Biomedical Engineering and Bioengineering Commons^™

Metabolic Profiling Of Radiation Resistance In Head And Neck Squamous Cell Carcinoma, Natalie Curry

Biomedical Engineering Undergraduate Honors Theses

Abstract

Head and neck squamous cell carcinoma is the sixth most common cancer worldwide. Radiation therapy is one of the most common treatments for HNSCC, however, many patients do not respond to radiation therapy. Currently, it takes about a month for clinicians to definitively determine whether a tumor is responsive to radiation therapy. Current studies have identified that the prevention of mitochondrial oxidative stress caused by reactive oxygen species can prevent DNA damage and lead to a decrease in apoptosis in radiation resistant cells Measuring the oxygen consumption rate through Seahorse metabolic assays allows us to quantify basal respiration, maximal …

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 …

Guide Rnas Preparation For In-Vitro Crispr-Cas9 Complex Delivery Targeting Genes That Affect Wound Healing., Prashant Khatiwada

Biomedical Engineering Undergraduate Honors Theses

CRISPR-Cas9 technology has widely been used as a viable genome engineering platform to make site-specific insertion, deletion, and breaks. The nuclease dead version of Cas9 or dCas9 can be used for the activation and repression of target gene sites using specific activation or repression domains. In this study, CRISPR guide RNAs were designed for a CRISPR inhibition approach to repress the transcriptional activity of the target genes. An expression plasmid vector composed of a U6 promoter sequence, BbsI restriction sites, and a chimeric gRNA sequence was digested, and the phosphorylated forward and reverse gRNAs were ligated with the plasmid vector. …

Using Deep Learning To Analyze Materials In Medical Images, Carson Molder

Computer Science and Computer Engineering Undergraduate Honors Theses

Modern deep learning architectures have become increasingly popular in medicine, especially for analyzing medical images. In some medical applications, deep learning image analysis models have been more accurate at predicting medical conditions than experts. Deep learning has also been effective for material analysis on photographs. We aim to leverage deep learning to perform material analysis on medical images. Because material datasets for medicine are scarce, we first introduce a texture dataset generation algorithm that automatically samples desired textures from annotated or unannotated medical images. Second, we use a novel Siamese neural network called D-CNN to predict patch similarity and build …

Glial Endothelial Brain Cell Co-Cultures For Testing Signaling Response And Delivery Of Novel Materials Across Blood Brain Barrier, Neela Prajapati

Doctoral Dissertations

The brain accounts for 20% of overall energy metabolism in the body though it just comprises 2% of the total body mass but has a limited capacity of storing energy unlike other critical organs in the body such as the heart and liver. This energy along with oxygen and nutrients is supplied by cerebral blood flow (CBF), any interruption of which can cease the brain function within seconds with a potential irreversible neuronal injury, within minutes. Vascular cells along with astrocytes and neurons are a part of a recently developed concept known as the Neurovascular Unit responsible for Neurovascular coupling …

Quantifying Blood Flow Patterns In The Pediatric Heart Using Blood Speckle Imaging, Harrison Dean

Biomedical Engineering Undergraduate Honors Theses

Congenital Heart Disease (CHD) is the most common type of congenital disease worldwide. Echocardiography using Doppler ultrasound is typically used to diagnose and monitor CHD; however, it is angle-dependent in nature and as a result is limited in its ability to accurately evaluate ventricular function. Blood Speckle Imaging (BSI) is a novel, angle-independent imaging modality that provides detailed blood flow information and visualization within a given area using speckle-tracking. In this study, velocity-field information obtained from BSI was used to calculate flow parameters such as kinetic energy (KE) and circulation using a custom created MATLAB program. BSI was performed on …

The Linear And Non-Linear Relationships Between Peripheral Venous Pressure, Arterial Circulation, And Patient Factors, Lauren Crimmins

Biomedical Engineering Undergraduate Honors Theses

Peripheral venous pressure (PVP) can be used to measure blood volume status with a minimally invasive procedure. The pediatric cohort undergoing surgery for pyloric stenosis was studied to determine how arterial circulation and patient factors linearly impact PVP. The relationship between PVP and these confounding factors can provide valuable information for future PVP researchers.

