oral language opportunities were encouraged through a variety of learning centres that included an art table, a drama centre, a science touch table, as well as various other language activities. Teachers shared stories of drama centres that included pretend restaurants, a doctor’s office, and a post office, as well as props to re-enact classroom read-alouds. These meaningful activities supported independent student exploration and meaning making. Using a multi-layered view of language writing, and employing a deductive approach, I identified understandings and beliefs using Ivanič’s (2004) framework of six discourses of writing and learning to write. Findings of this second layer of analysis indicated that teachers viewed writing as multimodal. Their description of daily classroom contexts reflected beliefs and perspectives within five of the six discourses. The use of all six discourses was found in only one participant’s narrative. Teachers’ narratives often included elements of three or more discourses (that were sometimes conflicting) in the same writing event. A complex understanding of emergent writing was found in all narratives.

Keywords: emergent writing
kindergarten
narrative
teacher knowledge
writing discourses
Advisor: Stagg-Peterson, Shelley
A Critical Evaluation of Surgical Therapy for the Management of Medication-Related Osteonecrosis of the Jaw

Introduction: Medication-related osteonecrosis of the jaw (MRONJ) is an adverse drug reaction to antiresorptive and antiangiogenic therapy, resulting in maxillofacial bony necrosis and significant negative effects to quality of life (QoL). With mixed evidence surrounding the effectiveness of surgical therapy for management of MRONJ, we aimed to evaluate the effects of surgery on both disease resolution and QoL. Methods: We conducted four studies for this dissertation. The first, a systematic review and meta-analysis, aimed to evaluate the effectiveness of the various therapies proposed for management of MRONJ. The second, a retrospective cohort study, compared surgical versus nonsurgical therapy for disease resolution. To allow us to measure QoL in these patients, the third study produced and validated a quality of life questionnaire (the MRONJ-QoL) for use in patients with MRONJ. Using this questionnaire, the fourth study prospectively compared the effects of various surgical techniques to nonsurgical therapy on both disease resolution and effects on QoL. Results: Our systematic review suggested, in contrast to the 2014 treatment guidelines by the American Association of Oral and Maxillofacial Surgeons, that surgical therapy may, on average, be favoured to nonsurgical treatment of MRONJ for disease resolution. This finding was confirmed in our retrospective review (adjusted odds ratio, 4.33; 95% confidence interval, 1.28 to 14.60). Evaluation of the MRONJ-QoL showed it to have high internal consistency (Cronbach’s alpha of 0.85) and good reliability (weighted kappa score of 0.65). Furthermore, cross-sectional and concurrent evaluation of validity suggested the questionnaire to be valid. Finally, our prospective evaluation showed sequestrectomy, debridement, and resection to be significantly associated with resolution of the disease (OR 36.0, 95% CI 2.7-477.2, p=0.007; OR 37.0, 95% CI 4.3-319.0, p=0.001; and OR 42.5, 95% CI 1.4-1257.6, p=0.03, respectively), and debridement and resection to be associated with improved QoL (MRONJ-QoL score improvement of 3.83, 95% CI 0.16-7.50, p=0.04; and MRONJ-QoL score improvement of 6.82, 95% CI 0.21-13.4, p=0.04, respectively). Conclusion: Our studies demonstrated that surgical therapy is suggested to be favourable to nonsurgical therapy for the management of MRONJ. Future multicentered randomized controlled trials will be required to confirm these findings.

Keywords: BRONJ
MRONJ
OMFS
Oral and Maxillofacial Surgery
Advisor: Azarpazhooh, Amir
Nonlinear Interferometers for Quantum Information Processing and Metrology

The ability to generate biphoton state with tunable properties in various degrees of freedom (DoFs) is always a challenging task in the field of quantum information processing. This arises from the fact that generating such biphoton state puts many constrains on the design and fabrication of the biphoton sources. In this thesis, I propose a novel common-path nonlinear interferometer (NLI) to generate biphoton states with tunable properties without the need for any modification to the biphoton source itself. I further utilize our NLI scheme to perform a precision dispersion measurement as well. First, I developed a comprehensive model, which accounts for the effects of the pump temporal coherence, as well as the chromatic dispersion and the birefringence of the linear medium inside the NLI. I have shown that through manipulating the dispersion and birefringence of the linear medium inside the NLI, biphoton properties in both frequency and polarization DoFs can be tuned (simultaneously or separately). Variants of all-fiber NLIs, consisting of periodically-poled silica fibers as the nonlinear media, which generate biphotons, and a single-mode fiber with an inline polarization controller as the linear section, are constructed for proof-of-principle demonstrations. Biphoton states with comb-like spectra are obtained from the NLI, without requiring any modification to the nonlinear media. Furthermore, biphoton states with tunable degree of polarization entanglement (in the range of 0 to 1) are predicted and experimentally generated with our interferometer. More significantly, through the simultaneous manipulation of the chromatic dispersion and birefringence of the linear medium, a novel class of biphoton states with coupled frequency and polarization DoFs is also obtained. The frequency-dependent polarization entanglement feature, which is the signature of such states, is experimentally verified. The abovementioned NLIs are also utilized to demonstrate precision dispersion measurement on a 5-m-long single-mode fiber sample, with a sensitivity of ~0.009 ps/nm. Our sensitivity is comparable to that of the existing state-of-the-art dispersion measurement techniques, but unlike the latter, ours eliminates the need for interferometer balancing, beam alignment, and phase stabilization. The simplicity, robustness and versatility of our demonstrated NLI technique illustrates its important role in quantum state engineering and quantum metrology.

