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Title: Pre-implant Brain Activation Modeling to Drive Placement of Depth Leads in White Matter for Direct Neurostimulation Therapy in Epilepsy
Creator: Cendejas Zaragoza, Leopoldo
Date: 2019
Description: A critical step towards applying direct brain stimulation therapy in focal onset epilepsy is to effectively interface with epileptogenic...
Show moreA critical step towards applying direct brain stimulation therapy in focal onset epilepsy is to effectively interface with epileptogenic neural circuits using a limited set of active contacts. This takes special relevance when interacting with networks that exhibit two or more foci. A strategy to influence the maximum extent of the epileptogenic circuit is to stimulate white matter pathways to enhance propagation to distant epileptic tissue.A significant number of elements must be considered in the clinical response to stimulation delivered directly to neuronal populations. These variables include: stimulation parameter settings, number and interdependence of anatomical targets, electrode number, electrode location and orientation, geometry or shape of the electrode contacts, contact polarity, biophysical properties of stimulated medium, andtrajectory of axonal bundles adjacent to the stimulation site.This document addresses the development of a computational model which takes into consideration all the mentioned variables to predict activation of distant sites via white matter pathways. A method to calculate the extracellular potential field, induced by the application of time-dependent stimulation waveforms, is discussed. Such a method considers both the anisotropic conductivity nature of neural tissue and the electrochemical phenomena of the electrode-tissue interface. The response of white matter fibers is then evaluated by solving a compartmental cable model based in the Hodgkin and Huxley membrane description.The model was integrated into a pre-surgical workflow and was used prospectively to guide stereotactic implantation of depth leads to apply direct neurostimulation therapy in four patients with refractory focal onset epilepsy.
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Title: THE EFFECT OF INTENTIONAL, PERSISTENT SMALL-GROUP LEARNING ON COLLEGE STUDENT ACHIEVEMENT AND RETENTION IN THE PRE-CALCULUS CLASSROOM
Creator: Peterson, Christy Lee
Date: 2019
Description: Various research studies have established that nearly half of all students who decide to pursuit a math, science, or engineering field change...
Show moreVarious research studies have established that nearly half of all students who decide to pursuit a math, science, or engineering field change their mind and seek a different major. The National Center for Education Statistics shows a decrease in the number of degrees in engineering and related fields from 36,900 degrees in the 2003 – 2004 academic year to 31,800 degrees in 2013 – 2014, a 13.8% decline. Not surprising, a report by the President’s Council of Advisors on Science and Technology in 2012 predicted that the United States workforce would see a deficit of one million college graduates in science, technology, engineering and math over the next decade. This study was designed to help answer the question, Is there a difference in achievement or retention for students participating in intentional, persistent small-group learning compared with randomly assigned small-groups in a college level pre-calculus course? This study compared the pre-calculus achievement scores, course pass rates and retention rates between two types of small-group membership, persistent and random. The study also compared students’ study habits throughout the semester and students’ experiences working in a small-group learning environment. Initial examination of the data showed that students participating in intentional, persistent small-groups had better course pass rates and consistently scored higher on unit exams and the final exam than students who participated in randomly assigned small-groups. The course pass rates for both types of small-group membership were similar to the pass rates for students in all other sections of pre-calculus offered at the college. The retention rate for the two courses was similar. However, when compared to the retention rate for all sections of pre-calculus offered at the college, retention was statistically higher in the two sections utilizing small-groups in this study. Given that retention is one of the challenges for pre-calculus, utilizing small-group learning might be a way to improve student retention in college pre-calculus. There were no significant findings for differences in students’ study skills or students’ experiences working in small-group learning environments. However, it was interesting to see that students in randomly assigned small-groups had stronger agreement on items related to working with multiple peers while students in the intentional, persistent small-groups had stronger agreement on items related to developing relationships. The results indicate there might be value to student achievement in utilizing persistent group membership over randomly assigned group membership or even whole-class lecture. Furthermore, the results of this study indicate that utilizing small-group learning in pre-calculus benefits the student retention rate.
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Title: INTERACTIVE MULTIPLE MODEL ESTIMATION FOR UNMANNED AIRCRAFT SYSTEMS DETECT AND AVOID
Creator: Canolla, Adriano Carlos
Date: 2018
Description: This research presents new methods to apply safety standards to Detect and Avoid (DAA) functions for Unmanned Aircraft Systems (UAS), using...
Show moreThis research presents new methods to apply safety standards to Detect and Avoid (DAA) functions for Unmanned Aircraft Systems (UAS), using maneuvering target tracking and encounter models.Previous DAA research methods focused on predefined, linear encounter generation. The new estimation and prediction methods in this research are based on the target tracking of maneuvering intruders using Multiple Model Adaptive Estimation and a realistic random encounter generation based on an established encounter model.When tracking maneuvering intruders there is limited knowledge of changes in intruder behavior beyond the current measurement. The standard Kalman filter (KF) with a single motion model is limited in performance for such problems due to ineffective responses as the target maneuvers. In these cases, state estimation can be improved using MMAE. It is assumed that the current active dynamic model is one of a discrete set of models, each of which is the basis for a separate filter. These filters run in parallel to estimate the states of targets with changing dynamics. In practical applications of multiple model systems, one of the most popular algorithms for the MMAE is the Interacting Multiple Model (IMM) estimator. In the IMM, the regime switching is modeled by a finite state homogeneous Markov Chain. This is represented by a transition probability matrix characterizing the mode transitions. A Markov Chain is a stochastic model describing a sequence of possible events in which the probability of each event depends only on the previous event.This research uses the hazard states estimates (which are derived from DAA standards) to analyze the IMM performance, and then presents a new method to predict the hazard states. To reduce the prediction error, this new method accounts for maneuvering intruders. The new prediction method uses the prediction phase in the IMM algorithm to predict the future intruder aircraft states based on the current and past sensor measurements. The estimation and prediction methods described in this thesis can help ensure safe encounters between UAS and manned aircraft in the National Airspace System through improvement of the trajectory estimation used to inform the DAA sensor certification process.
