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Title: Cardiolipin Modulates the Insertion of Adsorbed Helical Amyloid Beta Peptide Into Model Mitochondrial Membranes
Creator: Kaczmarek, Julia A.
Date: 2023
Description: The loss of mitochondrial phospholipid cardiolipin (CL) may play a role in both the pathogenesis of Alzheimer's Disease (AD) and its treatment...
Show moreThe loss of mitochondrial phospholipid cardiolipin (CL) may play a role in both the pathogenesis of Alzheimer's Disease (AD) and its treatment. An effector molecule of the disease, amyloid-beta (Aβ), has been observed to interact with lipid membranes, but its relevance to mitochondrial membranes containing CL remained elusive. The present study investigated if the presence of CL modulated the insertion of adsorbed helical amyloid beta (Aβ14-40) into model mitochondrial membranes, and if this effect was more pronounced for its N-terminus or C-terminus. I conducted a coarse-grained computer simulation using well-tempered metadynamics to traverse the free energy landscape that maps the translocation of Aβ14-40. Insertion into CL-containing bilayers created larger local membrane deformations and modulated the location of the transition path but had an inconclusive impact on the free energy cost of translocation. Since the generation of toxic calcium-permeable pores depends on the insertion of Aβ into the bilayer, the loss of CL seen in AD may prime the inner mitochondrial membrane for pore formation, but more research is needed to pursue this hypothesis.
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Title: Development of data assimilation for analysis of ion drifts during geomagnetic storms
Creator: Hu, Jiahui
Date: 2024
Description: The primary objective of this dissertation is to gain insight into geomagnetic storm effects at mid-latitudes induced by solar activity....
Show moreThe primary objective of this dissertation is to gain insight into geomagnetic storm effects at mid-latitudes induced by solar activity. Geomagnetic storms affect our everyday lives because they give rise to transient signal loss, data transmission errors, negatively impacting users of satellite navigation systems. The Nighttime Localized Ionospheric Enhancement (NILE) is a localized plasma enhancement that because it is not well understood, drives the design of satellite-based augmentationsystems. To better secure operation of technological infrastructure, it is essential to build a comprehensive understanding of the atmospheric drivers, especially during solar active periods. Instrument measurements and climate models serve as valuable tools in obtaining information regarding the occurrence of space weather events; nonetheless, both sources exhibit quantitative and qualitative limitations. Data assimilation, an evolving technique, integrates measurements and model information to optimize the state estimations. This dissertation presents developments in a data assimilation algorithm known as Estimating Model Parameters from Ionospheric Reverse Engineering (EMPIRE), and its applications in investigating the atmospheric behaviors under varying solar conditions. EMPIRE is a data assimilation algorithm specifically designed for upper atmospheric driver estimation of neutral wind and ion drifts at user-defined spatial and temporal scales. The EMPIRE application in this work aims to contribute to a more comprehensive understanding of the effects of the NILE. EMPIRE utilizes the Kalman filter to optimize state calculations primarily based on electron density rates, provided by other data assimilation algorithms. Earlier runs of the algorithm used pre-defined values for the background state covariance cross time. To address model limitations under changing geomagnetic conditions, the algorithm is enhanced by concurrently updating the background state covariance during assimilation processes. Additionally, representation error is incor- porated as a component of the observation error, and error analysis is performed through a synthetic-data study. Previously, EMPIRE fused Fabry-Perot Interferometer (FPI) neutral wind measurements, demonstrating increased agreement with validation neutral wind data. In this work, this approach is extended to augment Coherent Scatter Radar (CSR) ion drift measurements from Super Dual Auroral Radar Network (SuperDARN), providing additional insights into EMPIRE’s estimated field-perpendicular ion motion. For an in-depth exploration of storm-related NILE, both EMPIRE and another data assimilation method, the Whole Atmosphere Community Climate Model with thermosphere and ionosphere eXtension coupled with Data Assimilation Research Testbed (WACCM-X + DART), is implemented for a storm event to test the proposed NILE driving mechanism. Furthermore, this dissertation introduces a Kalman smoother technique into the EMPIRE to enhance its ability to assess past storm events, and to explore the potential for algorithm improvements.
