Biomedical Engineering and Bioengineering Commons^™

Modeling Residence Time Distribution Of Chromatographic Perfusion Resin For Large Biopharmaceutical Molecules: A Computational Fluid Dynamic Study, Kevin Vehar

KGI Theses and Dissertations

The need for production processes of large biotherapeutic particles, such as virus-based particles and extracellular vesicles, has risen due to increased demand in the development of vaccinations, gene therapies, and cancer treatments. Liquid chromatography plays a significant role in the purification process and is routinely used with therapeutic protein production. However, performance with larger macromolecules is often inconsistent, and parameter estimation for process development can be extremely time- and resource-intensive. This thesis aimed to utilize advances in computational fluid dynamic (CFD) modeling to generate a first-principle model of the chromatographic process while minimizing model parameter estimation's physical resource demand. Specifically, …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Technology Aiding In Neonatal Lung Developmental Care, Megan Kirk

Undergraduate Honors Theses

In this paper, old as well as new technological findings to decrease premature infant mortality are reviewed. This paper discusses fetal development throughout pregnancy from conception to full-term status as well as fetal lung development specifically from conception until full-term status. Several ideas to rapidly develop and mature fetal lungs are discussed such as mothers ingesting artificial surfactant supplements, either independently or coupled with antenatal corticosteroids, as well as intra-amniotic instillation prior to 28 weeks gestational. Drawbacks regarding these two are mentioned as well such as the fetus’s lungs not being mature enough to use the artificial surfactant leading into …

An Impedimetric Aptasensing System For The Rapid Detection Of Salmonella Typhimurium, America Sotero

Graduate Theses and Dissertations

Salmonella Typhimurium is a foodborne pathogen associated with raw and undercooked eggs, poultry, beef, fruits, and vegetables. In the United States, Salmonella is responsible for approximately 1.2 million illnesses, 23,000 hospitalizations, and 450 deaths annually. For many years, conventional detection methods such as culture-dependent and PCR-based methods have been the “golden standards” for the detection of this pathogen due to their high sensitivity and reliability. However, they still have some disadvantages such as long enrichment steps and high costs that need to be overcome. The development of a rapid and reliable method for the detection of S. Typhimurium is needed …

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 …

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 …

Dectin-1 Mediated Mechanical Force Generation In Candida Albicans Fungal Pathogen Recognition, Rohan Choraghe

Biomedical Engineering ETDs

Candida spp. pathogens continue to be a major health care burden with high mortality and exceeding a billion dollars in terms of healthcare cost. Candidainfection ranges from superficial dermatological infection to more serious blood stream infection in debilitated patients. One of the major lines of innate immune defense against Candidais phagocytosis. Dectin-1 is the antifungal receptor in myeloid cells responsible for most immune responses against fungi including phagocytosis. We looked into the signaling pathway coordinating this mechanical process downstream of Dectin-1. We found that Dectin-1 activation gives rise to a significant mechanical force generation mediated through RHOA-ROCK-MyosinII pathway. …

Pathophysiology And Proteogenomics Of Post-Infectious And Post-Hemorrhagic Hydrocephalus In Infants, Albert M. Isaacs

Arts & Sciences Electronic Theses and Dissertations

Post-infectious (PIH) and post-hemorrhagic (PHH) hydrocephalus occur as sequalae of neonatal sepsis or intraventricular hemorrhage (IVH) of prematurity, respectively. Together, PIH and PHH represent the most common form of infantile hydrocephalus, the most common indication for neurosurgery in children globally, and the leading cause of neurological morbidity and mortality worldwide. The lack of understanding of the pathophysiology of PIH and PHH, particularly with regards to the host central nervous system response to the antecedent infection and hemorrhage, perturbation of differentiating neural stems in the ventricular (VZ) and subventricular (SVZ) zones, and damage to periventricular white matter (PVWM) tracts carrying sensorimotor …

