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Title: Modeling, Analysis and Computation of Tumor Growth
Creator: Lu, Min-Jhe
Date: 2022
Description: In this thesis we investigate the modeling, analysis and computation of tumor growth.The sharp interface model we considered is to understand...
Show moreIn this thesis we investigate the modeling, analysis and computation of tumor growth.The sharp interface model we considered is to understand how the two key factors of (1) the mechanical interaction between the tumor cells and their surroundings, and (2) the biochemical reactions in the microenvironment of tumor cells can influence the dynamics of tumor growth. From this general model we give its energy formulation and solve it numerically using the boundary integral methods and the small-scale decomposition under three different scenarios.The first application is the two-phase Stokes model, in which tumor cells and the extracellular matrix are both assumed to behave like viscous fluids. We compared the effect of membrane elasticity on the tumor interface and the curvature-weakening one and found the latter would promote the development of branching patterns.The second application is the two-phase nutrient model under complex far-field geometries, which represents the heterogeneous vascular distribution. Our nonlinear simulations reveal that vascular heterogeneity plays an important role in the development of morphological instabilities that range from fingering and chain-like morphologies to compact,plate-like shapes in two-dimensions.The third application is for the effect of angiogenesis, chemotaxis and the control of necrosis. Our nonlinear simulations reveal the stabilizing effects of angiogenesis and the destabilizing ones of chemotaxisand necrosis in the development of tumor morphological instabilities if the necrotic core is fixed. We also perform the bifurcation analysis for this model.In the end, as a future work, we propose new models through Energetic Variational Approach (EnVarA) to shed light on the modeling issues.
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Title: GLOBAL ESTIMATION AND ANALYSIS OF IONOSPHERIC DRIVERS WITH A DATA ASSIMILATION ALGORITHM
Creator: López Rubio, Aurora
Date: 2022
Description: This dissertation studies a data assimilation algorithm that estimates the drivers of the ionosphere-thermosphere (IT) region of the Earth....
Show moreThis dissertation studies a data assimilation algorithm that estimates the drivers of the ionosphere-thermosphere (IT) region of the Earth. The algorithm, EMPIRE (Estimating Model Parameters from Ionospheric Reverse Engineering) can estimate 2 main drivers of the ionospheric behavior: neutral winds and electric potential by ingesting mainly ionospheric densities obtained through Global Satellite System (GNSS) measurements. Additionally, the algorithm can ingest FPI (Fabry-Perot interferometer) neutral wind measurements. The contributions include 1) Vector spherical harmonic basis function for neutral wind estimation, 2) Quantification of the representation error of the estimations of the algorithm EMPIRE, 3) Analysis of Nighttime Ionospheric Localized density Enhancement (NILE) events and 4) Ingestion of global ICON (Ionospheric Connection Explorer) neutral winds measurements. The IT region in the atmosphere is characterized by having a large concentration of free ions and electrons, electromagnetic radiation and Earth's magnetic field. The behavior of the region is dominated by the solar activity, that ionizes the free electrons of the region, forming ionospheric plasma and determining its density. Unusual solar activity or any atmospheric disturbance affects the distribution of the ionospheric plasma and the behavior of the IT region. The redistribution of the ionospheric density impacts technology widely used such as telecommunication or satellite navigation, so it is increasingly important to study the IT system response. The IT behavior can be characterized by what drives its changes. Two drivers that play a key role, the ones we focus on this dissertation, are electric potential, that directly affects the charged ions in the system, and neutral winds, that refers to the velocity of the neutral particles that form the thermosphere. To quantify these drivers, measurements and climate models are available. Measurements are limited as the IT region is vast and covers the entire globe. Climate models can provide information in all the region, but they are usually not as reliable during the unusual solar activity conditions or disturbances. In this dissertation we use a data assimilation algorithm, EMPIRE, that combines both sources of data, measurements and models, to estimate the IT drivers, neutral winds and electric potential. EMPIRE ingests measurements of the plasma density rate and models the physics of the region with the ion continuity equation. The drivers are represented with basis functions and their coefficients are estimated by fitting the expansions with a Kalman filter. In previous work and use of the algorithm, the neutral winds were expanded using power series basis function for each of the components of the vector. The first contribution of the dissertation is to use a vector spherical harmonic expansion to describe the winds, allowing a continuous expansion around the globe and self-consistent components of the vector. Before, EMPIRE estimated the correction of the drivers with respect climate model values. In this work, EMPIRE is also modified to directly estimate the drivers. Then, a study of the representation error, which is the discrepancy between the true physics and the discrete model that represents the physics of EMPIRE and its quantification is done. Next, EMPIRE is used to analyze two NILE events, using the global estimation of both winds, from the first contribution, and the electric potential, derived in previous work. Finally, global estimation of winds allows us to implement the ingestion of ICON global winds in EMPIRE, in addition to the plasma density rate measurements.
