Biomedical Engineering and Bioengineering Commons^™

Data-Driven And Cell-Specific Determination Of Nuclei-Associated Actin Structure, Nina Nikitina, Nurbanu Bursa, Matthew Goelzer, Madison Goldfeldt, Chase Crandall, Sean Howard, Janet Rubin, Anamaria Zavala, Aykut Satici, Gunes Uzer

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Quantitative volumetric assessment of filamentous actin (F-actin) fibers remains challenging due to their interconnected nature, leading researchers to utilize threshold-based or qualitative measurement methods with poor reproducibility. Herein, a novel machine learning-based methodology is introduced for accurate quantification and reconstruction of nuclei-associated F-actin. Utilizing a convolutional neural network (CNN), actin filaments and nuclei from 3D confocal microscopy images are segmented and then each fiber is reconstructed by connecting intersecting contours on cross-sectional slices. This allows measurement of the total number of actin filaments and individual actin filament length and volume in a reproducible fashion. Focusing on the role of F-actin …

Investigating The Presence Of Patented In Vitro Models For Cancer-Nerve Crosstalk Methods, Christoff Hauptmann

Biomedical Engineering Undergraduate Honors Theses

The purpose of this research project is to investigate the presence of patented in vitro models for perineural invasion (PNI) and tumor innervation, the two most prominent modes of cancer-nerve crosstalk that play an active role in cancer initiation and progression. PNI occurs through a positive feedback loop in which cancer cells invade passive nerves to metastasize. Tumor innervation is the process where tumor cells attract nearby nerves to the tumor microenvironment (TME) for tumor growth and metastasis. These crosstalk paths have been established for many types of cancer and result in poor patient prognosis. Recently, in vitro models have …

Evaluation Of The Efficiency Of Muscle-Specific Promoters To Express Non-Endogenous Proteins In Skeletal Muscle, Gabrielle Bulliard, Made Harumi Padmaswari, Christopher E. Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene therapies are emerging as powerful tools for treating genetic diseases and cancers, offering the potential for a permanent cure. Hemophilia B, affecting approximately 6,000 men in the U.S., results from a deficiency in coagulation factor IX protein (FIX), which is crucial for blood clotting. A substantial portion of patients, over 40%, suffer from severe hemophilia B, experiencing spontaneous, prolonged bleeding. Current prophylactic treatments involve frequent coagulation factor infusions, yet a curative approach would alleviate this burden. Gene editing technologies like CRISPR-Cas systems show promise for correcting genetic mutations, but the diverse nature of factor IX gene (F9) …

What Is Biological Engineering? – A Magazine, Morgan Christensen

Undergraduate Honors Capstone Projects

Biological Engineering is one of the less commonly known fields of engineering and can be challenging to describe to someone outside the discipline. The most common question I've been asked during my undergraduate career is "What is biological engineering?". My answer has changed throughout my time at Utah State University as I've had more experiences within the discipline. This project focuses on answering this question in the format of a magazine to help bridge the gap between those in the discipline and a general audience. By using a magazine as the format, the content must be organized and written in …

Testing Resilience Of Microalgae Biofilms When Exposed To Hydrothermal Liquefaction Aqueous Phase, Davis Riley Haag

Undergraduate Honors Capstone Projects

There are a multitude of experimental and processing techniques in the bioenergy field that produce sustainable and carbon negative to carbon neutral methods of converting renewable resources into biologically based hydrocarbons. One example of a process is hydrothermal liquefaction (HTL) which specializes in converting wet biomass into biocrude oil. One reason that these processes are not used outside experimental testing is due to the high cost of performing these processes. There is potential to move these processes to larger scale testing and eventually industrial adaptation if breakthroughs are made to offset the process expenses. There is a waste product produced …

Acoustofluidic Delivery Of Biomolecules To Cells: A Novel Approach For Preparing Car-T Cells., Madison C. Colebank

Electronic Theses and Dissertations

The continuous pursuit of effective methods for gene transfection in primary human T cells is crucial for advancing cell-based therapies. Viral vectors, currently used in cell-based therapies, involve a lengthy and costly process. This thesis explores the efficacy of coupling acoustofluidic and sonoporation techniques as an alternative non-viral gene transfection approach with primary T cells. Sonoporation, in conjunction with microbubbles, has been demonstrated to induce cavitation, resulting in the formation of pores in the cell membrane through which molecules can enter. Using flow cytometry, we compared the loading efficiency of primary T cells with that of Jurkat T cells to …

Rockin’ Rehab: Novel Rocking Chair For Children With Spinal Cord Injury To Enable Trunk Muscle Activation And Detect Muscle Activation Patterns., Johnathan Jay George

