Biological Engineering Commons^™

Comparative Performance Of Physiological Vital-Sign Forecasting Under Random And Patient-Wise Splitting Using Deep Learning, Lavanya Vasavi Chittem Reddy

Theses and Dissertations

Physiological vital-sign forecasting estimates future measurements based on recent temporal patterns and can support analysis of continuously recorded monitoring data. This study comparatively evaluated deep feedforward, recurrent, bidirectional recurrent, long short-term memory, and bidirectional long short-term memory architectures for one-step-ahead forecasting of peripheral oxygen saturation, heart rate, and pulse rate. Each model received consecutive observations of peripheral oxygen saturation, heart rate, pulse rate, respiratory rate, and age, while separate single-output models predicted the next value of the selected target.

Random and patient-wise data splitting were compared using identical input definitions, preprocessing procedures, model architectures, and training hyperparameters. The strongest architecture …

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

The Bacteriostatic, Regenerative, And Immunomodulatory Properties Of Extracellular Matrix Particles For Lung Injury, Keera P. Rhoads

Theses and Dissertations

Acute respiratory distress syndrome (ARDS) is a prevalent, life-threatening lung condition, affecting nearly 200,000 Americans annually, with a 40% international mortality rate. There is no cure for ARDS, and current pharmacological treatments have limited effectiveness. Symptoms can be mitigated with mechanical ventilation, though this often leads to ventilator-induced lung injuries (VILI) and puts critically ill patients at risk of infections, including ventilator-associated pneumonia (VAP). A promising therapeutic is the extracellular matrix (ECM), a complex network of structural proteins and bioactive molecules that has been shown to have anti-inflammatory properties and prevent fibrosis. We aim to utilize the regenerative and immunomodulatory …

Characterization Of Nanoplastic-Induced Exacerbation Of Asthmatic Pathophysiology In A Murine In Vivo Model, Keith Li

Theses and Dissertations

As global plastic production increases, so does the environmental and biological presence of nanoplastics (NPs), raising growing concerns about their potential impact on human health. These particles have been detected in various organs, including the lungs, yet their role in respiratory inflammation remains largely unexplored. Emerging evidence suggests that NP exposure may influence immune responses in the lungs, particularly in individuals with preexisting conditions such as asthma. However, the specific ways in which these particles interact with allergen driven inflammation are still unclear.

In this study, a murine model of allergic airway inflammation was used to investigate how surface modified …

Demonstrating Feasibility Of Ultrasound-Sensitive Microbubbles Delivery To Treat Disruptions In The Blood Brain Barrier Endothelium, Rubens Jourdain

Theses and Dissertations

Vascular cognitive impairment and dementia (VCID) is one of the main causes of dementia. VCID is caused by age and other genetic factors that lead to disruptions in the blood brain barrier (BBB) and allow blood components to enter the brain. The currently available treatments of VCID include opening the BBB with high-frequency-ultrasound to deliver drugs to the brain. However, this only treats the already developed disease. Consequently, we developed a new drug delivery system whose goal is to restore the brain capillary endothelial cells (BCEC) lining the blood vessel. The objective of this study was to demonstrate the feasibility …

Advancing Biofabrication Methodologies To Develop Biomimetic Tissue Scaffolds For Musculoskeletal Applications, Nashaita Yezdi Patrawalla

Theses and Dissertations

Musculoskeletal injuries impose a significant global burden, affecting millions and generating an economic toll exceeding $14 billion. Tissue engineering has gained traction as a promising strategy offering potential for functional restoration of damaged musculoskeletal tissues. This research aims to advance biofabrication techniques for generation of biomimetic tissue scaffolds, by optimizing scaffold design and modulating fabrication process parameters to generate scaffolds for musculoskeletal regeneration with application-specific tailored properties. In this realm, collagen-based biomaterials have been extensively investigated for tendon and ligamentous applications, and in combination with bioceramics incorporated into the collagen framework to produce composite scaffolds that better recapitulate the native …

Shape Memory Alloy Capsule Micropump For Drug Delivery Applications, Youssef Mohamed Kotb