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Title: DEVELOPING NON-LINEAR AND ADAPTIVE NEURONAL SYNCHRONY AND CONNECTIVITY ANALYSIS TO PERSONALIZE CLOSED-LOOP DBS THERAPY FOR TREATING EPILEPSY
Creator: Farahmand, Sina
Date: 2019
Description: Epilepsy disease afflicts more than seventy million people worldwide. In approximately one third of the cases, antiepileptic medications fail...
Show moreEpilepsy disease afflicts more than seventy million people worldwide. In approximately one third of the cases, antiepileptic medications fail to control seizures. Over the last few decades, electrical stimulation of the brain has been evaluated as a potential alternative to treat surgically and medically refractory epilepsy patients. Despite some successes, most of the devices using this protocol operate based on pre-determined stimulation parameters (e.g. frequency and location of stimulation) that have little or no relationship to the individuals’ underlying brain dynamics, which we hypothesize may explain their low clinical efficacy in preventing or terminating seizures.In this study, a non-linear adaptive neuronal synchrony and connectivity analysis was developed in order to extract stimulation parameters from endogenous, multi-site brain dynamics of epilepsy patients. A non-linear analytical methodology was proposed to assess phase-synchrony dynamics in epilepsy patients as seizures evolve. This study revealed a desynchronization around seizure onset. However, the synchrony level started to increase gradually towards seizure end and reached its maximum at seizure termination. This results reveal that hyper-synchronization of the epileptic network may be a critical self-regulatory mechanism by which the brain terminates seizures. In the other phase of this study, a non-linear adaptive phase-connectivity analysis was developed in order to extract frequency and locations of stimulation that match the synchronized network dynamics at seizure termination. Matching these parameters to the endogenous brain dynamics of epilepsy patients as seizure naturally terminates may not only terminate seizures prior to their development, but it may also lead to a personalized deep brain stimulation (DBS) therapy with higher clinical efficacy.
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Title: FRANK-KASPER PHASES IN THE CO-NB-NI TERNARY SYSTEM AND THE ISOTHERMAL SECTION OF THE CO-NB-NI SYSTEM AT 1473K
Creator: Jia, Hui
Date: 2019
Description: The present study is to determine the Frank-Kasper phases in the Co-Nb-Ni system. Frank-Kasper phases, also called topological close packed ...
Show moreThe present study is to determine the Frank-Kasper phases in the Co-Nb-Ni system. Frank-Kasper phases, also called topological close packed (TCP) phases are one of the largest groups of intermetallic compounds. They are classified into several phases: A15, Laves, σ, µ and the M, P, R phases. In the 1200°C-isothermal section of the Co-Nb-Ni system, the µ phase and Laves phases exist over large composition ranges. In this study, the Co-Nb-Ni ternary system was investigated using optical microscopy(OM), X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) and differential scanning calorimetry (DSC). The experimental results were compared with literature data and thermodynamic calculations. XRD was used to identify the Frank-Kasper phases. In comparison with previous investigations, the large extensition of µ phase in the Co-Nb-Ni system was verified. In addition, the small phase (~67at. % Nb) shown in the alloys with ~50at. % Nb is the unstablized impurity phase. On the other hand, according to the results of experiments and thermo-calc, C15 phase was found instead of C14 phase compared with Gupta's study.
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Title: ENHANCED DEGRADATION AND PEPTIDE SPECIFICITY OF MMP-SENSITIVE SCAFFOLDS FOR NEOVASCULARIZATION OF ENGINEERED TISSUES
Creator: Sokic, Sonja
Date: 2013, 2013-07
Description: Biomaterial strategies for engineering tissues of clinically relevant size require the formation of rapid and stable neovascularization. The...
