Biomedical Engineering and Bioengineering Commons^™

Development Of An In Vitro 3-Dimensional Co-Culture Human Colorectal Cancer Model In Microfluidic Devices, Abby Jens

Master's Theses

Colorectal cancer is the second most common cause of cancer-related deaths in the United States, with the relative 5-year survival rate for distant stage cancer being only 14%. The most common treatment for colorectal cancer is with chemotherapeutic drugs; however, the discovery of these drugs is costly, time-consuming, and often requires the use of animal models that do not yield results that translate to clinical trials. Due to these shortcomings, researchers seek to develop physiologically relevant in vitro tumor models that more accurately mimic the tumor microenvironment for cheaper and faster high-throughput drug screening. The aim of this research was …

Comparison Of Scanning Electron Microscopy And Confocal Laser Microscopy For Tissue Surface Roughness Characterization, Tarnvir Dhaliwal

Master's Theses

It was found that the measurements captured by confocal microscopy and scanning electron microscopy had a statistically significant difference for bovine tissue. There was not a statistically significant for porcine and poultry tissue.

The intent of the study is to perform a comparative study to examine efficacy of two distinct technologies for a singular purpose: tissue surface roughness characterization. The two technologies compared are a confocal reflectance microscope and a scanning electron microscope. The comparison was made by comparing two surface roughness parameters [Ra and Rq] within ImageJ.

The study examined three different animal species [porcine, bovine, and poultry] to …

Deep Learning And Generative Ai Approaches For Automated Diagnosis And Personalized Treatment: Bridging Machine Learning, Medicine, And Biomechanics In Predicting Tissue Mechanics And Biomaterial Properties., Yasin Shokrollahi

Theses and Dissertations

Machine learning, particularly deep neural networks, has demonstrated significant potential in predicting high-dimensional tasks across various domains. This work encompasses a detailed review of Generative AI in healthcare and three studies integrating machine learning with finite element analysis for predicting biomechanical behaviors and properties. Initially, we provide a comprehensive overview of Generative AI applications in healthcare, focusing on Transformers and Denoising Diffusion models and suggesting potential research avenues to address existing challenges.

Subsequently, we addressed soccer-related ocular injuries by combining finite element analysis and machine learning to predict retinal mechanics following a soccer ball hit rapidly. The prediction errors are …

Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov

Doctoral Dissertations

Reactive chemistries for protein chemical modification play an instrumental role in chemical biology, proteomics, and therapeutics. Depending on the application, the selectivity of these modifications can range from precise modification of an amino acid sequence by genetic manipulation of protein expression machinery to a stochastic modification of lysine residues on the protein surface. Ligand-Directed (LD) chemistry is one of the few methods for targeted modification of endogenous proteins without genetic engineering. However, current LD strategies are limited by stringent amino acid selectivity. To bridge this gap, this thesis focuses on the development of highly reactive LD Triggerable Michael Acceptors (LD-TMAcs) …

Free-Hand Photoacoustic Imaging Of Breast Cancer Tissue, Elina Rascevska

Electronic Thesis and Dissertation Repository

Approximately 19% of breast cancer patients undergoing breast conserving surgery (BCS) must return for a re-excision surgery due to positive margin reported by pathology. This problem is mainly associated with lack of intraoperative cancer margin assessment tools. Our previous work demonstrated that lipid-weighted photoacoustic imaging (PAI) can be used intraoperatively to successfully differentiate between cancerous and healthy tissue with high sensitivity. However, the technology was cumbersome and significantly prolonged the procedure time. The goal of this work was to develop a compact hand-held probe, working on lipid-weighted PAI principles, that can provide feedback during BSC without significantly altering the surgical …

Characterization Of Mammographic Dense Tissue Sub-Types Using Classification Algorithms On Metric Space Technique Output Functions, Madison Raza

Electronic Theses and Dissertations

In recent years breast cancer has become the leading cause of global cancer incidence. One of the most common forms of screening is through the use of digital x-ray screening mammography. Risk assessment models which help predict a patient’s risk of developing breast cancer rely mainly on patient history and qualitative breast density assessment from screening. The 2D wavelet transform maxima modulus (2D WTMM) method uses a sliding window approach to quantify the spatial organization of underlying mammographic tissue according to Hurst- exponent ranges (H) as fatty (H ≤ 0.45), healthy dense (H ≥ 0.55) and …

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …

Novel Magnetic Resonance Imaging-Compatible Mechatronic Needle Guidance System For Prostate Focal Laser Ablation Therapy, Eric R. Knull