The Investigation Of Surface Structures On Various Pathogens And Their Interactions With The Human Immune System, Carmen M. Villalobos

Biomedical Engineering ETDs

The cell surface is the first interface the host immune system encounters and

its investigation has led to a better understanding of cellular biology and types of

pathways that pathogens target in a host cell. The cell surface has evolved to include

many functions such as manipulation of the cytoskeleton, cell signaling, membrane

trafficking, adhesion, and integration into host tissue. The pathogens of interest are

the pathogenic fungus, Candida albicans, and the parasite, Giardia lamblia and we

investigate the consequences of drug treatments on the cell surface, leading to

promising new targets.

Deterministic Model Of The Voltage Dependent Anion Channel (Vdac) Kinetics, Viren Shah

Theses and Dissertations

The voltage-dependent anion channel (VDAC) is a voltage gated channel residing on the outer mitochondrial membrane (OMM) that facilitates the flow of metabolites between the cytosol and mitochondria. The channel is regulated through conformational changes driven by electrostatic effects along with numerous regulatory mechanisms. The aim of this study is to mechanistically model kinetics of substrate flow through VDAC and incorporate them into existing mechanistic computational models of mitochondrial function. The resulting model is used in two ways: 1) to establish mitochondrial bioenergetics (conductance, permeability, and current/flux) under physiological conditions, and 2) to conduct perturbations simulating the effect of altered …

Do Different Pathologies Affect The Relationship Between The Stiffness Of The Plantar Fascia And The Function Of The Mtp Joint?, Madeline Ryan Pauley

Biomedical Engineering Theses & Dissertations

Compared to healthy individuals, individuals with plantar fasciitis and diabetes experience material and structural property changes to soft tissues in the feet. The purpose of this study was to compare the relationship between material properties, power absorption, and energy storage characteristics to metatarsal power between healthy, plantar fasciitis symptomatic and asymptomatic, and diabetic participants. Investigating material change differences as well as energy storage and transfer trends in different pathology groups can lead to a better overall understanding of power transfer at the metatarsophalangeal joint (MTP). Participants were recruited for kinematic gait analysis and lower extremity shear wave elastography analysis and …

Validation Of Nanosecond Pulse Cancellation Using A Quadrupole Exposure System, Hollie A. Ryan

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric fields (nsPEFs) offer a plethora of opportunities for developing integrative technologies as complements or alternatives to traditional medicine. Studies on the biological effects of nsPEFs in vitro and in vivo have revealed unique characteristics that suggest the potential for minimized risk of complications in patients, such as the ability of unipolar nsEPs to create permanent or transient pores in cell membranes that trigger localized lethal or non-lethal outcomes without consequential heating. A more recent finding was that such responses could be diminished by applying a bipolar pulse instead, a phenomenon dubbed bipolar cancellation, paving the way …

Cardiac Modelling Techniques To Predict Future Heart Function And New Biomarkers In Acute Myocardial Infarction, Sergio C. H. Dempsey

Electronic Thesis and Dissertation Repository

Fundamental to treatment planning for patients that have suffered myocardial infarction are predictive biomarkers and risk factors. Important among these in terms of a patient’s treatment plan or prognosis are the contractility of the damaged myofibers, final infarct volume, and poor infarct healing rate. Proposed and developed in this thesis are techniques to predict these biomarkers and risk factors using cardiac biomechanical modelling. One of the developed techniques was a CT compatible shape optimization technique which can predict the contraction force of healthy, and stunned myofibers within 6.3% and the distribution of potentially necrotic myofibers within 10% accuracy. The second …

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 …

Quantitative Fluorescence Imaging For Investigation And Treatment Of Disease, Lemoyne Michael Habimana-Griffin

