Biomedical Engineering and Bioengineering Commons^™

Fungi In Flux | Designing Regenerative Materials And Products With Mycelium, Arvind Bhallamudi

Masters Theses

As the world grapples with the escalating crisis of climate threats and environmental degradation, this research delves into the synergistic potential of design and biology, developing safe and sustainable materials for applications in prototyping, furniture and interior design. Harnessing the power of a unique organism - fungi, the study proposes an accessible, efficient, and resilient material resource system. It utilizes local waste streams and mycelium (the vegetative part of fungi) to grow functional structures. An experimental and small-scale protocol is modeled by testing bio-fabrication and bio-printing methods. The composites' performance qualities and characteristics are evaluated through mechanical testing and a …

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 …

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 …

Development Of Non-Viral Nano-Carriers For Gene Delivery And Covid-19 Vaccines, Zhongyu Li

Dissertations

Gene therapy is one of the most promising medical fields with the potential to effectively advance the treatment of difficult diseases by producing therapeutic proteins or repairing defective gene sequences. However, gene therapy presents severe challenges in delivery including renal clearance, phagocytosis, enzymatic degradation, protein absorption, and cellular internalization barriers, which have been barriers for translation into the clinic. Naked nucleic acids, with their intrinsic negative charge, electrostatically repulse the anionic cell membrane, preventing cellular uptake. Also, they are considered foreign genetic material when introduced into the body and are rapidly cleared by the reticuloendothelial system or degraded by nucleases, …

Optical Perturbation Of Protein Kinase A Activity Via Photoactivatable Inhibitor Peptides, Peter Chen

McKelvey School of Engineering Theses & Dissertations

Protein Kinase A (PKA) plays important roles in diverse biological processes such as sleep, long term memory, and synaptic plasticity. In addition, PKA also acts as an integrator of neuromodulator signaling though G protein-coupled receptor activation. However, despite genetic knockout and pharmacological inhibition experiments that demonstrate the importance of PKA, it is unclear where, when, or how PKA plays these roles in cellular physiology and behavior. In order to better understand the function of PKA in these processes, and how neuromodulator signaling drives complex behavioral changes, there exists a need for a method to selectively activate/inactivate PKA with high spatial …

Preparing Non-Human Primates To Study Hand-Eye Coordination In Frontal Eye Fields (Fef) During Delayed Movement Task, Juliusz Cydzik

McKelvey School of Engineering Theses & Dissertations

ABSTRACT OF THE THESIS Preparing Non-Human Primates to Study Hand-Eye Coordination in Frontal Eye Fields (FEF) During Delayed Movement Task by Juliusz Cydzik Master of Science in Biomedical Engineering Washington University in St. Louis, 2023 Professor Lawrence Snyder, Chair Hand-eye coordination enables humans and non-human primates to use their hands and eyes to perform various tasks. We are interested in coordination at the systems level, where saccades and reaches are encoded. The parietal reach region (PRR), situated at the posterior end of the intraparietal sulcus (IPS) and overlapping portions of the medial intraparietal area (MIP) and V6a, is commonly attributed …

Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu

McKelvey School of Engineering Theses & Dissertations

Geobacter sulfurreducens are anaerobic bacteria capable of making electrical contacts with other organisms and extracellular electron acceptors. The challenge of imaging live Geobacter bacteria is maintaining anaerobic conditions during the imaging process. In this thesis, we augment a single-molecule localization microscope (SMLM) with a home-built anaerobic imaging chamber and use constant argon bubbling to maintain oxygen-free imaging conditions. To validate the imaging protocol, we use the transient binding of Nile red to resolve the spherical morphology of lipid-coated glass spheres with nanoscale resolution. However, when imaging Geobacter, the distribution of Nile red localizations is non-uniform, both between different cells …

Antimicrobial Activity And Mechanism Of Amyloid Proteins And Synthetic Conjugated Polyelectrolytes, Fahimeh Maghsoodi

