Engineering Commons^™

Quantitative Assessment Of Intra- And Inter-Modality Deformable Image Registration Of The Heart, Left Ventricle, And Thoracic Aorta On Longitudinal 4d-Ct And Mr Images, Alireza Omidi, Elisabeth Weiss, John S. Wilson, Mihaela Rosu-Bubulac

Biomedical Engineering Publications

Purpose

Magnetic resonance imaging (MRI)-based investigations into radiotherapy (RT)-induced cardiotoxicity require reliable registrations of magnetic resonance (MR) imaging to planning computed tomography (CT) for correlation to regional dose. In this study, the accuracy of intra- and inter-modality deformable image registration (DIR) of longitudinal four-dimensional CT (4D-CT) and MR images were evaluated for heart, left ventricle (LV), and thoracic aorta (TA).

Methods and materials

Non-cardiac-gated 4D-CT and T1 volumetric interpolated breath-hold examination (T1-VIBE) MRI datasets from five lung cancer patients were obtained at two breathing phases (inspiration/expiration) and two time points (before treatment and 5 weeks after initiating RT). Heart, LV, …

Applying Model Approaches In Non-Model Systems: A Review And Case Study On Coral Cell Culture, Liza M. Roger, Hannah Reich, Evan Lawrence, Shuaifeng Li, Whitney Vizgaudis, Nathan Brenner, Lokender Kumar, Judith Klein-Seetharaman, Jinkyu Yang, Hollie M. Putnam, Nastassja Lewinski

Chemical and Life Science Engineering Publications

Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The …

Machine Assisted Experimentation Of Extrusion-Based Bioprinting Systems, Shuyu Tian, Rory Stevens, Bridget T. Mcinnes, Nastassja Lewinski

Chemical and Life Science Engineering Publications

Optimization of extrusion-based bioprinting (EBB) parameters have been systematically conducted through experimentation. However, the process is time- and resource-intensive and not easily translatable to other laboratories. This study approaches EBB parameter optimization through machine learning (ML) models trained using data collected from the published literature. We investigated regression-based and classification-based ML models and their abilities to predict printing outcomes of cell viability and filament diameter for cell-containing alginate and gelatin composite bioinks. In addition, we interrogated if regression-based models can predict suitable extrusion pressure given the desired cell viability when keeping other experimental parameters constant. We also compared models trained …

Detection Of 2,4,6-Trinitrotoluene Using A Colorimetric Gold Nanoparticle Air Cassette Filter, Andrea I. Ferrer Vega

Theses and Dissertations

Trinitrotoluene (TNT) is an explosive commonly used during military and terrorist activities. Current methods to identify this compound require sampling, transport and analysis at a forensic lab using analytical instrumentation. However, on-site detection is needed to assist efforts to prevent detonation. Gold nanoparticles have been used as sensors throughout the years due to their versatility and surface enhanced Raman scattering properties in the presence of an analyte and low limits of detection. By taking advantage of the Meisenheimer complex that TNT forms in the presence of amines, it is possible to determine its presence at picogram levels. Subsequently, adhering amine …

The Critical Role Of Dynamic Surface Tension Of Surfactants On The Impact Dynamics Of Water Droplets, Amir Esmaeili, Reza Mohammadi

Graduate Research Posters

Due to their time-dependent surface tension, the addition of surface-active agents or surfactants to water for specific applications has made controlling the impact dynamics of these droplets a complex phenomenon. This work investigates the influence of the molecular weight, concentration, and ionic nature of the surfactants as well as the substrate surface characteristics on the impact dynamics of surfactant-laden droplets using a high-speed camera at 10000 frames per second. Sodium dodecyl sulfate, hexadecyltrimethylammonium bromide, and n-decanoyl-n-methylglucamine were used as anionic, cationic, and nonionic surfactants, respectively. We used hydrophilic glass slides, hydrophobic polytetrafluoroethylene, and superhydrophobic alkyl ketene dimer (AKD) as substrates. …

Equations Of State For Warm Dense Carbon From Quantum Espresso, Derek J. Schauss

Theses and Dissertations

Warm dense plasma is the matter that exists, roughly, in the range of 10,000 to 10,000,000 Kelvin and has solid-like densities, typically between 0.1 and 10 grams per centimeter. Warm dense fluids like hydrogen, helium, and carbon are believed to make up the interiors of many planets, white dwarfs, and other stars in our universe. The existence of warm dense matter (WDM) on Earth, however, is very rare, as it can only be created with high-energy sources like a nuclear explosion. In such an event, theoretical and computational models that accurately predict the response of certain materials are thus very …