Theses and Dissertations

Implantable drug delivery devices have many benefits over traditional drug administration techniques and have attracted a lot of attention in recent years. By delivering the medication directly to the tissue, they enable the use of larger localized concentrations, enhancing the efficacy of the treatment. Passive-release drug delivery systems, one of the various ways to provide medication, are great inventions. However, they cannot dispense the medication on demand since they are nonprogrammable. Therefore, active actuators are more advantageous in delivery applications. Smart material actuators, however, have greatly increased in popularity for manufacturing wearable and implantable micropumps due to their high energy …

Analysis And Evaluation Of Different Transformer Architectures For The Protein Sequence Representation And The Corresponding Hypothetical Applications, Mary Mao

Theses and Dissertations

This project is to investigate and assess several Transformer topologies for the modeling of protein sequences and their corresponding uses. Each major model for the protein sequence representations is inspected with its mathematical theory and analyzed for the different performance of the models with various validation repositories.

Controlled Delivery Of Peptide And Gasotransmitter For Promoting Vascular Endothelialization, Shirin Changizi

Theses and Dissertations

Endothelial cells (ECs) are vital for maintaining proper vascular function and regulating processes such as hemostasis and inflammation. Disruption of endothelial cells integrity can lead to several pathological conditions, including coronary artery disease, vascular cognitive impairment, and dementia (VCID). Alterations in ECs distribution may lead to compromised blood-brain barrier (BBB) function, facilitating the passage of blood components and contributing to conditions such as Alzheimer's disease. Additionally, disruptions in ECs function can lead to early-stage thrombosis and intimal hyperplasia, resulting in graft failure in small-diameter (

This study aimed to develop innovative approaches for drug delivery to the BBB and TEVGs …

Microwave Imaging Technique For Breast Cancer Detection, Nure Alam Chowdhury

Theses and Dissertations

Breast cancer is a global problem, and it is inevitable to detect cancerous cells at early stages. In recent years, microwave imaging technology has been widely applied in biomedical applications for its non-ionizing radiation. In this study, we design a micro-strip patch antenna with an inverted T-type notch in the partial ground to detect tumor cells inside the human breast. The size of the current antenna is small enough (18 mm × 21 mm × 1.6 mm) to distribute around the breast phantom. The operating frequency has been observed from 6–14 GHz with a minimum return loss of −61.18 dB …

Investigating Endothelial Damage During Ischemic Stroke Treatment Using In Vitro And Computational Models, Zackary Lorton

Theses and Dissertations

Large vessel occlusion during acute ischemic strokes requires mechanical thrombectomy (MT) procedures using stent retrievers (SR). However, complete clot removal typically takes several attempts, which can amplify endothelial cell injury (EI). This project aims to characterize the extent of EI during MT using an in vitro vascular platform and a finite-element model (FEM). Impact of SR diameter and characterization of SR mechanical forces are assessed and correlated with human umbilical vein endothelial cell (HUVEC) response. HUVECs were seeded on fibronectin (4 µg/cm²) coated true-scale PDMS arterial phantoms with 2.5 mm luminal diameter. Test groups (n=6) either …

The Effects Of Various Nanoplastics On The Inflammatory Response In Primary Alveolar Epithelial Cells, Eunice J. Pak

Theses and Dissertations

As plastic pollution begins to multiply in the environment and the workplace, gradual degradation of these plastics creates an unseen threat to biological health: nanoplastics. These nanoplastics are common in day-to-day life, and have been found in various internal organs of the human body. The biological and health effects of these nanoplastics are still widely unknown, and only recently has research focused on the impacts of these particles on human health at the cellular level.

In this thesis, poly(methyl methacrylate) and three forms of polystyrene (carboxyl-modified, amine-modified, and neutral surface charge) have been tested on submerged primary C57BL/6 mouse alveolar …

Study Of Surface And Groundwater Quality And Quantity At Watershed Scale In Mississippi, Dipesh Nepal

Theses and Dissertations

Hydrology and water quality are affected by land use and climate changes. Mississippi’s diverse agro–ecosystem comprises of a range of land use land cover (LULC) including agriculture, forest, wetlands, urban, and grasslands. The objectives of this study were to investigate the impacts of various factors such as Best Management Practices (BMPs), wetlands, LULC, and climate changes on water quality and quantity. The hydrologic and water quality responses to dynamic LULC input in Soil and Water Assessment Tool (SWAT) were evaluated. Results showed that agricultural and forest expansion were major drivers of hydrologic and water quality changes in Big Sunflower River …