Show moreBiomaterial strategies for engineering tissues of clinically relevant size require the formation of rapid and stable neovascularization. The ability of an engineered scaffold to induce vascularization is highly dependent on its rate of degradation. During the process of material degradation, the scaffold should degrade in a manner allowing for cellular infiltration, lumen formation, and extracellular matrix (ECM) synthesis. Matrix metalloproteinases (MMPs) play a key role in mediating cell-induced proteolytic matrix degradation, remodeling, and controlled neovascularization. Poly (ethylene glycol) PEG hydrogels have been extensively investigated as scaffolds for tissue engineering applications due to their ease of chemical modification allowing for the recapitulation of key aspects of the neovascularization process. The goal of the work described in this thesis was to develop strategies to enhance and control the degradation of MMP-sensitive PEG diacrylate (PEGDA) hydrogels without inducing changes to the bulk physical and mechanical properties of the material and to further study the effect of the cleavage site concentration and MMP-sensitive peptide substrate specificity on the rate of neovascularization and tissue remodeling in vitro and in vivo. In the first part of this study, a detailed investigation was completed to investigate the effects of the mechanical and physical properties of the scaffolds as well as the role of proteolytically mediated hydrogel degradation on 3D fibroblast invasion within MMPsensitive PEGDA hydrogels. Initial studies focused on the use of a modified version of a previously published multistep conjugation method to generate degradable PEGDA macromer conjugates containing variations in the number of MMP-sensitive domains. Theoretical and experimental characterization of this multistep conjugation demonstrated xi that this method leads to the formation of multiple species that directly affect the compressive modulus and degradation rate of the scaffold making it difficult to control degradation independent of alterations in the bulk physical and mechanical hydrogel properties. After manipulation of multiple polymerization conditions, hydrogels with similar compressive moduli but different hydrogel degradation rates were synthesized. These initial studies showed that an increase in the incorporation of proteolytically sensitive domains in PEGDA hydrogels of similar modulus lead to enhanced degradation and 3D fibroblast invasion. In this study, the role of soluble FGF-1 on fibroblast invasion within these scaffolds was investigated and it was demonstrated that the inclusion of FGF-1 in the scaffolds results in further enhancement of fibroblast invasion in a dosedependent fashion. Further studies were necessary to develop a more controllable and robust approach in tuning scaffold degradation independent of alterations in the bulk physical and mechanical properties. In order to address this, a novel approach was developed to engineer protease-sensitive peptides with multiple proteolytic cleavage sites that could be covalently crosslinked into hydrogels without compromising the physical and mechanical biomaterial properties. This approach avoided the need for utilizing a multistep conjugation process as peptides could be incorporated into the backbone of PEG using a single step conjugation. Using this approach, hydrogels formed with the engineered peptides led to significantly enhanced degradation and neovascularization in vitro as compared to scaffolds with a single protease sensitive peptide between crosslinks. In addition, hydrogels with enhanced susceptibility to degradation promoted vascularization over a wider range of matrix properties. This approach allowed for controlled xii concentration of the proteolytic cleavage sites within the matrix and thus tuning of hydrogel degradation for tissue engineering applications. In the final study, MMP-sensitive peptide substrates specific to degradation by MMPs known to be expressed during neovascularization were screened for degradation and their role in neovascularization. MMP-sensitive PEGDA hydrogels (SSite and TriSite) were synthesized with peptide substrates sensitive to cleavage by MMP-2, MMP- 9, MMP-14, a mixed sequence of MMP-2, 9 and 14, and compared to the peptide substrate used in the previous studies, which is degraded by collagenase enzymes. The hydrogels were evaluated for their sensitivity and specificity to degradation by MMPs, in terms of cleavage site concentration, and for their role in neovascularization and tissue remodeling in vitro and in vivo. The presented approach allows for the incorporation of varying cleavage site concentration and MMP-sensitive peptide substrates into PEG hydrogels without alterations in the mechanical and physical properties of the hydrogels. Results showed that without the incorporation of growth factors in this scaffold, vascularization and tissue invasion was supported in all MMP-sensitive hydrogel groups regardless of the MMP-sensitive peptide substrate embedded in the matrix. In addition, the cleavage site concentration had a profound impact in enhancing vascularization in vitro and tissue invasion in vivo. These techniques can be used to tune the properties of polymer scaffolds for neovascularization and tissue remodeling. In addition, these studies provide insight into the effect of the physical, mechanical, and degradative properties of these systems and on the role of cleavage site concentration, and MMP substrate specificity on xiii neovascularization and tissue invasion within proteolytically degradable PEG hydrogel constructs.
PH.D in Biomedical Engineering, July 2013
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Title: STEEL STRUCTURE RESPONSE UNDER FIRE CONDITIONS MODEL BASED SIMULATION (MBS)
Creator: Coughlin, Kevin James
Date: 2019
Description: This paper addresses the issue of structure design and analysis for conditions of fire loading. It includes an introductory section that...
Show moreThis paper addresses the issue of structure design and analysis for conditions of fire loading. It includes an introductory section that presents the historical and current state of practice using prescriptive methods of design, a qualitative and conceptual development (based on actual field observations) of what is expected to occur in a structure when subjected to fire, and a summary of the current state of research on the subject of structure design for fire loading. Next, a thermo-plastic non-linear finite element shell model was developed for a two member steel beam and column, bolted joint structure used in an actual physical fire test, subjected to beam a bending load and column compressive load, held constant, while the structure was heated up in a furnace. The beam / column bolted joint rotation for the test matched the simulation quite well. Next, further extending this modeling approach, a partial moment frame from the center of a 9 story building designed for dead, live, and seismic loading was modeled with non-linear thermo-plastic shell elements in the fire zone, along with linear elastic beam / line elements for structural components surrounding the fire zone. For this model, the gravity loading (no seismic loading included) was fully applied, and then a thermal load corresponding to the ASTM E119 fire test load was applied to the structure in the fire zone. Simulation of lateral torsional buckling, flange local buckling, web local buckling, and finally overall global buckling of the columns was accomplished in this effort, increasing confidence that complex thermo-plastic structural behavior can be modeled with advanced non-linear finite element technology. Boundary conditions on this model from the floor system had a significant impact on the mode of global buckling (strong axis or weak axis), warranting further investigation and possibly a 3-D frame with a floor system included in future work. Also, extending this modeling approach even further, in future work, using the entire 9 story moment frame, with shell elements in the fire zone and non-linear moment-curvature beam / line elements for surrounding members, is contemplated, the objective being to numerically model a progressive collapse event in a planar frame. Finally, an actual 10 story structure, converted to and industrial open floor structure, based on current design codes and standards, was modeled thermally using the industry standard Hydrocarbon (HC) Temperature vs time curve, and structurally using non-linear thermoplastic shell elements in the “fire room” (to better capture local buckling and overall structure collapse behavior), and thermoplastic beam elements for the rest of the structure. The thermal modeling was performed for steel members both without insulation (bare steel) and with minimal insulation (1/4” coated thickness), and these “decoupled” results then applied to the structural model. The use of even a small layer of insulation demonstrated the dramatic effect of such, insofar as the collapse time of the structure is concerned.
