VictorJuiz/thesis huggingface dataset:
MONITORING CYANOBACTERIA USING PHYCOCYANIN PROBES AND POTENTIAL RISK OF IN-PLANT ACCUMULATION

This thesis evaluates the effectiveness of phycocyanin fluorescence probes as monitoring tools for the presence of cyanobacteria and/or their associated toxins in source water, as well as determines the cyanobacterial accumulation inside low-risk water treatment plant. Previous work reported that the direct correlations between phycocyanin raw readings and cyanobacterial parameters (e.g., cell count, biovolume, and cyanotoxin concentration) are not always promising. In this work, a review of the phycocyanin fluorescence probes is presented, and a probability of exceedance plot is developed and presented to predict relevant cyanobacterial parameters. Critical probe RFU values in terms of corresponding cyanobacterial monitoring threshold with various confidence levels are determined at each study site. Cyanobacterial in-plant accumulation is determined and quantified in three water treatment plants in Ontario from 2016 to 2017. The results show evident cyanobacteria and cyanotoxin (i.e., microcystin and anatoxin-a) accumulations inside low-risk plants. The potential worst-case scenario is predicted and microcystin with a concentration above Ontario drinking water guideline (4.1 Âľg/L) might end up in the finished water. More work needs to be done to predict the risk of exposure when cyanotoxins enter the distribution system.

Keywords: Accumulation
Cyanobacteria
Cyanotoxin
Fluorescence probe
Monitoring
Advisor: Hofmann, Ron
Developing a Clostridial Heterologous Expression Host and Producing a Prenylated Flavin Cofactor: Steps in Elucidating an Anaerobic Mechanism for Activating Benzene

Benzene, a toxic aromatic compound, has become an increasingly prevalent environmental contaminant in anaerobic environments, but the initial degradation step used by microbes for breaking its unsubstituted aromatic ring is unknown. Proteogenomic studies have implicated the involvement of a putative benzene carboxylase operon belonging to a Peptococcaceae sp., but it remains uncharacterized. Methods for growing and transforming shuttle plasmids into C. acetobutylicum, a close phylogenetic relative of Peptococcaceae were developed. Screening of the E. coli proteome was able to elucidate two novel in vitro pathways for producing the prenylated FMN (prFMN), and two protein-free forms that could be used to activate UbiD-like enzymes were identified. The combination of a Clostridial expression platform and a purified prFMN cofactor working in conjunction could be the key to successful functional characterization of the putative anaerobic benzene carboxylase, which could serve as a biomarker for the substrate-specific monitoring of benzene bioremediation at contaminated sites.

Keywords: Anaerobic biodegradation
Benzene
Clostridium
Heterologous expression
Prenylated FMN
Advisor: Edwards, Elizabeth A
A RESEARCH PLAN FOR ASSESSING THE POWER AND ENERGY CAPABILITY OF A RIVER NETWORK UNDER AN INTEGRATED WIND/HYDRO–ELECTRIC DISPATCHABLE RÉGIME

The world strives for more clean and renewable energy, but the amount of dispatchable energy in river networks is not accurately known and difficult to assess. When wind is integrated with water, the dispatchable yield can be greatly increased, but the uncertainty of the wind further degrades predictability. This thesis demonstrates how simulating the flows is a river network integrated with wind over a long time domain yields a solution. Time-shifting the freshet and pumped storage will ameliorate the seasonal summer drought; the risk of ice jams and uncontrolled flooding is reduced. An artificial market eliminates the issue of surplus energy from wind at night. Furthermore, this thesis shows how the necessary infrastructure can be built to accomplish the goals of the intended research. While specific to Northern Ontario and sensitive to the lives of the Native peoples living there, it indicates where the research might be applicable elsewhere in the world.