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Title: #MeToo: What Urged Users to Post?
Creator: Hirsh, Rachel Anna
Date: 2023
Description: In this dissertation, I explore the motivations that compelled individuals to share their stories during the #MeToo movement, an unprecedented...
Show moreIn this dissertation, I explore the motivations that compelled individuals to share their stories during the #MeToo movement, an unprecedented digital phenomenon that thrust discussions of sexual harassment and assault into the public sphere. The central research question guiding this study was, "What urged users to post during the #MeToo movement?," which worked to uncover why and how the movement became so widespread.. Research demonstrates that when people are sexually harassed or assaulted, often times they do not come forward (Hlavka, 2014). Spencer et al. shares some of the common reasons women do not come forward are that they don’t classify their harassment or assault as a big enough deal, they do not know who or how to report it, they are afraid, they were drunk, they are ashamed, they don’t want to get their assailant in trouble, or they blame themselves (2017). However, those reasons fell by the wayside, as so many people came forward during the #MeToo movement. This paper aims to figure out why that was and how we can continuously get survivors to come forward. This paper also asks the question, did people come forward to share testimony, be part of a movement, or both?Two distinct hypotheses were formulated to unpack the complex dynamics at play The first hypothesis posited that users who engaged with central nodes, encompassing key figures within the #MeToo movement, original contributors, celebrities, and influencers, were more inclined to hold a positive outlook on the movement as a progressive step for women. This data was collected through a quantitative survey, and the analysis yielded inconclusive results, with 79.15% of the sample population expressing support for the movement while only 54.17% reported following central nodes. Qualitative interviews further underscored the multifaceted nature of motivations.The second hypothesis posited that individuals were more inclined to share their personal experiences of harassment or assault online when they observed weak ties within their social networks, such as acquaintances or friends of friends, sharing their own stories. The findings from survey data revealed that 68.87% of participants witnessed weak ties sharing personal experiences or using the #MeToo hashtag on their social media platforms. Qualitative interviews unanimously highlighted the significant influence of observing friends or weak ties posting about their experiences, further underscoring the diversity of motivators behind #MeToo participation.These findings shed light on the multifaceted nature of online activism and the pivotal role of personal networks in shaping the movement's trajectory. In essence, this research demonstrates that while the motivations for user participation in the #MeToo movement are diverse and complex, the presence of weak ties, or distant social relationships or relationships with infrequent interactions, within social networks emerges as a critical influence.
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Title: Optimization of Large-Scale NOMA With Incidence Matrix Design and Physical Layer Security
Creator: Hwang, Eli W.
Date: 2024
Description: The Non-Orthogonal Multiple Access (NOMA) system is recognized for its capability to achieve higher spectral efficiency and massive...