Improving Patient-Specific Assessments Of Regional Aortic Mechanics Via Quantitative Magnetic Resonance Imaging With Early Applications In Patients At Elevated Risk For Thoracic Aortopathy, Patrick A. Jones

Theses and Dissertations

Unstable aortic aneurysms and dissections are serious cardiovascular conditions associated with high mortality. The current gold standards for assessment of stability, however, rely on simple geometric measurements, like cross-sectional area or increased diameter between follow-up scans, and fail to incorporate information about underlying aortic mechanics. Displacement encoding with stimulated echoes (DENSE) magnetic resonance imaging (MRI) has been used previously to determine heterogeneous circumferential strain patterns in the aortas of healthy volunteers. Here, I introduce technical improvements to DENSE aortic analysis and early pilot application in patients at higher risk for the development of aortopathies. Modifications to the DENSE aortic postprocessing …

Detection Of 2,4,6-Trinitrotoluene Using A Colorimetric Gold Nanoparticle Air Cassette Filter, Andrea I. Ferrer Vega

Master of Science in Forensic Science Directed Research Projects

Trinitrotoluene (TNT) is an explosive commonly used during military and terrorist activities. Current methods to identify this compound require sampling, transport and analysis at a forensic lab using analytical instrumentation. However, on-site detection is needed to assist efforts to prevent detonation. Gold nanoparticles have been used as sensors throughout the years due to their versatility and surface enhanced Raman scattering properties in the presence of an analyte and low limits of detection. By taking advantage of the Meisenheimer complex that TNT forms in the presence of amines, it is possible to determine its presence at picogram levels. Subsequently, adhering amine …

Effect Of Stimulus Waveform On Transcranial Magnetic Stimulation Metrics In Proximal And Distal Arm Muscles, Christopher Lynch

Theses and Dissertations

Objectives: The purpose of this study was to determine the effect of common transcranial magnetic stimulation (TMS) waveforms (monophasic and biphasic) on resting motor threshold (RMT), active motor threshold (AMT), and motor evoked potential (MEP) amplitudes in the biceps and first dorsal interosseous (FDI) because waveforms may affect motor targets differently. Additionally, we determined the test-retest reliability of TMS metrics for each stimulation type and muscle.

Methods: Ten individuals participated in two sessions of single-pulse TMS delivered to the motor cortex perpendicular to the central sulcus. MEPs were normalized to the maximum EMG signal during contraction and were recorded at …

Applied Machine Learning In Extrusion-Based Bioprinting, Shuyu Tian

Theses and Dissertations

Optimization of extrusion-based bioprinting (EBB) parameters have been systematically conducted through experimentation. However, the process is time and resource-intensive and not easily translatable across different laboratories. A machine learning (ML) approach to EBB parameter optimization can accelerate this process for laboratories across the field through training using data collected from published literature. In this work, regression-based and classification-based ML models were investigated for their abilities to predict printing outcomes of cell viability and filament diameter for cell-containing alginate and gelatin composite hydrogels. Regression-based models were investigated for their ability to predict suitable extrusion pressure given desired cell viability when keeping …

Using Deep Learning-Based Framework For Child Speech Emotion Recognition, Gerald N. Onwujekwe

Theses and Dissertations

Biological languages of the body through which human emotion can be detected abound including heart rate, facial expressions, movement of the eyelids and dilation of the eyes, body postures, skin conductance, and even the speech we make. Speech emotion recognition research started some three decades ago, and the popular Interspeech Emotion Challenge has helped to propagate this research area. However, most speech recognition research is focused on adults and there is very little research on child speech. This dissertation is a description of the development and evaluation of a child speech emotion recognition framework. The higher-level components of the framework …

Impact Dynamics Of Surfactant-Laden Droplets On Non-Wettable Coatings, Amir Esmaeili

Theses and Dissertations

Owing to their excellent water repellency, non-wettable (superhydrophobic) coatings have gained tremendous attention in the past couple of decades. Alkyl ketene dimer (AKD), an inexpensive polymer frequently used in paper industry as a sizing agent, has shown potentials to become superhydrophobic. The formation of a porous structure after curing the solidified AKD for an extra-long time (4–6 days) results in superhydrophobicity, i.e., a static contact angle with water of >150° and a roll-off angle of <10°. In this work, a facile and low-cost method was used to turn the surface of AKD superhydrophobic in a very short period of time by briefly treating the coatings, obtained from isothermally heated molten AKD at 40 °C for 3 min, with ethanol. The resulting superhydrophobicity is due to the formation of porous, entangled irregular micro/nano textures that create air cushions on the surface leading to droplet state transition from Wenzel to Cassie. As a proof of concept, the same material was applied to the co-sputtered nickel-tungsten thin films, commonly used in micro/nano-electro-mechanical systems, to improve their hydrophobicity. According to the results, at least 20% increase was observed in the dynamic contact angles of the treated substrates.