Novel 3d Bench Top Model For Vascular Calcification Research, Ursla-Marie K. Offiah

Theses and Dissertations

Cardiovascular disease is the leading cause of non-communicable disease in the whole world killing 17 million people in 2012. Among the many vascular diseases is vascular calcification (VC) which is the mineral build up in the walls of blood vessels. Medial calcification is the plaque buildup in the medial layer of the blood vesicle that is characterized by arterial stiffness and high blood pressure. Current calcification research involves two dimensional (2D) lab methods such as flat petri dishes to investigate the mechanism that causes and inhibits vascular calcification. Research has shown that the use of three-dimensional (3D) models can be …

Design Of Plastic Contaminant Eliminator In Seed Cotton, Joshua H. Tandio

Theses and Dissertations

Plastic contamination in cotton is a problem in cotton industry and researchers have worked on this problem with different approaches. This thesis documents the design of mechanical and electronic real-time systems for detecting and removing plastic contaminants. The mechanical system was designed to expose plastic embedded inside the seed cotton to the sensor and to separate plastic contaminated cotton from the process stream. The detection system consisted of an embedded computer interfaced with a USB camera and Neural Network (NN) software running in it. Two NN models were tested, a transfer learning model and a built-from-scratch original model. The original …

Hydrology And Water Quality Analysis In The Big Black River Watershed, Mississippi, Moniba Shabbir

Theses and Dissertations

Evaluating hydrology and water quality for the Big Black River Watershed in Mississippi was accomplished by using the Better Assessment Science Integrating Point and Nonpoint Source (BASINS 4.5), Loading Simulation Program in C++ (LSPC), and Water Quality Analysis Simulation Program (WASP) models. The watershed model calibration was originally accomplished by using historical data collected from U.S. Geological Survey (USGS). The watershed model was calibrated using data from 2000 through 2018 in order to quantify stream flow and point source discharges under a variety of hydrologic conditions. The model predicted response of hydrology was consistent with the observed data range. The …

Therapeutic Modalities For Preventing Osteoarthritis Following Trauma To The Knee, Kayla M. Scott

Theses and Dissertations

Over 32.5 million adults in the United States and 300 million worldwide have osteoarthritis (OA). To date, there are no disease-modifying therapeutics, only strategies to slow OA progression through pain management, regenerative medicine approaches, and ultimately joint replacement.

On a microscale, a phenotypic shift of the normally quiescent articular chondrocytes leads to aberrant expression of pro-inflammatory and catabolic pathways, which are hypothesized to contribute to OA progression. Of note, interleukin-1β (IL-1β), tumor necrosis factor-α (TNF-α), and WNT/β-catenin signaling are key players disrupting cartilage homeostasis and driving inflammatory pathway activation. These pathways become dysregulated and form a positive feedback loop, increasing …

Extracellular Matrix Nanoparticles Effects On The Lung In Vivo, Brittaney E. Ritchie

Theses and Dissertations

Acute respiratory distress syndrome (ARDS) is a life-threatening condition that causes diffuse alveolar damage and a loss of the extracellular matrix (ECM). This leads to pulmonary edema and lung function deterioration. Our lab has created decellularized porcine lung, electrosprayed ECM nanoparticles that have been previously shown to have pro-regenerative capabilities in vitro.

In this study, the ECM nanoparticle effects on young murine lungs were tested in vivo. An ECM nanoparticle suspension, previously used for the in vitro studies, was aerosolized intratracheally into the lungs using a microsprayer. 24 hours later, the lung mechanics, bronchoalveolar lavage fluid, and histology …

Higher Tensile Forces Across Cellular Junctions And An Intact Nuclear Linc Complex Is Required For Epithelial Function And Stability, Fnu Vani Narayanan

