VictorJuiz/thesis huggingface dataset:
Process-yield-structure-bioconversion of Organosolv Lignin from Wheat straw

The goal of this study is to present a cohesive process that embraces separation and reaction steps for producing small molecules from organosolv lignin with white-rot fungus. This study contains novel findings on 1) the ability of B. adusta to produce intracellular laccase, 2) the comprehensive structural analysis of lignin molecules and 3) new results on lignin breakdown to small molecules after treatment by the fungus. For this purpose, the extraction of organosolv lignin in optimum operational conditions has been carried out in a reactor. After extraction without any catalysts, all the green solvents (ethanol/water) were recovered and reused. The highest yield of lignin (90%) was obtained under optimal conditions (120 min, 200 °C, and 400 psi). The extracted lignin also contained the lowest amount of carbohydrate impurities and ash. Furthermore, a detailed approach of the characterization of extracted lignin has been conducted by FTIR, NMR, TGA, DSC, SEC and MALDI-TOF techniques. The characterizations led to the identification of side chain moieties, vanillin, phenylcoumaran and others. The presence of different moieties such as Cγ–O group β-O-4 units, added value to the extracted lignin. Likewise, the ability of B. adusta to bio-transform extracted lignin into small molecules was evaluated. Lignin peroxidase, manganese peroxidase, laccase and versatile peroxidase had the main role in the biodegradation of lignin to small fractions such as syringylglycerol-B-guaiacyl ether, sinapyl alcohol diacetate and others. As a result, the extracted lignin after treatment with B. adusta showed significant changes in its physical and chemical structure, which makes it a novel candidate for yielding value-added products.

Advisor: Sain, Mohini
Understanding and Improving Wait Times for Hip Fracture Surgery

Although wait times for hip fracture surgery are linked to mortality and used as quality-of-care indicators worldwide, controversy exists about the duration of the wait that leads to complications. Using new surgical wait time data from a population based cohort in Ontario, Canada, objectives of the thesis were to: 1) establish a safe time window in which to conduct hip fracture surgery before risk of complications rise; 2) determine whether delayed surgery is associated with higher medical costs; and 3) assess wait times across Ontario to determine where performance improvement efforts need to be targeted. Validated data from linked health administrative databases were used to identify 42,230 adults aged 45 years and older receiving hip fracture surgery from 522 different surgeons at 72 different hospitals in Ontario between April 1, 2009 and March 31, 2014. The risk of developing mortality and other medical complications consistently rose when surgery was delayed more than 24 hours, after risk adjustment, and independent of the outcome or follow-up period assessed. Medical costs and postoperative length of stay were also increased when surgery was delayed. Two-thirds (66%) of patients did not receive surgery within 24 hours, with more than half of hospitals (52%), compared to 4.8% of surgeons and 0.2% of anesthesiologists, showing significant differences in the risk-adjusted likelihood of delayed surgery. Variables strongly associated with delay included hospital transfer and preoperative echocardiography. Findings pertain to increasing numbers of patients experiencing hip fractures and the different medical and surgical specialists treating them and may inform existing hip fracture care guidelines and policies. Methods from this thesis may be used to report and evaluate inpatient wait times for other surgical procedures in Canada.

Keywords: Hip fractures
Observational studies
Orthopaedic Surgery
Population based
Wait times
Advisor: Wodchis, Walter P
Integrating Neuroimaging and Genetics Data in a Bioinformatics-based Approach for the Study of Alzheimer’s Disease

Recent advances in the imaging-genetics field within Alzheimer’s disease (AD) have resulted in large amounts of data; however the challenge is filtering through the data and identifying meaningful genotype-phenotype relationships within AD. The overall goal of this thesis is to integrate existing tools to prioritize influential genetic variants and associated neuroanatomical measures in order to tease apart the etiology of AD and be able to use these markers in a predictive analysis of AD progression. The thesis is divided into four independent projects. The first project aims to reduce the burden of multiple testing correction by using a false discovery rate approach within strata defined by a novel biologically driven gene prioritization methodology. The overall aim of projects two and three is to estimate the heritability of neuroanatomical measures by preselection of regions with high heritability, allowing for reduction of the multiple testing burden. In project two, I investigated the influence of whole hippocampal volume and total brain volume on the heritability estimates of hippocampal subfields. In project three, I investigated heritability estimates of cortical thickness and surface area using both a vertex-wise and region of interest approach determining unreliability of smaller regions. The fourth project was a pilot study to investigate if combining genome wide association study data with neuroanatomical measures would improve the performance of common machine learning models in predicting cognitive decline in AD. These methods will aid in the identification of measurable robust and reliable quantitative markers, and have the potential to help predict AD onset and reveal more about the etiology of AD. In the future, such findings may allow targeted drug treatments to be delivered before the onset of clinical symptoms.