Nanoscience and Microsystems ETDs

Although the exact cause of Alzheimer’s disease (AD) is still unknown, it is widely considered that the accumulation of amyloid plaques composed of the amyloid-β (Aβ) peptide in the brain is linked to neurodegeneration. Co-localization of viral DNA with Aβ plaques, the association of brain infection and AD, and research indicating the protective effect of Aβ against bacteria and fungi in mice and human cells have led to the hypothesis that Aβ expression and deposition may be central to its function as an antimicrobial peptide (AMP). In my thesis research, we seek to elucidate how Aβ functions as an AMP …

The Development Of A Primer Payload With Microparticles For Uti Pathogen Identification Using Polythymidine- Modified Lamp Primers In Droplet Lamp, Jonas Otoo

KGI Theses and Dissertations

Nucleic acid amplification tests (NAATs) are among the diagnostic tests with the highest sensitivity and specificity. However, they are more complex to develop than other diagnostic tests such as biochemical tests and lateral flow immunoassay tests. Polymerase chain reaction (PCR) is the gold standard for NAATs. PCR requires thermal cycling to achieve clonal amplification of the target pathogen DNA for diagnosis. Thermal cycling poses a challenge in the development of PCR diagnostics for point-of-care (POC) settings. Loop-mediated isothermal amplification (LAMP) offers an isothermal method for NAATs diagnostics. The advancement of the microfluidics field significantly enhances the development of LAMP diagnostics …

Soil Respiration Measurements Reveal High Retention Of Organic Carbon From Corn Residue Derived High-Lignin Fermentation Byproduct Enabling Sustainable Lignocellulosic Biofuel Production, Michelle Sun Wang

Dartmouth College Master’s Theses

While 2G biofuel production can utilize non-edible, lignocellulosic feedstocks such as agricultural residues to produce liquid fuel, harvesting crop residues is unsustainable without careful management of the soil underneath. By harvesting a fraction of the crop residues left in the field after harvest, soil health can diminish and critically, the soil organic carbon (SOC) stored in agricultural fields can decrease. Currently, in the most popular 2G process models published, the issue of soil degradation remains unresolved with residue harvest strategies receiving considerable attention in the literature and other SOC management strategies receiving far less. Specifically, the strategy of returning the …

Growth Plate Cartilage: Understanding The Contribution Of Adhesion To Column Formation And Matrix Structure, Sydney E. Greer

Theses & Dissertations

Throughout fetal and adolescent development, bone growth is regulated by fine-tuned and controlled maturation of chondrocytes through a cartilaginous template called the growth plate. Bone growth rate is controlled through cell enlargement and extracellular matrix deposition, while the polarized arrangement of proliferative chondrocytes into columns aligned with the long axis of the bone potentiate growth. Chondrocytes are surrounded by a complex three-dimensional arrangement of matrix molecules, all of which are secreted by chondrocytes and assembled/remodeled to support the biological functions of the cell. Adhesion receptors found on the cell membrane of chondrocytes are crucial to the organization of matrix proteins …

The Future Is Now In Twisted Coil Polymer Actuators (Tcpa), Ryan Ronquillo

Electronic Theses and Dissertations

This thesis aimed to fabricate and test twisted coiled polymer actuators (TCPA) to understand the mechanical and thermal aspects of this artificial muscle fiber. The purpose of this thesis was to find a linear relationship using the LVDT sensor, fabricating TCPA fibers, and interpreting the data. The project tested whether nylon/polymer could be used as a better artificial muscle fiber.