Theses and Dissertations

Recent advances in three-dimensional (3D) cell culture systems have provided key insights into the understanding of biochemical and physiological states of native tissue. A significant progress in the field of mechanobiology involves measuring cellular traction forces in a more native 3D environment. However, the effects of mechanical forces exerted across cellular junctions and the nuclear LINC complex, in an organized 3D system has not been investigated thus far. Epithelial cells spontaneously form acini (also known as cysts or spheroids) with a single, fluid-filled central lumen, when grown in 3D matrices. The size of the lumen is dependent on apical secretion …

Development Of A Torque-Based Device For The Quantification Of Arm Rigidity In Patients With Parkinson’S Disease, Georgina O. Miller

Theses and Dissertations

Parkinsonian rigidity is caused by the inability of the muscles to relax and extend properly, due to reduced dopamine levels and often begins on one side of the body before spreading contralaterally. The current standard for determining joint rigidity in a clinical setting is a test completed by the clinician based on the feel of the relaxed wrist and elbow joints as they are passively flexed and extended and a series of ordinal rating scales, the Movement Disorder Society’s – Unified Parkinson’s Disease Rating Scale (MDS-UPDRS), Hoehn and Yahr Scale (H&Y), and Parkinson’s Disease Questionnaire-39 (PDQ-39). These methods are used …

The Impact Of Aging And Mechanical Injury On Alveolar Epithelial And Macrophage Responses In Acute Lung Injury And Inflammation, Michael S. Valentine

Theses and Dissertations

Patients with severe lung pathologies, such as Acute Respiratory Distress Syndrome (ARDS), often require mechanical ventilation as a clinical intervention; however, this procedure frequently exacerbates the original pulmonary issue and produces an exaggerated inflammatory response that potentially leads to sepsis, multisystem organ failure, and mortality. This acute lung injury (ALI) condition has been termed Ventilator-Induced Lung Injury (VILI). Alveolar overdistension, cyclic atelectasis, and biotrauma are the primary injury mechanisms in VILI that lead to the loss of alveolar barrier integrity and pulmonary inflammation. Stress and strains during mechanical ventilation are believed to initiate alveolar epithelial mechanotransduction signaling mechanisms that contribute …

Cell Type And Substrate Dependence Of Fibronectin Properties And Mechanotransduction, Navpreet S. Saini

Theses and Dissertations

Fibronectin is an important protein that is able to bind to other fibronectin molecules and to cell surface receptors. In doing so, the interactions fibronectin can perform is important for the processes of cell migration and tissue formation. Understanding the properties of fibronectin and fibril assembly is useful for areas such as wound healing, where fibronectin molecules are assembled to protect the tissue and to perform other tasks. Because of these reasons, it is important to understand how fibronectin is assembled and how its properties affect the fibril assembly, which in return affects the way the cell matrix operates. Previously …

The Role Of The Mechanical Environment On Cd117+ Endothelial Cell Angiogenesis, Patrick Link

Theses and Dissertations

Angiogenesis is a complex process coordinating cell migration, proliferation, and lumen formation. Changes to the microenvironment regulate angiogenesis through mechanotransduction and cytokine signals. In pulmonary hypertension, something in the process becomes abnormal, resulting in changes to the microenvironment and the formation of a glomerulus of dysfunctional capillaries, called a plexiform lesion. Endothelial cells, expressing CD117 (CD117+ EC clones) increase in the plexiform lesions of pulmonary hypertension, independent of pro-angiogenic VEGF signaling. We hypothesize that the mechanical environment and the macromolecular composition of the extracellular matrix, both, contribute to the aberrant angiogenesis. When we changed the mechanical environment, we changed the …

Exogenous Fniii 12-14 Regulates Tgf-Β1-Induced Markers, Hilmi M. Humeid

Theses and Dissertations

The extracellular matrix protein Fibronectin (FN) plays an important role in cell contractility, differentiation, growth, adhesion, and migration. The 12th -14th Type III repeats of FN (FNIII 12-14), also referred to as the Heparin-II domain, comprise a highly promiscuous growth factor (GF) binding region. This binding domain aids in cellular signaling initiated from the ECM. Additionally, FN has the ability to assemble into fibrils under certain conditions, mostly observed during cell contractile processes such as those that initiate due to upregulation of Transforming Growth Factor Beta 1 (TGF-β1) [1], [2]. Previous work from our lab has shown that self-assembly of …

Regulation Of Pituitary Progenitor Differentiation By Β-Catenin, Julie Leann Youngblood

Theses and Dissertations

The pituitary gland is a critical organ that is necessary for many physiological processes, including growth, reproduction, and stress response. These vital processes are regulated through the secretion of pituitary hormones from specialized cell types. Pituitary hormone-producing cells arise from a common pool of pituitary progenitors in the developing Rathke’s pouch, and mutations that disrupt the formation and differentiation of pituitary progenitors often result in hypopituitarism, pituitary adenomas, or craniopharyngiomas. Thus, it is necessary to determine the mechanisms of pituitary development in order to understand the ways in which these congenital defects and tumors develop and disrupt pituitary function. Canonical …

The Visual Ecology Of Speyeria Mormonia, Natalie Sanchez Gonzalez

Theses and Dissertations

Variations in environmental factors such as temperature, precipitation, and day length during larval development are known to affect morphological traits in butterflies related to their visual ecology, including eye size and wing color. These vision-related traits are important for the ability of diurnal butterfly species to detect mates, especially at long distances. Thus, changes in environmental conditions may result in phenotypic modifications to butterflies which may alter their visual ecology and subsequently, their reproductive fitness. To study the interaction of phenotypic plasticity and visual ecology in the Mormon Fritillary, Speyeria mormonia, I set up a natural-laboratory experiment at the Rocky …

Plants As Biofactories To Produce Mammalian Tumor Suppressor Micrornas, John Lachlan Macarthur

Theses and Dissertations

MicroRNAs (miRNAs) are small noncoding single stranded RNAs that are considered master regulators of gene expression. They are also an emerging class of therapeutic agents with significant potential for the prevention and treatment of many diseases, including cancer. Many different forms of cancer are associated with loss or reduced accumulation of one or more miRNAs that function as tumor suppressors. In animal models, restoration of missing tumor suppressor miRNAs prevents the initiation, progression and/or spread of the disease. However, the current absence of an efficient method for delivery of therapeutic miRNAs is a critical barrier to their use. The research …

Changes Of Dispersal Ability In An Isolated Population, Connor Bacon

Theses and Dissertations

Dispersal is a core mechanism in the maintenance of metapopulations. It maintains genetic diversity by connecting subpopulations and generates new populations to replace those that die out. However, as populations become more isolated, as occurs in habitat fragmentation, dispersal becomes more difficult. This should lead to selective pressure against dispersive individuals, causing a reduction in dispersal traits. Over time, this can lead to variation in dispersal traits among populations. We examine this idea using an extreme case of isolation in Euphydryas gillettii, a population that has remained completely isolated for forty years. By comparing this population to a baseline established …

Screening Of Novel Active Salicylic Acid Analogs And Identification Of A Bacterial Effector Targeting Key Proteins Involved In Salicylic Acid-Mediated Defense, Ian Palmer

Theses and Dissertations

The master regulator of salicylic acid (SA)-mediated plant defense, NPR1 (NONEXPRESSER OF PR GENES 1), and its paralogs NPR3 and NPR4 act as SA receptors. After the perception of a pathogen, plant cells produce SA in the chloroplast. In the presence of SA, NPR1 protein is reduced from oligomers to monomers, and translocated into the nucleus. There, NPR1 binds to TGA and WRKY transcription factors to induce expression of plant defense genes. EDS1 and PBS3 are two key proteins involved in SA biosynthesis. Previous research has shown that several plant pathogens produce SA hydroxylases. These pathogen-produced hydroxylases act to degrade …

Development And Validation Of A Novel Resonant Energy Transfer (Fret) Biosensor To Measure Tensile Forces At The Linc Complex In Live Cells, Paul Arsenovic

Theses and Dissertations

There is a large body of evidence supporting the theory that cell physiology largely depends on the mechanical properties of its surroundings or micro-environment. More recently studies have shown that changes to intra-cellular mechanical properties can also have a meaningful impact on cell function and in some cases lead to the progression of ailments or disease. For example, small changes to the protein sequence of a structural nuclear envelope protein called lamin-A is known to cause a variety of neurological and musculoskeletal diseases referred to as laminopathies. Currently, there is little incite into how these mutations lead to disease progression …