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Title: THE LATIN AMERICAN EXPORT: IMPLEMENTING LATIN AMERICAN URBAN STRATEGIES TO REDEVELOP AND RECONSTRUCT BRONZEVILLE
Creator: Saldaña Perales, Alejandro
Date: 2018
Description: The district and neighborhood of Bronzeville, located in the Near South Side of Chicago, suffers from crime, unemployment, abandonment, and...
Show moreThe district and neighborhood of Bronzeville, located in the Near South Side of Chicago, suffers from crime, unemployment, abandonment, and urban decay; more so than many of its metropolitan peers such as New York City, Los Angeles, or San Francisco.In Latin America, multidisciplinary operations and strategies focused on the investment in public spaces, mobility, and public assets have been successful in transforming decaying neighborhoods and redeveloping slums and blighted areas turning them into vibrant communities.Contextualizing and abstracting such strategies has the potential to import such ideas into new urban contexts; in this case, the United States of America, and to be implemented over the decaying North American urban fabric.
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Title: Implicit ligand theory: binding free energy calculations based on multiple rigid receptor snapshots
Creator: Xie, Bing
Date: 2018
Description: Binding affinity plays an important role in drug design. Accurate and fast prediction of binding free energies remains a major challenge for...
Show moreBinding affinity plays an important role in drug design. Accurate and fast prediction of binding free energies remains a major challenge for structure-based calculation. We have developed a fast free energy calculation program AlGDock and applied it to different systems. In this thesis, I will first demonstrate the feasibility of estimating protein-ligand binding free energies using multiple rigid receptor configurations on T4 lysozyme. Based on 576 snapshots extracted from six alchemical binding free energy calculations with a flexible receptor, binding free energies were estimated for a total of 141 ligands. For 24 ligands, the calculations reproduced flexible-receptor estimates with a correlation coefficient of 0.90 and a root mean square error of 1.59 kcal/mol. The accuracy of calculations based on Poisson-Boltzmann/Surface Area implicit solvent was comparable to previously reported free energy calculations. Then we evaluate a number of common snapshot selection strategies using a quality metric from stratified sampling, the efficiency of stratification, which compares the variance of a selection strategy to simple random sampling. For docking sets of over five hundred ligands to four different proteins of varying flexibility, we observe that for estimating ensemble averages and exponential averages, many clustering algorithms have similar performance trends: for few snapshots (less than 25), medoids are the most efficient while for a larger number, optimal (the allocation that minimizes the variance) and proportional(to the size of each cluster) allocation become more efficient. Proportional allocation appears to be the most consistently efficient for estimating minima. Finally, we attempted a blinded prediction challenge D3R and applied AlGDock on several systems. I will describe the performance of our calculation. Overall, the study shows that AlGDock can work well for predicting the binding affinities and it demonstrates a strategy for developing an understanding of protein-ligand interactions.
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Title: Critical Aspect Ratio And Flow Development In A Low Reynolds Number Variable Aspect Ratio Duct Utilizing Oil Film Interferometry
Creator: Chiu, Daniel P.
Date: 2019
Description: Within the realm of fluid mechanics, there has always been an interest of bridging the gap between ideal- and real fluid flows. Pertaining to...
Show moreWithin the realm of fluid mechanics, there has always been an interest of bridging the gap between ideal- and real fluid flows. Pertaining to the study of turbulent duct flow, an aspect ratio (AR) configuration that would behave in such a manner would be considered a critical aspect ratio. This would mean the flow core would be unaffected by any sidewall contributions. Such analysis is done through wall shear measurement techniques; this study used oil-film interferometry (OFI).The first steps of this study were to determine sufficient criteria to ensure that the data collected were representative of the tested configuration, e.g. parameter choice and flow development length. Previous studies used the bulk velocity U_b which is derived from the entirety of the flow. This study focuses on the flow core, thus the choice to use the center-line velocity U_C seemed appropriate. The development length pertains to testing downstream from the inlet such that parameters are independent in th`e streamwise direction. This study demonstrates that the previously held value of x/H = 100 is insufficient and that nearly twice that is required.Furthermore, this study shows three very important findings: the flow development length required for testing is x/H ≈ 200, the size of the test platform plays little part in the overall behavior of the flow, and that the critical aspect ratio is AR = 24. These findings correspond to an aspect ratio range of 12.8 ≤ AR ≤ 48 and a Reynolds number range of 0.5 × 10^4 < Re_H < 4.0 × 10^4 . From these data, the estimated relationship between the coefficient of friction and the Reynolds number is shown with the following relation:Cf,C = 0.05164 Re_H ^ −0.25
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Title: MODELING THE ORIGIN AND INCEPTION OF FATIGUE FAILURE IN METALS THROUGH A NON-LINEAR MECHANICAL SPRING SYSTEM
Creator: Divani, Abbas
Date: 2019
Description: Fatigue failure of metals is one of the aspects of material behavior that have not been explained through direct calculations or mathematical...