Show moreThe Non-Orthogonal Multiple Access (NOMA) system is recognized for its capability to achieve higher spectral efficiency and massive connectivity. NOMA is intended to transmit massive user communications. The incidence matrix governs the relationship between users and resources for the Code domain NOMA (CD-NOMA). However, NOMA studies focus less on the design and optimization of the incidence matrix.Therefore, this thesis aims to investigate the development of a secure and large-scale NOMA system based on incidence matrix design. The main contributions are outlined as follows: Firstly, this research introduces a novel NOMA system. Distinct from existing studies, the NOMA system is based on combinatorial design. This innovative approach, coupled with a unique constellation design, eliminates the surjective mapping from the linear adding data of multiusers, reducing the complexity of constellation design and Multiuser Detection (MUD). The characteristics of the incidence matrix designs, Simple Orthogonal Multi-Arrays (SOMA), are explored, which display a distinct Latin Square pattern. The SOMA design's unique structure allows for the creation of a highly flexible and fair resource allocation matrix. The NOMA system's theoretical performance analysis equations are established, supporting dynamic adaptability and optimization. The design is validated by Monte Carlo simulation. Compared to other NOMA schemes, it offers higher degrees of freedom and lower complexity while maintaining graceful error rates to transmit a larger number of users. Secondly, a novel NOMA system utilizing incidence matrix information in the uplink is investigated. The incidence matrix pattern is exploited for MUD to achieve large-scale user connectivity. The incidence matrix is designed based on two critical mathematical concepts: parallel classes in hypergraph theory and orthogonal arrays (OAs) in combinatorial designs. Unlike other NOMA schemes, which require modification of their receiver and transmitter to decode superimposed multiuser signals, the unique pattern of the OA structure enables the use of conventional modulators. Consequently, the system load increases and the complexity and latency are reduced. The order of magnitude of the decoding complexity can be significantly reduced from O(N^3) to O(N) compared to the conventional minimum mean-square estimation (MMSE) decoder. Monte Carlo simulation validates that this novel NOMA system outperforms other NOMA designs in terms of error rate, data rate, and system size. Finally, a reconfigurable convolutional encoder design that integrates security and error correction based on physical layer security (PLS) and randomness is developed. This design addresses concerns over privacy, security, and reliability of Internet of Things devices in edge computing networks. The lightweight Convolutional encoders are designed to ensure security by updating the transfer function dynamically with user data. The reconfigurability of the design is achieved by replacing the fixed adder that represents the generator polynomials with the switch adder, enabling the use of 87 billion distinct updating structures, thereby enhancing the versatility of the design. BER-based PLS paradigms are demonstrated in the simulation. In the simulation, the robustness and randomness of this design are further validated through tests suggested by the National Institute of Standards and Technology for cryptographically secure pseudorandom number generators, such as the monobits, longest one, and run tests.
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Title: A Kernel-Free Boundary Integral Method for Two-Dimensional Magnetostatics Analysis
Creator: Jin, Zichao
Date: 2023
Description: Performing magnetostatic analysis accurately and efficiently is crucial for the multi-objective optimization of electromagnetic device designs...
Show morePerforming magnetostatic analysis accurately and efficiently is crucial for the multi-objective optimization of electromagnetic device designs. Therefore, an accurate and computationally efficient method is essential. Kernel Free Boundary Integral Method is a numerical method that can accurately and efficiently solve partial differential equations. Unlike traditional boundary integral or boundary element methods, KFBIM does not require an analytical form of Green’s function for evaluating integrals via numerical quadrature. Instead, KFBIM computes integrals by solving an equivalent interface problem on a Cartesian mesh. Compared with traditional finite difference methods for solving the governing PDEs directly, KFBIM produces a well-conditioned linear system. Therefore, the numerical solution of KFBIM is not sensitive to computer round-off errors, and the KFBIM requires only a fixed number of iterations when an iterative method (e.g., GMRES) is applied to solve the linear system.In this research, the KFBIM is introduced for solving magnetic computations in a toroidal core geometry in 2D. This study is very relevant in designing and optimizing toroidal inductors or transformers used in electrical systems, where lighter weight, higher inductance, higher efficiency, and lower leakage flux are required. The results are then compared with a commercial finite element solver (ANSYS), which shows excellent agreement. It should be noted that, compared with FEM, the KFBIM does not require a body-fitted mesh and can achieve high accuracy with a coarse mesh. In particular, the magnetic potential and tangential field intensity calculations on the boundaries are more stable and exhibit almost no oscillations.Furthermore, although KFBIM is accurate and computationally efficient, sharp corners can be a significant problem for KFBIM. Therefore, an inverse discrete Fourier transform (DFT) based geometry reconstruction is explored to overcome this challenge for smoothening sharp corners. A toroidal core with an airgap (C-core) is modeled to show the effectiveness of the proposed approach in addressing the sharp corner problem. A numerical example demonstrates that the method works for the variable coefficient PDE. In addition, magnetostatic analysis for homogeneous and nonhomogeneous material is presented for the reconstructed geometry, and results carried out from KFBIM are compared with the results of FEM analysis for the original geometry to show the differences and the potential of the proposed method.
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Title: Modeling and Optimization of Embedded Active Flow Control Systems
Creator: Henry, James M.
