Other Biomedical Engineering and Bioengineering Commons^™

Conversion Of Multicellds Digital Snapshots To Isa-Tab Format., Corey P. Chitwood

Electronic Theses and Dissertations

The MultiCellular Data Standard (MultiCellDS) is an interdisciplinary effort to create a data standard for sharing multicellular experimental, simulation, and clinical data. The ultimate goal of the overall project is to allow for data sharing that will lead to better analyses and simulations for multicellular biology and predictive medicine in association with the PhysiCell, a software that allows for simulations of large numbers of cells in 3D tissues. Digital cell lines are files that contain a standardized representation of a biological cell line and include phenotypic parameters as well as microenvironmental conditions for use in simulations. A Digital Cell Line …

Noninvasive Measurement Of Arterial Compliance With A Blood Pressure Cuff Using A Surrogate Arm Bench Top Model For Oscillometric Use, Shane Wilsey

Master's Theses

A surrogate arm model was created that is capable of being used for oscillometry. This model is capable of being used as a bench top model for blood pressure cuff devices. The arm consists of endplates and internal supports that are 3D printed with ABS, a silicone rubber outer sleeve, and interchangeable arteries made from two silicone rubber strips glued together at the edges. The interchangeable arteries have varying compliances that can be used as different inputs for oscillometric testing. A process was established to measure the artery compliances with a curve fit correlation of 0.95. However, testing revealed that …

Modeling Action Potential Propagation During Hypertrophic Cardiomyopathy Through A Three-Dimensional Computational Model, Julia Elizabeth Kelley

Master's Theses

Hypertrophic cardiomyopathy (HCM) is the most common monogenic disorder and the leading cause of sudden arrhythmic death in children and young adults. It is typically asymptomatic and first manifests itself during cardiac arrest, making it a challenge to diagnose in advance. Computational models can explore and reveal underlying molecular mechanisms in cardiac electrophysiology by allowing researchers to alter various parameters such as tissue size or ionic current amplitudes. The goal of this thesis is to develop a computational model in MATLAB and to determine if this model can accurately indicate cases of hypertrophic cardiomyopathy. This goal is achieved by combining …

Hand Strength And Dexterity Enhancer, Julia Ann Denison, Autumn B. Rexford, Melissa A. Kurani, Christina K. Fong

Biomedical Engineering

Good Grips created the hand strength and dexterity enhancer project to meet the challenge presented by Bill Phelps. He has Inclusion Body Myositis (IBM), an inflammatory muscle disease characterized by progressive muscle weakness and atrophy. Bill has limited strength in both hands and lost the ability to bend his fingers, making it difficult to grip anything. He needed a device that would help with everyday tasks such as writing, lifting, and holding various objects.

Our team consists of four engineering students attending Cal Poly, San Luis Obispo. We researched, designed, manufactured, and tested a device that would fulfill the problem …

The Impact Of Myoblast Transplantation On Collateral Capillary Arteriogenesis And Macrophage Phenotype, Christine Hue Do

Biomedical Engineering

Gangrene, pain, loss of limb function, amputation, and death are only few of the grievous consequences associated with peripheral arterial disease (PAD), a vascular disease caused by an obstruction that narrows the blood vessels. Since some patients have collateral vessels that can re-route blood to its downstream destination, much focus has been spotlighted upon discovering the mechanism of this process, termed arteriogenesis, as well as cell therapies to increase arterial diameter of collateral vessels. Since some patients do not have native pre-existing collateral vessels, another method to re-route blood is through arterialized collateral capillaries (ACC), which is the conversion of …

Machine Learning Applied To Colloidal Properties Of Perfluorocarbon Nanoemulsions For Imaging In Ards/Ali, Marco Hosfeld

Electronic Theses and Dissertations

Acute Respiratory distress Syndrome (ARDS) and Acute Lung Injury (ALI) are inflammatory lung pathologies consisting of non-hydrostatic pulmonary edema leading to hypoxia and impaired gas exchange in the lungs. ARDS/ALI is both difficult to study and treat as it is not in itself a specific pathology but rather a syndrome consisting of many pathologies that vary case by case. It is, however, consistently characterized by an explosive acute inflammatory response in the lung parenchyma leading to hypoxia. Although time has seen to an increase in the understanding of ARDS/ALI, the mortality rate remains in the range of 30-50%. For these …

Expanding Image Datasets For Deep Learning By Evaluating Independence Through Coefficient Correlation And Mean-Squared Error, Ayman Yousef

