Biomedical Engineering and Bioengineering Commons^™

High Frequency Oscillations As Biomarkers Of The Epileptogenic Zone In Children With Drug Resistant Epilepsy, Lorenzo Fabbri

Bioengineering Dissertations - Archive

Epilepsy surgery stands out as the most effective treatment for patients dealing with focal drug-resistant epilepsy (DRE). Its effectiveness depends on successfully removing or disconnecting the epileptogenic zone (EZ), which is the brain area crucial for seizure generation. The seizure onset zone (SOZ) serves as the best approximation of the EZ; this is the region where most seizures begin, identified through invasive electroencephalographic (iEEG) recordings. However, the unpredictable nature of seizures means they can take hours or even days to occur, consuming valuable human and financial resources. As a result, there is a pressing need for an interictal biomarker that …

Strategies For Enhanced Meg Data Analysis In Clinical Practice And Emerging Frontiers, Pegah Askari

Bioengineering Dissertations - Archive

Epilepsy and dementia are debilitating neurological disorders that pose substantial challenges for patients, caregivers, and healthcare systems. Advances in magnetoencephalography (MEG) and signal processing offer new opportunities to improve diagnostic accuracy, surgical planning, and treatment monitoring. This dissertation presents a unified body of work comprising artifact removal, automated event detection, and deep learning-based biomarker discovery. These approaches collectively enhance the clinical utility of MEG for diverse patient populations.

The first study addresses a significant technical obstacle in the management of drug-resistant epilepsy. Patients receiving responsive neurostimulation (RNS) have historically been excluded from MEG as the data is contaminated by device-related …

Functional Enhancement Of Pancreatic Islets Through Photobiomodulation For Potential Diabetes Therapeutics, Kelli Fowlds

Bioengineering Dissertations - Archive

Islet transplantation is a potential therapeutic route for type 1 diabetic patients facing chronic ketoacidosis and/or hypoglycemia unable to be properly regulated with standard insulin administration. However, successful engraftment is hampered by a multitude of factors. Harvested islets face rapid, substantial degradation due to hypoxia and nutrient depletion once isolated. Transplanted islets are additionally susceptible to the instant blood-mediated inflammatory reaction (IBMIR). This combination of factors leads to more than half of transplanted islets failing to engraft post-surgery. Many areas of research are dedicated to investigating alternative approaches or supplemental treatments to improve the success rate of engraftment and insulin …

Novel Electrophysiological Biomarkers In Pediatric Drug Resistant Epilepsy And Genetic Epilepsy Syndromes, Sakar Rijal

Bioengineering Dissertations - Archive

Pediatric epilepsies, particularly those that are drug-resistant or genetically driven, represent some of the most complex neurological disorders encountered in childhood. Central to their pathophysiology is a disruption in the delicate balance between cortical excitation and inhibition (E/I), often resulting from impaired GABAergic interneuron function. This imbalance manifests as aberrant network dynamics and altered neural oscillations, giving rise to seizures and long-term cognitive impairments. In this thesis, we developed a translational framework to identify electrophysiological biomarkers that (i) assess cortical E/I imbalance and (ii) map epileptogenic zones, with the aim of enhancing diagnosis, guiding surgical planning, and informing therapeutic monitoring …

Vendor-Independent B0 Shimming Framework With Application To Metabolic Mri In Human Gliomas, Mahrshi Jani

Bioengineering Dissertations - Archive

High and ultra-high field MRI and MRSI offer markedly improved signal-to-noise ratio and spectral dispersion, enabling in-vivo characterization of tumor metabolism with unprecedented detail. However, these benefits are tightly coupled to high demands on static magnetic field (B₀) homogeneity, particularly in the brain where susceptibility interfaces near the skull base and paranasal sinuses generate complex, higher-order field perturbations. In glioma patients, additional susceptibility variations arise from surgical cavities, hemorrhage, calcifications, and cystic components, further degrading B₀ homogeneity. As a result, shimming often become the main bottleneck limiting robust, whole-brain spectroscopic imaging and, consequently, our ability to map metabolic …