In addition, this work presents a detailed high-speed imaging analysis of the influence of the molecular weight, concentration and ionic nature of surfactants on droplet …

Rheological Analysis Of The Mechanical Properties Of Murine Lungs Over The Lifespan, Olajumoke Olufunke Harrison

Theses and Dissertations

To study the effects of aging in murine lungs, we characterized C57Bl6j mice from neonatal to 24-month-old mice. Samples were divided into two groups: Young Mice (YM) and Middle Age/Old Age Mice (MOM). The YM group included the neonatal and 6-10week. The MOM group included 7- and 22–24-month-old mice. Rheological testing was performed using a TA Instruments DHR-2 Rheometer to collect the mechanics of each mice sample. Utilizing a 20-mm parallel plate fixture, a gap of 0.8-1.0-mm, and a temperature setting of 25C, we conducted a frequency sweep. Samples were the decellularized over a four-day process then lyophilized for mass …

Imaging Potential In Saturation Recovery Methods For Sarcoidosis Patients With Medical Devices, Samantha Zhao

Theses and Dissertations

Cardiovascular magnetic resonance (CMR) imaging is a preferred imaging methodology due to its lack of ionizing radiation and ability to detect myocardial inflammation and fibrosis using quantitative T1 mapping techniques. Cardiac sarcoidosis (CS) is characterized as the formation of granulomas in the myocardium. Current methods for detection include measuring non-cardiac specific C-reactive protein (CRP) levels, or PET imaging, which uses ionizing radiation, therefore CMR would make an ideal imaging option. However, many CS patients have implanted cardiac devices which can cause degradation in image. The modified Look-Locker inversion recovery (MOLLI) method is widely used in quantitative T1 mapping with high …

Estimating Affective States In Virtual Reality Environments Using The Electroencephalogram, Meghan R. Kumar

Theses and Dissertations

Recent interest in high-performance virtual reality (VR) headsets has motivated research efforts to increase the user's sense of immersion via feedback of physiological measures. This work presents the use of electroencephalographic (EEG) measurements during observation of immersive VR videos to estimate the user's affective state. The EEG of 30 participants were recorded as each passively viewed a series of one minute immersive VR video clips and subjectively rated their level of valence, arousal, dominance, and liking. Correlates between EEG spectral bands and the subjective ratings were analyzed to identify statistically significant frequencies and electrode locations across participants. Model feasibility and …

Preference-Aware Task Assignment In Mobile Crowdsensing, Fatih Yucel

Theses and Dissertations

Mobile crowdsensing (MCS) is an emerging form of crowdsourcing, which facilitates the sensing data collection with the help of mobile participants (workers). A central problem in MCS is the assignment of sensing tasks to workers. Existing work in the field mostly seek a system-level optimization of task assignments (e.g., maximize the number of completed tasks, minimize the total distance traveled by workers) without considering individual preferences of task requesters and workers. However, users may be reluctant to participate in MCS campaigns that disregard their preferences. In this dissertation, we argue that user preferences should be a primary concern in the …

Surface Characterization Of Accident Tolerant Fuel Claddings Candidates After Prolonged Exposure To Steam Oxidation, Connor F. Donlan

Theses and Dissertations

Accident Tolerant Fuel Claddings are designed to improve fuel performance and safety in abnormal reactor conditions. The development of these cladding materials has become a top priority for the nuclear community, with incidents such as the Three Mile Island accident and the Fukashima Dai-chi accident. The development of these claddings has resulted in 2 subsections: coating current claddings or replacing cladding materials with new materials. The claddings studied in this thesis are a Zircaloy-4 cladding coated with chromium through physical vapor deposition, Zircaloy-4, and a FeCrAl alloy, C26M. This thesis assessed the surface chemistry, roughness, and wettability after extended exposure …

Evaluating Neuromuscular Function Of The Biceps Brachii After Spinal Cord Injury: Assessment Of Voluntary Activation And Motor Evoked Potential Input-Output Curves Using Transcranial Magnetic Stimulation, Thibault Roumengous

Theses and Dissertations

Activation of upper limb muscles is important for independent living after cervical spinal cord injury (SCI) that results in tetraplegia. An emerging, non-invasive approach to address post-SCI muscle weakness is modulation of the nervous system. A long-term goal is to develop neuromodulation techniques to reinnervate (i.e. resupply nerve to) muscle fiber and thereby increase muscle function in individuals with tetraplegia. Towards this goal, developing monitoring techniques to quantify neuromuscular function is needed to better direct neurorehabilitation. Assessment of voluntary activation (VA) is a promising approach because the location of the stimulus can be applied cortically using transcranial magnetic stimulation (TMS) …

