Biomedical Engineering and Bioengineering Commons^™

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao

Dissertations

Traumatic brain injury (TBI) in children is a major public health concern worldwide. Attention deficits are among the most common neurocognitive and behavioral consequences in children post-TBI which have significant negative impacts on their educational and social outcomes and compromise the quality of their lives. However, there is a paucity of evidence to guide the optimal treatment strategies of attention deficit related symptoms in children post-TBI due to the lack of understanding regarding its neurobiological substrate. Thus, it is critical to understand the neural mechanisms associated with TBI-induced attention deficits in children so that more refined and tailored strategies can …

Motion-Resistant Pulse Oximetry, Ludvik Alkhoury

Dissertations

The measurement of vital signs ? such as peripheral capillary oxygen saturation (SpO₂) and heart rate (HR) levels ? by a pulse oximeter is studied. The pulse oximeter is a non-invasive device that measures photoplethysmography (PPG) signals and extracts vital signs from them. However, the quality of the PPG signal measured by oximetry sensors is known to deteriorate in the presence of substantial human and sensor movements contributing to the measurement noise. Methods to suppress such noise from PPG signals measured by an oximeter and to calculate the associated vital signs with high accuracy even when the wearer …

Biomechanical And Psychophysical Underpinnings Of Balance Dysfunction In Individuals With Traumatic Brain Injury, Naphtaly Ehrenberg

Dissertations

Falls are a major burden on healthcare infrastructure, especially in older adults and even more so in older individuals that are living in institutions. According to data from the Centers for Disease Control and Prevention (CDC), from 2010 to 2020, unintentional falls were the leading cause of nonfatal emergency department visits for all age groups except among individuals from 15-24 years of age, where unintentional falls ranked a very close second to being unintentionally struck by or against. Among older individuals living in the community, approximately 30-35% fall at least once in a given year, and around three times as …

Improving The Stimulation Selectivity In The Human Cochlea By Strategic Selection Of The Current Return Electrode, Ozan Cakmak

Dissertations

The hearing quality provided by cochlear implants are poorly predicted by computer simulations. A realistic cochlear anatomy is crucial for the accuracy of predictions. In this study, the standard multipolar stimulation paradigms are revisited and Rattay’s Activating Function is evaluated in a finite element model of a realistic cochlear geometry that is based on µ-CT images and a commercial lead. The stimulation thresholds across the cochlear fibers were investigated for monopolar, bipolar, tripolar, and a novel (distant) bipolar electrode configuration using an active compartmental nerve model based on Schwartz-Eikhof-Frijns membrane dynamics. The results suggest that skipping of the stimulation point …

Angiogenic Supports For Microvascular Engineering, Zain Siddiqui

Dissertations

Ischemic tissue disease is caused by a lack of circulation / blood supply to tissue. This can be treated by introducing a number of angiogenic (pro-blood vessel forming) factors into the tissue. This work presents strategies for ischemic tissue treatment utilizing a novel proangiogenic self-assembling peptide hydrogel platform. To demonstrate the utility of this platform, its use alone as an angiogenic therapeutic (both alone as a self-assembling hydrogel and with two-component systems), and its ability to vascularize implants is explored. Due to these angiogenic scaffolds demonstrating efficacy to regenerate microvasculature, this work evaluates diseases that can be treated by the …

Sensorimotor Content Of Multi-Unit Activity In The Paramedian Lobule Of The Cerebellum, Esma Cetinkaya

Dissertations

Based on Center for Disease Control and Prevention report 2016, around 39.5 million people in the United States suffer from motor disabilities. These disabilities are due to traumatic conditions like traumatic brain injury (TBI), neurological diseases such as amyotrophic lateral sclerosis (ALS), or congenital conditions. One of the approaches for restoring the lost motor function is to extract the volitional information from the central nervous system (CNS) and control a mechanical device that can replace the function of a paralyzed limb through systems called Brain-Computer Interfaces (BCI).