Electronic Theses and Dissertations

Introduction: Activity-based locomotor training improves trunk control in children with spinal cord injury (SCI), and there is need for additional activities to allow these children to activate trunk muscles. The purpose of this research was to design, fabricate, and evaluate a rocking chair for children with SCI, and to investigate the activation of muscles during use. Sensorization of the chair to confirm muscle activation is also explored. Methods: Quality Function Deployment (QFD) design methodologies identified and ranked needs and features for the rocking chair. A design was developed and evaluated via finite element analysis. The chair was fabricated and tested …

Transcriptomic Profiling Of Engineered Human Gene Integration In The Mouse Genome Following In Vitro Gene Editing, Ethan Potts, Made Harumi Padmaswari, Christopher Nelson

Biomedical Engineering Undergraduate Honors Theses

Gene replacement is a promising method of therapy for genetic diseases. However, safety and efficacy are areas that need more research. This experiment aims to use RNA sequencing and bioinformatic techniques to provide answers to these questions and provide direction to future studies to develop a gene replacement therapeutic. C2C12 mouse myoblast cells were transfected with a vector containing a CRISPR-Cas9 system and the Human Factor IX (hF9) gene in order to hijack target genes and integrate the hF9 gene. The two target genes, myoglobin (Mb) and creatine kinase (Ckm), were chosen for their high rate of expression and low …

Real-Time Measurements From Wearable Sensors To Enhance Stability On Uneven Terrain, Sophie Copelin

Biomedical Engineering Undergraduate Honors Theses

The presented thesis is a study of sensation associated with inversion/eversion movement about the anterior/posterior axis. The long-term goal is to create a system that provides feedback to a prosthesis user, so their chances of falling is decreased. This feedback system would use wearable sensors to detect certain angles, so that sensory feedback could be provided. The study aimed to determine if Xsens Movella DOT sensors could be used in a system like this, so the accuracy of the Xsens Movella DOT sensors was assessed and the difference in angles that could be determined by them when compared to that …

Detection Of Hypoxia Via Rgb Imaging, Nathania Nischal

Biomedical Engineering Undergraduate Honors Theses

Colorectal cancer is a common form of cancer, and is heavily researched in murine models. Colonoscopies are often performed in clinical settings to assess the health of the colon, as well as locate and assess the severity of tumors in a non-invasive way. As the quality of the images is dependent on the colonic environment and the light available, it is important to ensure the accuracy of the images via a normalization algorithm. The RGB images procured from these colonoscopies have great potential as a diagnostic tool for physicians, as varying scales of discoloration is common in hypoxic tissue. While …

Dorsal Root Ganglia Neurite Outgrowth Following Traumatic Spinal Cord Injury Repair: A Review, Adrienne Vaughan

Biomedical Engineering Undergraduate Honors Theses

Traumatic spinal cord injury (tSCI) can cause partial sensorimotor deficiency or total dysfunction, rendering patients unable to perform necessary tasks and dramatically decreasing their quality of life. tSCI is a very prevalent issue. In the United States alone, there are approximately 54 new cases of SCI per one million people each year, or 18,000 new cases annually. tSCI creates a lesion gap filled with axon-inhibiting fibrotic scar tissue. Comprehensive functional recovery following traumatic spinal cord injury (tSCI) requires axonal regeneration across wound site lesions. Dorsal root ganglia (DRG) neurite outgrowth is often evaluated in PNI therapeutic research since it can …

Computational Predictions Of Heart Failure Drug Effects On Cardiac Fibrosis, Aaron Gardner

Chemical Engineering Undergraduate Honors Theses

The extracellular matrix is a complex system surrounding cells that is crucial to all of the cardiovascular system’s functions. Fibrosis is an excessive accumulation (scarring) of the extracellular matrix. Fibrosis is typically a negative event, and the scarring must be reduced in the heart in order to maintain its functionality. Due to this, simulations are run using the software “Netflux” in order to determine the effects of different heart failure drugs on cardiac fibrosis. The drugs that were simulated were an ACE Inhibitor, BAR Beta Blocker, ARB Blocker, and Entresto. These drugs were simulated over 50 hours at three different …

Suppressing Reactive Oxygen Species Via Application Of Antioxidant Supramolecular Polymers, Zacchaeus Wallace

Honors Theses

Cardiovascular diseases along with various other disease conditions are characterized by an upregulation in reactive oxygen species (ROS), which can overwhelm homeostatic processes in the body, resulting in cellular apoptosis and severe oxidative damage. The lack of clinically approved treatments to regulate or alleviate this elevated ROS presence underscores the need for novel therapeutic strategies. While antioxidants promote cell rescue through ROS scavenging, their clinical translation is impeded by insufficient bioavailable concentrations at the source of injury. The opportunity to apply antioxidant supramolecular polymers of peptide amphiphiles (PAs) is an exciting prospect of research to combat corresponding issues. For this …