Keywords: Alzheimer's disease
Bioinformatics
Genome Wide Association Studies
Heritability
Neuroimaging
Advisor: Knight, Joanne
Voltage-drop and Electromigration in Chip Power Grids

A major challenge in modern chip design is the design and analysis of the chip's power grid -- the network that relays power from the external supply pins of an integrated circuit (IC) to the chip's transistors. The power grid must deliver a source of power that is fairly free from large fluctuations over the chip's target lifetime. Large voltage variations on the grid can easily put circuit performance and reliability at risk. The large switching currents drawn by the logic circuitry may result in unacceptable voltage levels on the grid in the short-term. In addition, Electromigration, a physical phenomenon that leads to the aging and deformation of the grid metal lines over an extended period of time, may result in unacceptable voltage levels in the long-term, which places a limit on the useful lifetime of the chip. In light of these two problems, this thesis develops a suite of computer-aided design (CAD) techniques to help analyze, verify, and design the power grid. This thesis is in three parts. The focus of the first part is to develop a systematic approach that generates power budgets which, if adhered to by the underlying logic circuitry, would guarantee safe voltage levels on the grid. The second part of the thesis develops a power scheduling framework for power-gated power grids, a modern type of grid designs that includes active devices that allow major circuit blocks to be turned OFF, for power and thermal management. During chip operation, a power scheduler monitors the on-chip hardware resources and manages chip workload (switching activity) to ensure the voltage levels on the grid remain within specifications. Finally, the third part of the thesis develops a power grid fixing scheme that introduces minimal modifications to the grid design to meet a target electromigration lifetime.

Keywords: Chip Power Grids
Computer-Aided Design
Electronic Design Automation
Power Distribution Network
VLSI
Voltage Integrity Verification
Advisor: Najm, Farid N
Integrated Framework of Departure Time Choice, Mode Choice, and Route Assignment for Optimal Design of Time-dependent Transit Pricing Strategies

Modern travel demand management (TDM) strategies, such as time and distance-based congestion pricing, require evidence-based quantitative assessment to measure the potential effects on the transportation network performance and people’s responses to the dynamic consequences of such applications. This thesis focuses on building an integrated framework of departure time choice, mode choice, and dynamic multi-modal route assignment for optimal design of TDM strategies applied to large-scale transportation networks, with the focus on time-based transit pricing. The proposed platform integrates a simulation-based dynamic multi-modal multi-user-class route assignment model with an econometric model that jointly estimates departure time and mode choices and a genetic algorithm engine. The proposed platform has been used in optimizing time-dependent fares as a potential strategy to manage peak-hour transit crowding. Considering the traffic and transit networks as one system, the objective is to minimize travel times during peak periods by influencing travellers to alter their choice of transport mode, departure time, and/or route. The anticipated effect is to pace and spread out demand across space and time to yield the optimal spatio-temporal distribution of demand that minimizes end-to-end travel time. The control variables are the time-dependent transit fares. As a large and realistic use case, a model of the Greater Toronto Area has been developed to demonstrate and validate the results of this research. The main contributions of this research include: (1) developing a simulation-based large-scale dynamic route assignment model that captures the interactions between the traffic and transit sides; (2) integrating the route assignment model with a joint econometric model of departure time and mode choice to build a comprehensive model (the METRO platform) that can be used to assess dynamic TDM strategies; (3) integrating the METRO model with a cloud-based genetic algorithm engine to enable optimizing the design of TDM policies with emphasis on transit fares; and lastly (4) optimizing time-dependent transit fares in Toronto to minimize average weighted door-to-door travel time of all individuals in the system using all driving and transit modes, and quantitatively assessing the impacts of the resulting time-dependent fares as a policy and its strengths and weaknesses in addressing transit crowding.