To investigate the linear relationship between PVP and electrocardiogram (ECG) the waveforms were transformed into the frequency domain. A power spectral density was plotted, and the Pearson correlation coefficients were calculated for both preoperative and intraoperative settings. Linear regression models were computed for PVP and varying …

Biomechanical Studies Of Developing Zebrafish Heart In-Vivo, Nabid Salehin

Bioengineering Dissertations - Archive

The heart is an electrically controlled mechanical pump that provides the cardiac output required by the body to function properly and flexibly adapts to changing demand and working conditions. In vertebrate embryos, the heart is the first organ that starts functioning and the function is initiated well before structural organogenesis is complete, with its early mechanical function affecting its own development. During development, the heart transforms from a valveless linear peristaltic tube into a multi-chambered pulsatile pump with blood flow regulating valves while continuing to serve the metabolic needs of the embryo. The zebrafish has emerged as a popular model …

Non-Invasive Profiling Of Molecular Markers In Brain Gliomas Using Deep Learning And Magnetic Resonance Images, Chandan Ganesh Bangalore Yogananda

Bioengineering Dissertations - Archive

Gliomas account for the most common malignant primary brain tumors in both pediatric and adult populations. They arise from glial cells and are divided into low grade and high-grade gliomas with significant differences in patient survival. Patients with aggressive high-grade gliomas have life expectancies of less than 2 years. Glioblastoma (GBM) are aggressive brain tumors classified by the world health organization (WHO) as stage IV brain cancer. The overall survival for GBM patients is poor and is in the range of 12 to 15 months. These tumors are typically treated by surgery, followed by radiotherapy and chemotherapy. Gliomas often consist …

Metabolic And Electrophysiological Effects Of Transcranial Photobiomodulation (Pbm) And Multi-Wavelength Pbm, Tyrell Byrom Pruitt

Bioengineering Dissertations - Archive

Photobiomodulation (PBM) with near infrared light may become a non-invasive, effective clinical tool after it is understood well for its mechanism of action. In my dissertation research, I have addressed three research questions as three aims to achieve. Aim 1 was to investigate and demonstrate the reproducibility of the effects of transcranial PBM (tPBM) with 1064-nm laser delivered on the right forehead of separate groups of healthy humans measured using different experiment setups in separate sites and years. In Chapter 2, I reported sham-controlled, tPBM-induced concentration increases in oxygenated hemoglobin (∆[HbO]) and oxidized cytochrome c oxidase (∆[oxi-CCO]) in both young …

An In Vitro Model To Study The Role Of Iol: Lens Capsule Interactions In Posterior Capsule Opacification, Arjun Jaitli

Bioengineering Dissertations - Archive

Posterior capsule opacification (PCO) is the most common complication associated with intraocular lens (IOL) implantation. Unfortunately, current in vitro models cannot be used to assess the potential of PCO due to their failure to simulate posterior curvature of the lens capsule (LC), contradicting observations, different testing conditions and inherent challenges associated with use of human capsular bag models, cells and other tissue substrates. To overcome such a challenge, a new system to study IOL: LC interaction and potentially predict PCO was developed in this effort. It is believed that the interactions between an IOL and the lens capsule (LC) may …

Optimal Analytical Methods For High Accuracy Cardiac Disease Classification And Treatment Based On Ecg Data, Jianwei Zheng

Computational and Data Sciences (PhD) Dissertations

This work constitutes six projects. In the first project, a newly inaugurated research database for 12-lead electrocardiogram signals was created under the auspices of Chapman University and Shaoxing People's Hospital (Shaoxing Hospital Zhejiang University School of Medicine). This database aims to enable the scientific community in conducting new studies on arrhythmia and other cardiovascular conditions. In the second project, we created a new 12-lead ECG database under the auspices of Chapman University and Ningbo First Hospital of Zhejiang University that aims to provide high quality data enabling detection of the distinctions between idiopathic ventricular arrhythmia from right ventricular outflow tract …

Quantifying Mucosal Hemodynamics In A Murine Model Of Ulcerative Colitis With Diffuse Reflectance Spectroscopy, Elizabeth A. Bullard, Ariel I. Mundo, Shelby N. Bess, Kathryn P. Miller

Biomedical Engineering Undergraduate Honors Theses

Ulcerative colitis (UC) is a gastrointestinal, autoimmune disease that causes ulceration and inflammation of the colon with an incidence 10 out of every 100,000 people in North America and Western Europe. Though the exact etiology is uncertain, a number of studies have shown that inflammatory cells along with environmental factors, genetics, and lifestyle habits can contribute to the sustained inflammatory response. In order to determine the cellular mechanism behind relapse and remission of UC, researchers have frequently employed immunohistochemistry, western blotting and gene sequencing, but these destructive analysis methods require the removal of a sample, necessarily limiting these methods to …

Evaluating Cellular Response Of Different Valve Interstitial Cell (Vic) Phenotypes To Angiotensin I, Smit Patel

Biomedical Engineering Undergraduate Honors Theses

Calcific Aortic Valve Disease (CAVD), one of the leading causes of death in the United States, is characterized by diminished functioning and limited movement of the aortic valve (AV) due to increased thickening, disorganized extracellular matrix elastin fibers, increased collagen content, and abnormal deposition and formation of calcium nodules on the AV [1, 2]. There are two types of CAVD: i) Aortic valve sclerosis (AVS), in which patients suffer from tissue hardening, fibrosis, and early calcification, and ii) calcific aortic stenosis (CAS), representative by excessive calcification on the AV and reduced AV opening, are the two main forms of CAVD …