One of the major challenges being faced in BCIs and also in general …

Improving The Performance And Evaluation Of Computer-Assisted Semen Analysis, Ji-Won Choi

Dissertations

Semen analysis is performed routinely in fertility clinics to analyze the quality of semen and sperm cells of male patients. The analysis is typically performed by trained technicians or by Computer-Assisted Semen Analysis (CASA) systems. Manual semen analysis performed by technicians is subjective, time-consuming, and laborious, and yet most fertility clinics perform semen analysis in this manner. CASA systems, which are designed to perform the same tasks automatically, have a considerable market share, yet many studies still express concerns about their accuracy and consistency. In this dissertation, the focus is on detection, tracking, and classification of sperm cells in semen …

The Interconnection Of The Vestibular And Oculomotor Systems Analyzed In Healthy Young Adults By Examining Postural Sway, Cassandra Martin

Theses

In order to study the human brain in a non-invasive way, the vestibular and oculomotor systems have been analyzed simultaneously. To achieve this, an eye movement and balance assessment was conducted for 29 (23 male; 21.6 ± 3.8 years) healthy participants with no history of concussions, brain injuries, vertigo, migraines, brain surgeries, eye surgeries, or amblyopia. The tasks consisted of eyes open, eyes closed, horizontal saccades, vertical saccades, vergence jumps, horizontal vestibulo-ocular reflex (VOR), and vertical VOR. Each task was completed in two stances: feet shoulder width apart and feet together. Distance, velocity, sway area, center of pressure (COP) frequency, …

Assessing Structural And Functional Brain Alterations And Work-Related Fatigue In Non-Hyposmic And Hyposmic Covid-19 Survivors, Rakibul Hafiz

Dissertations

In the year 2019, life began to change at the advent of a global pandemic caused by the novel coronavirus. Mask mandates and mass vaccinations have mitigated the effects significantly, yet cases keep rising with new variants, especially, in densely populated countries, like India. Recent neuroimaging evidence shows the virus can attack the central nervous system (CNS). However, exactly which brain regions undergo structural and functional changes remain largely unknown. Many patients experience 'loss of/reduced sense of smell' (i.e., hyposmic) and an alarming number of survivors develop persistent symptoms ('long-COVID') for several months after initial infection. Fatigue is the most …

Gradient Free Sign Activation Zero One Loss Neural Networks For Adversarially Robust Classification, Yunzhe Xue

Dissertations

The zero-one loss function is less sensitive to outliers than convex surrogate losses such as hinge and cross-entropy. However, as a non-convex function, it has a large number of local minima, andits undifferentiable attribute makes it impossible to use backpropagation, a method widely used in training current state-of-the-art neural networks. When zero-one loss is applied to deep neural networks, the entire training process becomes challenging. On the other hand, a massive non-unique solution probably also brings different decision boundaries when optimizing zero-one loss, making it possible to fight against transferable adversarial examples, which is a common weakness in deep learning …

Towards Adversarial Robustness With 01 Lossmodels, And Novel Convolutional Neural Netsystems For Ultrasound Images, Meiyan Xie

Dissertations

This dissertation investigates adversarial robustness with 01 loss models and a novel convolutional neural net systems for vascular ultrasound images.

In the first part, the dissertation presents stochastic coordinate descent for 01 loss and its sensitivity to adversarial attacks. The study here suggests that 01 loss may be more resilient to adversarial attacks than the hinge loss and further work is required.

In the second part, this dissertation proposes sign activation network with a novel gradient-free stochastic coordinate descent algorithm and its ensembling model. The study here finds that the ensembling model gives a high minimum distortion (as measured by …

Towards Understanding The Role Of Central Processing In Release From Masking, Nima Alamatsaz

Dissertations

People with normal hearing have the ability to listen to a desired target sound while filtering out unwanted sounds in the background. However, most patients with hearing impairment struggle in noisy environments, a perceptual deficit which current hearing aids and cochlear implants cannot resolve. Even though peripheral dysfunction of the ears undoubtedly contribute to this deficit, surmounting evidence has implicated central processing in the inability to detect sounds in background noise. Therefore, it is essential to better understand the underlying neural mechanisms by which target sounds are dissociated from competing maskers. This research focuses on two phenomena that help suppress …