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Title: Machine learning applications to video surveillance camera placement and medical imaging quality assessment
Creator: Lorente Gomez, Iris
Date: 2022
Description: In this work, we used machine learning techniques and data analysis to approach two applications. The first one, in collaboration with the...
Show moreIn this work, we used machine learning techniques and data analysis to approach two applications. The first one, in collaboration with the Chicago Police Department (CPD), involves analyzing and quantifying the effect that the installation of cameras had on crime, and developing a predictive model with the goal of optimizing video surveillance camera location in the streets. While video surveillance has become increasingly prevalent in policing, its intended effect on crime prevention has not been comprehensively studied in major cities in the US. In this study, we retrospectively analyzed the crime activities in the vicinity of 2,021 surveillance cameras installed between 2005 and 2016 in the city of Chicago. Using Difference-in-Differences (DiD) analysis, we examined the daily crime counts that occurred within the fields-of-view of these cameras over a 12-month period, both before and after the cameras were installed. We also investigated their potential effect on crime displacement and diffusion by examining the crime activities in a buffer zone (up to 900 ft) extended from the cameras. The results show that, collectively, there was an 18.6% reduction in crime counts within the direct viewsheds of all of the study cameras (excluding District 01 where the Loop -Chicago's business center- is located). In addition, we adapted the methodology to quantify the effect of individual cameras. The quantified effect on crime is the prediction target of our 2-stage machine learning algorithm that aims to estimate the effect that installing a videocamera in a given location will have on crime. In the first stage, we trained a classifier to predict if installing a videocamera in a given location will result in a statistically significant decrease in crime. If so, the data goes through a regression model trained to estimate the quantified effect on crime that the camera installation will have. Finally, we propose two strategies, using our 2-stage predictive model, to find the optimal locations for camera installations given a budget. Our proposed strategies result in a larger decrease in crime than a baseline strategy based on choosing the locations with higher crime density.The second application that forms this thesis belongs to the field of model observers for medical imaging quality assessment. With the advance of medical imaging devices and technology, there is a need to evaluate and validate new image reconstruction algorithms. Image quality is traditionally evaluated by using numerical figures of merit that indicate similarity between the reconstruction and the original. In medical imaging, a good reconstruction strategy should be one that helps the radiologist perform a correct diagnosis. For this reason, medical imaging reconstruction strategies should be evaluated on a task-based approach by measuring human diagnosis accuracy. Model observers (MO) are algorithms capable of acting as human surrogates to evaluate reconstruction strategies, reducing significantly the time and cost of organizing sessions with expert radiologists. In this work, we develop a methodology to estimate a deep learning based model observer for a defect localization task using a synthetic dataset that simulates images with statistical properties similar to trans-axial sections of X-ray computed tomography (CT). In addition, we explore how the models access diagnostic information from the images using psychophysical methods that have been previously employed to analyze how the humans extract the information. Our models are independently trained for five different humans and are able to generalize to images with noise statistic backgrounds that were not seen during the model training stage. In addition, our results indicate that the diagnostic information extracted by the models matches the one extracted by the humans.
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Title: EXAMINING PERFORMANCE DEGRADATION OF LI-ION BATTERIES WITH SILICON-BASED ANODE AND POSSIBLE SOLUTIONS TO IMPROVE THE SILICON ANODE BEHAVIOR
Creator: Luo, Mei
Date: 2022
Description: Si has been investigated as a promising alternative to conventional graphite because of its high specific capacity and wide operating voltage;...
Show moreSi has been investigated as a promising alternative to conventional graphite because of its high specific capacity and wide operating voltage; however, technical challenges related to volume change in the silicon anode have hampered their practical application. In this work, the effects of silicon volume change on electrochemical performance has been studied in NMC532/Si full cells. First, different area specific capacity ratios of the negative to positive electrode (N:P ratio) were investigated using three-electrode cells. With individual electrode potentials monitored by a reference electrode, different depths of lithiation/delithiation at the anode and cathode were found to play an important role on cell performance; the cell with higher N:P ratio displays superior electrochemical performance due to its smaller silicon volume change. Further, calendar-life aging and cycle-life aging of NMC532/Si cells were compared with their electrode potentials monitored using a reference electrode. The observation of larger capacity decay and impedance growth of cycle-life aging cells illustrates the important effect of silicon volume change; significant capacity decay of calendar-life aged cell was observed as well, revealing an essential role of chemical effect of ongoing side reactions at Si anode. Specially-designed silicon with different protocols and electrolyte additives were investigated to address the intrinsic challenges of Si anodes for lithium-ion batteries.