Evaluation And Development Of Tourniquet Test Methods, Catherine Pitts

All Theses

Since the beginning of the 21^st century the general perspective on tourniquets has changed to a more positive outlook on their life saving abilities. The US has seen a greater number of mass casualty events, and conflicts across the globe have led to an increased use of tourniquets. The increased demand has also led to faulty counterfeit tourniquets and improvised tourniquets that don not properly occlude blood flow or cause significant nerve damage to the injured limb.

ASTM started designing a tourniquet testing standard with experts in the tourniquet community to cut down on the dangers of tourniquet use. …

The Effect Of Central Screw And Post Vault Containment On Reverse Total Shoulder Arthroplasty (Rsta) Baseplate Stability, Mickaela J. Gunnison

All Theses

Reverse total shoulder arthroplasty (RTSA) is a procedure that aims to fix irreversible rotator cuff damage and degenerative glenohumeral joint diseases that hinder arm abduction. One major complication of RTSA is glenoid baseplate failure resulting from increased movement at the bone-baseplate interface. This study examined 36, 12 PCF composite Sawbones® scapulae. The specimens were split equally into 6 study groups, each having different implant configurations with varying baseplate lateralization and central screws or posts. Each specimen was subjected to cyclic shear loading and failure testing on an Instron to determine implant micromotion and load values.

After testing, ANOVA tests were …

Light-Induced Phase Separation Purification For Monoclonal Antibodies, Xuyang Chen

All Theses

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Analyzing Diverse Student Experiences: The Intersection Of Equity, Inclusivity, And Biomedical Engineering Education Through A Clinical Observations And Needs Finding Course, Jacquelynn Horsey

Biomedical Engineering Undergraduate Honors Theses

In the field of biomedical engineering, needs identification and solution development are an important element of the design process. In our undergraduate curriculum, a course was designed to allow clinical observation and provide an opportunity for students to learn about engineering design and engage with clinicians via completing rotations in medical facilities near our campus. While this type of course is not unique, evaluating its efficacy is not simple. Given the broad range of institutional resources available- such as proximity to a medical school, or residency programs- reporting the quality of such courses within the context of such available resources …

The Determination Of Macrophage Localization In Muscle Injuries Using Spatial Transcriptomics, Julliana Renales

Biomedical Engineering Undergraduate Honors Theses

The repair of traumatic muscle injury is often a long process which can in many cases be insufficient and incomplete. In such cases, scar tissue may form, leading to high risk of re-injury and the prevention of muscle regeneration. An important part of decreasing this risk is gaining a better understanding of the cellular complexities of injury repair. More specifically, macrophage cells are an important piece in the regulation of inflammation and repair. In this project, computational analysis spatial transcriptomic data was performed to examine mouse muscle injury and its development over time. This analysis was used to examine the …

Investigation Of Early Stage Wound Healing In Volumetric Muscle Loss, Sean Ong

Biomedical Engineering Undergraduate Honors Theses

Volumetric muscle loss (VML) refers to the substantial removal of tissue from skeletal muscle due to surgery or lesions. This condition disrupts the normal regenerative process of injured muscles, leading to significant loss of muscle function. This study examines the progression of VML injury, approximately 20% of the muscle mass being removed, in the tibialis anterior (TA) muscle of a mouse model over a 15-day post-injury period. The injured muscles exhibited discoloration indicative of reduced blood flow and experienced a decrease in muscle mass throughout the study duration. Furthermore, the maximum force output of the injured TA was significantly lower, …

Quantification Of Age-Related Changes In The Structure And Mechanical Function Of Skin With Multiscale Imaging, Alan E. Woessner, Nathan J. Witt, Jake D. Jones, Edward A. Sander, Kyle P. Quinn

Biomedical Engineering Faculty Publications and Presentations

The mechanical properties of skin change during aging but the relationships between structure and mechanical function remain poorly understood. Previous work has shown that young skin exhibits a substantial decrease in tissue volume, a large macro-scale Poisson’s ratio, and an increase in micro-scale collagen fiber alignment during mechanical stretch. In this study, label-free multiphoton microscopy was used to quantify how the microstructure and fiber kinematics of aged mouse skin affect its mechanical function. In an unloaded state, aged skin was found to have less collagen alignment and more non-enzymatic collagen fiber crosslinks. Skin samples were then loaded in uniaxial tension …