Keywords: Biphoton shaping
biphoton spectral engineering
Dispersion measurement
Entanglement tuning
Nonlinear interferometer
Advisor: Qian, Li
A Data-driven Study of Connected Residential Thermostats to Investigate user Behavior, Thermal Modelling, and Optimal Control of HVAC Systems

Approximately a tenth of North America’s total energy usage is for space conditioning of residential buildings -- the majority of which is controlled by a thermostat. Despite these energy implications, thermostats have been difficult to study and their controls have remained reactive and heuristic-driven. Fortunately, with the latest generation of devices, connected thermostats, it is now possible to address these limitations. This thesis is among the first major bodies of research to exploit the emerging data from connected thermostats. Specifically, we seek to accomplish three main objectives: (1) extend the understanding of how users utilize these devices to manage their preferences, (2) develop predictive models of occupant behavior and thermal response of houses, and (3) optimize the control of residential HVAC systems using only existing available data.For objective (1), we determined that factors such as location and seasonality affected setpoint preferences, but that it was unclear if truly distinct user types emerged -- instead users appeared more on a spectrum of preferences. With schedule overrides, the behavior of users was found to be more complex than previously understood, with ultimately only a small group of users remaining in permanent and energy-intensive overrides. For objective (2), we found standard, well-tuned machine learning models (namely, random forest and ridge regression) were the most robust performers beating simple baseline and deep learning methods for predicting occupancy and thermal responses of the houses. Finally, for objective (3), we found that a data-driven model predictive controller outperforms a model-free reinforcement learning method and a standard deadband controller. In summary, this thesis makes multiple novel and significant contributions which improve the understanding of connected thermostat users, how to develop customized data-driven models, and how to improve the comfort and energy use associated with connected thermostats controlling the HVAC in our homes.

Keywords: HVAC control
residential buildings
Advisor: Sanner, Scott
O'Brien, Liam
Observation of a Transition Between Dynamical Phases in a Harmonically Trapped Degenerate Fermi Gas

A proposed paradigm for out-of-equilibrium quantum systems is that an analog of quantum phase transitions exists between parameter regimes of qualitatively distinct time-dependent behaviour. Here, we present evidence of such a transition between dynamical phases in a cold-atom quantum simulator of the collective Heisenberg model. The crux of this work is the conceptual mapping of a 3D harmonic optical trap onto a mode-space lattice in which the collective Heisenberg model lives. We show that this mapping is valid for our system in the regime of weak pair-wise interactions and explore the limits of this regime. This mapping enables study of spin models on lattices using simple optical traps -- without the use of optical lattice beams. The spatial extent of the harmonic oscillator wavefunctions gives rise to long-range collective interactions. We find that below a critical interaction strength, magnetization of an initially polarized fermionic gas decays quickly, while above the transition point, the magnetization becomes long-lived because of an energy gap that protects against dephasing by the inhomogeneous axial field. Our quantum simulation reveals a non-equilibrium transition predicted to exist but not yet directly observed in quenched s-wave superconductors. To facilitate our quantum simulation, we measured the zero-crossing near 209 G of the Feshbach resonance between the lowest two spin states in 40K to greater precision than ever before. We also compare our experimental measurements to several levels of theory and find excellent agreement. Further, in our system, we find that the dynamics of the collective Heisenberg model can be reversed by applying a many-body reversal.

Keywords: Atomic Physics
Degenerate Fermi Gases
Quantum Simulation
Ultracold Atoms
Advisor: Thywissen, Joseph H
Estimating and Evaluating Predictive Uncertainty in Deep Object Detectors

Object detection is a robot perception task that requires classifying objects in the scene into one of many predefined categories, as well as localizing these objects through estimating their tightest fitting bounding boxes. Modern deep object detectors produce point estimates of object categories and bounding boxes in the scene, making it difficult for subsequent components of a robot system from quantifying the trustworthiness of the objects detected in the scene. A solution to this problem is to construct probabilistic object detectors, models that can predict probability distributions rather than point estimates of object categories and bounding boxes in the scene. In this dissertation, we present several contributions to deterministic and probabilistic object detectors. We first present AVOD, one of the first deterministic object detectors to efficiently solve the 3D object detection problem. We then present BayesOD, a probabilistic object detector that provides a Bayesian treatment for every step of the neural network inference procedure. We show the effectiveness of AVOD and BayesOD on multiple standard object detection datasets in 2D and 3D. We then highlight statistical issues with training and evaluation trends followed by modern probabilistic object detectors and propose novel training and evaluation metrics to avoid the pitfalls of these trends. We demonstrate the effectiveness of our solutions on in-distribution, domain-shifted, and out-of-distribution 2D object detection datasets.

Advisor: Waslander, Steven