VictorJuiz/thesis huggingface dataset:
Native Trees, Urban Forest Management Planning, and Residents: Knowledge, Attitudes, and Actions

In the past decade, municipalities across North America have increased investment in their urban forests in an effort to maintain and enhance the numerous benefits provided by them. Some municipalities have drafted long-term urban forest management plans (UFMPs) that emphasize the planting of native trees to improve ecological integrity, and participation of residents, since the majority of urban trees are typically located on residential property. Yet it is unclear if municipal foresters are mindful of UFMP goals or what residentsâ level of knowledge, attitudes, and actions are regarding native trees and urban forestry goals. Through a case study of southern Ontario municipalities, I administered interviews with municipal foresters and a survey exploring residentsâ ability to identify the native status of common tree species, as well as their attitudes and actions regarding urban forest issues. The results indicate that all municipalities with management plans emphasize native species, and many justify their planting as a way to increase ecological integrity. However, only a fraction of species native to the region are available through nursery stock, meaning many are not planted by municipalities. The results of the survey indicate that residents are better able to identify common native trees than non-native trees, although knowledge-levels are low, and there are failures of resident outreach within the case study municipalities. Although residents generally have positive attitudes towards native trees, few are interested in planting native species if they create a hazard or increase costs. These positive attitudes do not translate into emphasizing native species when actually selecting tree species to plant. This dissertation adds to existing research surrounding native species management in urban ecosystems, and understandings about how urban forestry policy influences residents and municipal actors. Future research is needed to determine species suitability for urban plantings and meaningful ways of engaging with new residents.

Keywords: Assisted Migration
Ecological Integrity
Ecosystem Services
Native Species
Residents
Urban Forest
Advisor: Conway, Tenley M.
Computational Acquisition of Robust Motor Skills

Humans have the ability to learn complex motor skills like ballet dancing, breakdancing, gymnastics and riding a bicycle. Ideally, these skills are robust to many conditions: they can be performed whether the day is windy or the ground is slippery. This thesis introduces computational tools for physics-based simulated characters to acquire robust motor skills. We show how to optimize control solutions to produce complex motor skills, such as breakdancing, handstands and hand walks. The cost function is specified in terms of intuitive motion properties (e.g., place the hands close to the ground, place the feet as high as possible, maximize angular momentum in some direction, etc.). Unlike previous work, our method does not require contacts to be pre-specified, which simplifies the synthesis process and allows tackling motions that were previously outside the scope of physics-based methods. Our approach is currently too slow for online applications that require control solutions for a range of tasks to be performed. We show that if we restrict the problem to specific movements, it is possible to design online controllers that achieve a range of tasks and that are robust to disturbances. We demonstrate this for a variety of rotational movements, including cartwheels, dives, flips and handsprings. The control solutions described so far are only valid for a small set of states of the character. We develop a method to systematically expand this set, thereby increasing the robustness of our control solutions and allowing for their sequencing. Once a skill is learned by a character with a particular body shape, we show how it can be transferred to a character with a different body shape. The method discovers surprisingly natural results, such as a heavier character avoiding losing balance by taking extra steps and stretching out its arms. For a given character, this opens up a large reservoir of skills that can be acquired.

Advisor: Fiume, Eugene
Fracture of Underfilled and Edge-Bonded BGA-PCB Assemblies: Effects of Joint Geometry, Strain Rate and Stiffness