This research accomplished three goals: (1) designing and fabricating a system capable of creating supercoiled muscle fibers consistently, (2) calibrating the Linear Variable Differential Transformer (LVDT) and Core, and (3) analyzing/interpreting the data of the Twisted Coiled Polymer Actuators (TCPA) …

Cardiac Ablation And Stimulation With Nanosecond Pulsed Electric Fields (Nspefs), Federica Serra

Biomedical Engineering Theses & Dissertations

Surgical ablation of cardiac tissue is the definitive treatment for the most common arrhythmia, atrial fibrillation. In current medical practice, myocardial tissue is often ablated by the application of radiofrequency (RF) currents which are delivered through an electrode to create lesions that block the electrical pathways that sustain reentrant arrhythmias and restore the normal heart rhythm. An alternative to RF is cryoablation, during which the endocardial or epicardial tissue is brought in contact with a cryoprobe. Both RF ablation and cryoablation have significant limitations. In RF ablation, tissue is heated in order to ablate it, but it is an open …

Rattus Norvegicus As A Biological Detector Of Clandestine Remains And The Use Of Ultrasonic Vocalizations As A Locating Mechanism, Gabrielle M. Johnston

Master's Theses

In investigations, locating missing persons and clandestine remains are imperative. One way that first responder and police agencies can search for the remains is by using cadaver dogs as biological detectors. Cadaver dogs are typically used due to their olfactory sensitivity and ability to detect low concentrations of volatile organic compounds produced by biological remains. Cadaver dogs are typically chosen for their stamina, agility, and olfactory sensitivity. However, what is not taken into account often is the size of the animal and the expense of maintaining and training the animal. Cadaver dogs are typically large breeds that cannot fit in …

Trace Dna Detection Using Diamond Dye: A Recovery Technique To Yield More Dna, Leah Davis

Master's Theses

This study aspires to find a new screening approach to trace DNA recovery techniques to yield a higher quantity of trace DNA from larger items of evidence. It takes the path of visualizing trace DNA on items of evidence with potential DNA so analysts can swab a more localized area rather than attempting to recover trace DNA through the general swabbing technique currently used for trace DNA recovery. The first and second parts consisted of observing trace DNA interaction with Diamond Dye on porous and non-porous surfaces.

The third part involved applying the Diamond Dye solution by spraying it onto …

Laser Inscribed Graphene Aptasensor For Detection Of Apple Stem Pitting Virus, Yifan Tang

All Theses

Apple stem pitting virus (ASPV) is a latent RNA virus that could cause significant loss to apple production; early-stage field diagnosis could reduce the economic loss caused by ASPV infection. Biosensor is a promising user-friendly detection tool that could transduce biological or chemical interactions into electric signals. Among various types of biosensors, aptasensor, which use aptamers as recognition elements show potential as a high throughput, in-field test. The goal of this thesis is to develop an electrochemical aptasensor testing system for ASPV detection. The quality control study of laser inscribed graphene (LIG) based working electrode of the biosensor was conducted …

Assesment Of Structure, Function, And Microevolutionary Dynamics Of Extrachromosomal Circular Dna In Chinese Hamster Ovary Cells, Dylan Chitwood

All Dissertations

Chinese hamster ovary (CHO) cell lines are among the most popular expression hosts used in biopharmaceutical manufacturing due to relative ease of culture, capacity to perform human-like post-translational modifications, and non-susceptibility to viruses. However, the intrinsic plasticity of the CHO genome can lead to undesired genetic rearrangements, phenotypic shifts, reduced product quality, and early culture termination that prevents continuous biomanufacturing. A characteristic of plastic and unstable genomes that is poorly understood in CHO cells is extrachromosomal circular DNA (eccDNA). EccDNAs are focal amplifications of the genome that reside in the extranuclear space. These plasmid-like entities are structurally complex and are …

Mitral Valve Imaging And Biomechanics: A Workflow Towards Computational Modeling And Validation, Sam Stephens

Graduate Theses and Dissertations

The mitral valve serves a critical role in healthy cardiac function by ensuring the unidirectional flow of oxygenated blood from the left atrium into the left ventricle. It experiences the highest pressures found within the heart and its closure is the result of a complex interaction of several different structures that, furthermore, are unique to each individual. Despite the valve’s vital role however, the specific function of these constituent structures is not fully understood. This, confounded by its asymmetric, personalized nature, make surgical interventions for the mitral valve far less effective than for its neighboring aortic valve. Efforts to overcome …