McKelvey School of Engineering Theses & Dissertations

Molecular imaging is a powerful tool that enables interrogation of basic molecular mechanisms, diagnosis of disease, guidance of therapeutic modalities and monitoring of treatment response. Among the various imaging modalities, optical imaging is particularly suited for preclinical molecular imaging owing to its high sensitivity, lack of exposure to ionizing radiation, low cost, portability and scalability of imaging from the microscopic to macroscopic scale. In particular, fluorescence molecular tomography (FMT) provides quantitative 3D reconstructions of fluorescence distributions down to picomole quantities allowing for whole animal molecular imaging. In this work, FMT is applied to detect disease-specific molecular probes, to monitor and …

Joint Estimation Of Perceptual, Cognitive, And Neural Processes, Katherine Heisey

Arts & Sciences Electronic Theses and Dissertations

Humans are remarkable in their ability to perform highly complicated behaviors with ease and little conscious thought. Successful speech comprehension, for example, requires the collaboration of multiple sensory, perceptual, and cognitive processes to focus attention on the speaker, disregard competing cues, correctly process incoming audio stimuli, and attach meaning and context to what is heard. Investigating these phenomena can help unravel crucial aspects of human behavior as well as how the brain works in health and disease. However, traditional methods typically involve isolating individual variables and evaluating their decontextualized contribution to an outcome variable of interest. While rigorous and more …

Phantoms To Placentas: Mr Methods For Oxygen Quantification, Kelsey Meinerz

Arts & Sciences Electronic Theses and Dissertations

Molecular oxygen (O2) is vital for efficient energy production and improper oxygenation is a hallmark of disease or metabolic dysfunction. In many pathologies, knowledge of tissue oxygen levels (pO2) could aid in diagnosis and treatment planning. The gold standard for pO2 measures in tissue are implantable probes, which are invasive, require surgery for placement, and are inaccessible to certain regions of the body. Methods for determining pO2 both non-invasively and quantitatively are lacking. The slight paramagnetic nature of O2 provides opportunities to non-invasively characterize pO2 in tissue via magnetic resonance (MR) techniques. As such, O2 can be treated as a …

Investigatin Actin-Myosin Mechanics To Model Heart Disease Using Fluorescence Microscopy And Optical Trapping, Justin Edward Reynolds

Honors Theses

Hypertrophic cardiomyopathy (HCM) is a hereditary disease in which the myocardium becomes hypertrophied, making it more difficult for the heart to pump blood. HCM is commonly caused by a mutation in the β-cardiac myosin II heavy chain. Myosin is a motor protein that facilitates muscle contraction by converting chemical energy from ATP hydrolysis into mechanical work and concomitantly moving along actin filaments. Optical tweezers have been used previously to analyze single myosin biophysical properties; however, myosin does not work as a single unit within the heart. Multiple myosin interacts to displace actin filaments and do not have the same properties …

Pilot Study Exploring The Effect Of Targeted Cox-2 Inhibition In Macrophages Responding To Neuronal Injury; Promoting Enhanced Axonal Regeneration, Alyssa Brauckmann

Electronic Theses and Dissertations

Celecoxib nanoemulsion (CXB-NE) has been developed as a macrophage targeted analgesics by Dr. Janjic and her team at Duquesne University, (Janjic et al, 2018; Liu et al, 2020; Saleem et al, 2019b; Vasudeva et al, 2014). The CXB-NE nanoemulsion carrying a Nonsteroidal Anti-inflammatory (NSAID) inhibitor of COX-2 activity result in a reduction in PGE2 expression in macrophages. Using CXB-NE in rats that have peripheral nerve injury constricting the sciatic nerve relieves hypersensitivity, a pain-like behavior. The treatment also decreases inflammation associated with this chronic constriction injury (Janjic et al, 2018; Saleem et al, 2019b; Stevens et al, 2019). In this …

Dose Response Effect Of Mycobacterium Smegmatis-Derived Lipomannan In Raw 264.7 Murine Macrophages, Cassandra Robertson