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Title: Mothers’ Vaccination Decision: The Relation Between Science Skepticism, Social Networks, Vaccination Beliefs, and Fear of ASD
Creator: Lockwood, Maria Izabel Kugelmas Guarita
Date: 2021
Description: Vaccines are instrumental in stopping the spread of disease, yet some parents choose to not vaccinate their children. Despite scientific...
Show moreVaccines are instrumental in stopping the spread of disease, yet some parents choose to not vaccinate their children. Despite scientific evidence that childhood vaccines are safe, there is an increasing number of children in the United States and the United Kingdom who are not getting vaccinated. The current study investigates different factors that may be associated with mothers’ decision to vaccinate their children. This study examines the relations between skepticism in science, vaccination beliefs, fear of having a child with Autism Spectrum Disorder (ASD), social network recommendations, and maternal decision to vaccinate. Participants included 293 expectant mothers in the United States and the United Kingdom. Results indicated that mothers who are pro-vaccine and mothers who are vaccine-hesitant have different score profiles across scales that measure skepticism in science, vaccination beliefs, and fear of having a child with ASD. Specifically, we found that relative to mothers who are vaccine-hesitant, mothers who are pro-vaccine: (1) indicated less skepticism in science; (2) had fewer anti-vaccination beliefs; (3) did not statistically differ on their fear of having a child with ASD; and (4) had a smaller percentage of their social network advocating against vaccination. Thus, the study adds to the research literature, as it illustrates that mothers who are vaccine-hesitant differ from mothers who are pro-vaccine on key factors.
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Title: Data-Driven Methods for Soft Robot Control and Turbulent Flow Models
Creator: Lopez, Esteban Fernando
Date: 2022
Description: The world today has seen an exponential increase in its usage of computers for communication and measurement. Thanks to recent technologies,...
Show moreThe world today has seen an exponential increase in its usage of computers for communication and measurement. Thanks to recent technologies, we are now able to collect more data than ever before. This has dawned a new age of data-driven methods which can describe systems and behaviors with increasing accuracy. Whereas before we relied on the expertise of a few professionals with domain-specific knowledge developed over years of rigorous study, we are now able to rely on collected data to reveal patterns, develop novel ideas, and offer solutions to the world’s engineering problems. No domain is safe. Within the engineering realm, data-driven methods have seen vast usage in the areas of control and system identification. In this thesis we explore two areas of data-driven methods, namely reinforcement learning and data-driven causality. Reinforcement learning is a method by which an agent learns to increase its selection of ideal actions and behaviors which result in an increasing reward. This method was applied to a soft-robotic concept called the JAMoEBA to solve various tasks of interest in the robotics community, specifically tunnel navigation, obstacle field navigation, and object manipulation. A validation study was conducted to show the complications that arise when applying reinforcement learning to such a complex system. Nevertheless, it was shown that reinforcement learning is capable of solving three key tasks (static tunnel navigation, obstacle field navigation, and object manipulation) using specific simulation and learning hyperparameters. Data-driven causality encompasses a range of metrics and methods which attempt to uncover causal relationships between variables in a system. Several information theoretic causal metrics were developed and applied to nine mode turbulent flow data set which represents the Moehlis model. It was shown that careful consideration into the method used was required to identify significant causal relationships. Causal relationships were shown to converge over several hundred realizations of the turbulent model. Furthermore, these results match the expected causal relationships given known information of self-sustaining processes in turbulence, validating the method’s ability to identify causal relationships in turbulence.
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Title: ARCHITECTURE FOR COLLABORATIVE CREATIVITY - SPACE WE-Q: SPACE INTELLIGENCE EMPOWERING CREATIVE WE CULTURE IN LEARNING-DRIVEN ENVIRONMENTS
Creator: Mor-Avi, Anat
Date: 2020
Description: Changes in societal culture, along with research on how we learn, challenge current architectural solutions. Education’s shifting paradigms...