The reliability of the solder joints connecting microelectronic components to printed circuit boards (PCBs) is a serious concern in the design of many electronic devices. The focus of the present research was the fracture performance of component-solder-PCB assemblies with and without underfill adhesives under bending loading conditions. Fracture tests of copperâ solderâ copper double-cantilever-beam (DCB) specimens with a single continuous solder layer showed that for joints shorter than a characteristic length the fracture load increased with increasing solder joint length. Also, the fracture tests of DCBs with two discrete solder joints showed the strength was maximum at an optimal joint spacing. An analytical solution was developed for the characteristic length of mode I DCB specimens with a single continuous solder layer as well as the optimal spacing of double-joint DCBs, taking into account the mechanical properties and dimensions of the substrates and solder. Fracture experiments with underfilled ball grid array (BGA)- PCB specimens in a DCB configuration showed that the specimens always failed in the PCB. The strength of the underfilled BGAs was solely a function of the fillet size, and independent of the underfill thermal and mechanical properties. Edge-bonding is a less expensive alternative to underfilling, in which only the edges or corners of the component are bonded to the PCB using a viscous adhesive. Edge-bonded and underfilled specimens with fillets of the same size and shape tested using DCB specimens failed at the same load, because the stress distribution in the PCB near the PCB-fillet interface was only a function of the adhesive fillet size and shape, and independent of the extent of the adhesive layer between the PCB and the BGA. Finally, a cohesive zone model (CZM) was developed to predict the PCB delamination bending loads in underfilled BGA-PCB assemblies. The cohesive parameters were obtained from fracture tests of bending test specimens consisting of PCB substrates bonded with the underfill adhesive. The model provided relatively accurate predictions of the failure mode and fracture load of the underfilled BGA-PCB assemblies for a range of PCB stiffnesses, adhesive fillet sizes, and strain rates.

Keywords: Ball grid array (BGA) package
Finite element analysis (FEA)
Printed circuit board (PCB)
Solder joints
Underfill adhesives
Advisor: Spelt, Jan K.
Biochemical Interrogation of Rare Cystic Fibrosis Mutations Informs Strategies for Future Therapeutic Intervention

There are over 2000 mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene associated with Cystic Fibrosis (CF) disease, and to date, the two recently FDA-approved drugs KalydecoTM and OrkambiTM have been effective in rescuing functional expression of the two most common CFTR mutations, G551D and ΔF508, respectively, representing approximately 90% of the patient population worldwide. However, potential efficacy of these therapies for the remaining ~2000 mutations is unknown. Thus, biochemical characterization of each rare variant is needed to assess potential clinical benefit. My thesis attempts to understand molecular defects associated with less common CFTR mutations, mainly c.3700A>G (causing abberant splicing and subsequent translation of ΔI1234_R1239-CFTR) and c.2052_2053insA (Q685TfsX4-CFTR), with the goal of determining whether current CF therapies (specifically designed for G551D and ΔF508) could be used for these rare variants. Additionally, my work aims to identify unique molecular aberrations for these rare, mutant CFTR proteins in order to facilitate development of mutation-specific therapeutics. Through a collaborative initiative involving clinicians, biochemists and biophysicists, we found that ΔI1234_R1239-CFTR shared certain biochemical attributes with ΔF508-CFTR, however contained intrinsic defects which differed significantly (i.e. poorer interdomain assembly between the amino- and carboxy-termini, and decreased functional responses to cAMP agonists, CFTR correctors and potentiators). When CFTR activity was evaluated in nasal epithelial cultures from siblings homozygous for c.3700A>G, we likewise found that ΔI1234_R1239-CFTR responded poorly to small molecules. For Q685TfsX4-CFTR, we found that this variant was prematurely truncated, and therefore did not respond to CFTR-specific therapies. However, a proof-of-concept in vitro strategy to ‘skip’ the exon containing the c.2052_2053insA mutation led to an incomplete, yet partially mature CFTR molecule which exhibited channel activity, albeit this function was unregulated. In parallel to these studies, we generated and functionally characterized several other rare CFTR mutations using novel mutagenesis and high-throughput functional screening methods, allowing for rapid identification and stratification of genotypes that could potentially benefit from current CF therapies. Furthermore, our efforts described here aim to facilitate future mutation-specific CF drug discovery, as well as a ‘personalized medicine’ approach to assist in the development of novel strategies to combat this fatal genetic disease.