Drug Releasing Hydrogels For Opioid Use Disorder, Kaytlyn M. Crowe

Theses

Ease of access to prescription opioids and the strength of synthetic opioids have contributed to the rise in over use disorders, overdose, and death rates during the opioid epidemic. The current overdose standard of care, rescue NLX (NLX), is a competitive antagonist to the μ-opioid receptor but has a relatively short period of action compared to opioid agonists, especially synthetic agonists. Rises in the abuse of these synthetic and semi-synthetic agents in recent years have shown the weaknesses of rescue NLX, as it can leave overdose patients vulnerable to renarcotization and precipitated withdrawal. To prevent both from occurring, we developed …

Alcohol As A Catalyst For Hiv-Associated Neuroinflammation And Tbi-Induced Iron Toxicity, Agnieszka Agas

Dissertations

Alcohol has long been considered an exacerbator of diseases, disorders, and injuries as well as many of the accompanying symptoms. As an alternative approach, this dissertation explores alcohol as a catalyst for two different human disease conditions, human immunodeficiency virus (HIV)-associated neuroinflammation and traumatic brain injury (TBI)-induced iron toxicity. In HIV-1 infection, this dissertation presents a novel anti-viral drug, called Drug-S, for a possible inhibition and treatment of HIV-1 disease progression.

The first aim explores the influence of alcohol with HIV-associated neuroinflammation on macrophage migration across an in vitro model of the blood brain barrier. There is a gap in …

Development Of Deep Learning Neural Network For Ecological And Medical Images, Shaobo Liu

Dissertations

Deep learning in computer vision and image processing has attracted attentions from various fields including ecology and medical image. Ecologists are interested in finding an effective model structure to classify different species. Tradition deep learning model use a convolutional neural network, such as LeNet, AlexNet, VGG models, residual neural network, and inception models, are first used on classifying bee wing and butterfly datasets. However, insufficient data sample and unbalanced samples in each class have caused a poor accuracy. To make improvement the test accuracy, data augmentation and transfer learning are applied. Recently developed deep learning framework based on mathematical morphology …

The Effects Of Design Parameters On The Neural Recordings With Micro-Ecog Arrays, Manan Amish Sethia

Theses

In the field of neural prosthetics, electro-cortico-graph (ECoG) arrays are commonly used to record neural activity of the brain cortex both in animal and human subjects. A finite element model (FEM) was developed to simulate the electric field generated by a single neuron in the rat brain cortex and a micro ECoG array (µECoG) placed on the pia surface for recording the neural signal. The neuron was simulated as a dipole current source with a magnitude of 1µA and placed at three different depths in the motor cortex corresponding to different layers under the µECoG array. The array design was …

Using Fnirs As An Objective Measure Of Susceptibility To Informational Masking, Min Zhang

Dissertations

Resolving complicated auditory scenes is crucial for daily communication where background sound is often present. However, most hearing aid (HA) and cochlear implant (CI) users have difficulties understanding speech when competing sound sources are present, resulting in reduced job opportunities and increased risk for social isolation. Perceptual interference from background sound is called auditory masking. At least two distinct masking phenomena exist, called energetic and informational masking (EM and IM).

In the first masking phenomenon, EM, target and masker energies coincide at the same time and frequency. Computational and physiological models of cochlear auditory processing can reliably predict listeners' performances …

Real Time Analysis Of Eye Movements Using Computer Aided Software, Farhan Ahmad

Theses

Eye movement analysis is a slow and tasking job that require a trained vision analyst to sift through hundreds of eye movements. The difficulty of the task increases when a subject has undiagnosed eye related disorders. One such disorder is Convergence insufficiency (CI) which affects nearly 12 million people in the US. Convergence insufficiency occurs when the eyes are unable to coordinate simultaneous inward movement for near focal tracking. Individuals with CI are unable to coordinate eye movements this can result in many symptoms such as double vision, blurred vision, headaches, vision strain, and fatigue. A diagnosis for CI relies …