Keywords: Civil Engineering
Dispatchable Energy
Hydraulic Engineering
Hydro-Electricity
Renewable Energy
Sustainable Energy
Advisor: Karney, Bryan
The Comparative Impacts of Meadow and Sedum Species on Green Roof Hydrology

The goal of this thesis is to compare the stormwater management potential of two common green roof plant communities – native grasses and forbs, known as “meadow” species, and Sedum species – over a range of irrigation volumes. The physical and biological mechanisms involved in water retention provided by the green roof vegetation was measured and compared. Plants retain stormwater through three different mechanisms: water consumed through the roots which remains in the biomass, water transpired through the leaves during photosynthesis, and water intercepted by the leaves which then evaporates. Overall, the meadow species consumed roughly 50% more water through their roots, while Sedum intercepted roughly 70% more water; however, these processes occurred over different timescales and at different magnitudes, and were significantly impacted by variations in climate. This study highlights the complexities of plant water relations, and will contribute to a more holistic understanding of green roof performance and benefits.

Keywords: green roof
hydrology
LID
stormwater
vegetation
Advisor: Drake, Jennifer
Low-tech Photocatalysts for Solar Water Disinfection (SODIS)

Solar water disinfection (SODIS) is a household water treatment technique that involves adding microbiologically contaminated water to clear bottles and leaving them in full sunlight for at least 6 hours. While SODIS is a low-cost technique that requires few resources, it is a time-consuming process. In order to make SODIS more effective, this work investigated the use of low-tech photocatalysts. Initial experiments examined the ability of fired clay coated with TiO2 and urea to remove colour from a methylene blue solution, but results indicated that bare fired clay performed similarly to the coated pieces. Therefore, different bare clays were investigated further as photocatalysts for SODIS. One of the clays, Low Red, was able to inactivate E. coli within 1 hour of sunlight exposure. Based on the results of these experiments, certain fired clays may be able to serve as photocatalysts for SODIS.

Keywords: Clay
Low-tech
Photocatalysis
SODIS
Titanium dioxide
Advisor: Andrews, Susan
Internal Oxidation of Alloy 690

This dissertation studies the anomalous internal oxidation of Alloy 690 in a simulated primary water environment using time-resolved studies. Experiments were carried out in a steam/hydrogen mixture at atmospheric pressure and 480 ยบC in a tube reactor. Samples were exposed for a total of 100 hours with several interruptions and were studied between consecutive exposures. Scanning Electron Eicroscopy (SEM) imaging was used to observe changes on the surface, and Energy Dispersive X-Ray (EDX) elemental analyses was performed on the grain boundaries and within grains. Crystallography of grain boundaries was also carried out using Electron Backscatter Diffraction (EBSD). Results showed that the surface coverage of nodules increased with exposure time. The external oxide formed near grain boundaries had a fairly constant width over time, but the grain boundary region was dynamic, with signs of temporary internal oxidation, accompanied by stress relief due to diffusion of nickel to the grain boundary.

Advisor: Newman, Roger C
Evaluating the Remaining GAC Bed Life for MIB and Geosmin with a Laboratory-scale Test and Predictive Model

A challenge in applying GAC for taste and odour (T) control is the difficulty in predicting the remaining bed life of a partially-spent GAC. This study evaluated the validity of a promising tool developed by Gillogly et al. (1999) and Schideman et al. (2012) which combines a bench-scale column test with a predictive model to estimate the percent T removal across pilot- and full-scale contactors under variable conditions. In this study, the theoretical basis of scaling down large-scale filters to bench-scale columns was first verified using a pore and surface diffusion model (PSDM). The impact of operational parameters (e.g., sieve method, temperature) on both bench- and pilot-scale column performance were then examined for refinements to the test protocol. Finally, comparison of the results of bench-scale column tests and predictive model predictions with those of pilot-scale column tests at four water treatment plants validated the accuracy of this tool.

Advisor: Hofmann, Ronald
Optimal Inventory Policy Through Dual Sourcing

We consider a risk-averse firm that utilizes dual-sourcing for perishable or seasonal goods with uncertain customer demand. Using real options theories, we provide two models aimed at determining optimal order quantities to maximize the firm's expected profit. Furthermore, we can consider the demand to be an observable process correlated to a traded, which can be hedged to reduce profit uncertainty. A single offshore single local order period (SOSLOP) model provides a pseudo-analytical solution which can be easily solved to determine an optimal offshore and local order quantities based on the manufacturers' lead times, and a more realistic single offshore multiple local order period (SOMLOP) model uses numerical methods to determine optimal order quantities. Finally, a method for matching distributions of expected demands based on managerial estimates can be applied to any of the aforementioned models and be easily incorporated into the industry.