Keywords: Departure time choice
Dynamic route assignment
Large-scale network
Mode choice
Optimization
Time-based transit fares
Advisor: Abdulhai, Baher
Age-related Differences in Oscillatory Activity in Hippocampal and Neocortical Networks

The brain adapts to structural and functional changes that naturally occur over the latter half of the human lifespan, enabling people to maintain cognitive function. However, the nature of these changes has not yet been fully characterized. The present dissertation examines the extent to which aging is associated with changes in the recruitment of oscillatory activity within hippocampal and neocortical regions to support relational memory performance on a short delay visuospatial memory task. Structural magnetic resonance imaging and magnetoencephalography were used to characterize potential age-related changes in hippocampal volume, oscillatory activity, and subsequent memory performance, and the relationships among them. Sixteen younger and 16 older adults were sequentially presented with three objects during a study phase. Following a short delay, the objects were re-presented simultaneously, and participants had to determine whether the spatial relations among the objects had been maintained. Older and younger adults showed similar task accuracy, and older adults had preserved hippocampal volumes, but had longer response latencies relative to younger adults. Age-group differences in oscillatory activity were observed during the pre-stimulus, study, and test phase. Younger adults had higher theta (~5Hz) and lower beta (~20Hz) than older adults during pre-stimulus. Younger adults also uniquely showed theta power increases in medial temporal and frontal medial regions during the study and test phase that predicted higher task accuracy, whereas older adults showed widespread alpha (~10Hz) and beta power decreases during the study and test phase, which predicted longer response latencies during the test phase. Taken together with the literature reviewed in this dissertation, these findings begin to provide a better understanding of how different oscillatory mechanisms may support the maintenance of cognitive abilities across the lifespan. Specifically, the hippocampal theta power increases in younger adults may reflect relational memory processes, whereas the neocortical alpha and beta power decreases in older adults may reflect a sensory reactivation and attention-based process operating on holistic low-resolution representations.

Keywords: Aging
Hippocampus
Magnetoencephalography
Relational Memory
Advisor: Ryan, Jennifer D
In the Service of Kaiser and King: State Sovereignty, Nation-building, and the German Army, 1866-1918

From its creation during the Wars of Unification (1864-71) until its defeat at the end of the First World War, the German army remained a federal institution. To be sure, the imperial constitution recognized the Kaiser as commander-in-chief of Germany’s land forces. Under the Kaiser’s direction, the Prussian war ministry prepared the military budget and the Prussian General Staff drafted operational plans for future wars. A patchwork of military agreements nevertheless limited the authority of the Kaiser and Prussia’s military leaders over nearly one-quarter of the German army. According to these agreements, separate war ministries, cadet schools, and general staffs oversaw the arming, clothing, feeding, housing, and training of Bavarians, Saxons, and Württembergers, while the monarchs of Germany’s three smaller kingdoms determined personnel appointments, the deployment of units, and even the design of insignia and uniforms. The army’s contingent-based structure ensured that Prussians and non-Prussians served alongside, but only rarely with, one another after 1871. Based on research in archives and libraries in Germany, Austria, England, and the United States, this dissertation explores the means by which the smaller armies of Bavaria, Saxony, and Württemberg were integrated into Prussia’s much larger military structure after 1871 and seeks to understand why the German army, burdened by numerous loyalties and overlapping spheres of control, did not simply fall apart during the First World War. It argues that even though the decentralization of military authority and the presence of dual loyalties among Bavarian, Saxon, and Württemberg soldiers remained serious concerns for Prussian authorities, the German army proved remarkably durable because the empire’s monarchs and their advisors preferred compromise, rather than conflict, with one another. This dissertation contributes to ongoing historiographical debates concerning the process of nation-building and the consolidation of state power across Europe since the French Revolution; the evolution of the relationship between monarchs and their militaries in a period characterized by public opinion shaped by parliamentary debates and a mass press; and the ability of multiethnic and multinational empires to mobilize their diverse societies for war at the turn of the twentieth century and on the eve of two global conflicts.

Keywords: Federalism
German army
German empire
Germany
Monarchy
Nation-building
Advisor: Retallack, James
Characterizing Mechanisms of Double-stranded DNA Break Repair during AID-mediated Genome Rearrangements

Maintenance of genome integrity is fundamental to gene expression, cell growth, and cell differentiation. Paradoxically, B cells induce programmed double-strand DNA breaks (DSBs) at the immunoglobulin heavy chain (Igh) locus by upregulating the DNA mutagen activation-induced cytidine deaminase (AID) during the germinal center reaction. Mutagenic repair of AID-mediated DSBs increases diversity in effector function within the antibody repertoire, a process known as class switch recombination (CSR). However, repair of AID-mediated DSBs can occasionally result in unwanted genome rearrangements such as chromosomal translocations. Therefore, B cells must harbor mechanisms for recognizing and repairing AID-mediated DSBs that largely preserve genome integrity, promote humoral immunity, and prevent chromosomal aberrations. However, our understanding of these mechanisms remains incomplete. In my thesis research, I explored the mechanisms by which B cells recognize and repair AID-mediated DSBs. Using CRISPR/Cas9 technology, I generated DSB structures in vivo modeling AID-mediated DSBs to induce CSR and chromosomal translocations in mouse and human B cells. By analyzing intra- and interchromosomal recombination junctions, I found that DSB polarity is sufficient to bias repair towards either non-homologous end-joining or alternative end-joining. My findings establish a critical role for DSB structure and polarity in modulating DSB end-joining in mouse and human B cells. I also found that E3 ubiquitin ligases RNF20 and RNF40, which monoubiquitinate histone H2B upon DNA damage, are required for DSB repair during CSR and homologous recombination. I demonstrate that H2B ubiquitination occurs independently of the canonical DDR factors H2AX, ATM, and DNA-PKcs, suggesting that ubiquitination of H2B could represent a newly identified axis of DSB repair. My thesis research reveals novel mechanisms of DSB repair and maintenance of genome integrity in B cells, which could in turn inform therapeutic interventions for cancer and humoral immunity.

