VictorJuiz/thesis huggingface dataset:
A Hopeful Research of a Necessary Revolution: Influences of Turkish Political Theatre
Keywords: 1960-1980
autoethnography
capitalism
political theatre
socialism
Turkish theatre

As a Turkish artist who grew up influenced by the works of left-wing figures, the author sets out to research how Turkish political theatre from 1960 to 1980 impacted the period as well as future generations. Through autoethnographic methods, this paper aims to examine the chain of artistic and political influence between Nâzım Hikmet, Genco Erkal, and the author. By referring to existing scholarship and privileging materialist analysis, the depoliticization of post-1980 is observed as the result of capitalist development, oppressive propaganda, and active dismantling of socialist movements and organizations. The paper ends with two original artistic creations by the author, presented as the inspired results of the research, to move forward the chain of influence. The writing of the paper itself is offered as a political performance that calls for collective action. Yazar, solcu figürlerin eserlerinden etkilenerek büyüyen bir Türk sanatçı olarak 1960'tan 1980'e kadar Türk politik tiyatrosunun dönemi ve gelecek nesilleri nasıl etkilediğini araştırmaya koyulur. Bu makale, Nâzım Hikmet, Genco Erkal ve yazar arasındaki sanatsal ve politik etki zincirini otoetnografik yöntemlerle incelemeyi amaçlamaktadır. 1980 sonrasının depolitizasyonu mevcut bilime atıfta bulunularak ve materyalist analize öncelik verilerek, kapitalist gelişmenin, baskıcı propagandanın ve sosyalist hareketlerin ve örgütlerin kasıtlı olarak dağıtılmasının bir sonucu olarak gözlemlenir. Makale, etki zincirini ilerletmek için araştırmanın ilham verici sonuçları olarak sunulan yazarın iki orijinal sanatsal yaratımıyla sona ermektedir. Makalenin yazılışı da, kolektif eylem çağrısı yapan politik bir performans olarak sunuluyor.
Evaluating Stream Fish Community Responses to Environmental Change through Biological Indices
Keywords: fish
freshwater
health
index
temperature

Freshwater fish species require, and compete for, suitable habitats to maximize various physiological and behavioral processes. Yet, the habitats on which they rely are being modified by localized human activities and global climate change, resulting in increased temperatures and decreased health. Monitoring fish communities in areas affected by these modifications (i.e., urban areas) allows for responses to be tracked and trends identified. Biological indices are often used in these areas as they can succinctly communicate community responses to resource managers and the public, but are also criticized based on the metrics and scoring used and their lack of consideration for sampling variability. Here, long-term stream fish community monitoring data, different indices, and their responses in both urbanized and less impacted areas are evaluated, contributing to the confidence with which monitoring programs can interpret sampling results and identify areas for improvement when using or developing new indices.
Open-source Implementation and Clinical Acceptability Assessment of Organ-at-risk auto-segmentation in Head Neck Cancers
Keywords: auto segmentation
deep learning
head and neck cancer
oar
organs at risk
unet

Auto-segmentation of organs at risk (OAR) in cancer patients holds the potential to improve efficacy and reduce inter-observer variability in radiotherapy planning. While studies have shown that deep learning auto-segmentation models can reach high accuracy, they often fail to reach the level of transparency and reproducibility required to assess the models’ generalizability and clinical acceptability, hindering the adoption of auto-segmentation systems in clinical environments. In this study, we leverage the recent advances in deep learning and open science platforms to reimplement and compare the performance of eleven published OAR auto-segmentation models on the largest compendium of head and neck cancer imaging datasets to date. We further provide examples as to how clinical acceptability assessment could accelerate the adoption of auto-segmentation systems in the clinic by establishing ‘baseline’ clinical acceptability threshold(s) for nineteen organs-at-risk in the head and neck region. Our data, open-source models and computational framework are providing a strong foundation for benchmarking segmentation tools, a key challenge for accelerated clinical adoption of these methods.
Further Investigating the Transformation of Benzene Derivatives in Acidic Conditions by the Fungus Hormoconis Resinae
Keywords: Benzene derivatives
Bioremediation
Groundwater
Hormoconis resinae