Plasmonic Nanopore Sensing For The Characterization Of Viruses And Biomolecules, Scott Renkes

Bioengineering Dissertations - Archive

The rapid advancement of nanomedicine has enabled increasingly precise nanotherapeutic platforms, including targeted nanoparticles, monoclonal antibodies, and viral gene delivery vectors. As these technologies mature, quality control and analytical characterization have emerged as critical bottlenecks, particularly in systems where functional outcomes depend on one-to-one molecular or particle–biological interactions. Conventional ensemble-averaged techniques obscure heterogeneity that is often central to therapeutic efficacy, safety, and manufacturability. A prominent example is adeno-associated virus (AAV)–based gene therapy, where production yields heterogeneous populations of empty, partially loaded, and fully loaded capsids. Genome fill percentage and integrity directly influence therapeutic efficacy and dosing accuracy, while limited understanding …

Emotion Processing In Adolescents With Epilepsy And Healthy Controls Using Multi-Modal Neuroimaging, Frances Kathryn E. King

Bioengineering Dissertations - Archive

Epilepsy is increasingly recognized as a disorder not only of seizures but also of widespread network dysfunction, impacting cognitive and emotional processing. One critical cognitive process affected in epilepsy is emotional conflict processing, which relies on the interplay of multiple brain networks. However, the spatiotemporal dynamics of emotional conflict processing in epilepsy, particularly in adolescents, have remained poorly understood. This dissertation investigated the neural mechanisms underlying emotional conflict processing in typically developing adolescents and adolescents with epilepsy using magnetoencephalography (MEG). The first study elucidated the spatiotemporal profile of emotional conflict processing in 24 typically developing adolescents using magnetoencephalography (MEG). Cluster-based …

Human System Composite Performance Measures: General Systems Performance Theory Insights, Lawrence Disalvi

Bioengineering Dissertations - Archive

Composite Performance Measures (CPMs) of human performance are widely employed in applications that range from mundane to life-changing, yet they are frequently presented without explanation or reference to theoretical underpinnings. The conceptual soundness of a widely used CPM approach, based on additive combination of constituent components, has been called into question by Kondraske. He argues the relevance of General Systems Performance Theory (GSPT) and performance capacity envelope concepts when applied to multidimensional CPM measures.

To obtain evidence-based answers to assertions regarding CPM types and rationale employed in medical and non-medical contexts, a Systematic Descriptive Review was conducted. Separately, the GSPT-based …

Computational And Experimental Analysis Of Silica Nanoparticles Under Dc And Ac Electric Fields Using A Self-Induced Back Action Actuated Nanopore Electrophoresis (Sane) Sensor, Homayoun Asadzadeh, Scott Renkes, George Alexandrakis, Minjun Kim, Scott Turpin

Bioengineering Dissertations - Archive

In this dissertation I have studied a novel single-molecule nanosensor that integrates a Solid-State Nanopore (SSNP), milled in silicon nitride with a Double Nanohole (DNH) nanoaperture, milled in gold. This device leverages Self-Induced Back-Action (SIBA) for optical trapping with ssNP electrical sensing and is called the SIBA-Actuated Nanopore Electrophoresis (SANE) sensor. My lab has previously shown that simultaneous acquisition of bimodal optical and direct current (DC) electrical signatures enables more detailed characterization of nanoscopic analytes compared to using electrical data alone, which are typically collected by ssNP sensors. In this work I have first studied by COMSOL Multiphysics simulations the …

Spray-On Sensor Formulations That Enable Detection Of Physical And Chemical Stimuli, Priyanka Shiveshwarkar