Keywords: CFTR
Cystic Fibrosis
Drug Discovery
Personalized Medicine
Rare Mutations
Small Molecules
Advisor: Bear, Christine E
Studying Guidance Cues in Collective Cell Migration: Tools and Metrics

Directed cell migration is essential in morphogenesis, regeneration and pathological conditions. Of particular interest is collective cell migration, in which groups of cells migrate in a coherent and coordinated manner while remaining in contact with one another. In vivo, migratory cells are exposed to a complex signalling milieu that directs their migration; however, how cells prioritize and translate these cues into directed migration is not fully understood. In vitro systems simplify the systematic study of the effect of guidance cues in cell migration by providing increased flexibility to manipulate these cues. This work describes novel in vitro tools and analytical metrics for the analysis of collective cell migration and utilizes them to probe the effects of combinations of guidance cues on cell migration. This includes an improved analytical methodology for the classical scratch wound assay in which individual cell migratory behaviour is characterised with high spatial and temporal resolution; a novel metric designed specifically for measuring cell-cell coordination during collective cell migration is also suggested. The tools described in this work were used to investigate the mechanism for propagation of guidance cues in epithelial cells. Migration guidance from topographical features was found to propagate to cells not directly exposed to them through mechanical interactions between cells not mediated by cell-cell junctions or intracellular tension, but arising rather from volume exclusion. Additionally, the tools proposed were also used to characterise the effect of modifying the expression of the Planar Cell Polarity signalling protein Vangl1 on the collective migration of endothelial cells. Vangl1 expression was found to influence the migration of endothelial cells by modulating directedness in the scratch wound assay, but not in a variety of other migration assays, implying damage signals from the scratch were necessary for a Vangl1 migration phenotype. The work presented here is a first step to an improved experimental and analytical pipeline to understand the effect of combinations of guidance cues on directed collective cell migration.

Keywords: Cell Streaming
Collective cell migration
Grooves
Guidance cues
Planar Cell Polarity Signalling
Wound Healing
Advisor: McGuigan, Alison P
Development of Polymer-based Gels for Multimodal Medical Imaging Phantoms

Development of Polymer-based Gels for Multimodal Medical Imaging Phantom By Eunji In Doctor of Philosophy Department of Mechanical and Industrial Engineering University of Toronto 2016 Abstract In the field of medical imaging, there have been numerous efforts to combine multiple imaging modalities such as ultrasound (US), Magnetic Resonance Imaging (MRI), x-rays and Computed Tomography (CT), positron emission tomography (PET), ultrasound (US), and single photon emission CT. Multimodal imaging allows the fusion and analysis of various image data to provide morphological and functional information. With the progress in medical imaging technology and increased importance of quality assurance, the research in medical imaging phantom is necessary. Phantom is an anthropomorphic object that mimics the properties of human tissue for calibration, training and surgical planning purposes. This research thesis examines four different types of polymer-based materials for constructing medical phantoms: carrageenan-based polymer gel, polymer cross-linked aerogels, UV-curable silicone and self-healing polymer materials. In the first study, water-based carrageenan gel found to have a good correlation with the imaging properties of human tissue, but its long-term stability issue restricts its applicability as commercial phantoms. Since samples contained high water content, mechanical and imaging properties of carrageenan-based gel fluctuated due to water expulsion and absorption cycles over six-week period. In the second study, silica and cellulose aerogel cross-linked with polymer was also investigated as a phantom material. Contrast agents are cross-linked to fabricate an MRI/CT-compatible material. Results demonstrate that the imaging properties of these aerogels met the values of some human tissue values but due to volume shrinkage and complex fabrication process restricts its production in large scale. Furthermore, in the third study UV-curable silicone material was considered as a 3D printable phantom material. The addition of hydrophilic silicone and water is shown to improve the curing time and imaging properties of silicone. With suitable properties of UV-curable silicone, it will assist to produce real-size liver phantom using 3D printing technique for a patient-specific phantoms. There is an increased demand for phantom application in clinician training and surgical planning with needle-insertion or dissection is necessary. In the final chapter, self-healing silicone with microcapsule healing mechanism was investigated as proof-of-concept for surgical planning tool. Throughout four different studies, different polymer-based materials are examined subsequently with novelty in each study.