Show moreFatigue failure of metals is one of the aspects of material behavior that have not been explained through direct calculations or mathematical modeling. This research is to undertake the development of an innovative model that can be used in predicting the fatigue behavior of metals. This model is based on the behavior of a system of large number of parallel elements, each composed of two springs, a string, and a mass block, that undergo cyclically varying or random load cycles. Failures among the elements occur at random and can be used as a means to simulate fatigue damage and fatigue behavior. Initial studies on this model have produced promising results. This research is intended for full development and implementation of the model including procedures for Development of a method for calibration of the model parameters using the common mechanical properties of steel, extension of the model to incorporate the hysteresis behavior of steel under cycling loading, and development of Constant Fatigue Life diagrams Such as Goodman diagram.
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Title: SUSTAINED RELEASE OF PHOSPHATE-BASED THERAPEUTICS FOR ATTENUATION OF PATHOGEN-INDUCED PROTEOLYTIC MATRIX DEGRADATION
Creator: Bittencourt Pimentel, Marja
Date: 2019
Description: Loss of the normal intestinal microbiome community structure and its replacement by pathogenic microbes contributes to severe persistent...
Show moreLoss of the normal intestinal microbiome community structure and its replacement by pathogenic microbes contributes to severe persistent inflammation in diseases such as ulcerative colitis and inflammatory bowel disease. While host-derived proteases are known to contribute to this pathogenesis, the role of increased production of microbial-secreted proteases due to virulent phenotypes remains unclear. Following surgical removal of diseased intestinal tract, increased bacterial protease expression is a key phenotype involved in intestinal healing impairment. Antibiotic administration is ineffective for treating these complications as it inadvertently eliminates normal flora while allowing pathogenic bacteria to acquire antibiotic resistance. Prior research has shown that intestinal phosphate depletion in the surgically stressed host triggers bacterial virulence which is suppressed under phosphate abundant conditions. To address this issue our previous work has demonstrated that the use of free monophosphate (-Pi) and polyphosphate (-PPi), as well as post-loaded PPi nanoparticles (NP-PPi) attenuate collagenase production of gram-negative (Pseudomonas aeruginosa and Serratia marcescens) but not gram-positive (Enterococcus faecalis) pathogens expressing high collagenolytic activity. Due to the variation in phosphate metabolism among microbial species we investigated the in vitro efficacy of a combination treatment of phosphates delivered in a sustained release format using NP-PPi and NP-Pi on collagenase and biofilm attenuation across gram-positive and gram-negative test pathogens.Collagenase screening was assessed using two in vitro models. The first in vitro assay involved culturing pathogens in the presence and absence of NP-Pi and/or NP-PPi treatment using two-dimensional (2D) commercially available fluorogenic protease-sensitive peptide substrates. Although these substrates are among the most commonly used for screening protease activity and inhibition in vitro, their application does not translate to three-dimensional (3D) matrix degradation. Additionally, the addition of drug-loaded nanoparticles directly in bacterial culture does not recapitulate the in vivo sustained release of phosphates due to nanoparticles embedded within tissue. Thus, the second model involved the development of a novel cell culture platform which utilized a proteolytically degradable hydrogel scaffold and a non-degradable nanocomposite hydrogel scaffold. In this assay NP-Pi and NP-PPi were entrapped in a non-degradable poly(ethylene) glycol (PEG) hydrogel to form of a nanocomposite matrix which served as a reservoir for sustained release of phosphates. Bacteria producing high levels of proteases were cultured in the presence of the nanocomposite phosphate releasing reservoir and the proteolytically degradable PEG hydrogel scaffold to determine the efficacy of sustained release of phosphates in attenuating proteolytic hydrogel degradation. To correlate matrix degradation with bacterial enzymes secreted in the culture medium, we also developed a method to efficiently measure hydrogel degradation rate until complete material degradation with a greater degree of accuracy compared to the commonly employed method utilizing gravimetric measurements in gel wet weight. Combined, the in vitro platform and our proposed degradation assay provide a novel approach for screening the effect of therapeutics for attenuation of bacterial protease-induced matrix degradation.The 2D in vitro study demonstrated that the combination treatment (NP-PPi + NP-Pi) confers broad spectrum efficacy for suppression of collagenase and biofilm production across test pathogens. Conversely, the 3D in vitro model demonstrated that the combination treatment (NP-PPi + NP-Pi) attenuated protease production for gram-negative pathogens, while the gram-positive test pathogen exhibited significant decreases in protease levels only in the presence of NP-Pi. Finally, our novel Sirius red absorbance assay for quantifying hydrogel degradation was found to provide greater accuracy when compared to gravimetric measurements in gel wet weight. It also enabled real-time monitoring of 3D matrix degradation kinetics as well as the time required for complete material dissolution in the presence of bacterial proteases and active human MMP-9 enzyme solutions. These findings highlight the importance of designing relevant in vitro platforms for screening therapeutic efficacy in the presence of cells and nanomaterials.