Show moreChanges in societal culture, along with research on how we learn, challenge current architectural solutions. Education’s shifting paradigms align with these changes and move teaching strategies from teacher-centered to learner-centered, and from formal and passive, to informal and active modes. Another shift emphasizes collaboration and participatory creativity, which evolve the idea of the “collective,” or “We” versus “I” scenarios. In addition, studies show that creativity flourishes in specific contradictory performances. Supporting these reported changes, new knowledge, and paradigm shifts, this research studied how an active, adaptive architectural design approach might emerge into the learning and creative processes. Evidence indicates that “design and space do matter,” particularly in learning- and working-driven domains. Empirical research has been weak in addressing this understanding relative to architectural solutions, affordances, behaviors, and emotions, promoting collaborative creativity. This research aimed to investigate patterns of architectural affordances believing to impact and empower collaborative cultures and behaviors in learning environments (“WE CULTURE”), specifically motions and emotions. A Mixed-method research design was conducted, using two techniques: (a) a content analysis of awarded learning and working environments, and (b) a post-occupancy evaluation using ethnographic techniques to study the Kaplan Innovation Institute at the Illinois Institute of Technology in Chicago, Illinois, USA. In an effort to provide an applied design study, a visual pattern language related to cultures of learning, environment behavior, and emotions was developed. The pattern language is the platform for designing intelligent spaces, SPACE WE-Q, promoting collaborative behaviors, and creativity through adaptive and behavior-based systems of active affordances. SPACE WE-Q offers a planned adaptive system for unplanned creative processes that emerges into learning and suggesting a new relationship between architecture and education, between architects and users, and between users and space.
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Title: Promoting Healthy Lifestyle Behaviors for African Americans with Serious Mental Illness and Weight Concerns
Creator: Nieweglowski, Katherine
Date: 2022
Description: People with serious mental illness face greater rates of chronic illness and obesity compared to those without mental illness. These rates are...
Show morePeople with serious mental illness face greater rates of chronic illness and obesity compared to those without mental illness. These rates are disproportionately higher for those who are part of racially minoritized groups. For example, African Americans are more likely to be obese compared to their white counterparts. This study sought to test a diet and exercise program—developed through community-based participatory research—called “Behaviors for Healthy Lifestyles” (BHL) for African Americans with serious mental illness and weight concerns. The impact of this program, also combined with peer health navigation (PHN), was tested on various physical and mental health outcomes. Participants were randomly assigned to either integrated-care treatment as usual (IC-TAU), BHL, or BHL+PHN. Data was collected at baseline, 4-month, 8-month, and 12-month follow up for outcomes measuring general health, bodily pain, physical functioning, emotional well-being, depression, recovery, quality of life, weight efficacy, and emotional eating. Monthly data collection was also conducted on frequency of healthy lifestyle behaviors related to diet and physical activity. Findings from group by trial analyses of variance on these outcomes did not show any significant impact. Implications for testing diet and exercise interventions combined with PHN for this population are discussed along with future research considerations related to increasing attendance and participation for greater health improvements.
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Title: Development and evaluation of high resolution MRI templates and labels of the MIITRA atlas
Creator: Niaz, Mohammad Rakeen
Date: 2022
Description: A digital human brain atlas consisting of MRI-based multi-modal templates and semantic labels delineating brain regions are commonly used as...
Show moreA digital human brain atlas consisting of MRI-based multi-modal templates and semantic labels delineating brain regions are commonly used as references for spatial normalization in a wide range of neuroimaging studies. Magnetic resonance imaging (MRI) studies of the aging brain is of significant interest in recent times to explore the role of brain characteristics associated with cognitive functions. The introduction of advanced image reconstruction techniques, and the recent trend in MRI acquisitions at submillimeter in-plane resolution have resulted in an easier availability of MRI data on older adults at high spatial resolution. An atlas with a comprehensive set of high-resolution templates representative of the older adult brain and detailed labels accurately mapping brain regions can increase the sensitivity and specificity of such neuroimaging studies. Additionally, most neuroimaging studies can benefit from a high-resolution atlas with templates where fine brain structures are resolved and, where the transition between different tissue can be more accurately defined. However, such an atlas is not publicly available for older adults. Hence the goal of this thesis is to develop a comprehensive, high-resolution digital human brain atlas for older adults termed as Multi-channel Illinois Institute of Technology and Rush University Aging (MIITRA) atlas.This dissertation aims a) to develop a new technique based on the principles of super-resolution for the construction of high-resolution structural and diffusion tensor templates, and evaluate the templates for use in studies on older adults, b) to construct and evaluate high-resolution structural and diffusion tensor templates constructed using the method developed in (a) for the MIITRA atlas using MRI data collected on 400 nondemented older adults, c) to investigate and develop a technique for the construction of high-resolution labels and evaluate the performance of gray matter labels constructed using this technique in segmenting the gray matter of older adults, and d) to develop and evaluate a comprehensive set of high-resolution labels using the technique developed in (c) for the MIITRA atlas using data on 400 non-demented older adults. Based on the aforementioned points, the thesis is structured as follows: Firstly, this thesis presents a novel approach for the construction of a high-resolution T1-weighted structural template based on the principles of super resolution. This method introduced a forward mapping technique to minimize signal interpolation, and a weighted averaging method to account for residual misregistration. The new template was shown to resolve finer brain structures compared to a lower resolution template constructed using the same data. It was demonstrated through systematic comparison of this new template to several other standardized templates of different resolutions that a) it exhibited high image sharpness, b) was free of image artifacts, c) allowed for high spatial normalization accuracy and detection of smaller inter-group morphometric differences compared to other standardized templates, d) was highly representative of the older adult brain. This novel approach was further modified for the construction of a high spatial resolution diffusion tensor imaging template. The new DTI template is the first high spatial resolution population-based DTI template of the older adult brain and exhibits high image quality, high sharpness, is free of artifacts, resolves fine white matter structures, and provides higher spatial normalization accuracy of older adult DTI data compared to other available DTI templates. Secondly, the aforementioned techniques were utilized in the development of high resolution T1-weighted and DTI templates, and tissue probability maps for the MIITRA atlas using high quality MRI images on 400 diverse, community cohort of non-demented older adults. Thirdly, a novel approach for generating high resolution gray matter labels is presented that involves a) utilization of the super resolution technique to ensure sharp delineation of structures, and b) a multi atlas based correction technique to reduce errors due to misregistration. High-resolution gray matter labels were constructed using the super resolution technique. When used for regional segmentation of the gray matter of older adults, the new gray matter labels of the showed high overlap, high geometric correlation, and low dissimilarity with the manually edited reference labels, demonstrating that there is a high agreement between the new labels and the manually edited Freesurfer labels. Finally, this thesis presents the development of a comprehensive array of gyral-based, cytoarchitecture-based, and functional connectivity-based gray matter labels in MIITRA space utilizing the aforementioned techniques. These labels include gyral-based, cytoarchitecture-based, and functional connectivity-based labels which will enhance the functionality of the MIITRA atlas. The new labels will also enhance the interoperability of MIITRA with the source atlases.
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Title: The Detection of Emerging Pathogenic Arcobacter Species In Poultry and Poultry By-Products
Creator: Nguyen, Paul
Date: 2022
Description: Arcobacter species are emerging foodborne pathogens that are associated with human gastrointestinal illness. Typical symptoms of Arcobacter...
Show moreArcobacter species are emerging foodborne pathogens that are associated with human gastrointestinal illness. Typical symptoms of Arcobacter infection that have been reported include diarrhea, abdominal cramps, nausea, vomiting, and in severe cases, bacteremia. Consumption of contaminated food and water is the most common transmission source that leads to human infection. When consumed, pathogenic Arcobacter spp. pass through the stomach and establishes themselves in the host intestinal tract, where they cause gastroenteritis. Currently, there is no standard isolation method to detect pathogenic Arcobacter spp. from food and environment sample matrices. The research detailed in this thesis describes the development of the Nguyen-Restaino-Juárez Arcobacter detection system (NRJ) comprised of a selective enrichment broth and a chromogenic agar plate used to isolate three pathogenic species: Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. Results revealed that NRJ yielded 97.8% inclusivity and 100.0% exclusivity when evaluating against select bacterial strains found in foods. Our research group internally validated the novel chromogenic detection system by comparing its efficacy against the modified Houf reference method (HB). Method-performance evaluations determined the NRJ method was significantly more sensitive and specific than modified HB when isolating the three Arcobacter species from ground chicken samples. Furthermore, 16S amplicon sequencing data identified that greater than 97% of bacterial isolates recovered using the NRJ detection system were Arcobacter species. This thesis presents the development and validation of a new gold standard method for isolating these emerging pathogens in food, clinical and environmental sampling.
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Title: Synthesis and Photophysical Characterization of Novel Aromatic Triplet Dyes for Photodynamic Therapy Applications
Creator: Morgan, Jayla A
Date: 2022
Description: Photodynamic therapy is a biomedical approach to treating specific types of cancerous tumor cells and harmful bacteria. The core principle of...
Show morePhotodynamic therapy is a biomedical approach to treating specific types of cancerous tumor cells and harmful bacteria. The core principle of photodynamic therapy involves the usage of a photosensitizer, which is an agent with the capability of transforming molecular, triplet state oxygen, into a reactive oxygen species upon a reaction with near-infrared (NIR) light. The reactive oxygen species has been demonstrated to cause apoptosis among harmful cells without damaging cancer free cells. The effectiveness of photodynamic is highly dependent upon the identity of the photosensitizer; a powerful and efficient photosensitizer should be non-toxic, exhibit high light absorption capabilities, and should produce large amounts of the reactive oxygen species. A novel chromophore bis-iodo-dipyrrolonaphthyridine-dione was demonstrated to have all vital characteristics of an ideal photosensitizer, however produced low amounts of the reactive oxygen species of interest due to the chemical instability of a carbon-halogen bond present in the molecule. Various subsequent halogenations (bis-bromo and bis-chloro) completed in order to remedy this instability revealed specific regioselectivity in regards to the dipyrrolonaphthyridinedione parent that are exhibited upon substituents effects by the substrate, electronic effects exhibited by the reagents of interest, and overall photophysical characterization of the molecules.