Bioengineering Dissertations - Archive

Polydiacetylene based materials have been used for a variety of liquid phase sensing applications. There remains a need for low cost, easy-to-read gas phase sensors for continuous monitoring of physiological parameters and environmental hazards at work or at home. Such sensors could have applications in everyday life, for example as point-of-care or at home testing devices to enable early detection of disease to reduce healthcare costs. Making accessible and non-invasive technologies for monitoring of health and health risks provides individuals with the ability to be proactive in regard to their health and safety. In other examples, environmental monitoring systems could …

Development Of Anti-Microbial Nanocoatings On Metallic Surfaces To Prevent Infections, Luis Fernando Soto Garcia

Bioengineering Dissertations - Archive

Healthcare-associated infections have a prevalence of about 7% in the United States and up to 50% in some developing nations. They not only present a constant risk for inpatients and healthcare workers but are also a serious challenge to human health services worldwide. These infections can be transmitted via contaminated non-critical surfaces like doorknobs and bedrails, which are routinely cleaned with low-level disinfectants approved by the U.S. Environmental Protection Agency. However, this strategy has limited efficacy since recontamination occurs, resulting in these surfaces again becoming vectors of infection. In this work, we addressed this issue by developing a self-disinfecting nanocomposite …

An In-Vitro Model For Visualizing Intraocular Lens And Lens Capsule Interaction In Posterior Capsule Opacification, Amjad Chatila

Bioengineering Dissertations - Archive

Posterior Capsule Opacification (PCO) is a common complication post cataract surgery. It is believed that Intraocular Lens (IOL) physical and chemical properties would affect their PCO potential. The tight binding between IOL and posterior lens capsule (PLC) is believed to have a negative impact on PCO formation, as suggested in the “No space, no cell, no PCO” hypothesis. To test the hypothesis, we have recently developed an in vitro 3D system to simulate IOL and PLC physical interaction. To expand the function and capability of this system, one objective of my work was to develop the next generation adhesion force …

Novel Engineering Approaches For Orthopedic Injury Treatment And Infection Diagnosis, Cynthia Co

Bioengineering Dissertations - Archive

Bioengineering has made significant contributions to the treatment of orthopedic injury through interdisciplinary approaches. Central to these advancements are many orthopedic implants, including anchors and joint replacements, which have been designed to restore mobility. Despite their functional efficacy, these products have limited lifespan and are associated with many complications, such as implant-associated infection. The success of implant design and function, both in the short and long term, is paramount for enhancing patient outcomes and overall well-being. Therefore, my thesis work is dedicated to addressing these critical challenges, aiming to maximize their treatment effect while minimizing the implant-associated complications.

Long-term patient …

Noninvasive Mapping Of Global And Regional Functional Connectivity In The Brain Of Children With Drug Resistant Epilepsy And Healthy Controls, Ludovica Corona

Bioengineering Dissertations - Archive

For patients with drug resistant epilepsy (DRE), resective surgery is the most effective treatment to achieve seizure-freedom. Its success largely depends on the resection, ablation, or disconnection of the epileptogenic zone (EZ), defined as the minimal area indispensable for the generation of seizures, with minimal or no functional deficits. To date, there is no clinical exam to delineate the EZ unambiguously. Instead, the EZ is indirectly defined through multiple noninvasive diagnostic tests used by the multidisciplinary epilepsy team, whose results are often insufficiently concordant or inconclusive. Thus, extra-operative intracranial electroencephalography (iEEG) monitoring may be needed to precisely define the EZ …

Lung Cancer Growth Forecasting And Classification Models By Machine Learning Using A Novel 2d Co-Culture High Throughput Device, Adam Adrien Germain

Bioengineering Dissertations - Archive

Co-culture devices have commonly been used during in vitro experimentation to create therapeutic testing devices for lung cancer that more closely mimic the in vivo environment to gain better insights into new therapies and the reasons for inconsistency for current therapies. Moreover, AI (artificial intelligence) in the form of convolutional neural networks (CNN) and convolutional long-short term memory neural networks (convLSTM) are being used to classify, diagnose, and predict drug outcomes from the visual data provided by clinical imaging modalities, such as CT-scans, MRIs, or histopathological slides among others, or from numerical and textual data gathered from the genetic testing …