Nanosecond Pulsed Electric Field Modulates Electron Transport And Mitochondrial Structure And Function, Lucas Nelson Potter

Biomedical Engineering Theses & Dissertations

Pulsed power treatment has been used to induce regulated cell death (RCD) in cells or ablate tumors in animals. A subset of pulsed power as electroporation with high voltage and pulse duration of milliseconds is used for biomedical treatment to induce pores in the plasma membrane of cells. Nanosecond Pulsed Electric Fields (nsPEFs)– an extension of electroporation, uses waveforms with pulse durations on the order of 10-900 nanoseconds. nsPEF treatment has demonstrated intracellular effects for potential biomedical applications. In this work, nsPEF treatment is used to demonstrate changes that affect viability, plasma membrane permeability ROS (Reactive Oxygen Species) in the …

Wearable Sensor Gait Analysis For Fall Detection Using Deep Learning Methods, Haben Girmay Yhdego

Electrical & Computer Engineering Theses & Dissertations

World Health Organization (WHO) data show that around 684,000 people die from falls yearly, making it the second-highest mortality rate after traffic accidents [1]. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. In light of the recent widespread adoption of wearable sensors, it has become increasingly critical that fall detection models are developed that can effectively process large and sequential sensor signal data. Several researchers have recently developed fall detection algorithms based on wearable sensor data. However, real-time fall detection remains challenging because of the wide …

Evaluating Foot-Drop Interventions For Multiple Sclerosis Using A Multimodal System, Laura Marie Byrnes-Blanco

USF Tampa Graduate Theses and Dissertations

This dissertation explores how multimodal walking impacts quantitative and qualitative aspects of gait for persons with multiple sclerosis (pwMS) experiencing foot-drop. Foot-drop can dramatically impede mobility and clinicians routinely prescribe ankle-foot-orthosis (AFO) and functional electrical stimulation (FES) devices to alleviate its impacts on daily life. However, little is known about how these devices affect pwMS while traversing environments with real-world complexity. To explore this topic, an interventional, parallel assigned study was conducted. A realistic nature pathway containing changes in floor pitch, audiovisual stimulation, and during-trial tasks (for dual-tasking) was generated in an immersive virtual reality system called CAREN: Computer Assisted …

Multi-View Contrastive Learning For Unsupervised Domain Adaptation In Brain-Computer Interfaces, Sepehr Asgarian

Electronic Thesis and Dissertation Repository

Electroencephalography (EEG) has been widely used to record electromagnetic fields for motor imagery (MI)-based brain-computer interfaces (BCIs). However, collecting MI signals is often time-consuming and challenging to classify due to the inter-subject variability of EEG signals. To address these issues, we propose a novel framework MACNet, which stands for Multi-view Adversarial Contrastive Network. MACNet employs a contrastive learning approach to learn spatial and temporal features in two views, using Riemannian and Euclidean encoders. By jointly extracting underlying features and learning domain-invariant representations in both source and target features, MACNet improves the alignment and accuracy. In addition, we propose a domain …

Human Spacesuit Interaction During Eva Of The Legs Using A Force Sensing System, Niraliben D. Patel

USF Tampa Graduate Theses and Dissertations

Astronauts perform a multitude of tasks in space, both in the spacecraft and outside of the spacecraft. Extravehicular Activity (EVA) refers to any activity that is completed outside of the spacecraft, whether it is work on the actual spacecraft, spacewalks, or conducting sample collections on other planets and moons. To do this safely, a pressurized Extravehicular Mobility Unit (EMU) or commonly known as the spacesuit is used. There have been multiple iterations of the United States EMU with advances to further optimize the astronaut safety and EVA tasks. However, there is still relatively little information on the movement of the …

Comparison Of In-Vitro 3d Human Embryoids With Current Models For Gastrulation, Jin Park