Different strains of H. resinae have been found to use several pathways to transform a number of benzene derivatives. Further study of the transformation of toluene, benzaldehyde, and benzyl alcohol by H. resinae ATCC 34066 was carried out in acidic solutions, with different fungus culturing media, both with and without glucose. It was found that H. resinae ATCC 34066 is not able to transform toluene at all, though it is tolerant to concentrations up to 50 ppm. The fungus was able to reduce benzaldehyde to benzyl alcohol up to concentrations of 500 ppm, both in the presence of glucose and without it. Glucose was found to be a preferred culturing media to PDA with smaller observed transformation lag times. Benzaldehyde to benzyl alcohol conversion ratios by the fungus were found to be higher in the presence of glucose. Further study is needed to better understand the benzene derivative transformation pathways.
Constructing Points Systems in Accumulative and Independent Sports via Bayesian Regression
Keywords: Bayesian Regression
Ranking System
Simulations
Sports Analytics

The goal of ranking systems is to objectively evaluate multiple performances over a certain period of time. Concerns with current points ranking systems stem from reward imbalance across tiers and selective participation. This has implications on athlete funding through national team selections and Olympic qualifications. We propose a Bayesian framework for designing and evaluating an accumulative points system that can be applied to any multi-competitor sport. In a case study for slopestyle snowboarding, we used data from world, continental, and national events between 2016 and 2019. We demonstrate through Monte Carlo simulation experiments that our Bayesian points system is both more accurate at calculating athlete ranks and more consistent when athletes attempt to game the system.
Environmentally Induced Changes to Neuron Connectivity and Morphology in the Brain of the C. elegans dauer
Keywords: Behavior
C. elegans
Connectomics
Development
Electron Microscopy

An organism’s survival relies on the ability of the nervous system to convert a vast array of sensory information into appropriate motor responses. Processing conducted by the nervous system is complex, even in simple animals. In the nematode C. elegans, sensory neurons connect to an intricate, layered network of interneurons and motor neurons. Many neuron-to-neuron connections are stable from birth to adulthood, but recent developments show that even some of the most stable connections in the nervous system can change in response to environmental stress. In this thesis, I describe the significant changes to network connectivity and neurite morphology in a C. elegans model of environmental stress, the dauer stage. I show that one of the most prominent dauer-specific changes, the loss of the RIC-to-AVA connection, correlates with behavioural responses. The dauer is not simply a paused developmental state, but has active remodeling of neuron connectivity.
Identifying Susceptibility Factors of Psoriatic Disease using Single-cell RNA Sequencing
Keywords: Biomarkers
Psoriasis
Psoriatic Arthritis
scRNA-seq
Single-cell RNA sequencing
TCR

Psoriatic arthritis (PsA) is an immune mediated musculoskeletal inflammatory disease that manifests itself in approximately a third of psoriasis patients – an immune mediated disease characterized by hyperproliferative keratinocytes and T-cell infiltration. An accurate and timely diagnosis is essential to prevent irreversible joint and bone damage, yet there are currently no validated biomarkers for PsA. To identify possible biomarkers, we employed single-cell RNA sequencing on peripheral blood mononuclear cells of PsA, psoriasis, and healthy controls. We focused on two proteins A20 and IkBα that were dysregulated in PsA cell subsets in addition to numerous interferon stimulated genes that were differentially expressed. Confirming interferon-mediated influence on immune activity serum IFNα levels were higher among PsA patients with four or more swollen joints than patients with less than two. Future studies should explore the predictive value of IFNα serum levels as a biomarker of PsA patients that will develop more severe disease.
A Scheduling-based Constraint Programming Approach to Solving a Complex Two-dimensional Two-stage Cutting Stock Problem
Keywords: Constraint Programming
Cutting Stock Problem
Guillotine Cuts
Heuristics
Mixed-Integer Linear Programming
Optimization