Advances And Applications In Ultrasound-Switchable Fluorescence Imaging, Liqin Ren

Bioengineering Dissertations - Archive

Cancer diagnosis is a prerequisite for further medical therapy and treatment. Near-infrared (NIR) fluorescence imaging is a desirable modality without invasiveness and nonionizing radiation. However, fluorescence suffers from a strong light scattering in tissues, leading to a low spatial resolution and low sensitivity in centimeter-deep tissue (limited to several millimeters). To enhance spatial resolution and avoid the high scattering of conventional fluorescence imaging in deep tissue, ultrasound-switchable fluorescence (USF) imaging has emerged as a highly promising technique for biomedical imaging and research. The principle of improving spatial resolution in USF imaging is to confine the fluorescence emission from thermosensitive fluorophores …

Development Of Multiscale And Multidimensional Light Sheet Microscopy For Image-Based Modelling Of Organogenesis, Tanveer Ashwini Ashwini Teranikar

Bioengineering Dissertations - Archive

Behavioral analysis of individual cells, in the form of structural phenotypes arising in response to mechanical stimuli or genomic alterations as small molecule intermediates of disease, are instrumental for understanding organogenesis. In this regard, dynamic cell tracking or temporal changes in cell shape, area and size are vital for modelling tissue interactions. However, optical diffraction limits imposed by lenses, hinders high resolution volume reconstruction of microscale biological processes and subcellular organelles. Thereby, isotropic intensity is restricted to limited focal volumes, reducing imaging distance to less than 1 mm for high magnification. To combat this, Light Sheet Microscopes (LSM) have emerged …

Quantification And Identification Of Neuro-Electrophysiological Markers And Brain Network For Biomedical Applications, Shu Kang

Bioengineering Dissertations - Archive

Electroencephalogram (EEG) can detect and monitor neuro-electrophysiological signals in the human brain, including assessing brain function in newborns at risk of neurological injury and healthy adults undergoing intervention with prefrontal transcranial photobiomodulation (tPBM). Moreover, EEG-based brain functional connectivity can be assessed in either resting-state or task-based measurements using graph-theoretical network modeling. However, the management of newborns with mild hypoxic ischemic encephalopathy (HIE) is controversial, and no study has investigated the EEG-based brain network and information flow resulting from HIE. Also, the underlying electrophysiological mechanism of tPBM is still unclear, and further research is needed to determine optimal parameters for tPBM …

An In Vitro 3d Model To Investigate Iol: Posterior Lens Capsule Interactions On Lens Epithelial Cell Responses, Joyita Roy

Bioengineering Dissertations - Archive

ABSTRACT: Posterior Capsule Opacification (PCO) is the most common complication associated with Intraocular Lens (IOL) implantation. The disease is caused by the infiltration and proliferation of Lens Epithelial Cells (LEC) into the interface between the IOL and Posterior Lens Capsule (PLC). The severity of these cell responses depends on a lot of factors like the IOL design, IOL material, and interaction between the IOL and the posterior lens capsule. While some studies have also shown that adsorption of certain proteins present in the PLC, like fibronectin, may affect IOL-induced PCO in the clinical setting, the mechanism governing such interactions is …

Targeted Drug-Loaded Nanoparticle System (Tdnps) To Ameliorate And Treat Idiopathic Lung Fibrosis, Harish Ramachandramoorthy

Bioengineering Dissertations - Archive

Idiopathic pulmonary fibrosis (IPF) is a fatal progressive disease with a dismal prognosis and 3-5 years of survival. Up to date, there are no effective treatments, and a few current therapies that do not ameliorate the pulmonary fibrosis but rather just increase the survival time by 2-3 years. The major factor limiting the treatment is the lack of targeted therapies to deliver the drugs past the mucosa, into the disease microenvironment. To combat this disease, we proposed a localized therapy via our targeted drug-loaded nanoparticles (TDNPs) to effectively deliver drugs and treat lung fibrosis. Our objective was to design TDNPs …