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Title: Non-Hermitian Phononics
Creator: Mokhtari, Amir Ashkan
Date: 2021
Description: Non-Hermitian and open systems are those that interact with their environment by the ﬂows of energy, particles, and information. These systems...
Show moreNon-Hermitian and open systems are those that interact with their environment by the ﬂows of energy, particles, and information. These systems show rich physical behaviors such as unidirectional wave reflection, enhanced transmission, and enhanced sensitivity to external perturbations comparing to a Hermitian system. To study non-Hermitian and open systems, we first present key concepts and required mathematical tools such as the theory of linear operators, linear algebra, biorthogonality, and exceptional points. We first consider the operator properties of various phononic eigenvalue problems. The aim is to answer some fundamental questions about the eigenvalues and eigenvectors of phononic operators. These include questions about the potential real and complex nature of the eigenvalues, whether the eigenvectors form a complete basis, what are the right orthogonality relationships, and how to create a complete basis when none may exist at the outset. In doing so we present a unified understanding of the properties of the phononic eigenvalues and eigenvectors which would emerge from any numerical method employed to compute such quantities. Next, we apply the mentioned theories on the phononic operators to the problem of scattering of in-plane waves at an interface between a homogeneous medium and a layered composite. This problem is an example of a non self-adjoint operator with biorthogonal eigenvectors and a complex spectrum. Since this problem is non self-adjoint, the degeneracies in the spectrum generally represent a coalescing of both the eigenvalues and eigenvectors (exceptional points). These degeneracies appear in both the complex and real domains of the wavevector. After calculating the eigenvalues and eigenvectors, we then calculate the scattered fields through a novel application of the Betti-Rayleigh reciprocity theorem. Several numerical examples showing rich scattering phenomena are presented afterward. We also prove that energy flux conservation is a restatement of the biorthogonality relationship of the non self-adjoint operators. Finally, we discuss open elastodynamics as a subset of non-Hermitian systems. A basic concept in open systems is effective Hamiltonian. It is a Hamiltonian that acts in the space of reduced set of degrees of freedom in a system and describes only a part of the eigenvalue spectrum of the total Hamiltonian. We present the Feshbach projection operator formalism -- traditionally used for calculating effective Hamiltonians of subsystems in quantum systems -- in the context of mechanical wave propagation problems. The formalism allows for the direct formal representation of effective Hamiltonians of finite systems which are interacting with their environment. This results in a smaller set of equations which isolate the dynamics of the system from the rest of the larger problem that is usually infinite size. We then present the procedure to calculate the Green's function of effective Hamiltonian. Finally we solve the scattering problem in 1D discrete systems using the Green's function method.
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Title: TWO ESSAYS IN SUSTAINABILITY AND ASSET RETURN PREDICTABILITY
Creator: Nguyen, Lanh Vu Thuc
Date: 2021
Description: Our paper consists of two chapters in Financial Modeling for Sustainability and Asset Return Predictability. Recent developments in data...
Show moreOur paper consists of two chapters in Financial Modeling for Sustainability and Asset Return Predictability. Recent developments in data scraping and analytical methods have enhanced the possibility to construct the data and modeling required to examine the topics in each chapter. Chapter 1 proposes a simple yet strategic model involving a personal financial system to achieve a sustainable and prosperous future. The proposed model emphasizes the optimization of carbon footprints of one person at a time through the decentralization of the electricity use. While describing steps to develop a decentralized system considering electricity as a credit product, the model also underlines the importance of geographic economic dimensions and energy market prices due to their anticipated impact on the effectiveness of designing strategies for optimizing individuals’ energy use habits. Geographical conditions as well as market electricity prices can be used to signal individual energy use scores over time, therefore could also be instrumental in customizing energy use habits as the users realize variations in their energy use scores resulting from hourly electricity price changes at their locations. In other words, not only the changes in the individual’s behavior, but also the changes in the geographical conditions and community of users will affect the improvement of energy use behaviors of an individual over time using our model. We believe that the proposed model can be efficiently adopted to take on challenges threatening the future sustainability. While describing the basic characteristics of the model, we also open the possibility for future studies its capabilities to reduce carbon footprints from other societal choices, for example, using water, managing waste, or designing sustainable transportation systems. In Chapter 2, we examine asset return predictability, which is an important topic in finance with rich literature. Much of the current literature considers dividend yield as the main predictor for expected returns, and the main discussion centers around confirming or rejecting the predictive power of dividend yield with mixed evidence. However, dividend payments have been consistently declining and public firms have been increasingly using stock repurchase as the alternative to return values to shareholders. We aim to contribute to the literature by investigating a panel data of total equity payout, which takes into account not only dividend payout but also other forms of payment such as stock repurchase, as the main predictor for expected returns. In the asset return predictability literature, existing studies gather stock repurchase data from financial statements. In this paper, we manually construct our database of returns and payouts of public companies from various sources to create precise firm-level total equity payout dataset without relying on approximations from annual financial statements. This study adds to understanding of total equity payout and stock returns by analyzing a finer granularity than an annum and cross section of stock returns.