A General Framework For Characterizing And Evaluating Attacker Models For Cps Security Assessment, Christopher S. Deloglos, Christopher Deloglos

Theses and Dissertations

Characterizing the attacker’s perspective is essential to assessing the security posture and resilience of cyber-physical systems. The attacker’s perspective is most often achieved by cyber-security experts (e.g., red teams) who critically challenge and analyze the system from an adversarial stance. Unfortunately, the knowledge and experience of cyber-security experts can be inconsistent leading to situations where there are gaps in the security assessment of a given system. Structured security review processes (such as TAM, Mission Aware, STPA-SEC, and STPA-SafeSec) attempt to standardize the review processes to impart consistency across an organization or application domain. However, with most security review processes, the …

Linear And Nonlinear Optical Effects In High Carrier Concentration Oxides And Nitrides At Epsilon-Near-Zero, Ray Secondo

Theses and Dissertations

Nonlinear optics has been an important method for achieving ultrafast light manipulation. Recently, ENZ material have gained interest due to inherent advantages such as slow light, improved confinement, and ideal relaxation times, the nonlinear response of these materials, such as the intensity-dependent-refractive-index, are ultra-large yet remain ultra-fast. This experimental discovery of epsilon-near-zero enhancement has thus opened new avenues in nonlinear optics research in recent years, and while experiments have continued to progress a theoretical understanding of the processes and origins of nonlinear optical enhancement at epsilon-near-zero has lagged.

To fill this gap, the work herein focuses on uncovering the mechanisms …

Nebulizer-Based Systems To Improve Pharmaceutical Aerosol Delivery To The Lungs, Benjamin M. Spence

Theses and Dissertations

Combining vibrating mesh nebulizers with additional new technologies leads to substantial improvements in pharmaceutical aerosol delivery to the lungs across therapeutic administration methods. In this dissertation, streamlined components, aerosol administration synchronization, and/or Excipient Enhanced Growth (EEG) technologies were utilized to develop and test several novel devices and aerosol delivery systems. The first focus of this work was to improve the poor delivery efficiency, e.g., 3.6% of nominal dose (Dugernier et al. 2017), of aerosolized medication administration to adult human subjects concurrent with high flow nasal cannula (HFNC) therapy, a form of continuous-flow non-invasive ventilation (NIV). The developed Low-Volume Mixer-Heater (LVMH) …

Deep Learning Assisted Intelligent Visual And Vehicle Tracking Systems, Liang Xu

Theses and Dissertations

Sensor fusion and tracking is the ability to bring together measurements from multiple sensors of the current and past time to estimate the current state of a system. The resulting state estimate is more accurate compared with the direct sensor measurement because it balances between the state prediction based on the assumed motion model and the noisy sensor measurement. Systems can then use the information provided by the sensor fusion and tracking process to support more-intelligent actions and achieve autonomy in a system like an autonomous vehicle. In the past, widely used sensor data are structured, which can be directly …

Information Architecture For A Chemical Modeling Knowledge Graph, Adam R. Luxon

Theses and Dissertations

Machine learning models for chemical property predictions are high dimension design challenges spanning multiple disciplines. Free and open-source software libraries have streamlined the model implementation process, but the design complexity remains. In order better navigate and understand the machine learning design space, model information needs to be organized and contextualized. In this work, instances of chemical property models and their associated parameters were stored in a Neo4j property graph database. Machine learning model instances were created with permutations of dataset, learning algorithm, molecular featurization, data scaling, data splitting, hyperparameters, and hyperparameter optimization techniques. The resulting graph contains over 83,000 nodes …

Perovskite Thin Films Annealed In Supercritical Fluids For Efficient Solar Cells, Gilbert Annohene

Theses and Dissertations

In the field of photovoltaics, scientists and researchers are working fervently to produce a combination of efficient, stable, low cost and scalable devices. Methylammonium lead trihalide perovskite has attracted intense interest due to its high photovoltaic performance, low cost, and ease of manufacture. Their high absorption coefficient, tunable bandgap, low-temperature processing, and abundant elemental constituent provide innumerable advantages over other thin film absorber materials. Since the perovskite film is the most important in the device, morphology, crystallization, compositional and interface engineering have been explored to boost its performance and stability. High temperatures necessary for crystallization of organic-inorganic hybrid perovskite films …

Computational Analysis And Prediction Of Intrinsic Disorder And Intrinsic Disorder Functions In Proteins, Akila I. Katuwawala

Theses and Dissertations

COMPUTATIONAL ANALYSIS AND PREDICTION OF INTRINSIC DISORDER AND INTRINSIC DISORDER FUNCTIONS IN PROTEINS

By Akila Imesha Katuwawala

A dissertation submitted in partial fulfillment of the requirements for the degree of Engineering, Doctor of Philosophy with a concentration in Computer Science at Virginia Commonwealth University.