Novel Nanoparticles To Stimulate Therapeutic Angiogenesis For The Treatment Of Peripheral Arterial Diseases, Tam Phung Nguyen

Bioengineering Dissertations - Archive

Peripheral arterial disease (PAD) is a severe impairment of arterial vessels resulting in obstruction of normal blood flow in the legs, leading to acute or chronic lower limb ischemia and subsequently high morbidity and mortality rates. Common treatments for PAD, such as medications and surgical revascularization, have several limitations. For instance, medications used to lower cholesterol, reduce high blood pressure, control blood sugar, prevent blood clots, and reduce/delay symptoms such as leg pains. Still, they cannot treat the established disease directly and often cause side-effects, including bleeding, headache, and diarrhea. Meanwhile, many elderly PAD patients cannot undergo surgical options. Therefore, …

Engineering Elastic And Functional Electrospun Nano-Fibers For Potential Heart Repair, Alan Mark Taylor

Bioengineering Dissertations - Archive

In the United States and around the world, cardiovascular disease (CVD) has been one of the main causes of death since 1921, responsible for approximately 1 in 4 deaths domestically. Myocardial infarction (MI), or commonly called a heart attack, is a subset of CVD that often ends in heart failure (HF). Cardiac cells are incapable of regeneration, leading to severe impacts on quality of life. Current treatments for MI fail to target left ventricular remodeling and therefore do little to address the progression towards HF. Cardiac scaffolds for tissue engineering (TE) are a prominent solution in recent research. Developing various …

Advancing The Radiation Oncology Clinic With Motion Management And Automatic Treatment Planning, Damon Anton Sprouts

Bioengineering Dissertations - Archive

The leading cause of premature death (death under the age of 70) is cancer. The top five cancers for both male and female are: lung, colorectum, pancreas, breast cancer, and prostate. In 2020 there was an estimated 19.3 million new cases with an estimated 9.9 million deaths. The cancer burden is expected to grow to 28.4 million by the year 2040. Surgery, chemotherapy, and radiotherapy are the three pillars in the modern clinic for cancer treatment. In radiotherapy, ionizing radiation particles can travel through the patient body, deposit energy along the way and damage the DNA Structure. There needs to …

Electrophysiological, Hemodynamic, And Metabolic Effects Of Transcranial Photobiomodulation (Tpbm) On Topographical And Physiological Connectivity In The Human Brain, Sadra Shahdadian

Bioengineering Dissertations - Archive

Transcranial photobiomodulation (tPBM) targets the human brain with near-infrared (NIR) light and is shown to affect human cognitive performance and neural electrophysiological activity as well as concentration changes of oxidized cytochrome-c-oxidase ([CCO]) and hemoglobin oxygenation ([HbO]) in human brain. Brain topographical connectivity, which shows the communication between regions of the brain, and its alteration can be assessed to quantify the effects of external stimuli, diseases, and cognitive decline, in resting-state or task-based measurements. Furthermore, understanding the interactions between different physiological representations of neural activity, namely electrophysiological, hemodynamic, and metabolic signals in the human brain, has been an important topic among …

Mapping Of Electroencephalogram (Eeg) Responses To Newsvendor Decision Model And Cerebral Hemodynamic Responses To Transcranial Photobiomodulation (Tpbm) In Humans, Cong Dung Nghi Truong

Bioengineering Dissertations - Archive

Decision-making is one of the most critical activities of human beings. Various studies have investigated the brain responses to a variety of decision tasks by deploying the EEG data. The first aim of my dissertation was to investigate the neurocognitive mechanisms and correlations across multiple subjects when people make risky economic decisions. A decision-making task was designed based on the newsvendor problem (NP) with two scenarios: low-profit margins (LM) as the more challenging scenario and high-profit margins (HM) as the less difficult one. The EEG signals were acquired from healthy humans while subjects were performing the task. The Correlated Component …