We investigate the novel Two-Dimensional Two-stage Cutting Stock Problem with Flexible Length, Flexible Demand, Order-to-Order Marriageability, and Scheduling Costs (2SCSP-FFMS): orders for rectangular items must be cut from treated rectangular stocks using guillotine cuts with the objective to minimize waste, inventory cost, and tardiness cost. Different from problems in the literature, the 2SCSP-FFMS allows the item length and total order demands to vary within customer-specified intervals. We first investigate a variation of the problem that ignores marriageability (pairwise conflicts between orders) and scheduling costs, proposing constraint programming models, mixed-integer programming models, and heuristics. Then, we study a second variation that adds the marriageability requirement before examining the full 2SCSP-FFMS problem. Accordingly, we extend the approaches that performed best in the first variation to the second one and the full 2SCSP-FFMS. For each of these problems, we perform empirical analysis on both generated and real-life industrial instances. Notably, our scheduling-based constraint programming model has orders-of-magnitude smaller memory requirements over other exact methods and can be competitive with a customized multi-phase heuristic.
Investigating the Establishment of the Developmental Transitions of Cortical Neural Precursors at the Transcriptional Level
Keywords: Cortex
Development
Neural stem cells
Neurogenesis

Adult neural stem cells (NSCs) arise from radial precursor cells (RPs) in the embryo that build the brain by generating different neural cell types in a temporally and regionally defined manner. An emerging model proposes that adult NSCs transition from RPs which can generate different neural cell types in response to signals in the environment. In Chapter 3 of this thesis, I have tested the hypothesis that developing cortical neural precursors are multipotent and show that they may have the potential to generate both excitatory and inhibitory neurons. In Chapter 4, I hypothesize that the time around birth is an important developmental period for neural precursors as they transition gradually from RPs to adult NSCs. I show that perinatal neural precursors take on a unique transition state, undergoing transcriptional changes within the first few days after birth.
Intercultural Bilingual Education (IBE) and the Image of Indigenous People and Quechua Speakers in the Peruvian Andes
Keywords: Churcampa
Education
Intercultural Bilingual Education
Language
Peruvian Andes
Quechua

In Peru, there are currently more than 27,000 government-funded IBE schools located mostly in rural areas. These schools were created to redress the historical marginalization of indigenous languages like Quechua and to narrow the achievement gap between indigenous and non-­indigenous students linked with the privileging of Spanish linguistic and cultural practices. While Quechua is recognized in the Peruvian constitution as an official language and is spoken by roughly 4 million Peruvians, parents continue to equate education with Spanish language education. They do not encourage their children to learn Quechua due to its low status. This linguistic bias is related to many factors including the social stigma attached to Quechua as the language of illiterate indigenous. This study examines how discourse in various IBE policies imagines Indigenous people and Quechua speakers to be. I also include my voice through my own personal experience as the daughter of Quechua speakers.
An Optimal Control Approach to Model-based Stimulation of Phase-reduced Networks of Spiking Neurons
Keywords: deep brain stimulation
neuronal dynamics
optimal control

As the dynamics of artificial neural networks are increasingly more influenced by their biological roots, important insight lies at the intersection of neuroscience and control theory. The high-dimensionality of these networks and the nonlinearity of microscopic neuronal dynamics often preclude direct applications of conventional control. Mean-field models offer alternative low-order descriptions of the collective macroscopic behaviour of neurons. These orders may be bridged through the study of neuronal synchronization, which is believed to underlie several brain disorders. We propose a model-based control framework to regulate neuronal spiking activity based on a synchronization observable. It is inspired by the neurosurgical procedure of deep brain stimulation, whereby an implanted open-loop neurostimulator injects high-frequency current pulses into the affected brain region. While the desynchronization of neuronal activity is a leading hypothesis behind its effectiveness, the mechanism remains poorly understood. We turn to optimal control to tailor the stimulation to the observed pathophysiology.
Lake Ice in a Rainfall Dominated Southern and Central Ontario
Keywords: lake ice
limnology
modelling
Ontario
precipitation
winter rain