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Title: Leakage Power Attack-Resilient Designs of A SRAM Cell in 7nm FinFET Technology
Creator: Chen, Kangqi
Date: 2019
Description: Recently, the classic metal-oxide-semiconductor field-effect-transistor (MOS- FET) has reached its limit for scaling. Another transistor...
Show moreRecently, the classic metal-oxide-semiconductor field-effect-transistor (MOS- FET) has reached its limit for scaling. Another transistor structure, FinFET, gradually has become the alternative choice for next generation of integrated circuits. Excellent features like reduced short channel effects, low threshold-voltage variability, less random dopant fluctuation, etc, offer this transistor model more stability, less leakage and faster performance. In particular, scaling trends force SRAM cells to be more vulnerable while using conventional MOSFET. The application of FinFET helps SRAM cell designs to overcome stability issues and achieve less power and faster speed. Another critical feature of an SRAM cell that needs to be considered is the correlation between data stored in cell and leakage of this cell. Side-Channel Attacks (SCA) like Leakage Power Analysis (LPA) would exploit this correlation to decrypt the secret key inside the memory. SCA has been proved to be a non-invasive but dangerous threat. Therefore, LPA would be the main focus of this thesis research.In this thesis, firstly, threshold voltage of various models are investigated using fundamental logic circuits including full-adders built with pass transistors, CLRCL and SERF. Secondly, conventional 6T SRAM cell design and single-ended 9T SRAM cell design targeting high stability and low power, are implemented and compared. Thirdly, the leakage balance method is applied to 9T cell design. Two novel solutions for LPA prevention of 9T design are proposed, implemented and compared against the original 9T design and conventional 6T design. The results confirm improved leakage balance and attack resilience while maintaining the stability and low-power features of the original 9T SRAM cell.
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Title: Simple Entropy Terms for End-Point Binding Free Energy Calculations
Creator: Menzer, William Michael
Date: 2019
Description: We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are...
Show moreWe introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average receptor−ligand interaction energies in simulations of a noncovalent complex, to improve the treatment of entropy: second- and higher-order terms in a cumulant expansion and a confining potential on ligand external degrees of freedom. We also consider a filter for snapshots where ligands have drifted from the initial binding pose. The variations were tested on six sets of systems for which binding modes and free energies have previously been experimentally determined. For some data sets, none of the tested estimators led to results significantly correlated with measured free energies. In data sets with nontrivial correlation, a ligand RMSD cutoff of 3 Å and a second-order truncation of the cumulant expansion was found to be comparable or better than the average interaction energy by several statistical metrics.
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Title: SHARING COMMUNITY HOUSING YOUNG PROFESSIONALS IN CHINESE BIG CITIES
Creator: ZHANG, HAOYU
Date: 2018
Description: In the past few decades, China has achieved an unbelievable fast development, from a poor after-war country to the second largest economy in...
Show moreIn the past few decades, China has achieved an unbelievable fast development, from a poor after-war country to the second largest economy in the world. Under the leadership of the Chinese central government and people’s corporate effort, China made significant achievements in its economic growth, modernization construction. With these achievements, Chinese urbanization has gone through a rapid development and expansion process. Nowadays, city living quality and urban development became one of the most popular focal points in Chinese people’s daily life.The Chinese urbanization enters rapid expansion era. Urbanization with Chinese characteristics does bring a rich material life and improve the standard of people’s living. Meanwhile, city problems started to appear and bring inexpediency and troubles to urban resident’s daily life. At the same time when cities are developing, the distance between people seems to get further. Comparing to other groups of people, the young professionals, are facing more challenges in the cities. They are under pressure from intense competition and high living cost. Most of them must live in space with bad conditions and gradually lose confidence under the heavy load from life. They are also in self-enclosed status, losing normal social relationships and scare to communicate with others. In Chinese big cities, having a comfortable space to live and not being lonely seems to be an unattainable wish for the young generation. Meanwhile, as an emerging economic pattern, Sharing Economy started to appear in most countries of the world during past years. China, as one of the largest economies, and a country with extremely high population base and rapid development speed became the best place for sharing economy to be developed. The Chinese urbanization situation gave a massive push to the sharing economy which is highly expected and considered to be able to solve the problem of conflict between people and urban. This thesis aims to prove that the idea of sharing can create an efficient, economical and comfortable living environment for young professionals in Chinese big cities, by looking at the urbanization with Chinese characteristics, young professionals living conditions, the development of sharing economy in China and developing a community prototype. This community will help young people to relieve living stress and rebuild social connections, also become a solution to reduce the conflict between young professionals and urban environment.
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Title: Hutong Skyscraper high-rise studio
Creator: Zhang, He
Date: 2012-05-02, 2012-05

Title: INVESTIGATION OF OXIDATIVE DEGRADATION AND DEGRADATION MITIGATION IN POLYMER ELECTROLYTE FUEL CELLS USING IN-SITU FLUORESCENCE SPECTROSCOPY
Creator: Prabhakaran, Venkateshkumar
Date: 2014, 2014-05
Description: Hydrogen/air polymer electrolyte fuel cells (PEFCs) possess high efficiency and modularity. However, significant technical advances are...