Virginia Commonwealth University, 2021

Director: Lukasz Kurgan, Professor, Department of Computer Science

Proteins, as a fundamental class of biomolecules, have been studied from various perspectives over the past two centuries. The traditional notion is that proteins require fixed and stable three-dimensional structures to carry out biological functions. However, there is mounting evidence regarding a “special” class …

Nature-Inspired Material Strategies Towards Functional Devices, Sayantan Pradhan

Theses and Dissertations

Naturally sourced, renewable biomaterials possess outstanding advantages for a multitude of biomedical applications owing to their biodegradability, biocompatibility, and excellent mechanical properties. Of interest in this dissertation are silk (protein) and chitin (polysaccharide) biopolymers for the fabrication of functional biodevices. One of the major challenges restricting these materials beyond their traditional usage as passive substrate materials is the ability to combine them with high-resolution fabrication techniques. Initial research work is directed towards the fabrication of micropatterned, flexible 2D substrates of silk fibroin and chitin using bench-top photolithographic techniques. Research is focused on imparting electrochemical properties to silk proteins using conducting …

Accident Tolerant Fuels Claddings And The Evolution Of Their Surface Characteristics Under Critical Heat Flux, Rajnikant V. Umretiya

Theses and Dissertations

Enhanced Accident Tolerant Fuels (ATFs) systems for light water reactors require higher temperature oxidation resistance in steam environments than the current UO₂ – zirconium fuel system. Investigating the ATF materials’ surface properties is needed as they have evidenced to affect the Critical Heat Flux (CHF), which is an important parameter of the thermal-hydraulic performance required to provide safety margins. In this dissertation, the surface properties of FeCrAl alloys (APMT and C26M), Zircaloy-2, Zircaloy-4, and Cr-coating on Zircaloy-4 substrates produced by Physical Vapor Deposition (PVD) and Cold Spray (CS) were investigated according to their chemistry, topography, and wettability. The static …

Learning-Based Predictive Control Approach For Real-Time Management Of Cyber-Physical Systems, Roja Eini

Theses and Dissertations

Cyber-physical systems (CPSs) are composed of heterogeneous, and networked hardware and software components tightly integrated with physical elements [72]. Large-scale CPSs are composed of complex components, subject to uncertainties [89], as though their design and development is a challenging task. Achieving reliability and real-time adaptation to changing environments are some of the challenges involved in large-scale CPSs development [51]. Addressing these challenges requires deep insights into control theory and machine learning. This research presents a learning-based control approach for CPSs management, considering their requirements, specifications, and constraints. Model-based control approaches, such as model predictive control (MPC), are proven to be …

A Mechanism Behind The Mechanotransduction Of Surface Characteristics In Osteoblasts, Otto J. Juhl Iv

Theses and Dissertations

Biomaterials for use in bone regeneration and healing range from metal and metal alloy implants to hydrogel-based solutions. These materials can be optimized to increase bone healing and integration by improving the mechanical and biological properties. Regardless of the material itself, the cell-substrate interaction is key to the success of the biomaterial once implanted. Substrate surface characteristics such as roughness, wettability, and particle density are well-known contributors to a substrate’s overall osteogenic potential, and therefore the substrate's overall success. Unfortunately, it is still unknown how these substrate surface characteristics are transduced into intracellular signals by cells, preventing specific tailoring of …

Intermittent Theta Burst Stimulation: Application To Spinal Cord Injury Rehabilitation And Computational Modeling, Neil Mittal

Theses and Dissertations

Loss of motor function from spinal cord injuries (SCI) results in loss of independence. Rehabilitation efforts are targeted to enhance the ability to perform activities of daily living (ADLs), but outcomes from physical therapy alone are often insufficient. Neuromodulation techniques that induce neuroplasticity may push the limits on recovery. Neuromodulation by intermittent theta burst transcranial magnetic stimulation (iTBS) induces neuroplasticity by increasing corticomotor excitability, though this has most frequently been studied with motor targets and on individuals not in need of rehabilitation. Increased corticomotor excitability is associated with motor learning. The response to iTBS, however, is highly variable and unpredictable, …