Winter precipitation long-term (1900 - 2019), short-term (1990 - 2019) and projected (2015 - 2099) trends were studied over central and southern Ontario. Precipitation trends, especially rainfall, increased over the long-term and projections. The increase in winter rainfall motivated the development of a new version of the Canadian Lake Ice Model (CLIMo), CLIMo - Temperate Rain, which incorporates the heat fluxes and mass contributions of rainfall. CLIMo-TR improved simulations of lake ice thicknesses during thaw and rainfall events, however break-up tended to be overestimated. Rainfall primarily affected lake ice through its mass contribution to the lake ice surface, which led to a thicker snow layer and white ice formation. Few short-term lake ice trends were seen, while projected trends expect significantly shorter ice cover durations and decreases in maximum, mean and SD of thickness. As winter seasons become warmer and winter rainfall increases, understanding rainfall effects on lake ice will be of importance.
The ‘Paper and Pencil’ Operations of Interdisciplinarity: Interdisciplinary Integration as Information Practice
Keywords: Information Practice
Interdisciplinarity
Meta-Research
Research Practice

Interdisciplinary research produces innovative solutions to complex problems by integrating information from multiple disciplines. At present, despite the positioning of integration as the defining activity of interdisciplinarity, interdisciplinary work tends to be evaluated on the basis of final outcomes, at the expense of a clear understanding of what interdisciplinary integration actually is. This thesis problematizes this outcome focus and makes the case for a practice-focused approach, using conceptual modeling and network analysis of the data holdings of in-progress interdisciplinary research projects to explore how researchers integrate data from multiple disciplines. These case studies demonstrate that even in ostensibly interdisciplinary research, data tend to be analyzed in disciplinary silos, leaving any integration that occurs to take place in an ad-hoc, after-the-fact fashion. The adverse implications of this finding on interdisciplinarity are discussed, and a framework for the repositioning of integration as a research practice is proposed as a potential solution.
Anti-degradative Self-etch Adhesive to Preserve Bonded Interfaces
Keywords: Hybrid layer preservation
interfacial fracture toughness
resin
self-etch adhesive

Objective: Investigate the effect of adding drug-silica co-assembled particles containing Octenidine Dihydrochloride (DSPs) into a commercial self-etch adhesive (SE) on the degradation of resin-dentin interface aged in simulated human salivary esterase (SHSE). Methods: Miniature short rod specimens (mini-SR) were fabricated from human dentin bonded to composite using unmodified commercial SE (negative control), SE+10%w/w calcined particles without drug (CDSP-SE) (positive control) or SE+10% w/w DSPs (DSP-SE) (experimental). Specimens were tested for interfacial fracture toughness (FT) and fracture mode after incubation for 0, 30, or 180-days in SHSE. Media were analyzed for presence of resin degradation by-product 2,2-Bis[4(2,3-hydroxypropoxy)phenyl]propane (BisHPPP). Results: FT among all specimens and periods were similar (p>0.05). Fracture plane for all groups moved from dentin to resin layer over time, with the control groups significantly more into resin and with more BisHPPP in their media (p<0.05). Conclusion: The incorporation of DSPs and CDSPs into SE appears to preserve the resin layer of SE interfaces.
The Effects of Seasonality on Ecological Interactions Between Fishes in Different Thermal Guilds
Keywords: acoustic telemetry
coexistence
fish
seasonality
stable isotope
trophic niche

Seasonality may play a crucial, yet understudied, role in structuring species interactions. I used acoustic telemetry, stomach contents, and stable isotopes to determine the seasonal niche overlap of a native cold-water species (lake trout) and a range-expanding warm-water species (smallmouth bass) in two northern temperate lakes. I found that niche overlap between lake trout and smallmouth bass was the highest in the spring, when both species were active and using littoral resources. In contrast, lake trout and smallmouth bass spatially partitioned their niches in the summer. Activity diverged during the winter, with lake trout remaining active with a littoral diet, while smallmouth bass activity was minimal. This thesis demonstrates that both temporal (seasonal activity) and spatial (habitat and diet) niche components structure species interactions and suggests that the impacts of smallmouth bass on lake trout may be greatest in the spring, a season that may lengthen due to climate change.
A Real-time Robotic System for the Continuous Automation of Single Cell Surgery and Embryo Biopsy
Keywords: 3D Reconstruction
Automatic biopsy
Image-feedback control
Real-time
Robotic manipulation
Single-cell surgery