Show moreHydrogen/air polymer electrolyte fuel cells (PEFCs) possess high efficiency and modularity. However, significant technical advances are required to facilitate their commercialization in targeted applications. A key issue is component durability under an array of adverse operating conditions. The polymer electrolyte membrane (PEM) in a PEFC is one of the components whose long-term durability is of concern since it undergoes mechanical, thermal, and chemical degradation during fuel cell operation. The chemical (oxidative) degradation processes that take place in a PEM are attributed to reactive oxygen species (ROS) that are generated in-situ during PEFC operation. It is essential to quantify the rate of ROS generation within the PEM during PEFC operation prior to proposing an effective degradation mitigation strategy. This is a daunting challenge, given the high reactivity and very short lifetime of these species. The rate of generation of ROS within the PEM of an operating PEFC was accurately measured, for the very first time, using in-situ fluorescence spectroscopy. The influence of fuel cell operating parameters (temperature, relative humidity, and electrode potential/current density) on the rate of ROS generation was studied. The ROS generation reaction rate constant (estimated from the in-situ fluorescence experiments) correlated perfectly with the macroscopic rate of PEM degradation (estimated from the ex-situ fluoride emission rate) across all conditions, demonstrating unequivocally for the first time that a direct correlation existed between in-situ ROS generation and PEM macroscopic degradation. The utility of using regenerative free radical scavengers (FRS) such as CeO2 nanoparticles to mitigate ROS induced PEM degradation was also demonstrated using xxii xxii in-situ fluorescence spectroscopy. Though CeO2 was shown to scavenge the generated ROS, its scavenging efficacy declined with time and hence it was not truly a regenerative scavenger. The FRS efficacy was found to scale with the number of surface oxygen vacancies in its non-stoichiometric lattice. The regenerative FRS activity of CeO2 nanoparticles was improved by tuning its lattice via nitrogen doping (N-doping). It was demonstrated that N-doping increased both the number of Ce3+ active clusters in the lattice and the Ce-O bond distance; these structural attributes enhanced the regenerative ROS scavenging activity of CeO2. In addition, the influence of catalyst support on PEM degradation during PEFC operation was studied. A novel and highly corrosion-resistant non-carbon catalyst support (RuO2-SiO2; RSO) developed by our group was compared against a benchmark carbonbased catalyst support (Vulcan XC 72; C). It was found that the ROS generation rate, and hence the macroscopic PEM degradation rate, was lower when RSO was used as the electrocatalyst support in place of C. In conjunction with its remarkable corrosionresistance, this finding further illustrated the viability of RSO as an outstanding PEFC electrocatalyst support. Apart from PEM degradation, the applications of fluorescence spectroscopy in the context of other electrochemical devices was also discussed. Proofof- concept studies to study the Pt dissolution rate (in PEFC electrodes) and vanadium crossover rate (in vanadium redox flow batteries) were successfully undertaken; these areas, along with probing degradation processes secondary batteries, would be rich grounds for future study.
PH.D in Chemical Engineering, May 2014
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Title: WIND TURBINE FARMS IMPACT ON POLLEN TRANSPORT DISPERSION PATTER S
Creator: Hsu, Chin Yu
Date: 2012-11-28, 2012-12
Description: Wind energy has become more and more popular because electricity generation by wind power brings much less environmental impacts than...
Show moreWind energy has become more and more popular because electricity generation by wind power brings much less environmental impacts than conventional energy generation using coal. Also, energy generated by wind power does not require expensive fuel imported from overseas. Since the land in between turbines is still cultivated for crops and grazing, it is important to know the potential interference of wind turbines with pollen transport and dispersion, or the possible change of patterns established for thousands of years. However, these issues have not been studied in the literature. The co-existence of conventional crops with genetically modified (GM) crops has become a subject of debate. In particular, pollen transfer from GM crops to non-GM crops might result in the introgression of transgenes into natural populations as maize is mainly wind-pollinated. This study thus reports and assesses a comprehensive method that estimates maize pollen transport in the presence of turbines to ascertain the potential for maize pollen transport. The study on the concentrations of maize pollen transport affected by the wind turbines considers different dispersion parameters given the additional mechanical turbulence introduced by the presence of operating wind turbines. For instance, the wind turbines can increase surface roughness which subsequently causes increased mechanical turbulence. A high mechanical turbulence subsequently reduces downwind concentrations because of the mixing higher and wider into the atmosphere, which dilutes the maize pollen plume with more clean air. This study compares maize hourly concentrations and ground level flux levels inside and outside a virtual maize flux in the presence and absence of operating wind turbines. Results from a 14-day simulation of maize transport xii with and without operating wind turbines indicate that each difference of corresponding concentration and flux levels is statistically significant. Likewise, patterns of maize pollen transport inside the farm with turbine effects are significantly different from those without turbine effects. Overall, the average maize pollen concentration inside the farm in the absence of turbine effects is about 5 times greater than the corresponding maize pollen concentration with turbine effects. The total mass of maize pollen released into the air is the same whether the wind turbines are present or not. The portion of maize pollen staying inside the farm, on the other hand, is influenced by turbulence. For instance, the increased surface roughness caused by the turbine effects will increase the mechanical turbulence. Because the high mechanical turbulence carries a large portion of maize pollen away from the farm, only a small portion of maize pollen stays inside the farm due to the high turbulence that lifts maize pollen into higher levels of flow where the wind speed is stronger. In contrast, without turbine effects, a small portion of maize pollen leaves the farm while most of it deposits on the ground much sooner than it would with turbine effects. Therefore, maize pollen concentration and ground level flux in the presence of turbine effects will be greater than they are without turbine effects at a relatively far distance from the farm.