Keywords: CT
Medical Imaging
MRI
Phantom
Polymer
US
Advisor: Naguib, Hani E
Unsupervised Indoor Localization for Smartphones

In this work, the problem of indoor localization for smartphones is investigated. An indoor localization system is designed, that relies on two general techniques: received signal strength based localization and dead reckoning. The system is designed to be trained by the collected data via crowdsourcing, with no need for active human intervention. Sensor fusion techniques are used to resolve different issues of the localization problem. The combination of accelerometer and gyroscope are used as a dead reckoning system to measure the user's displacement. Graph matching algorithms are used to merge crowdsourced data to make a unified data structure, in a fully unsupervised fashion. We investigate the problem of translating topological indoor localization to geographical localization, by modeling the building map and the semantic maps as graphs. Two matching algorithms are proposed along with a node similarity measure based on finding the minimum distance between all sets of permutations of two vectors. We provide an efficient algorithm to calculate the similarity measure, and prove its correctness via a theorem. The proposed systems are implemented and shown to perform well, both in simulations and on real data. A novel magnetic sensor based localization system is also introduced and implemented that does not require any available infrastructure in the indoor area. Sensor fusion techniques are used to improve the system's accuracy.

Keywords: Localization
Smartphones
Tracking
Wi-Fi
Wireless communications
Wireless sensor networks
Advisor: Valaee, Shahrokh
Applied Plasmonics for the Cultivation and Study of Photosynthetic Microorganisms

This thesis explores nano-scaled plasmonic solutions to the problem of light capture and distribution in microalgae cultivation schemes. An evaluation of the effect of light quality on productivity under different photobioreactor geometries shows a 2x increase in productivity under 630-nm red light for low density cultures under low light intensity, compared to 534-nm green light. The opposite was true however when high density cultures are exposed to high intensity light â 534-nm performed 4x better than strongly ab-sorbed 630-nm red light. These results highlight the coupled influence of light quality and conventional photobioreactor design parameters. Wavelength specific, near-field plasmonic phenomena are then used as a means to couple light into cyanobacteria biofilms showing that plasmonic fields can be used to drive photosynthesis in living cells. 10-Âľm thick biofilms with maximum cell volume density of 20% vol/vol (2% more total accumulation than control experiments with direct light) were cultivated over three days. Far-field plasmonic phenomena were also applied to bulk cyanobacteria cultures to demonstrate a 6.5% enhancement in productivity. Resonant light is scattered back towards the culture increasing total ab-sorption while off-resonance light is transmitted. Supporting technology that enables patterning of plas-monic nano-features with a commercial CO2 laser system is also presented. Patterning speeds of 30 mm2/min and patterning costs of $0.10/mm2 are demonstrated which are ~30 fold faster and ~400 fold less expensive than e-beam lithography. Finally, crude oil characterization based on surface plasmon reso-nance is demonstrated, with applicability to both conventional and alternative energy industries. Bitumen-toluene mixture tests show a measurement sensitivity of 74o RIU-1, and a limit of detection below 1% toluene. Seven crude oils from around the world are differentiated with refractive indices spanning 1.44 to 1.56, with a sensor limit of detection of 0.0006 RIU.

Keywords: biofuels
cyanobacteria
microalgae
photobioreactor
plasmonics
solar energy
Advisor: Sinton, David
Impacts of High-depth of Wind Power Penetration on Interconnected Power Systems Dynamics