Date: 2024
Description: This thesis presents research focused on the aerodynamic performance of circulation control on two-dimensional and quasi-two-dimensional wings...
Show moreThis thesis presents research focused on the aerodynamic performance of circulation control on two-dimensional and quasi-two-dimensional wings. Aerodynamic loads, namely lift, drag, and moment coefficients, are measured through Reynolds Averaged Navier Stokes (RANS) modeling and wind tunnel experiment. A simplified and parameterized RANS model is presented as a rapidly iterable approach to estimating the performance of trailing-edge circulation control on two dimensional airfoils, with the hypothesis that an optimized airfoil shape can be found which maximizes the lift coefficient increment generated by circulation control, through modification of the wing profile. The simplified modeling setup is compared with more conventional approaches to numerical simulation of circulation control. The performance of the simplified modeling scheme is then compared with wind tunnel studies, for both steady-state and dynamic performance, as functions of both momentum coefficient dCμ and chord-based Reynolds number Re_c. The dynamic performance for the model is studied to find an analog to the theoretical unsteady models of Wagner and Theodorsen. An adjoint optimization framework is used to find an optimal airfoil profile for circulation control. The optimized profile is then compared in both a simulation and a wind tunnel test study against a NACA0015 airfoil. In simulation, improvement between 12% and 15% is seen for the lift control authority for all values of dCμ and Re_c tested. In experiment, the optimized profile demonstrated improvements of up to 28% in lift control authority, dCL/dCμfor values of Cμ, and decreased performance for higher values of Cμ.
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Title: Evaluation of the efficacy of power ultrasound technology coupled with organic acids to reduce listeria monocytogenes on peaches and apples
Creator: Joshi, Mayura Anand
Date: 2024
Description: Fresh fruits and vegetables are prone to microbial contamination throughout different phases of human handling, processing, transportation,...
Show moreFresh fruits and vegetables are prone to microbial contamination throughout different phases of human handling, processing, transportation, and distribution. Emerging technologies, such as power ultrasound, have received attention due to their capacity to reduce or eliminate foodborne bacterial pathogens on these commodities. Power ultrasound, when combined with certain antimicrobials, has demonstrated its effectiveness as a valuable tool for washing fresh produce. The objective of this study was to examine the effectiveness of power ultrasound combined with organic acids on the reduction of Listeria monocytogenes on fruits. In this study, peaches and apples were subjected to surface inoculation with a four-strain cocktail of L. monocytogenes and dried for 1 h. Stomacher bags, containing 225 mL of citric, lactic, or malic acids at concentrations of 1%, 2%, or 5%, were employed for treating inoculated peaches and apples. The acid treatment was used alone, or in combination with power ultrasound for 2, 5, or 10 min. Water was used for controls. Before treatment, the initial population of L. monocytogenes on apples was lower compared to the initial population on peaches, with apples showing a 1.94 log CFU/fruit reduction. Water controls demonstrated no significant log reduction in both apples and peaches. The greatest L. monocytogenes reduction on apples occurred when treated with 1% citric acid for 2 min with power ultrasound where L. monocytogenes was significantly reduced from 6.98±0.88 log CFU/fruit to 5.56±0.91 log CFU/fruit. The greatest L. monocytogenes reduction on peaches occurred when treated with 5% citric acid for 5 min with power ultrasound where L. monocytogenes was significantly reduced from 7.44±0.45 log CFU/fruit to 6.68±0.40 log CFU/fruit. Overall, the combined effect of acid and power ultrasound was more pronounced in apples than in peaches. The survival of L. monocytogenes on apples and peaches appeared to be highly dependent on the specific treatment and hurdle technology applied. The combination of ultrasound hurdle technology with acid washing has proven effective in reducing L. monocytogenes on both peaches and apples, with a more significant impact observed on apples. While acid washing is a more economical option compared to ultrasound technology, the efficiency of microorganism reduction is considerably enhanced when power ultrasound is combined with organic acids. Looking ahead, the development of cost-effective power ultrasound methods could facilitate widespread adoption of ultrasound hurdle technology in the produce industry.