PH.D in Environmental Engineering, December 2012
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Title: RESILIENT CITIES OF THE FUTURE UTILIZING NATURAL INTELLIGENCE TO RETROFIT THE URBAN SYSTEMS
Creator: Naik, Vaidehi
Date: 2017, 2017-07
Description: Accentuated by the industrial revolution, the climate change is aging our cities, which are now facing an ecological, economical, and...
Show moreAccentuated by the industrial revolution, the climate change is aging our cities, which are now facing an ecological, economical, and political imbalance resulting into the degraded quality of urban living. Not only has global warming altered the earth’s natural patterns, but it also altered the economic and socio-cultural urban patterns. With the growing needs of rapidly expanding urban population due to the industrial revolution, the cities underwent unplanned sprawling of urban agglomerations. However, our globalized economic system has evolved the way we live, work, and play, transforming the modern infrastructure growth models significantly. Our architects, urban planners, and policy makers are powered by the environmental scientist’s years of research and analysis, yet are struggling to replenish the post-industrial age rust belt mayhem with sustainable solutions. As the transition from industrial to ecological age become eminent, by investigating into the natural intelligence’s survival techniques, we could extract practical solutions to using clean and renewable energy systems to support life. This thesis aims at analyzing the current trends in redesigning and retrofitting the urban-systems with the eco-systems at the micro- and macro- scales, thus providing with sustainable solutions to the new city center of the sixth largest town in Canada, Mississauga. Caused by rapid urbanization, population growth & migration, increased emission of green house gases, and overuse & pollution, our deteriorating infrastructure is grappling for mitigation against climate change, and global warming. Using natural intelligence to shift from linear to a closed loop system, the solutions provided herein aims at increasing the infrastructure’s resource efficiency and changing from fossil fuel to solar economy. Catalyzed by the proposed Midwestern high-speed rail line, the project in Mississauga (Ontario, Canada) seeks to introduce the hybrid, mixed-use, transit oriented development to instigate the shift towards eco-cities. These intermodal transit infrastructure aims to bring a strategically sustainable change at a neighborhood scale, thus eventually refurbishing the entire city, one territory at a time. The idea of these utopian cities may seem unachievable at a larger scale, but the cities like Hammarby Sjöstad, Tianjin, and Dongtan seem to lead, inspire, and equip the ignorant with their sustainable approach to growth. By transitioning towards an ecological age, there seems a way to negating the effects of human induced climate change, and make our planet sustainable for the future generations to survive.
M.S. in Architecture, July 2017
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Title: LAND USE EFFECTS ON WATER QUALITY: BUILDING A FRAMEWORK FOR CHICAGO RIVER WATERSHED
Creator: Mahdi, Naila Ghidey Ismail
Date: 2012-05-09, 2012-05
Description: The purpose of this study is to introduce a framework that enables a holistic watershed approach that models the dynamics of water quality and...
Show moreThe purpose of this study is to introduce a framework that enables a holistic watershed approach that models the dynamics of water quality and landuse in a highly urbanized watershed. The landuse-water quality relationship is a complex relationship and has not been adequately addressed for highly urbanized watersheds. Factors such as inadequate urban planning, increase of impervious areas and dynamics of population growth are some of the reasons for the complex relationship. Also point sources are always easy to be identified and controlled unlike nonpoint sources such as urban storm runoff. Both quantities and transport pathways of pollutant inputs are impacted by land use in the watershed. So, examining the factors that govern the relationship between different land uses and water quality within a watershed can give insights and important information about existing and potential sources of contamination. The two backbone concepts in this study are the holistic watershed perspective and the role of historical data records as part of assessment, modeling and integration tools of the watershed framework. Analysis of the records will explain watershed conditions identifying the major problem areas and justify the modeling and post analysis procedures. Data sources are often important but data availability, heterogeneity and conformity are the main challenges in integrating these sources. This research presents an approach to integrate the watershed data in a single repository and methodologies for analyzing and assessing the watershed using data warehouse and data mining technologies. A multi-dimensional model that supports complex querying of watershed data and discovery of trends and patterns in data by incorporating 40 years worth of watershed data from different source agencies in a central repository is introduced. Also, the discipline of data driven modeling was introduced in this thesis using the developed central repository. Several regression and classification algorithms were presented and assessed for their appropriateness for predicting total nitrates using few watershed attributes. The results show acceptable prediction accuracy. Five years of water quality simulation using the multi-purpose environmental analysis system BASINS coupled with the comprehensive, conceptual, and continuous simulation watershed scale model HSPF resulted in export coefficients for level (III), detailed land use for the Chicago River watershed. The water quality simulation approach utilized in this research to generate the coefficients constitutes a new contribution to the Chicago River watershed and other highly urbanized watersheds. The continuous calibrated and validated model can be used in the investigation and analysis of different scenarios and possible future conditions, thus providing a planning tool for regulatory environmental agencies. The data driven models developed can be used as operation tool to maintain the water quality parameters especially if TMDL and WQS are developed for Chicago River Watershed. So the framework proposed for this study can be considered robust with the proposed integration, planning and operating techniques and tools. Furthermore, an optimization tool is introduced in the future work section.
Ph.D. in Environmental Engineering, May 2012
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