Biomedical Engineering Undergraduate Honors Theses

With deep learning being leveraged more regularly in the field of image classification, particularly in medical imaging, network optimizations have become a field in and of itself. With open source, comprehensive medical image datasets few and far, computational dataset expansion has become a useful tool for researchers without the ability to further manually collect data. However, with the rich amount of data that imaging modalities like multi-photon microscopy collect at a time, there is potential to expand datasets through proper utilization of this data that often time goes unused. Previous deep learning studies have shown that improper expansion can conflate …

Isomotive Dielectrophoresis For Enhanced Analyses Of Cell Subpopulations., Mohamed Zakarya Rashed

Electronic Theses and Dissertations

As the relentless dream of creating a true lab-on-a-chip device is closer to realization than ever before, which will be enabled through efficient and reliable sample characterization systems. Dielectrophoresis (DEP) is a term used to describe the motion of dielectric particles/ cells, by means of a non-uniform electric field (AC or DC). Cells of different dielectric properties (i.e., size, interior properties, and membrane properties) will act differently under the influence of dielectrophoretic force. Therefore, DEP can be used as a powerful, robust, and flexible tool for cellular manipulation, separation, characterization, and patterning. However, most recent DEP applications focus on …

Simulation Of Fracture Strength Improvements Of A Human Proximal Femur Using Finite Element Analysis., Waleed Ebraheem Alim

Electronic Theses and Dissertations

The most common hip fracture in the elderly occurs as a result of a fall to the side with impact over the greater trochanter resulting in a fracture of the proximal femur. The fracture usually involves the femoral neck or the intertrochanteric region. It has recently been determined that the fracture crack of a hip fracture typically initiates on the superior-lateral cortex of the femoral neck and then propagates across the femoral neck, resulting in a complete fracture. The strength of the superior-lateral cortex of the femoral neck is likely determined by the combined properties of the generally thin cortex …

Automated Conversion Of Multicellds Digital Cell Lines And Isa-Tab Filesets., Connor Joseph Burns

Electronic Theses and Dissertations

Biological simulation tools are a valuable asset to bridge the gap between biological experimentation and biological theory. As systems thinking has become more regularly applied to biological materials and processes, these materials and processes have been characterized in multi-disciplinary, computational manners. This characterization has yielded an ability to create more realistic simulation tools that can provide in silico experiments for a wider range of scenarios. One prominent simulation tool is PhysiCell, an open-source physics-based multicellular simulation program which utilizes input Digital Cell Lines or Digital Snapshots from the MultiCellular Data Standard (MCDS) project.

This project aims to allow data exchange …

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, …

Understanding The Effect Of Adaptive Mutations On The Three-Dimensional Structure Of Rna, Justin Cook

Undergraduate Research and Scholarship Symposium

Single-nucleotide polymorphisms (SNPs) are variations in the genome where one base pair can differ between individuals.¹ SNPs occur throughout the genome and can correlate to a disease-state if they occur in a functional region of DNA.¹According to the central dogma of molecular biology, any variation in the DNA sequence will have a direct effect on the RNA sequence and will potentially alter the identity or conformation of a protein product. A single RNA molecule, due to intramolecular base pairing, can acquire a plethora of 3-D conformations that are described by its structural ensemble. One SNP, rs12477830, which …

Pneumonia Radiograph Diagnosis Utilizing Deep Learning Network, Wesley O'Quinn

Honors College Theses

Pneumonia is a life-threatening respiratory disease caused by bacterial infection. The goal of this study is to develop an algorithm using Convolutional Neural Networks (CNNs) to detect visual signals for pneumonia in medical images and make a diagnosis. Although Pneumonia is prevalent, detection and diagnosis are challenging. The deep learning network AlexNet was utilized through transfer learning. A dataset consisting of 11,318 images was used for training, and a preliminary diagnosis accuracy of 72% was achieved.

Primer Payload System For Higher-Order Multiplex Lamp: Design And Development Of Unit Processes, Tochukwu Dubem Anyaduba

KGI Theses and Dissertations

Design and Development of Platforms for the Application of Loop-mediated Isothermal Nucleic Acid Amplification, LAMP, in the Diagnosis of Polymicrobial Diseases

Tochukwu Dubem Anyaduba, Travis Schlappi (PI)

For the past two decades, several isothermal nucleic acid amplification technologies have emerged. These are mostly in response to the need for robust molecular diagnostic tools amenable to point-of-care and limited-resource settings. Of these, loop-mediated isothermal amplification, LAMP, stands out as a highly specific and rapid alternative to the polymerase chain reaction, PCR. One of LAMP's significant characteristics involves using four essential and two loop (rate increasing) primers to recognize six to eight …