Development Of Novel Inks And Approaches For Printing Tissues And Organs, Shen Ji

Dissertations

Tissue engineering is a multidisciplinary field that investigates and develops new methods to repair, regenerate and replace damaged tissues and organs, or to develop biomaterial platforms as in vitro models. Tissue engineering approaches require the fabrication of scaffolds using biomaterials or fabrication of living tissues using cells. As the demands of customized, implantable tissue/organs are increasing and becoming more urgent, conventional scaffold fabrication approaches are difficult to meet the requirements, especially for complex large-scale tissue fabrication. In this regard, three-dimensional (3D) printing attracted more interest over the past decades due to its unrivaled ability to fabricate highly customized tissues or …

Experiments And Modeling Of The Chemo-Mechanically Coupled Behavior Of Polymeric Gels, Nikola Bosnjak

Dissertations

Polymeric materials consist of mutually entangled or chemically crosslinked long njitmolecular chains which form a polymer network. Due to their molecular structure, the njitpolymeric materials are known to undergo large deformation in response to various njitenvironmental stimuli, such as temperature, chemical potential and light.

When a polymer network is exposed to a suitable chemical solvent, the solvent molecules are able to diffuse inside the network, causing it to undergo a large volumetric deformation, known as swelling. In addition to volumetric deformation, this process involves the chemical mixing of the polymer network and solvent molecules, and is typically environmentally responsive. A …

Cycloidal-Drive Joint Design For Wearable Exoskeletons, Abhi J. Rawal

Theses

This thesis's scope was to construct a highly back drivable and compact joint design that can be used for wearable exoskeletons specifically designed to assist with rehabilitation. A compact cycloidal gear transmission was designed to satisfy the compactness requirement while ensuring the minimum torque is required for backdriving the mechanism. The joint was designed based on the compact cycloidal drive specifications, and the backdrivability test was performed to measure the minimum torque required (1.20 Nm) to backdrive. The joint design incorporates various important features such as rotation lock feature to prevent hyperextension, a housing design that offers the benefit of …

Blast Shock-Wave Characterization In Experimental Shock Tubes, Sudeepto Kahali

Dissertations

Blast-induced traumatic brain injuries have affected U.S. soldiers deployed for extended periods in the gulf and Afghanistan wars. To identify the biomechanical and biochemical mechanisms of injury, critical in the identification of diagnostic and therapeutic tools, compressed gas-driven shock tubes are used by investigators to study shockwave-animal specimen interactions and its biological consequences. However, shock tubes are designed and operated in a variety of geometry with a range of process parameters, and the quality of shock wave characteristics relevant to field conditions and therefore the study of blast-induced traumatic brain injuries suffered by soldiers is affected by those conditions. Lab-to-lab …

Biomechanical Loading Changes Between Species In Mild Blast-Induced Traumatic Brain Injury, Jose Juan Rodriguez

Dissertations

Blast-induced traumatic brain injury (bTBI) has become one of the leading injury modalities in military personnel and is considered a signature injury in veterans returning from conflicts in the Middle East. One of the main concerns in studying bTBI is translating animal experiments to clinical applications that can service veterans. Significant advances have been made using animal models in relating external shock waves to emerging neuropathophysiological and behavioral outcomes. However, it is unknown if these results are applicable to humans; and if so, can an interspecies transfer function be developed based on size, shape, and material response. This work aims …

Comparison Of Longitudinal Changes In Resting State Functional Magnetic Resonance Imaging Between Alzheimer’S And Healthy Controls, Berk Can Yilmaz

Theses

Resting State Functional Magnetic Resonance Imaging (rs-fMRI) is a technique that is widely used for analyzing brain function using different approaches and methods. This study involves rs-fMRI analysis of Blood Oxygenation Level Dependent (BOLD) signals acquired from Alzheimer’s disease (AD) Patients and Healthy Controls (HC). Each subject in the study had both functional and anatomical images with at least one rs-fMRI scan with their Anatomical (T1) scans. Previous rs-fMRI studies have demonstrated that AD shows differences in Amplitude of Low Frequency (<0.1 Hz) Fluctuations (ALFF), and Regional Homogeneity (ReHo) measures according to HCs.