Undergraduate Theses and Capstone Projects

Tuberculosis is a debilitating respiratory disease caused by the bacterial species Mycobacterium tuberculosis, which acts by infecting the host’s macrophages and evading their immune responses. The purpose of the study was to determine if RAW 264.7 murine macrophage activity could be facilitated and intensified by stimulation with LAM from M. smegmatis. Stimulation with bacterial LAM, and lipopolysaccharide (LPS) as a positive control, yields functional endpoints: nitric oxide (NO) production measured by nitrites (NO2) in the culture supernatant and expression of proteins, such as tumor necrosis factor-α and inducible nitric oxide synthase (iNOS). RAW 264.7 cells were stimulated dose-responsively with LAM …

Comparing Economics Of Traditional Carbonation Method And A Novel Carbonation Invention For Craft Beer, Kira Simonson

Biological and Agricultural Engineering Undergraduate Honors Theses

The traditional method for the carbonation of beer includes bubbling CO₂ through a pressurized brite tank until the desired level of carbonation concentration is reached. The gas either dissolves in the liquid volume or passes through the beer into the gas headspace above the bulk volume of beer. The gas that passes through the liquid can strip the beer of flavors, and this undissolved gas is vented to the atmosphere. To reduce the gas lost to the atmosphere, the CO₂ is dissolved into the beer slowly over a long period of time, which increases gas-use efficiency but sacrifices …

Design Of A Deep Flow Technique Hydroponic System And An Elementary Education Module For Tri Cycle Farms, Cady Rosenbaum

Biological and Agricultural Engineering Undergraduate Honors Theses

Hydroponics is an agricultural technique in which plants are grown without soil and are instead grown in water systems that include nutrients and other growth-supporting media. Hydroponic systems typically reside inside, so that the system can be fully controlled by the grower by manipulating the temperature and amount of light the plants receive. The benefits of growing plants using hydroponics include: the amount of water used is reduced, it is less labor to grow organic produce with an indoor system, less space used, and it allows for growing food anywhere. Tri Cycle Farms is planning for the construction of a …

Comparative Genomics Of Human Mesenchymal Stem Cells And Human Mesenchymal Stem Cells Derived Vascular Smooth Muscle Cells, Samia Ismail

Biomedical Engineering Undergraduate Honors Theses

As of 2017, vascular diseases contributed to 23.1% of all deaths in America. To address the need for more effective and sustainable treatment options for these ailments, stem cell differentiation and implantation has emerged as a viable alternative to standard bypass and graft insertions. A completely autologous treatment can be achieved by extracting adult stem cells, differentiating them into vascular smooth muscle cells (VSMCs), and then reimplanting these cells at the affected tissue site. This study aims to investigate the efficiency of the VSMC differentiation from human mesenchymal stem cells (hMSCs) by comparing 4 cell lines of untreated hMSCs with …

Quantitative Optical Imaging Of Metabolic And Structural Biomarkers In Rodent Injury Models, Shima Mehrvar

Theses and Dissertations

The assessment of organ metabolic function using optical imaging techniques is an overgrowing field of disease diagnosis. The broad research objective of my PhD thesis is to detect quantitative biomarkers by developing and applying optical imaging and image processing tools to animal models of human diseases. To achieve this goal, I have designed and implemented an optical imaging instrument called in vivo fluorescence imager to study wound healing progress. I have also developed a 3-dimensional (3D) vascular segmentation technique that uses intrinsic fluorescence images of whole organs.

Intrinsic fluorophores (autofluorescence signals) provide information about the status of cellular bioenergetics in …

Transcriptomic Analysis Of Cytokine-Treated Tissue-Engineered Cartilage As An In Vitro Model Of Osteoarthritis, Jiehan Li

McKelvey School of Engineering Theses & Dissertations

Osteoarthritis (OA), as the most common form of arthritis and a leading cause of disability worldwide, currently has no disease-modifying drugs. Inflammation plays an important role in cartilage degeneration in OA, and pro-inflammatory cytokines, IL-1β and TNF-α, have been shown to induce degradative changes along with aberrant gene expression in chondrocytes, the only resident cells in cartilage. The goal of this study was to further understand the transcriptomic regulation of tissue-engineered cartilage in response to inflammatory cytokines using an in vitro miPSC model system. We performed RNA sequencing for the IL-1β or TNF-α treated tissue-engineered cartilage derived from murine iPSCs, …