McKelvey School of Engineering Theses & Dissertations

Gastrulation is an early morphogenetic process that is conserved across most metazoans and lays out the future body plan through the formation and shaping of the three germ layers: endoderm, mesoderm, and ectoderm. Despite its importance, not much is known about the events surrounding human gastrulation that occurs in utero due to ethical and technical limitations on studying human embryos. Therefore, many researchers have devised protocols for creating in vitro models of gastrulation using embryonic stem cells. Initially starting with mouse embryonic stem cells, the field of in vitro embryo models has advanced rapidly, with protocols using human embryonic stem …

Making Sense Of Big (Kinematic) Data: A Comprehensive Analysis Of Movement Parameters In A Diverse Population, Naomi Wilma Nunis

University of the Pacific Theses and Dissertations

OBJECTIVE

The purpose of this study was to determine how kinematic, big data can be evaluated using computational, comprehensive analysis of movement parameters in a diverse population.

METHODS

Retrospective data was collected, cleaned, and reviewed for further analysis of biomechanical movement in an active population using 3D collinear resistance loads. The active sample of the population involved in the study ranged from age 7 to 82 years old and respectively identified as active in 13 different sports. Moreover, a series of exercises were conducted by each participant across multiple sessions. Exercises were measured and recorded based on 6 distinct biometric …

Development Of A Portable Device For Quantifying Internal-External Rotational Laxity Of The Knee In Vivo, Haley Kuralt

Graduate College Dissertations and Theses

Osteoarthritis (OA) is the leading cause of mobility-related disability. Post-traumatic osteoarthritis (PTOA) is a form of OA that occurs after an acute injury to the affected joint. In the case of the knee, rupture of the anterior cruciate ligament (ACL) is the most common acute injury. ACL injury occurs in sports that involve cutting and pivoting motions, such as soccer, football, and skiing. Many patients opt to undergo ACL reconstructive surgery (ACLR) so that they may return to their sport with restored knee stability and function. Unfortunately, ACLR does not completely restore the knee to its original state, resulting in …

Tdcs Effects On Synaptic Plasticity And Motor Skill Learning, Forouzan Vasheghani Farahani

Dissertations and Theses

Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique that involves the application of low-intensity constant current to the brain through electrodes placed on the scalp. Its potential to enhance brain function and treat brain-related disorders has led to its increasing popularity due to its safety, simplicity, and affordability. However, its effectiveness remains a topic of debate.

Quantifying Cartilage Composition And Arthrokinematics: Application To Short-Term Biomechanical Outcomes After Sports-Related Knee Injury And Surgery, John Curtis Ramsdell

Graduate College Dissertations and Theses

The long-term consequence for many individuals who suffer ACL injury, especially when the meniscus suffers injury as well, is the development of early-onset osteoarthritis (OA), commonly referred to as post-traumatic OA (PTOA). Target therapies to reduce PTOA incidence are desperately needed, as upwards of 200,000 ACL injuries occur each year in the United States; however, therapeutic advancements are hindered by the lack of understanding for the mechanisms that drive PTOA onset and progression. A prevailing hypothesis is that post-surgical alterations to the injured knee’s arthrokinematics (the way the cartilage surfaces of the femur and tibia articulate) introduce an unusual loading …

Exploring Ph Gradient Phenomena In Non-Linear Electrokinetic Microfluidic Devices, Azade Tahmasebi

Dissertations, Master's Theses and Master's Reports

Electrokinetic microfluidics is a versatile technology utilized within lab on a chip (LOC) devices for diagnostic and analytical applications; advantages include reduced resource demands, flexibility, and simplicity of use. Dielectrophoresis (DEP) is a precision nonlinear electrokinetic tool utilized within microfluidic microdevices to induce polarization and control bioparticle motions for applications that range from hemoglobin separations to cancer cell isolation and detection. Despite promising results, undesired side phenomena can occur in electrokinetic systems which impede reproducibility and accuracy. These unfavorable phenomena have not been comprehensively explored in the literature. Prior preliminary research suggests the fundamental phenomena originate from microelectrodes utilized in …

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 …