Electronic Thesis and Dissertation Repository

Advances in prostate cancer (PCa) screening techniques have led to diagnosis of many cases of low-grade and highly localized disease. Conventional whole-gland therapies often result in overtreatment in such cases and debate still surrounds the optimal method of oncologic control. MRI-guided prostate focal laser ablation (FLA) is a minimally invasive treatment option, which has demonstrated potential to destroy localized lesions while sparing healthy prostatic tissue, thereby reducing treatment-related side effects. Many challenges still exist in the development of FLA, including patient selection; tumour localization, visualization, and characterization; needle guidance; and evaluation of treatment efficacy. The objective of this thesis work …

Cad System For Early Diagnosis Of Diabetic Retinopathy Based On 3d Extracted Imaging Markers., Ahmed Sleman

Electronic Theses and Dissertations

This dissertation makes significant contributions to the field of ophthalmology, addressing the segmentation of retinal layers and the diagnosis of diabetic retinopathy (DR). The first contribution is a novel 3D segmentation approach that leverages the patientspecific anatomy of retinal layers. This approach demonstrates superior accuracy in segmenting all retinal layers from a 3D retinal image compared to current state-of-the-art methods. It also offers enhanced speed, enabling potential clinical applications. The proposed segmentation approach holds great potential for supporting surgical planning and guidance in retinal procedures such as retinal detachment repair or macular hole closure. Surgeons can benefit from the accurate …

Design Of Asic Based Electrical Impedance Tomography Microendoscopic System For Prostate Cancer Surgical Marginal Assessment, Mohsen Shahghasemi

Dartmouth College Ph.D Dissertations

Prostate cancer is the second most common cancer in the United States. It is typically treated by surgically excising the cancerous section of the prostate. Because there is not always a visible distinction between the healthy and cancerous sections, surgery often leaves some cancerous tissue behind. This is referred to as a positive surgical margin and it requires adjuvant treatment with adverse side effects. Electrical impedance tomography (EIT) is a low-cost low-form-factor method that can be used to assess surgical marginal intraoperatively to ensure that no cancerous tissue is left behind. EIT-based surgical margin assessment works on the principle that …

Intraoperative Quantification Of Bone Perfusion In Lower Extremity Injury Surgery, Xinyue Han

Dartmouth College Ph.D Dissertations

Orthopaedic surgery is one of the most common surgical categories. In particular, lower extremity injuries sustained from trauma can be complex and life-threatening injuries that are addressed through orthopaedic trauma surgery. Timely evaluation and surgical debridement following lower extremity injury is essential, because devitalized bones and tissues will result in high surgical site infection rates. However, the current clinical judgment of what constitutes “devitalized tissue” is subjective and dependent on surgeon experience, so it is necessary to develop imaging techniques for guiding surgical debridement, in order to control infection rates and to improve patient outcome.

In this thesis work, computational …

Neural Correlates Of Post-Traumatic Brain Injury (Tbi) Attention Deficits In Children, Meng Cao

Dissertations

Traumatic brain injury (TBI) in children is a major public health concern worldwide. Attention deficits are among the most common neurocognitive and behavioral consequences in children post-TBI which have significant negative impacts on their educational and social outcomes and compromise the quality of their lives. However, there is a paucity of evidence to guide the optimal treatment strategies of attention deficit related symptoms in children post-TBI due to the lack of understanding regarding its neurobiological substrate. Thus, it is critical to understand the neural mechanisms associated with TBI-induced attention deficits in children so that more refined and tailored strategies can …

Dual Color Optogenetic Control For Analyzing Cardiac Function In Drosophila, Jiantao Zhu

McKelvey School of Engineering Theses & Dissertations

Prolonged consumption of carbohydrate-rich diets and immobile lifestyles frequently cause metabolic disorders and obesity and, as a result, may lead to progressive heart dysfunction among broad social groups of the population. Drosophila melanogaster serves as an essential model organism in cardiovascular disease research due to conserved physiological and genomic traits shared with humans, its genetic and molecular toolbox versatility, and cost-effective maintenance. Here, we combine optogenetics and optical coherence tomography to study cardiovascular function in D. melanogaster. A new optogenetic pacing system has been developed, employing a transgenic line carrying two opsins: ChR2 and NpHR2.0. A custom-built hardware setup …

Synthesis, Radiolabeling And Evaluation Of A Suite Of Tracers With 44Sc For Detecting Extracellular Dna, Zhiyao Li

McKelvey School of Engineering Theses & Dissertations

Neutrophil extracellular traps involve the rapid translocation of DNA to the outside of the cell under certain stimuli. This structure forms a fibrous network that is able to limit the spread of pathogens and to kill microorganisms. It has also been shown to be present in various pathological processes such as inflammation, autoimmune diseases, and cancer metastasis. Currently, the formation process of NETs in vivo is being extensively studied. However noninvasive detection and quantitation has yet to be achieved. A class of PET tracers are described here that consists of a DNA dye as the backbone that is labeled with …