The aim of the study is to investigate individual and group level differences using ReHo and mALFF related …

A Model For Thermal Diffusion And Local Tissue Damage From The Measurement Of Temperature In Electrosurgical Incision, Marek Vira

Theses

The extremely high temperatures applied over extremely short time intervals that are characteristic of electrosurgery result in a unique tissue damage pattern. Cesarean delivery and hysterectomy, the two most frequently performed procedures in obstetrics and gynecology (OB/GYN), commonly employ electrosurgical incision. While it is controversial, it has been suggested that tissue damage produced by electrosurgery could increase surgical site infection rates. While recommendations for the settings in the use of the electrosurgical unit do exist, there is no current technique for real time assessment of the viability of tissue around the site of the electrosurgical incision. Current methods for analyzing …

Investigating The Combined Effects Of Whole Body Vibration And Vestibular Stimulation On Spasticity And Dystonia In Cerebral Palsy, Peter A. Michael

Dissertations

This study identifies and addresses three voids and potential shortcomings associated with the classification, assessment and management of Cerebral Palsy (CP). These concerns should not undermine the significant advancement that has been made in this specific branch of rehabilitation, but addressing them is necessary. Cerebral Palsy is a group of motor impairments due to hypoxic-ischemic brain damage around the time of birth and very commonly manifests as excessive muscle tone and poor motor control. There are classifications within CP including spasticity and dystonia.

First, a level of discrepancy is present in the classification of CP between the clinical and research …

Modulation Of Cerebellar Purkinje Cell Activity With Low Intensity Electric And Ultrasound Stimulation, Ahmet S. Asan

Dissertations

Non-invasive brain stimulation (NIBS) techniques garner significant interest due to their potential to offer instantaneous and region-specific treatments to neurological disorders. The cerebellum is one of the target sites for NIBS methods due to its central role in motor and cognitive functions. Among several modulation techniques, transcranial electric stimulations (tEs), in particular, transcranial direct and alternating current stimulations (tDCs/tACs), and low intensity focused ultrasound stimulation (LIFUS) show encouraging outcomes in clinical applications. tDCs and tACs are favored due to their low cost and accessibility while LIFUS offers high spatial resolution and deeper penetration without affecting the surrounding structures. In order …

Mechanical Characterization Of Animal Derived Starting Materials For Tissue Engineering, Bin Zhang

Dissertations

Animal derived starting materials are well established in the production of Tissue Engineered Medical Devices. Porcine specifically can be found in products ranging in application from hernia repair to breast reconstruction. Although this material has been largely accepted in the Tissue Engineering industry, little is known of its material properties and mechanical characteristics. A review of the scientific literature describes limited mechanical measures only on uncontrolled research grade material. The objective of this work is to mechanically characterize porcine starting material used in the medical device industry. Porcine skin is provided by Midwest Research Swine, LLC (MRS) an established supplier …

Scanless Optical Coherence Tomography For High-Speed 3d Biomedical Microscopy, Yahui Wang

Dissertations

Optical coherence tomography (OCT) is a high-resolution cross-sectional imaging modality that has found applications in a wide range of biomedical fields, such as ophthalmology diagnosis, interventional cardiology, surgical guidance, and oncology. OCT can be used to image dynamic scenes, in quantitative blood flow sensing and visualization, dynamic optical coherence elastography, and large-scale neural recording. However, the spatiotemporal resolution of OCT for dynamic imaging is limited by the approach it takes to scan the three-dimensional (3-D) space. In a typical OCT system, the incident light is focused to a point at the sample. The OCT system uses mechanical scanners (galvanometers or …