Keywords: Inventory Control
Optimization
Stochastic
Advisor: Lawryshyn, Yuri
Towards hydrophobin-mediated surface modification of lignocellulosic fractions: characterization of Class I hydrophobin interactions with cellulose and lignin and subsequent impact on T. reesei cellulase CBHI binding and activity

Class I hydrophobins have the ability to form amyloid-like rodlets upon exposure to an air-water interface, but the role of assembly in surface modification is unclear. Their binding to lignocellulose, a potential feedstock for chemicals, materials and energy, was tested, using aeration to induce hydrophobin assembly. Five class I hydrophobins were tested, both with and without aeration, for their ability to bind to cellulose and lignin, and significant differences in film mass and viscoelasticity could be observed. Films were further characterised by testing the binding of the Trichoderma reesei enzyme cellobiohydrolase I (CBHI) to lignin and cellulose after hydrophobin binding. Again, aeration was observed to alter the interactions hydrophobins had with both the surface and enzyme. This study displays the importance of hydrophobin assembly on observed properties of the protein, and highlights the possibility of tuning hydrophobin interactions with surfaces and proteins by aeration.

Keywords: Hydrophobin
Lignocellulose
Quartz Crystal Microbalance
Surface modification
Advisor: Master, Emma R
A Comparative Analysis of Agent-Based Pedestrian Modelling Approaches

Pedestrian simulation models are becoming more frequently relied upon by researchers and practitioners when designing or evaluating transit stations, event venues, and other large facilities. However, the computational performance of these models can vary greatly and their relative accuracy is generally unexplored, leaving users with little guidance when selecting a model for their needs. Here, models based on the Social Forces, Optimal Steps, and static graph concepts are coded into MassMotion, then calibrated against observed pedestrian flow data using Genetic Algorithms. Using two transit station scenarios, each modelâ s ability to match observed and increased volume pedestrian flows is explored and their relative speeds are compared, generally showing significant speed advantages over the default MassMotion model, but also indicating that the graph and Optimal Steps models are note sufficiently sensitive to congestion. Additionally, this work explores the behaviour of these models within various facility elements, including corridors, corners, and open spaces.

Keywords: Agent-Based Modelling
Genetic Algorithm
Pedestrian Simulation
Social Forces
Advisor: Shalaby, Amer S
Free Radical Scavenging in Health and Disease — a Basic Science Approach in Clinical Scenarios

Free radicals have been implicated in a variety of acute and chronic disease processes. Recent studies have focused on free radical scavenging and hydrogen gas has emerged as a novel scavenger. Hydrogen delivery at adequate concentrations in solution has posed a significant problem given hydrogenâ s low solubility and quick precipitation out of solution. A custom-built canister was developed to dissolve, store and deliver hydrogen enriched fluids at sustained concentrations. This canister was successfully utilized in a hemorrhagic shock rat model which showed upregulation of superoxide dismutase, which may provide a clue as to the mechanism by which hydrogen is protective against free radical damage.

Advisor: Goh, M. Cynthia
Coupled Oscillators Model of Hyperexcitable Neuroglial Networks

Presented in this thesis is an oscillator-based neuroglial model capable of generating Spontaneous Electrical Discharges (SEDs) in hyperexcitable conditions. The network is composed of 16 coupled Cognitive Rhythm Generators (CRGs), which are mathematical constructs that represent one of the following populations of excitable cells: an excitatory pyramidal cell population, an inhibitory interneuron population, an astrocyte population, or a microglial population. Various mechanisms leading to hyperexcitability were investigated, and results suggest an important role for astrocytes and microglia in the generation of SEDs of various durations. Analysis of the resultant SEDs revealed two underlying distributions with differing properties. Particularly, short and long SEDs are associated with deterministic and random processes, respectively. Furthermore, there was evidence of theta-HFO phase-amplitude cross-frequency coupling (CFC) in the short SEDs, and delta-HFO CFC in the long SEDs, as was previously reported in a mouse model of Seizure-Like Events (SLEs) and in human patients with epilepsy.