A Comparison Of Optical Measurement Methods For The Growth Of S. Cerevisiae, Jackson Black

Chemical Engineering Undergraduate Honors Theses

Genetic engineering of living organisms provides the opportunity to express and harvest different proteins from cell surfaces. Yeast (S. cerevisiae) is one such organism and is capable of being grown on an industrial scale. Cellular concentration is an important parameter to monitor while fermentation processes are underway, in order to control the environment inside the growth medium and maximize yields. Spectrophotometry is a conventional method for measuring concentration, but is limited by a narrow absorbance range, and the need for on-site periodic sampling. A continuous method of measurement, as provided by Bug Labs BE2100 non-invasive biomass monitor, would …

Computational Design Of Fiber-Optic Probes For Biosensing, Suwarna Karna

Electrical Engineering Theses

This thesis presents a study on the optical characteristics of hollow-core photonic crystal fibers (HC-PCFs) with a band gap cladding structure and their applications in optical fiber sensing. This 800B HC-PCF exhibited excellent optical properties and has a flexible structure, which makes them suitable for a wide range of industrial applications. Finite element simulations and structural optimization designs were conducted using the surface plasmon resonance (SPR) technique to determine the optimal performance parameters of the 800B HC-PCF. The fiber was further modified using the SPR technique to improve its practical detection capabilities. The performance of the modified fiber was observed …

Efficient Scopeformer: Towards Scalable And Rich Feature Extraction For Intracranial Hemorrhage Detection Using Hybrid Convolution And Vision Transformer Networks, Yassine Barhoumi

Theses and Dissertations

The field of medical imaging has seen significant advancements through the use of artificial intelligence (AI) techniques. The success of deep learning models in this area has led to the need for further research. This study aims to explore the use of various deep learning algorithms and emerging modeling techniques to improve training paradigms in medical imaging. Convolutional neural networks (CNNs) are the go-to architecture for computer vision problems, but they have limitations in mapping long-term dependencies within images. To address these limitations, the study explores the use of techniques such as global average pooling and self-attention mechanisms. Additionally, the …

Improving The Reliability And Accessibility Of Ct Perfusion Imaging In Acute Ischemic Stroke, Kevin J. Chung

Electronic Thesis and Dissertation Repository

CT perfusion (CTP) imaging is a validated treatment decision support tool in acute ischemic stroke. Automated analysis of CTP cerebral blood flow (CBF) and Tmax maps produces estimates of ischemic core and penumbra volumes used to determine target mismatch profiles for treatment. However, availability and utilization of CTP is low due to diagnostic variability between CTP software and technical, logistical, and radiation dose considerations that may limit its routine adoption. The objective of this doctoral research was to improve the reliability and accessibility of CTP by (1) improving diagnostic agreement between CTP software, (2) enabling perfusion imaging with standard acute …

Using Paired-Agent Imaging To Track Changes In Head And Neck Cancers After Undergoing Photodynamic Therapy Treatment, Reeham M. Choudhury

Dartmouth College Master’s Theses

Head and neck cancers affect thousands of people across the world, and photodynamic therapy (PDT) has been shown to have great potential to treat said cancers in a noninvasive manner. However, imaging head and neck cancers has been difficult, and molecular changes caused by PDT are not well-understood. Therefore, we propose the use of paired-agent imaging (PAI) to track changes in these cancers after after PDT treatment. For these studies, we primarily used benzoporphyrin derivative monoacid (BPD) for our photosensitizer, which is activated by a 690 nm laser. We first looked at changes in EGFR expression in vitro, and …

A Wearable Fiber-Free Optical Sensor For Continuous Measurements Of Cerebral Blood Flow And Oxygenation, Xuhui Liu

Theses and Dissertations--Biomedical Engineering

Wearable technologies for continuous monitoring of cerebral hemodynamics in freely behaving subjects not only advance our understanding of cognitive processing and adaptive behavior, but also provide vital information for diagnosis and therapeutic assessment of cerebral diseases associated with hypoxia/ischemia. Wearable near-infrared diffuse optical techniques have been used at the bedside to probe deep cerebral hemodynamics, including near-infrared spectroscopy (NIRS) for cerebral oxygenation measurement and diffuse correlation spectroscopy (DCS) for cerebral blood flow (CBF) measurement, respectively. However, most systems are relatively large and expensive, and use rigid fiber-optic probes that significantly constrain subject’s movement. A novel, wearable, fiber-free diffuse speckle contrast …

Verification Of Proton Range Predictions In Proton Treatment Planning Using X-Ray Ct Or Proton Ct Imaging, Nicholas S. Yee