In Vivo Analysis Of A Proprietary Glass-Based Adhesive For Sternal Fixation And Stabilization Using Rabbit And Sheep Models, Cina Mehrvar, Emily Deignan, Mark Hurtig, Gideon Cohen, Paul Zalzal, Oleg Safir, Adel Alhalawani, Marcello Papini, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Wire cerclage remains the standard method of care for sternal fixation, following median sternotomy, despite being beset with complications. An emerging treatment option has been to augment the wires with an adhesive. A patented ionomeric glass (mole fraction: SiO₂:0.48, ZnO:0.36, CaO:0.12, SrO:0.04) has been used to formulate GPC+, a glass polyalkenoate cement (GPC), by mixing it with poly(acrylic) acid (PAA) and de-ionized water. In a human cadaver study, this material, when applied with wire cerclage, was able to significantly reduce sternal instability. However, the material has yet to be tested in pertinent animal models. Here, after a series …

Involvement Of The Ino80 Chromatin Remodeling Complex In Cell Division And Genomic Stability, Ethan Chen

Biomedical Engineering Undergraduate Honors Theses

Cell division is a vital biological process for growth and development in both single and multi-cellular organisms—whereby the cell must duplicate its organelles and genome in entirety and appropriately distribute the copied contents to the daughter cells. Cells undergo a cycle of two distinct phases: interphase and mitosis. During interphase, the cell replicates its genomic DNA (in the form of chromosomes) located within the nucleus. DNA replication is carried out in a euchromatin state, where the chromosome structure is loose and easily accessible by DNA polymerase and other replication enzymes. Upon the completion of replication, chromatin is condensed into highly …

Quantification Of Superoxide Production In Cells Treated With L-Buthionine Sulfoximine, Rebekah Townsley

Biomedical Engineering Undergraduate Honors Theses

Hydroxyl radicals, superoxides, and hydrogen peroxides are common reactive oxygen species (ROS) that are produced by the mitochondria during cellular respiration [1]. Signal transduction pathways in the mitochondria are used to maintain the balance of ROS. However, when these mechanisms fail to regulate ROS properly, it causes oxidative damage and can lead to the development of various diseases such as cancer, respiratory, neurodegenerative, and cardiovascular diseases. L-buthionine sulfoximine (BSO) has been used previously to induce oxidative stress by inhibiting the γ-GCS enzyme used to synthesize glutathione, an antioxidant used to convert ROS to water [3]. BSO reduces glutathione production, thus …

New Force Transducer For Mitral Valve Chordae Tendinea, Joseph Berryman

Biomedical Engineering Undergraduate Honors Theses

In order to inform the future of mitral valve repair and replacement, more investigation into the mechanics of the sub-valvular structure is needed. Understanding the roles of each chord during valve closure requires a sensor capable of detecting these small forces with enough sensitivity to determine the characteristics of each of the chordal types. The focus of the cantilever force transducer is to maximize this sensitivity while also minimizing the invasiveness of the sensor on the overall function of the chord. The design utilizes flexible yet strong 3D printed resin and cantilever arms to improve the strain exerted on a …

Use Of 3d-Printed Surgical Spoons Compared To Other Cystotomy Methods In Dogs, Davina D'Angelo

Animal Science Undergraduate Honors Theses

Bladder stones, also known as uroliths, are not an uncommon condition in domestic dogs. To remove these uroliths, which occur in various sizes, shapes, and compositions, veterinarians will perform a surgical procedure called a cystotomy. A cystotomy consists of creating a small incision into the lumen of the urinary bladder and the utilization of various methods to extract the uroliths. For general veterinary practitioners, the laparoscopic-assisted technique is unavailable. As a result, the methods available for urolith extraction are often limited to flushing the stones out by inserting a urinary catheter through the urinary tract and the use of off-label …

Static Force Analysis Of A Porcine Mitral Valve To Determine Self-Supporting Capabilities Of The Leaflets, Jacob Paris

Biomedical Engineering Undergraduate Honors Theses

The mitral valve (MV) is responsible for controlling the flow between the left atrium (LA) and left ventricle (LV). This includes maintaining valve closure under high systolic pressures. Mitral regurgitation (MR) occurs when the valve fails to completely close and blood flows in the reverse direction, from the LV to the LA, during ejection. This type of valvular heart disease is prevalent among elderly individuals and is becoming increasingly common as the population ages. In order to better understand how to properly treat this large group of affected individuals, the mechanics of the MV during high systolic pressures must be …