The main objective of this work is to investigate the impact of the high-depth, e.g., 35%, of penetration of the wind power, as Wind Power Plants (WPPs), on the low-frequency (0.1-2Hz) dynamics of interconnected power systems. Due to the lack and/or inadequacy of the analytical and the digital time-domain simulation tools for this class of studies, this undertaking 1. Develops enhanced nonlinear dynamic models of Type-3 and Type-4 WPPs for transient stability studies. 2. Develops a MATLAB-based transient stability time-domain simulation tool and integrates the WPP models in the tool. 3. Develops small-signal (linearized) models of Type-3 and Type-4 WPPs from their corresponding enhanced nonlinear models. 4. Develops a MATLAB-based linear platform for eigen analysis of large power systems including linearized models of Type-3 and Type-4 WPPs. 5. Introduces and develops a measurement-based coherency identication method for power system coherency identication in the presence of WPPs. Based on the develops of items 1-5 above, this thesis investigates the impacts of the (i) depth of wind power penetration, (ii) locations of WPPs and (iii) types of WPPs on transient stability, damping ratios of electromechanical modes and coherency phenomena of the New York/New England power system. The studies conclude that: i. Addition of WPPs do not introduce new inter-area oscillatory modes however it can aect existing ones. ii. Impact of WPPs on the damping ratio of an inter-area mode is determined based on the location(s) of the added WPP(s) with respect to the areas. If the WPPs increase the power exchange between two areas, the damping of the inter-area mode decreases. iii. Addition of WPPs close to synchronous generators equipped with DC exciters re- sults in the reduction of the damping ratio of the corresponding local modes due to interactions among the fast reactive power controllers of the WPPs and the slow excitation systems of the generators. iv. As the depth of penetration of wind power increases, the power system exhibits higher degree of nonlinearity and the impact of wind power on the system transient stability can be determined only from the time-domain simulation of the system nonlinear model. This indicates that the results of the transient stability assess- ment of the power system for lower depth of penetration of wind power cannot be extrapolated to higher levels. v. Addition of WPPs to a power system results in altering the coherency structure. Based on the WPPs allocation patterns, the impact of wind power on the system coherency is limited to the formation of new areas that are totally dominated by the added WPPs and the base case coherency structure of the synchronous generators is preserved.

Advisor: Iravani, Mohammad Reza
Adaptive Decision Feedback Equalization With Continuous-time Infinite Impulse Response Filters

In high-speed (10+Gb/s) chip-to-chip links, the primary impairments to signal integrity are noise, crosstalk, and a smooth tail in the pulse response resulting in inter-symbol interference (ISI) sometimes spanning more than 10 unit intervals (UIs). Although often simple in their implementation, continuous time linear equalizers amplify high-frequency noise and crosstalk and consume extra power. A conventional discrete-time (DT) decision feedback equalizer (DFE) is well-suited and power efficient for channels with a few dominant post-cursor ISI terms, however, the power can become prohibitive for channels with many post-cursor ISI terms. Infinite impulse response (IIR) DFEs can equalize post-cursor ISI persisting 10 or more UIs while consuming low-power comparable to just one DT tap. DFE architectures with varying numbers of DT and IIR taps are compared for use in typical wireline channels, and it is found that 2 IIR taps can offer an excellent compromise between power consumption and performance. However, an IIR DFEâ s performance degrades significantly as the feedback loop delay increases. Fortunately, adding a single DT tap can eliminate the degradation. The first ever hybrid DFE combining 1 DT and multiple (2) IIR taps is presented equalizing 24dB loss at half the bitrate while consuming 4.1mW at 10Gb/s. A novel edge based adaptation algorithm is also presented for DT DFEs which converges faster than previous algorithms while using the same high-speed circuitry and signals required for clock recovery. The edge based algorithm is extended to work for a 1 DT + 1 IIR DFE. The 1 DT + 1 IIR DFE along with integrated clock recovery and adaptation is demonstrated in 28nm FD-SOI CMOS. At 16Gb/s with a 30dB-loss channel, a BER below 10â 12 is measured over a 0.3UI timing window. The novel edge-based algorithm adapts both IIR and discrete-tap equalizer coefficients using the same high-speed circuitry and signals required for clock recovery. The adaptive DFE converges within 5us and is robust in the presence of poorly-conditioned data.

Keywords: Clock and data Recovery
Decision Feedback Equalization
Equalization
Infinite Impulse Response DFE
Wireline
Advisor: Chan Carusone, Tony