The success rates of manually performed embryo biopsies in Preimplantation Genetic Diagnosis (PGD) are low due to human errors, excessive embryo damage and prolonged surgery times. To increase the procedure the success rate, a robotic system for the biopsy of early-stage 2-cell embryos is proposed. The system consists of robotic manipulators, a camera, sensors, a laser, and set of end-effector tools to perform different procedures on the embryo. The system is comprised of six continuous phases, implemented successively, with neither manual intervention nor software interruption. All six phases are under image-based feedback control and use linear and nonlinear controllers to move micromanipulators with high precision, reject external disturbances, and follow reference trajectories accurately. Significantly, this leads to very rapid processing of embryos. Experimental results on 2-cell and 4-cell cleavage stage embryos validate the effectiveness of the methods proposed.
Longevity of Metal-Acrylic Implant-Supported Fixed Complete Dental Prostheses: A Retrospective Study
Keywords: implant-supported fixed complete dental prostheses complications
implant-supported fixed complete dental prostheses success
implant-supported fixed complete dental prostheses survival
multivariate analysis
refurbishing
retread

Objective: To assess the longevity and survival of metal acrylic implant-supported complete fixed dental prostheses (MA-ICFDPs). Material and methods: This retrospective cohort study included patients treated with MA-ICFDPs at the University of Toronto. Data analyses were carried out to determine rate of complications, and survival analyses were carried out for refurbishing and failure of prosthesis. Results: A total of 156 MA-ICFDPs were included, with a mean follow-up of 9.3 ± 4.8 years. A total of 38 (24%) prostheses were refurbished after an average of 7.8 ± 4.9 years. A total of 18 (11%) prostheses failed, the most common reason being the failure of supporting implants. There was increased hazard ratio (HR) between bruxism for both refurbishing (HR= 3.1, 95% CI= 1.8-5.1, P<.001) and failure of prostheses (HR=2.1, 95% CI= 1.0-4.3, P=0.46). Conclusions: MA-ICFDPs have a good long-term prognosis. Refurbishing is a common repair procedure carried out to address extensive wear.
Novel Problems and Challenges in Language-based Conversational Recommender Systems
Keywords: Bias and Discrimination
Clarification-based Critiquing
Contextual Language Models
Conversational Recommendation Systems
Distributional Latent Embedding
Language-based Conversational Recommendation Systems

Language-based Conversational Recommender Systems (CRSs) have attracted growing attention as they allow users to express and interactively refine their preferences in natural language. However, there exist open problems in CRSs relating to the challenges users face when articulating accurate natural language preferences and the underlying technologies required to facilitate language-based interactions. Our first contribution addresses the challenge that users have trouble specifying preferences with the right level of specificity. We propose a clarification-based extension of a critiquing-based interaction workflow for CRSs that outperforms state-of-the-art models. In our second contribution, we explore the novel issue of unintended bias in language model-driven conversational recommendation by proposing novel bias evaluation metrics and performing source of bias analysis. In summary, this thesis investigates novel and important challenges in the deployment of language that can help users express their preferences more accurately and allow the identification and resolution of bias that arises in language-model-driven CRSs.
suPAR to Risk-stratify Children with Malaria
Keywords: malaria
mortality outcome
prognostic marker
risk-stratification
soluble urokinase-type plasminogen activator receptor (suPAR)
triage

Severe malaria is a leading global cause of childhood morbidity and mortality, particularly in sub-Saharan Africa. However, current malaria diagnostic tests do not reliably identify children at risk of severe disease and death. Host immune and endothelial activation contribute to severe malaria pathogenesis. Soluble urokinase-type plasminogen activator receptor (suPAR) is a marker of these pathways. Here, in a large cohort of Ugandan children with Plasmodium falciparum infection, we showed that suPAR levels at first clinical presentation are associated with disease severity and mortality. Furthermore, suPAR improved the predictive accuracy of a validated malaria clinical scoring system. We provide the first clinical evidence in a large prospective cohort that suPAR is a reliable marker to risk-stratify children with severe and fatal malaria. Together, our data provide proof-of-concept for prospective trials evaluating whether suPAR point-of-care measures can enhance triage, management and outcome of children with malaria in low-resource community settings.