Study Of The Therapeutic Effects Of Synchronization-Modulation Of The Na/K Pump On Muscle Fatigue, Jason E. Mast

USF Tampa Graduate Theses and Dissertations

It has been shown that by applying a specially designed oscillating external electric field to a cell membrane that the membrane's sodium/potassium pumps can be synchronized to all work at the same rate. Then by slowly increasing the electric field's frequency the pumps' turnover rate can also be increased. By increasing the pumps' turnover rate, the sodium and potassium concentration gradients can be increased, this type of stimulation is called synchronization-modulation. There are three generations of the synchronization-modulation waveform each with different utilities. In particular, the third generation of synchronization-modulation has the ability to use the energy of the external …

Impedance Analysis Of Tissues In Nspef Treatment For Cancer Therapy, Edwin Ayobami Oshin

Biomedical Engineering Theses & Dissertations

Nanosecond pulsed electric field (nsPEF) for cancer therapy is characterized by applications of high voltage pulses with low pulsed energy to induce non-thermal effects on tissues such as tumor ablation. It nonthermally treats tissues via electroporation. Electroporation is the increase in permeabilization of a cell membrane due to the application of high pulsed electric field. The objective of this study was to investigate the effect of nsPEF on tissue by monitoring the tissue’s impedance in real-time. Potato slices (both untreated and electroporated), and tumors extracted from female BALBc mice were studied. 100ns, 1-10kV pulses were applied to the tissues using …

Flexible Electrochemical Lactate Sensor, Peyton Miesse

Biomedical Engineering Theses & Dissertations

Lactic acid is a vital indicator for shock, trauma, stress, and exercise intolerance. It is a key biomarker for increases in stress levels and is the primary metabolically produced acid responsible for tissue acidosis that can lead to muscle fatigue and weakness. During intensive exercise, the muscles go through anerobic metabolism to produce energy. This leads to decreases in the blood flow of nutrients and oxygen to the muscles and increases in lactate production, which in turn cause lactic acidosis. Currently, changes in blood lactate concentrations are monitored by sensors that can be invasive via blood or wearable based sensors …

Extracellular Matrix-Derived Modular Bioscaffolds For Soft Connective Tissue Regeneration, Pascal Morissette Martin

Electronic Thesis and Dissertation Repository

Human decellularized adipose tissue (DAT) represents a promising extracellular matrix (ECM) source for the development of biomaterials, with its properties conductive of angiogenesis, adipogenesis, and scaffold remodelling. This thesis sought to provide new fundamental insight into the design of ECM-derived bioscaffolds by developing novel modular biomaterials for soft connective tissue regeneration and by studying the effects of ECM composition on cell function and fate.

Initial studies explored the effects of ECM composition of pre-assembled bead foams derived from DAT or commercially-sourced bovine collagen (COL) on human wound edge dermal fibroblasts (weDFs) sourced from chronic wounds. In vitro testing under conditions …

Using An Internal Auditory Stimulus To Activate The Developing Primary Auditory Cortex: A Fetal Fmri Study, Estee Goldberg

Electronic Thesis and Dissertation Repository

Insight into the rapidly developing brain in utero is scarce. Fetal functional magnetic resonance imaging (fMRI) is a technique used to gain awareness into the developmental process. Previous auditory task-based fMRI studies employed an external sound stimulus directly on the maternal abdomen. However, there has since been recommendation to cease doing so. We sought to investigate a reliable paradigm to study the development of fetal brain networks and postulate that by using an internal stimulus, such as the mother singing, it would result in activation of the fetal primary auditory cortex. Volunteers carrying singleton fetuses with a gestational age of …