Advisor: Bardakjian, Berj L
Comparing Favorable and Unfavorable Attachment of Colloids in a Discrete Sandstone Fracture

This study compares the results of cationic amine-modified latex (favorable attachment) and anionic carboxylate modified latex (unfavorable attachment) microsphere transport through a discrete sandstone fracture. Two microsphere sizes (200 nm and 1000 nm), two ionic strengths (5 mM and 10 mM), and two specific discharges (0.35 mm.s-1 and 0.70 mm.s-1) were tested to observe the impact on transport under both attachment conditions. The effect of ionic strength was significant for unfavorable attachment due to the presence of a secondary minimum, but not significant for favorable attachment conditions. The recovery of anionic microspheres resembled favorable attachment when cationic microspheres attached to the sandstone surface and created surface charge heterogeneities. For all conditions tested there was less separation between favorable and unfavorable attachment than would be expected in a comparable porous media study, which was attributed to less contact between the colloid and collector and higher specific discharge in fractured media.

Keywords: Colloid
Fractured Rock
Advisor: Sleep, Brent E
Parallel Algorithms and Methods for FPGA Placement

This thesis evaluates new parallel approaches for simulated annealing-based placement, and also leverages recent processor features such as hardware transactional memory (TM) and thread-level speculation (TLS) that aim to make parallel programming easier. Our contributions include a quantitative comparison of the speedup and quality-of-results obtained with various parallel algorithmic and programming approaches. We find that while TM and TLS simplify parallel programming, neither can achieve a compelling combination of speedup and placement quality. Our best algorithms require more programming effort than TM or TLS, but outperform prior approaches: without loss of placement quality, we can reach 5.9x speedup with a deterministic algorithm and 34x speedup with a non-deterministic one. We also evaluate the impact of hardware platforms on placement time. We find that while the greatest speedups occur on systems with many (57) simple cores, the fastest execution is achieved by systems with fewer (16) more complex cores.

Keywords: FPGA placement
parallel programming
transactional memory
Advisor: Betz, Vaughn
Steffan, John G
Data-Driven Mesoscopic Simulation of Large-Scale Surface Transit Networks

The planning of transit services, assessment of operational strategies, and evaluation of service changes can benefit tremendously from high-fidelity transit network models. Traditional microsimulation models are infeasible for large networks due to onerous model construction and calibration and prohibitive computational requirements. They are typically only used to model individual corridors or small sub-networks. This study presents a data-driven mesoscopic simulation method that models surface transit movement based on open data and machine learning. After a comprehensive comparison of running speed models using multiple linear regression, support vector machine, linear mixed effect model, regression tree and random forest, the random forest running speed models and lognormal dwell time distribution models were used to perform stop-to-stop mesoscopic simulations. The model results adequately replicated variation in headways, delays, and dwell times. Validation at the stop level and the route level demonstrated the need to capture passenger demand and congestion variations in future studies.

Keywords: machine learning
mesoscopic
modeling
open data
planning
public transport
Advisor: Shalaby, Amer
The adaptation of the plant pathogen Pseudomonas syringae onto the novel host Arabidopsis thaliana through experimental evolution

The bacterial plant pathogen Pseudomonas syringae is a highly diverse species complex that can infect and cause disease on a wide range of hosts. Despite this broad host range, individual strains of P. syringae are highly host specific. In this thesis, we used in planta serial passaging to experimentally evolve twelve independent lineages of P. syringae pathovar phaseolicola (Pph) 1448A, a bean pathogen, on the novel host Arabidopsis thaliana (Arabidopsis), with the goal of characterizing the early adaptive steps towards host adaptation. Twelve hypermutating lineages of Pph 1448A were constructed for this experiment to increase the evolvability of lineages, and to efficiently study mutations associated with adaptation towards Arabidopsis. After eighty days of passaging on the novel host, lineage 7 has shown a significant gain in fitness on Arabidopsis. Population sequencing of this lineage may provide novel insights into the adaptive processes underlying host specificity in P. syringae.