Graduate Research Theses & Dissertations

The objective of this paper is to compare the range errors for two treatment plans; one using x-ray CT and the other using proton CT for calculating dose distributions in an animal tissue phantom. We shot 150 MeV proton beam through a meat phantom to a film stack to measure the exponential drop of dose at the Bragg peak until zero dose remained. Plotting the depth dose curves and performing gamma analyses are two ways to quantify the proton range errors when comparing them to depth dose curves from film measurements in the phantom. The depth dose curves give us …

Measurement Of Fluid Movement Throughout The Brain Via Multiple Magnetic Resonance Imaging Techniques During High-Definition Transcranial Direct Current Stimulation, Jack W. Beaty Mr

Dissertations and Theses

Transcranial Direct Current Stimulation (tDCS) is a non-invasive method of neuromodulation with applications in neuroscience, clinical care, and biomedical engineering. tDCS has been well established as a safe method of applying low amplitude current between two or more electrodes to alter excitation thresholds and neuroplasticity. Recently, in-vitro and clinical studies have suggested that DC stimulation can induce a transient, polarity-specific, effect of increased water exchange across the blood-brain barrier (BBB). The electroosmotic effect, the proposed phenomenon driving water exchange, is a biophysical response of charged ions moving across an oppositely-charged surface, i.e., the tight junction, when subjected to an electric …

Advancing Fluorescent Contrast Agent Recovery Methods For Surgical Guidance Applications, Brook Kennedy Byrd

Dartmouth College Ph.D Dissertations

Fluorescence-guided surgery (FGS) utilizes fluorescent contrast agents and specialized optical instruments to assist surgeons in intraoperatively identifying tissue-specific characteristics, such as perfusion, malignancy, and molecular function. In doing so, FGS represents a powerful surgical navigation tool for solving clinical challenges not easily addressed by other conventional imaging methods. With growing translational efforts, major hurdles within the FGS field include: insufficient tools for understanding contrast agent uptake behaviors, the inability to image tissue beyond a couple millimeters, and lastly, performance limitations of currently-approved contrast agents in accurately and rapidly labeling disease. The developments presented within this thesis aim to address such …

The Role Of Generative Adversarial Networks In Bioimage Analysis And Computational Diagnostics., Ahmed Naglah

Electronic Theses and Dissertations

Computational technologies can contribute to the modeling and simulation of the biological environments and activities towards achieving better interpretations, analysis, and understanding. With the emergence of digital pathology, we can observe an increasing demand for more innovative, effective, and efficient computational models. Under the umbrella of artificial intelligence, deep learning mimics the brain’s way in learn complex relationships through data and experiences. In the field of bioimage analysis, models usually comprise discriminative approaches such as classification and segmentation tasks. In this thesis, we study how we can use generative AI models to improve bioimage analysis tasks using Generative Adversarial Networks …

Development Of Optical Coherence Tomography Angiography System For Mouse Eye Imaging And Measurement Of Vasodilation, Yilin Li

McKelvey School of Engineering Theses & Dissertations

Optical coherence tomography angiography (OCTA) is broadly known as a non-invasive technology that allows examining the retinal and choroidal vasculatures, alternative to fluorescein angiography. In this study, we have developed an optical coherence tomography (OCT) system for imaging the mouse eye. We measure the retinal thickness, which is 216.53um. We apply OCTA to characterize the quantitative change in vessel diameter and the perfusion density of the retina after the wild-type mice are administered the adenosine or inhale carbon dioxide. Comparing the images acquired one minute and 5 minutes after the injection or CO₂ inhalation with the baseline, distinct changes …

Iron Nanoparticles For Magnetic Imaging Applications, Aleia Williams

Masters Theses

Extensive research on iron oxide nanoparticles for various applications including nanomedicine, energy applications, environmental remediation, and magnetic imaging have previously been performed. Many are currently FDA approved as magnetic resonance imaging contrast agents and tracers for magnetic particle imaging applications. Magnetic properties of such materials are crucial to obtain good contrast and resolution. However, studies have shown the magnetic properties of iron oxide nanoparticles are less in comparison to those found in pure iron nanoparticle.

This research involves the synthesis and characterization of iron nanoparticles for applications in magnetic resonance imaging contrast agents, magnetic particle imaging tracers, and therapeutic agents …

Seeing The Big Picture: System Architecture Trends In Endoscopy And Led-Based Hyperspectral Subsystem Intergration, Craig M. Browning

<strong> Theses and Dissertations </strong>

Early-stage colorectal lesions remain difficult to detect. Early development of neoplasia tends to be small (less than 10 mm) and flat and difficult to distinguish from surrounding mucosa. Additionally, optical diagnosis of neoplasia as benign or malignant is problematic. Low rates of detection of these lesions allow for continued growth in the colorectum and increased risk of cancer formation. