Engineering Commons^™

Introduction To Neuroengineering, Mercedes Terry, Abigail Tubbs, Blair Dupre, Brandon Fugger, Enrique Alvarez Vazquez

Open Educational Resources

"Introduction to Neuroengineering" serves as a comprehensive guide to the fast evolving field at the intersection of neuroscience, engineering, and technology. This book covers foundational concepts like neuron structure, action potentials, and neural modeling, moving through advanced topics like brain-computer interfaces (BCIs), neurostimulation, and imaging technologies (EEG, MEG, fMRI). Each chapter combines theory with practical exercises and lab examples, accessible through a GitHub repository to enhance hands-on learning. Aimed at students, educators, and professionals, this resource offers a foundation and inspiration for innovation in neuroengineering, promoting ongoing exploration in this impactful field.

Sustainable Waste-To-Bioproducts Engineering Center Laboratory Safety Project, Claudine Mock

All Graduate Reports and Creative Projects, Fall 2023 to Present

Laboratory accidents are common in teaching and research labs; these accidents can be injurious or even fatal. The consequences of each type of laboratory accident are different based on the activities performed and the hazardous materials used in each facility. However, the most common issue related to laboratory accidents is the lack of proper safety measures (e.g., poor handling of hazardous materials, not reporting incidents immediately, etc.). This project aimed to establish and strengthen best practices and procedures to ensure laboratory safety at the Utah State University Sustainable Waste-to-Bioproducts Engineering Center. To achieve this goal, different practices and measures were …

Development Of A High-Throughput Screening Platform To Profile Gene Delivery And Transcriptional Control In Macrophages, Alexis Ivy

Graduate Theses and Dissertations

Macrophages are an important cell type in the body responsible for orchestrating the inflammatory response and return to homeostasis. Macrophages are often implicated in a multitude of disease pathologies including delayed wound healing, excessive fibrosis, autoimmune disease, and immunosuppression within the tumor microenvironment. Although macrophages have been targeted for therapeutic applications, success in utilizing them has remained elusive due to their relative ease of phenotype switching between inflammatory and anti-inflammatory. The challenge that remains is developing clinically relevant delivery vehicles that can target macrophages without causing a phenotypic switch counter-productive to the desired response. This is especially important when targeting …

The Role Of Kinases Signaling In Organogenesis, Fatemeh Nasehi

All Dissertations

Kinases are crucial regulators of organ development and differentiation. This thesis investi- gates the roles of TAK1, TGFbeta-Activate Kinase 1 (TAK1/Map3K7), and Akt3 kinases in skeletal, cardiac muscle, and cartilage. TAK1 is pivotal for the differentiation of various organ systems, including sinoatrial node and cartilage, and is responsible for phosphorylat- ing a diverse array of downstream kinases. We identified several novel proteins, including phospho-Akts, that are upregulated in response to TAK1 activation. We discovered severe Dilated Cardiomyopathy (DCM) and cartilage defects in Akt3 mutant mice. Although this mouse mutant has been studied for over two decades, we are the first …

Novel Meta-Materials Application For Pressure-Offloading Of Diabetic Foot Ulcers, Kyle Walker

All Dissertations

Diabetes and its associated complications have seen their prevalence sharply rise in the United States over the past few decades. In fact, the prevalence of diagnosed diabetes has nearly doubled from 5.1% of the US population in 1988, to 9% in the most recent CDC report, which does not include the large percentage of the population with undiagnosed or prediabetes. Of this diabetic population, it is estimated that up to 34% will experience at least one foot ulcer during their lifetime. In worst case scenarios, these ulcers can become infected and eventually require amputation of a portion of, or the …

Bioaffinity Analysis Of Aptamer-Target Interactions, Pooja Karunanithi

Honors Theses

This study explores the bioaffinity of aptamer-target interactions through a comprehensive analysis. Aptamers, oligonucleotides that can bind to target molecules, have emerged as powerful tools in various fields, including diagnostics and therapeutics. The primary objective of this research was to assess the binding affinity and specificity of selected aptamers to their respective targets using a combination of experimental techniques and computational models. The binding affinity of 10 different complexes were measured through surface plasmon resonance (SPR) followed by molecular simulations. The results showed that the 6th complex had the best binding affinity. The data suggest that these aptamers could be …

Denoising And Super-Resolution Of In-Vitro 4e Flow Mri In A Stenotic Phantom Model Using Physics-Informed Neural Networks., Shrouk M. Wally

Electronic Theses and Dissertations

In recent years, the use of 4D flow MRI has revolutionized cardiovascular imag- ing by providing comprehensive data on blood flow dynamics over time. However, the limited spatial and temporal resolution of this imaging modality can hinder the accurate assessment of complex hemodynamic phenomena. This thesis explores the application of Physics-Informed Neural Networks (PINNs) to enhance the resolution of 4D flow MRI data, thereby improving its clinical utility. PINNs are a class of neural networks that integrate physical laws into their training process. By embedding these physics equations, PINNs can discover the underlying physics of fluid dynamics to produce more …

Engineered Nucleic-Acid Binding Intrinsically Disordered Proteins For Biomedical Applications, Telmo Diez Perez

Biomedical Engineering ETDs

This dissertation explores the use of intrinsically disorder proteins (IDPs) in biomedical applications related to the detection and biosensing of nucleic-acid species. We engineer several low critical solution temperature (LCST) nucleic-acid binding elastin-like polypeptides (ELPs) as model IDPs and study their potential in biomedical application via interactions with short single-stranded (ss) DNA, tRNA and viral RNAs. First, we engineer a simple polycationic ELP capable of recruiting DNA on demand in a DNA-protein-rich condensate via LLPS. Moreover, we develop a modified Flory-Huggins theory to quantify the partitioning of DNA and protein upon coacervate formation with and without salts. We then design …

Data Files For Optical Imaging Provides Flowcytometry-Like Single Cell Level Analysis Of Hif-1Α Mediated Metabolic Changes In Radio-Resistant Head And Neck Squamous Carcinoma Cells, Jing Yan, Carlos Frederico Lima Goncalves, Pranto Soumik Saha, Cristina M. Furdui, Caigang Zhu

Biomedical Engineering Faculty Publications

No abstract provided.

Penetration Thresholds Of Porcine Limbs For Low Sectional Density Projectiles In High-Rate Impact, Joseph Lesueur, Jared Michael Koser, Carolyn E. Hampton, Michael Kleinberger, Frank A. Pintar

Biomedical Engineering Faculty Research and Publications

Introduction

With similar prevalence to injuries from fires, stings, and natural disasters, soft tissue injuries may occur from fireworks, industrial accidents, or other explosives. Surgeons are less familiar with treating high-velocity penetration from small debris, which may increase the chance of infection and subsequent fatality. Penetration risk curves have been developed to predict V₅₀, the velocity with 50% probability of penetration, for various sized projectiles. However, there has been limited research using nonmetallic materials to achieve lower density projectiles less than 1 g cm−2, such as sand or rocks.

Material and Methods

To emulate the size and density …

Hyperspectral Image Classification Of Bacteria Using A Deep Convolutional Neural Network, Bruce S. Vogelsberg Jr

All Theses

Hyperspectral imaging is a non-invasive imaging method capable of collecting both spatial and spectral information. However, because of the large volume of data collected, much of it is redundant or not useful for classification. Deep learning is a subset of machine learning that uses artificial neurons in a multilayered structure to learn representations from data. One of the main advantages of deep learning is the powerful feature extraction capabilities, which allow the model to learn both high- and low-level features. Convolutional neural networks are a type of deep learning model that have alternating convolutional and pooling layers capable of extracting …

Expandable Tissue-Engineered Living Surgical Pulmonary Heart Valve For Pediatric Patients, Jacob M. Lautenschlager

All Theses

Cardiovascular disease is the most common cause of mortality in developed countries, with 607.74 million cases globally in 2020.^1,2 Advances in medicine have changed the current demographic suffering from heart valve disease into an aging population suffering from degenerative heart valve disease, creating a growing population treated by surgical or transcatheter intervention.^3-6 Current treatments of valvular heart disease are therefore directed toward valve replacements for the adult population, leaving a treatment gap for pediatric patients suffering from heart valve disease.^7-10

Congenital heart defects are defined as structural abnormalities of the heart or intrathoracic great vessels and are …

Epidural Stimulation For Urogenital Dysfunction In The Spinal Cord Injured Rat., Natasha Lorraine Wilkins

Electronic Theses and Dissertations

Spinal cord injury (SCI) is a devastating, life changing event that greatly impacts quality of life. SCI can have body-wide, multi-system consequences including dysfunction within the urogenital system. Challenges with the urinary system include urinary incontinence, urine retention, and detrusor-sphincter dyssynergia all of which require maintenance through the regular use of catheters. Sexual dysfunction in men, who comprise nearly 80% of the SCI population, includes erectile dysfunction, anejaculation, retrograde ejaculation, poor expulsive force during ejaculation, and poor sperm quality. The treatment for sexual function in SCI men is focused more on fertility through the collection of sperm for insemination procedures …

Fluid-Solid Coupled Analysis Of Biological Samples In A Flow Chamber Using Optical Coherence Tomography, Reece W. Fratus

All Dissertations

Forces from fluid flow on a tissue or cellular boundary can drive remodeling processes through mechanotransduction pathways. In most cases, the exact mechanisms are not understood, such as in marine biofilm development or vascular remodeling. To gain a better understanding of these interactions, the flow profile at a solid boundary and the mechanical changes of that solid can be coupled together to determine the impact of fluid flow on mechanical remodeling. To achieve this, optical coherence tomography (OCT) is used to image the fluid and solid simultaneously. Fluid seeded with particles can be imaged and run through a particle image …

Computer Vision Algorithms For Assessment Of Surgical Suturing Skill Using Hand And Needle Motion, Jianxin Gao

All Dissertations

Surgical suturing skill assessment is a crucial part of surgical education. Vascular surgery educators have developed a simulation-based examination called Fundamentals of Vascular Surgery, which includes a clock-face model for assessing open surgical suturing skills. The clock-face model, however, requires the valuable time of expert surgeons to determine examinees' skills. Moreover, expert surgeons have different judgments for appropriate sutures, which leads to inconsistent grading. These limitations motivate us to use sensors to measure examinees' needle motions and hand motions during the clock-face suturing exercises, and then use the measurements for objective suturing skill assessment.

To assess suturing skills based on …

Contribution Of Collagen Type I To The Mechanical Properties Of Myocardial Tissues At The Micron Level, Adam Baker

All Dissertations

Collagen is a critical component of the organization and one of the key factors contributing to the mechanical stability of the myocardium. Where cardiomyocytes actuate to contract the heart and deliver blood to the lungs and the entire body, the local collagen network must be able to support the mechanical needs of the heart by enhancing rigidity, reducing the mechanical responsibility of cells, and increasing compliance to add loading capacity during diastole. At an organ-wide level, this has been measured and modeled in many ways. At the tissue level, the mechanical properties have been evaluated using techniques such as bi-axial …

The Development Of A Novel Cartilage Analog Scaffold For Chondral Regeneration, Vishal Thomas

All Dissertations

Focal Chondral Defects (FCDs) are cartilage injuries that affect about 900,000 Americans every year. Left untreated, these may lead to osteoarthritis and eventually necessitate painful knee replacements. Current treatment options are limited in terms of durability, cost, and availability of grafts. Tissue engineering, using natural scaffolds, are a highly attractive alternative promising cost efficiency, abundance, and long-term benefits. However, their low mechanical strength and dense matrices are impediments that could lead to sub-optimal repair.

In this work, a natural biomaterial, the bovine nucleus pulposus (bNP), derived from intervertebral disc tissue, was identified as a candidate scaffold for cartilage regeneration. Mechanical …

Tissue Engineered Models Of Environmental And Metabolism-Driven Cancer-Nerve Crosstalk, Emory Gregory

Graduate Theses and Dissertations

Purpose: Within the last 30 years, cancer-nerve interactions have garnered attention for causing patient pain, increasing the risk of recurrence, and decreasing patient prognosis. There are 2 key forms cancer-nerve crosstalk takes: perineural invasion (PNI), in which cancer cells infiltrate nerves as a route for metastasis, and tumor innervation (TI), in which neurites penetrate solid tumors to promote tumor progression. Present in vitro models of cancer-nerve crosstalk primarily include Matrigel® mouse matrix and collagen I hydrogels; whereas collagen I hydrogels neglect tumor extracellular matrix (ECM) complexity, Matrigel® is controversial for its batch-to-batch inconsistencies and inclusion of experiment-altering growth factors. Decellularized …

Feasibility Study For The Application Of A Solar Powered Absorption Chilling System For Cooling Poultry Houses In Northwest Arkansas, Matthew James Kelly

Graduate Theses and Dissertations

This paper investigates the economic feasibility of utilizing a solar-powered absorption chiller to provide cooling for poultry houses in northwest Arkansas. An existing thermodynamic model of a poultry house was modified to account for cooling. A simulation was performed using actual weather data from Fayetteville, Arkansas for 26 flocks of broilers at four cooling capacities for the 2020, 2021, and 2022 calendar years. Based on the simulation, the savings from reduced electricity use for ventilation and the cost of the required absorption chiller and solar thermal array for an 8-house farm were calculated. While providing cooling was found to reduce …

Measuring Cannulation Behavior On A Sensorized Simulator: Development, Verification, And Testing Of System Components, Lydia Petersen

All Dissertations

End Stage Kidney Disease (ESKD) is a significant public health burden in the United States. Life-sustaining hemodialysis, required up to three times a week for ESKD patients, necessitates a functioning vascular access. For proper cannulation, cannulators have many factors to consider, including an AVF’s geometry, depth, diameter, and other details. Poor cannulation can lead to infiltration, where the needle punctures the vessel wall. Infiltration occurs in as many as 50% of cannulations, causing complications ranging from hematoma and swelling to delayed treatment or loss of vascular access. This highlights the need for objective, standardized training methods to improve cannulation skills …

Optimization Of And Mechanistic Insights Into Photocatalytic And Non-Thermal Plasma Degradation Of Organic Pollutants For Sustainable Wastewater Treatment, Yiting Xiao

Graduate Theses and Dissertations

Water pollution by organic pollutants poses a significant environmental threat, necessitating the development of advanced treatment technologies to ensure sustainable and efficient remediation. This dissertation explored innovative approaches to enhance the degradation of organic pollutants through the integration of photocatalytic and plasma-assisted systems, with a focus on optimizing these processes using methodologies ranging from response surface methodology (RSM) to advanced machine learning techniques. The first part of the dissertation investigated the degradation of organic pollutants in flocculated liquid digestate using photocatalytic titanate nanofibers (TNFs) synthesized via a hydrothermal method. This study represents the first application of TNFs, with a bandgap …

Selective Bacterial Biofilm Removal Using Image-Guided Detection And Cold Atmospheric Pressure Plasma, Michael Okebiorun

Boise State University Theses and Dissertations

This dissertation explores the use of cold atmospheric pressure plasma (CAP) technology in eradicating bacterial biofilms from tissue surfaces, using Ps. fluorescens on chicken tissue to model human chronic wounds. It introduces a novel image-guided technique for precise biofilm removal, employing trypan blue staining coupled with advanced computer vision analysis, enhancing the CAP treatment's precision and efficacy. The study demonstrates the CAP device's ability to effectively disrupt biofilms through a non-thermal mechanism, based on its electrical characteristics and operational parameters. The success of the treatment is evident in the significant reduction of biofilm thickness of 49 -185 µm, with the …

A Model-Based Reverse System Engineering Methodology For Analyzing Complex Biological Systems With A Case Study In Glycolysis, Gerald L. Fudge, Emily Brown Reeves

Faculty Publications

We propose a model-based reverse systems engineering (MBRSE) methodology for biological systems that relies on requirements analysis in conjunction with model-based systems engineering (MBSE). The goal of this methodology is to better understand complex multiscale biological systems, discover knowledge gaps, and make testable predictions. The similarities between human-engineered and biological systems motivate this approach. Furthermore, traditional reductionist paradigms in biology have proven insufficient for understanding and accurately predicting complex biological systems, as opposed to systems engineering approaches that have proven effective in supporting the design and analysis of complex engineered systems spanning multiple spatiotemporal scales. We employ our MBRSE methodology …

Medial Patellofemoral Ligament Augmented With A Reinforced Bioinductive Implant Is Biomechanically Similar To The Native Medial Patellofemoral Ligament At Time Zero In A Cadaveric Model, Sean Mcmillan, Seth Sherman, Zachary Brown, Erik Brewer, Elizabeth Ford

Rowan-Virtua School of Translational Biomedical Engineering & Sciences Departmental Research

Purpose: To biomechanically compare primary medial patellofemoral ligament (MPFL) repair (MPFLr) augmented with a reinforced bioinductive implant (RBI) to the native MPFL ligament and a semitendinosus (semi-T) MPFL reconstruction (MPFLR) at time zero. Methods: Four fresh-frozen matched pair cadavers (8 knees) were used to biomechanically compare the native MPFL to augmented MPFLr (n = 4) and semi-T MPFLR (n = 4). The native MPFL (n = 8) was isolated, preserving the femoral and patellar attachments, and pulled to failure. The semi-T was harvested from 1 of the matched pairs and whipstitched, as was a 250-mm × 5-mm RBI. A standard …

Segmentation And Classification Of Left Ventricular Abnormalities In Cardiac Mri Using Initial Point Prediction Based Deformable Model, Md. Asadur Rahman, Md. Al Noman, A. B. M. Aowlad Hossain

Future Computing and Informatics Journal

The shape of the left ventricle (LV) of a cardiac magnetic resonance image (CMRI) helps physicians to diagnose different cardiac abnormalities. The similarity of pixel intensity and shape of LV with neighbor tissues, the imprecision of boundaries, and the presence of noise are the challenges to accurate segmentation of LV. This paper contributes to the successful implementation of an automatic edge contouring method to segment LV area from CMRI and detect whether the ventricle belongs to abnormalities. This method proposes the regression-based artificial neural network to predict the possible initial position of the deformable edge-based active contour model for precise …

Auxiliary Diagnosis Of Dental Calculus Based On Deep Learning And Image Enhancement By Bitewing Radiographs, Tai Jung Lin, Yen Ting Lin, Yuan Jin Lin, Ai Yun Tseng, Chien Yu Lin, Li Ting Lo, Tsung Yi Chen, Shih Lun Chen, Chiung An Chen, Kuo Chen Li, Patricia Angela R. Abu

Ateneo Laboratory for Intelligent Visual Environments

In the field of dentistry, the presence of dental calculus is a commonly encountered issue. If not addressed promptly, it has the potential to lead to gum inflammation and eventual tooth loss. Bitewing (BW) images play a crucial role by providing a comprehensive visual representation of the tooth structure, allowing dentists to examine hard-to-reach areas with precision during clinical assessments. This visual aid significantly aids in the early detection of calculus, facilitating timely interventions and improving overall outcomes for patients. This study introduces a system designed for the detection of dental calculus in BW images, leveraging the power of YOLOv8 …

Pulsing-Induced Healing Of A Surface Crack Of A Nickel-Based Alloy, Liwei Wang, Mingming Quan, Zhen Tan, Ming Liu, Dianlong Wang, Xiao Yang, Ying Liu, Yaning Mao, Zhimin Liang, Fuqian Yang

Chemical and Materials Engineering Faculty Publications

In this work, we demonstrate the feasibility of applying electric pulses to heal surface cracks on nickel-based alloy GH4169 under compressive load. There exists an incubation time for the onset of the healing of a crack, which is associated with local temperature at the crack tip. The crack size decreases with increasing the pulsing time at a constant healing rate prior to complete healing of the crack. Increasing compressive load accelerates the healing process. The electric pulsing leads to the formation of an influential zone surrounding the crack with the finest grain sizes in the healed crack and the coarsest …

A Kinematic Analysis Of The Shoulder During The Volleyball Attack Using Euler And Helical Axis Methods, Victoria Jolliff

Biomedical Engineering Theses & Dissertations

The shoulder is a complex joint with a wide range of motion, including flexion, extension, abduction, adduction, and internal and external rotation. In volleyball, repetitive overhand movements can cause shoulder overuse injuries. The primary offensive move, the attack, involves the approach, arm cocking, arm acceleration, and follow-through phases. Motion capture analysis and techniques like calculating Euler angles and rotation about a mean helical axis can evaluate shoulder movements. This study aimed to calculate shoulder movements during each phase of the volleyball attack using the Euler angle YXY sequence and the helical axis method. Different attack types, such as cross-court and …

Innovative 4d Printing Of Biomimetic Collagen-Tcp Scaffolds For Bone Regeneration, Karly Morgan Liebendorfer

Theses and Dissertations

Bone tissue engineering (BTE) is a promising alternative approach to autografts and allografts when treating various bone diseases and disorders. BTE enables the fabrication of biocompatible, biomimetic, and osteo-stimulating constructs for the repair and regeneration of damaged bone tissue. The native bone environment primarily consists of anisotropic type 1 collagen (organic) and hydroxyapatite nanocrystals (inorganic). Composite biomimetic scaffolds fabricated by combining collagen with bioceramics have shown immense promise for BTE applications. Prior work has reported on different biofabrication methods to synthesize collagen-based composite scaffolds for use in BTE applications. However, to date, a customizable 3D composite scaffold that resembles the …

Investigating The Effects Of Calcitonin Gene Related Peptide On Heart Failure And The Gut Microbiome, Talia Charlotte Kepniss

Theses and Dissertations

Heart failure affects millions of people worldwide with current available treatments that are limited in their efficacy. The financial burden for care of those with heart failure is over 20 billion dollars in the US alone. Calcitonin gene related peptide has demonstrated cardioprotective and powerful vasodilator effects. In this study our objective is to prevent the onset of heart failure and treat early stages of heart failure with injections of calcitonin gene related peptide in C57BL/6 mice. In order to model heart failure, experimental mice underwent a transverse aortic constriction surgery. Echocardiograms and fecal collections were completed to observe changes …