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Title: Pilgrim Baptist Church, Chicago, Illinois, ca. 1964
Creator: Weil, F. Peter
Date: 1964
Description: Pilgrim Baptist Church (3301 S. Indiana Ave, Chicago, IL) photographed by Institute of Design student F. Peter Weil. Date is estimated as 1964...
Show morePilgrim Baptist Church (3301 S. Indiana Ave, Chicago, IL) photographed by Institute of Design student F. Peter Weil. Date is estimated as 1964 from other evidence in the collection.
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Collection: F. Peter Weil photographs, 1952-1964

Title: Correlating Microstructural Properties to Macroscopic Shear Mechanics to Improve the Understanding of Tissue Biomechanics
Creator: Cahoon, Stacey Marie
Date: 2023
Description: Understanding tissue biomechanics is of interest for modeling organ injury from external loads, development of tissue surrogate materials, and...
Show moreUnderstanding tissue biomechanics is of interest for modeling organ injury from external loads, development of tissue surrogate materials, and creating new biomarkers for disease. Probing the response of soft tissue in shear can provide information on histopathology, provided a methodology exists that connects the macroscopic mechanical properties with cell-level properties. Two of the available methods to measure the macroscopic shear viscoelastic properties of soft tissue are oscillatory shear rheometry and ultrasound shear wave elastography (SWE). Due to its accuracy, rheometry is the gold standard, but it is destructive, requires excised homogeneous samples, and can only be applied ex-vivo. SWE is an emerging non-invasive imaging technique which requires validation, ostensibly by comparing with rheometry. Histology is the gold standard for providing morphological information on the cell level, which can determine tissue pathology. The challenge is to connect the macroscopic mechanical metrics derived from SWE and rheometry to the tissue microstructure. To address this challenge, mathematical models can be used that employ multiple, judiciously chosen measurements of macroscopic shear properties and histology to estimate intrinsic mechanical properties at the cell level.A class of homogeneous and composite lipid phantoms mimicking the mechanical properties of brain white matter were fabricated to test a novel stereotactic system and an optimized SWE imaging protocol. The shear stiffness measurements obtained with SWE on the whole phantom were validated with rheometry performed on a series of samples made with the same material as the phantoms. The same procedure was applied to porcine brain white matter excised from fresh whole brains (n=3). Cylindrical cores were extracted from the corpus callosum area, sliced into discs and microscopic sections were subsequently removed for histology. Good agreement was found between the SWE and rheometry measurements of shear stiffness, which generally increases with the level of compressive prestress. Immunofluorescence was used to stain separately the axon neurofilaments and myelin sheaths, and digital image analysis of the confocal microscopy images allowed the estimation of axon volume fraction and axon-to-myelin ratio in the corpus callosum. Using these metrics and a composite mechanical model, a connection between the macroscopic shear measurements and the viscoelastic properties of axon and glia matrix was made for porcine brain tissue. Similarly, rheometry was used to measure the macroscopic properties of decellularized porcine myocardium extracellular matrix (ECM) in two different fiber locations, and for three different fiber orientations. The mechanical properties were found to be dependent upon fiber location, but not on fiber orientation. Since collagen is a primary supportive structure for the ECM, several microscopic slices were probed with immunofluorescence to compute the collagen I and collagen IV volume fractions. Another mechanical model was employed to establish a connection between the macroscopic properties and the mechanical properties of the collagen matrix in decellularized porcine myocardial ECM.This dissertation highlights the use and integration of three different experimental techniques (rheometry, ultrasound SWE, and histology) to correlate key microstructural properties of soft, fibrous tissues (ex-vivo healthy porcine brain white matter and myocardium ECM) with macroscopic shear mechanics. The consideration of the effect of compressive prestress is noteworthy. The reported baseline data for the tissues under shear loading and prestress are pertinent to the physiological function of these tissues, and therefore constitute preliminary data and a necessary first step before a systematic study of the biomechanics of the same tissues in vivo is performed.
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