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Title: Video Object Detection using CenterNet
Creator: Mondal, Madhusree
Date: 2021
Description: This thesis investigates the options of video object detection with key-point-based approaches. The problem of recognizing, locating, and...
Show moreThis thesis investigates the options of video object detection with key-point-based approaches. The problem of recognizing, locating, and tracking objects in videos has been a challenging task in the computer vision area. There are few applications on key-point-based object detectors like CornerNet and CenterNet. At the first stage, this work involves the use of the previously proposed CenterNet module as a baseline detector on each frame of the Imagenet Video dataset. Then we apply an RNN module to exploit the temporal information from the past frames for better results.There are challenges in video object detection compared to still image-based object detection. It is not efficient to apply a still-image-based detector on each frame independently because we cannot exploit the temporal contextual information in videos since neighboring frames in a video are highly correlated. Object detection from videos suffers from motion blur, video focus, rare poses, etc. To overcome these issues one way of improving CenterNet for video object detection is to propagate the previous reliable detection results to boost the detection performance.
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Title: REDUCED-ORDER MODELING OF UNSTEADY FLOW OVER TWO COLLINEAR PLATES AT LOW REYNOLDS NUMBERS
Creator: Almashjary, Abdulrahman N
Date: 2021
Description: Wakes of bluff bodies that exhibit unsteady behavior are a topic of great interest in the study of fluid dynamics. Vortex formation in these...
Show moreWakes of bluff bodies that exhibit unsteady behavior are a topic of great interest in the study of fluid dynamics. Vortex formation in these wakes depends significantly on the Reynolds number and the arrangement of the bluff bodies in the computation domain. To attain a comprehensive understanding of the unsteady wakes of adjacent bodies, we examine the emerged flow patterns in the wake of two bodies when subjected to different flow regimes and geometric configurations. This work aims to develop a reduced-order model that can capture the dynamics and predict the time evolution of specific parameters in the flowfield. Investigations including direct numerical simulations of two collinear plates normal to the flow were performed. Flowfield data and forces exerted on the plates were collected using a numerical code of an immersed boundary projection method (IBPM). The conducted numerical simulations pursued classifying the flow patterns by systematically varying the Reynolds number and the gap between the two plates. It was found that at small gap spacings, a typical von Karman vortex street is observed. Whereas at larger gap spacings, both a biased and a flip-flopping gap flow are detected. Prevalent coherent structures present in various flow regimes can be extracted via data-driven modeling techniques. The proper orthogonal decomposition (POD) method is used in this framework, from which projection-based reduced-order models are developed utilizing the governing equations of fluid flows. Single and broadband spectra are observed in the unsteady wake of the two-plate configuration. The amplitude and frequency of the time-evolution of the true POD modes and the predicted models are assessed using the spectral proper orthogonal decomposition (SPOD), an empirical method to extract coherent structures one frequency at a time from fluid flows. It was found that these reduced-order models are able to recover the frequency content from non-time resolved data.
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Title: DEVELOPING FUSION BACTERIOCINS FOR ERADICATING PSEUDOMONAS AERUGINOSA BIOFILMS
Creator: An, Sungjun
Date: 2022
Description: The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of morbidity and mortality in cystic fibrosis patients and...