Gyroscopic Human Balance Device, Randy Lam Hau, Spencer Ross, Yael Farkash

Biomedical Engineering

This project’s sponsor, Charlie Guitierrez, has decades of experience building assistive walking devices for the wheelchair bound population. During his work, he noticed that many of his clients retained some ability to balance themselves and so theorized that they would be able to walk independently if given some form of assistance. This assistance could potentially be in the form of a wearable gyroscope. Gyroscopes are commonly used to stabilize objects subjected to instability, such as bicycles, motorcycles, and ships. Thus, a wearable gyroscope would assist its user in maintaining overall stability by imparting reactive torques and forces if the user …

Development Of The Cell-Free Protein Biomanufacturing Platform For The Therapeutic Human Protein Production And The Topical Delivery Applications Using The Nanosized Hydrogel System, Jeehye Kim

LSU Doctoral Dissertations

Proteins are highly structural polymers, performing an enormous range of roles within organisms. Unlike synthetic polymers, proteins have a significant hierarchical ordering that can be disrupted by many environmental factors, which limits the scale-up manufacturing capability as well as the utilization of proteins as therapeutic agents. In this study, the Cell-Free Protein Synthesis (CFPS) system was developed to enhance the production capacity and applications of the therapeutic proteins. The CFPS is an advanced biosynthetic and genetic-engineered system. It enables the efficient production of proteins when the conventional cell-based protein synthesis systems cannot be applied, and when sophisticated control is required …

An Adaptive Model To Support Biofeedback In Ami Environments: A Case Study In Breathing Training For Autism, Arturo Morales, Franceli L. Cibrian, Luis A. Castro, Monica Tentori

Engineering Faculty Articles and Research

Biofeedback systems have shown promising clinical results in regulating the autonomic nervous system (ANS) of individuals. However, they typically offer a “one-size-fits-all” solution in which the personalization of the stimuli to the needs and capabilities of its users has been largely neglected. Personalization is paramount in vulnerable populations like children with autism given their sensory diversity. Ambient intelligence (AmI) environments enable creating effective adaptive mechanisms in biofeedback to adjust the stimuli to each user’s performance. Yet, biofeedback models with adaptive mechanisms are scarce in the AmI literature. In this paper, we propose an adaptive model to support biofeedback that takes …

Facilitating Analysis Of Toxoplasma Gondii Bradyzoite Metabolic Activity Via Image Processing And Multivariate Logistic Regression For High Throughput Classification Of Mitochondrial Morphologies, Brooke Place

Theses and Dissertations--Biomedical Engineering

Approximately a third of the population worldwide is chronically infected by the parasite Toxoplasma gondii. During chronic infection the parasite resides within tissue cysts as the poorly understood bradyzoite form. Observation of these bradyzoites via microscopic imaging within tissue cyst purified from infected mouse brains has shown metabolic activity with heterogeneous replication potential. With fluorescence microscopy imaging targeting the parasite’s actively respiring mitochondria, the parasite’s metabolic state can be further investigated as the morphology of mitochondria can be associated with specific physiologic states. However, manually classifying mitochondrial morphologies from these images can be tedious and prone to error as …

Comparative Analysis Of Computationally Accelerated Ngs Alignment, Ada Chaeli Van Der Zijp-Tan

Honors Theses

The Smith-Waterman algorithm is the basis of most current sequence alignment technology, which can be used to identify similarities between sequences for cancer detection and treatment because it provides researchers with potential targets for early diagnosis and personalized treatment. The growing number of DNA and RNA sequences available to analyze necessitates faster alignment processes than are possible with current iterations of the Smith-Waterman (S-W) algorithm. This project aimed to identify the most effective and efficient methods for accelerating the S-W algorithm by investigating recent advances in sequence alignment. Out of a total of 22 articles considered in this project, 17 …

Ogt Glycosylation Of Histones In T Cells May Participate In Systemic Lupus Erythematosus, Jared Luke Ridgeway

Honors Theses

Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease that primarily affects women. The etiology is not known yet, but genetics and environmental factors trigger the disease. These epigenetic changes modify gene expression and contribute to the development of the disease. It is known that T cells from patients with lupus overexpress genes that may contribute to the onset and progression of the disease. Dr. Gorelik has shown that OGT (O-linked N-acetyl-Glucosamine Transferase), which is an X-linked gene, is overexpressed in women with SLE. OGT adds b-N-acetylglucosamine (O-GlcNAc) to serine and threonine residues of proteins. …