Keywords: B cells
Chromosomal translocations
Class switch recombination
CRISPR/Cas9
DNA repair
Genome integrity
Advisor: Martin, Alberto
Distributed Coordination Theory for Ground and Aerial Robot Teams

This thesis investigates distributed coordination problems for two important classes of robots. One class corresponds to ground-based mobile robots, each modelled as a kinematic unicycle. The second corresponds to flying robots, each propelled by a thrust vector and endowed with an actuation mechanism producing torques about three orthogonal body axes. The following coordination problems are studied in this thesis: rendezvous, formation control, linear and circular formation flocking and formation path following. For rendezvous of kinematic unicycles, a smooth, time-independent control law is presented that drives the unicycles to a common position from arbitrary initial conditions, under the assumption that the sensing digraph is time-invariant and contains a globally reachable node. The proposed feedback is very simple and is local and distributed. For rendezvous of flying robots, a control strategy is presented that makes the centres of mass of the vehicles converge to an arbitrarily small neighborhood of one another. The convergence is global, and each vehicle can compute its own control input using local and distributed feedback. For formation control, the objective is to make an ensemble of kinematic unicycles achieve pre-defined inter-agent spacings with parallel heading angles. We consider scenarios where the formation either stops or moves with a final collective motion. In the latter case, problems of linear and circular formation flocking and formation path following are studied. A control law is presented in each case that solves the problem for almost all initial conditions. For stopping and flocking formations, the proposed control laws are local and distributed while for formation path following, the control laws additionally require each agent to measure its displacement from the path. The idea used to solve the formation control problems is to rigidly attach an offset vector to the body frame of each unicycle. It is shown that stabilizing the desired formation amounts to achieving consensus of the endpoints of the offset vectors, and simultaneously synchronizing the unicycles' heading angles. Extension of formation control to flying robots using strictly local and distributed feedback is not addressed in this work and remains a challenging open problem.

Keywords: Autonomous robotics
Cooperative control
Distributed control
Stability of nonlinear systems
Advisor: Maggiore, Manfredi
Scardovi, Luca
Liberating the Family: Education, Aspiration and Resistance Among South African University Students

In October 2015, South Africa witnessed the largest student protests since the end of apartheid over rising tuition costs. Based on qualitative research conducted between 2015-2016, this dissertation analyses these protests through the experiences of working-class students from Khayelitsha, an urban township in Cape Town, South Africa. Education-based resistance since the end of apartheid occurs in a context of rapid and shifting patterns of class formation, in which higher education is both critical to ensuring social mobility and avoiding chronic unemployment. At the same time, higher education access is constrained by the endurance of racial and spatial inequalities, and limited forms of state support for working class students. My research reveals how working-class students develop aspirations toward higher education and how these are intimately connected to circumstances of household poverty. For these students, support for the protests did not merely involve opposition to commodification, but was connected to shared experiences of racialized poverty, aspirations toward collective social mobility, and the debilitating role of student debt. By focusing on how higher education reconfigured young people’s bonds with family and generated anticipated financial obligations, I highlight how the protests spoke to a crisis of social reproduction affecting working-class households. In doing so, I highlight young people’s role as economic actors in household distributive economies. This dissertation also reveals how higher education is frequently a contradictory resource for working class youth. It provides pathways toward social mobility for a limited number, while simultaneously binding them into systems that reproduce wider forms of social inequality. Rather than simply struggles against neoliberalism then, the protests reveal the multiple and contradictory functions of higher education in South Africa, as it is aimed at addressing racialized inequalities while meeting the human capital requirements of a globalized economy. Finally, I highlight the importance of relational approaches to youth studies, that understand young people’s agency as embedded within wider social, political and economic structures.

Keywords: Aspirations
Debt
Higher Education
South Africa
Student Activism
Youth
Advisor: Hunter, Mark