Show moreThe opportunistic pathogen Pseudomonas aeruginosa is a leading cause of morbidity and mortality in cystic fibrosis patients and immunocompromised individuals. Due to its remarkable ability to resist antibiotics, eradicating P. aeruginosa has become increasingly difficult. As previously reported, we have successfully engineered a colicin-secretion system that kills target biofilm cells rapidly and selectively in multispecies biofilms as well as demonstrated the potential of using live microorganisms engineered to produce antimicrobial colicin protein to treat biofilm-associated infections. In this study,we constructed a fusion colicin-pyocin that could target P. aeruginosa by DNase activity of colicin E2. The newly engineered bacteriocin-secretion system upon the shift in target, maintained biofilm inhibition capacity. Both during biofilm formation and after its development, the system was able to suppress the P. aeruginosa biofilm. This result opened up the possibility that it could be used for novel live biotherapeutics. A further study was conducted to overcome the challenge of requiring an exogenous inducer. We applied the concept of Quorum-Sensing signal that recognize autoinducer as a trigger of fusion colicin-pyocin producing genetic circuit so that it automates the production and secretion of fusion colicin-pyocin as soon as the genetic circuit senses the target population growing. This study demonstrated that combining the domains of colicin and pyocin could broaden the genetic circuit target range, maintaining strain specificity, while employing the QS system could remove the fundamental problem of diffusion or degradation of extra compounds as they approach engineered cells.
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Title: Asztalos_iit_0091N_11584

Title: Ausloos_iit_0091N_11542

Title: FUNCTIONAL CONNECTIVITY LABELS FOR THE MULTICHANNEL IIT AND RUSH UNIVERSITY AGING (MIITRA) ATLAS
Creator: Badhon, Rashadul Hasan
Date: 2022
Description: In the field of medical imaging, a brain atlas refers to a specific model of the brain of a population where different parts of the atlas...
Show moreIn the field of medical imaging, a brain atlas refers to a specific model of the brain of a population where different parts of the atlas correspond to different anatomical parts of the average brain of the population. A brain atlas is composed of MRI templates and semantic labels and is a crucial component of neuroscience for its critical role in facilitating spatial normalization, temporal characterization and automated segmentation for the purposes of voxel-wise, region of interest and network analyses. Building a brain atlas requires registering multi-dimensional brain datasets from a population into a reference space and, during the last decade, the advent of new technologies and computational modeling approaches has made it possible to build high-quality, detailed brain atlases. At the same time developments in data acquisition now allow the construction of comprehensive brain atlases containing a variety of information about the brain. The Multichannel Illinois Institute of Technology and Rush university Aging (MIITRA) atlas project is developing a high-quality comprehensive atlas of the older adult brain containing a multitude of templates and labels. These templates are constructed with state-of-the-art spatial normalization of high-quality data and as a result, they are characterized by higher image quality, are more representative of the brain of non-demented older adults and provide higher inter-subject spatial normalization accuracy of older adult data compared to other available templates. The methodology used in the development of the MIITRA templates facilitates the construction of accurate structural and connectivity labels. Functional connectivity MRI reveals sets of functionally connected brain regions, forming networks, by investigating synchronous fluctuations in MRI signal over time across these brain regions during rest. The purpose of this work was to generate functional connectivity labels for several brain networks in MIITRA space.
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Title: DEEP LEARNING IMAGE-DENOISING FOR IMPROVING DIAGNOSTIC ACCURACY IN CARDIAC SPECT
Creator: Liu, Junchi
Date: 2022
Description: Myocardial perfusion imaging (MPI) using single-photon emission computed tomography (SPECT) is a noninvasive imaging modality widely utilized...
Show moreMyocardial perfusion imaging (MPI) using single-photon emission computed tomography (SPECT) is a noninvasive imaging modality widely utilized for diagnosis of coronary artery diseases (CAD) in nuclear medicine. Because of the concern of potential radiation risks, the imaging dose administered to patients is limited in SPECT-MPI. Due to the low count statistics in acquired data, SPECT images can suffer from high levels of noise. In this study, we investigate the potential benefit of applying deep learning (DL) techniques for denoising in SPECT-MPI studies. Owing to the lack of ground truth in clinical studies, we adopt a noise-to-noise (N2N) training approach for denoising in full-dose studies. Afterwards, we investigate the benefit of applying N2N DL on reduced-dose studies to improve the detection accuracy of perfusion defects. To address the great variability in noise level among different subjects, we propose a scheme to account for the inter-subject variabilities in training a DL denoising network to improve its generalizability. In addition, we propose a dose-blind training approach for denoising at multiple reduced-dose levels. Moreover, we investigate several training schemes to address the issue that defect and non-defect image regions are highly unbalanced in a data set, where the overwhelming majority by non-defect regions tends to have a more pronounced contribution to the conventional loss function. We investigate whether these training schemes can effectively improve preservation of perfusion defects and yield better defect detection accuracy. In the experiments we demonstrated the proposed approaches with a set of 895 clinical acquisitions. The results show promising performance in denoising and improving the detectability of perfusion-defects with the proposed approaches.
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