Keywords: Arabidopsis thaliana
experimental evolution
Pseudomonas syringae
Advisor: Guttman, David S
Capacity Analysis of the Union Station Rail Corridor using Integrated Rail and Pedestrian Simulation

The capacity evaluation of railway station areas is essential for accommodating future growth in demand and new rail services. Conventional capacity analysis methodologies (analytical, optimization) have limitations due to over-simplified assumptions. While simulation tools have proven effective in analyzing complex station areas, the interactive effects between pedestrian and train movements are hardly captured properly. The study analyzed representative analytical and railway simulation methods, and applied an integrated simulation platform â Nexus (connected with OpenTrack and MassMotion) â to perform a comprehensive capacity analysis of the Union Station Rail Corridor. A 9% drop in on-time performance was observed and passengersâ average duration at LOS F tripled with the increase of train and passenger volumes. Both length and variation of dwell time due to pedestrian movement were recognized as the main factors of performance deterioration. The study also reveals the applicability and benefits of using such integrated simulation tools in other complex transit systems.

Keywords: Capacity
Integrated Simulation
Pedestrian
Railway
Simulation
Station
Advisor: Shalaby, Amer
An Analysis of Factors Affecting the Design and Performance of Storm Sewer Systems

Storm sewer systems today are typically designed using the Rational Method. In order to assess the effectiveness of the Rational Method, five models, four theoretical and one calibrated and validated model, are used to explore the influence of hydrologic factors such as soil saturation, depression storage, and peak rainfall timing, and hydraulic factors such as network interactions, backwater effects, and storage on the performance of storm sewer systems. Simulations were run in EPA SWMM 5.1, and peak runoff rates, runoff volumes, and key pipe flow values were recorded, compared, and analyzed to quantify the influence of these hydrologic and hydraulic factors. It is found that the Rational Method is a reasonable starting point for design; however it often underestimates runoff values and cannot assess network and backwater effects. It is recommended that Rational Method designs incorporate basic dynamic analysis as a means to identify and address potential design weaknesses.

Keywords: Design Storm
Hydraulic
Hydrologic
Influence
Performance
Rational Method
Advisor: Karney, Bryan
Drake, Jennifer
Water Recovery from Inorganic Solutions via Natural Freezing and Melting

A combined natural freezing and melting water recovery process was evaluated for a 0.5 molal magnesium sulphate solution. 500 mL of solution was placed in a container open to the air, and the temperature was lowered to between -2 and -26 째C. At equilibrium the solid produced, consisting of ice and entrapped solution or solute crystals, was removed and thawed at either 3 째C or 25 째C. The resulting liquid was analysed for magnesium. Microscopy of the solid was also performed. Although the purity of the liquid was not affected by the thawing temperature, solid frozen at -26 째C yielded the best purity when melted, as 40% of the original water could be recovered at a concentration of 0.075 molal magnesium sulphate. This is because during melting entrapped solution drains from the solid faster than the ice melts, increasing liquid concentration at earlier stages of melting.

Keywords: eutectic freeze
freeze concentration
ice
melting
natural freezing
water recovery
Advisor: Papangelakis, Vladimiros
Characterization of the Microbial Community and Activity of Nitrate-Reducing, Benzene-Degrading Enrichment Cultures

Benzene is a natural component of crude oil. It is highly toxic, carcinogenic, and persistent contaminant. This work studied anaerobic benzene-degrading, nitrate-reducing enrichment cultures that were previously cultivated for over twenty years. Amplicon sequencing of nitrate-reducing cultures amended with benzene and benzene degradation intermediates provided evidence for a process by which Peptococcaceae is responsible for initial substitution of the benzene ring, followed by further degradation by Azoarcus. A qPCR study found an increase in copy number of Peptococcaceae and the abcA subunit of a putative anaerobic benzene carboxylase (Abc) associated with Peptococcaceae was correlated with benzene degradation. Further study of an Azoarcus-enrichment culture found that it was capable of degrading the BTEX compounds, but only under limited conditions. Finally, a metagenome was assembled for the benzene-degrading, nitrate-reducing culture. Annotation of metatranscriptome data to this metagenome provided further evidence for carboxylation of the benzene ring by Peptococcaceae.

Advisor: Edwards, Elizabeth A