Engineering Enzymatic Pathways In The Gut Microbiome To Control Dietary Isoflavone Metabolism, Lenaiya Allisen Kydd

Bioengineering Dissertations - Archive

ABSTRACT: Observing how plasmids persist within the gut can help us understand how newly introduced genes are transmitted within the gut microbiome. I sought to determine the persistence of genetic constructs introduced to the murine gut and then develop our own genetic system to be delivered to the gut to engineer the microbiome in its ability to convert certain dietary isoflavones. In my initial experiments, mice were given bacteria containing a genetically engineered plasmid and were examined for the persistence of the plasmid in the gut. I found long-term persistence of the plasmid in the gut for up to 2 …

Novel Nanocomposites For The Treatment Of Lung Infections, Uday Kumar Chintapula

Bioengineering Dissertations - Archive

Lung infections, especially lower respiratory tract infections and their associated pneumonias, are one of the leading causes of death, accounting for more than 4 million fatalities every year worldwide. Bacterial pathogens are involved in many lower respiratory tract infections including emerging antibiotic resistant respiratory pathogens such as methicillin-resistant staphylococcus aureus (MRSA). Current interventions for MRSA lung infections include systemic antibiotic treatments for an extended period leading to various side effects such as acute kidney injury, nephrotoxicity, and so on. To overcome these limitations, the goal of this dissertation research is to develop a drug delivery system, which includes pathogen-specific drug-loaded …

Development Of Algorithms To Analyze Electrogastrography (Egg) For Neonatal Gastrointestinal Development And Electroencephalography (Eeg) For Effects Of Led-Based Pre-Frontal Light Stimulation, Akhil Mahendra M Chaudhari

Bioengineering Dissertations - Archive

Algorithm development, and biological signal processing are the key components for new applications of successful medical diagnosis that can provide physiological and functional information to better understand human condition for either patients with certain diseases or healthy human beings. Neuroimaging tools, such as functional near infrared spectroscopy (fNIRS), and electrogastrography (EGG) have been used to investigate the gut maturity in diseased and healthy state; and electroencephalogram (EEG) have been used to investigate brain functions in response to neuromodulated or task-based interventions. Accordingly, my dissertation focused on algorithm development and signal processing for two major topics: (1) to outline EGG response …

Designing And Advancing Contrast Agents For Ultrasound-Switchable Fluorescence Imaging, Yang Liu

Bioengineering Dissertations - Archive

Fluorescence imaging is a remarkable tool for molecular targeting and multicolor imaging, but it suffers from poor resolution in centimeters-deep tissues. The recently developed ultrasound-switchable fluorescence (USF) imaging has overcome this challenge and achieved in vivo imaging with the help of the indocyanine green (ICG)-encapsulated poly(N-isopropylacrylamide) (ICG-PNIPAM) contrast agent. As USF imaging advances, there is a great demand to expand the contrast agent bank so that applications can be achieved using different types of contrast agents. Also, there is a need to improve the current ICG-PNIPAM nanogel. This study focused on improving the ICG-PNIPAM nanogel, formulating a novel contrast agent, …

Poly(Lactic-Co-Glycolic Acid) Nanoparticle Delivery Of Notch Intracellular Domain Plasmid To Restore Notch Signaling, Victoria L. Messerschmidt

Bioengineering Dissertations - Archive

Notch signaling is a highly conserved signaling system that is required for embryonic development and regeneration of organs. When the signal is lost, maldevelopment occurs and leads to a lethal state. Delivering exogenous genetic materials encoding Notch into cells can reestablish downstream signaling and rescue cellular functions. Here, we utilized the negatively charged and FDA approved polymer poly(lactic-co-glycolic acid) to encapsulate Notch Intracellular Domain-containing plasmid in nanoparticles. We show that primary human umbilical vein endothelial cells (HUVECs) readily uptake the nanoparticles with and without specific antibody targets. We demonstrated in vitro that our nanoparticles are nontoxic, stable over time, and …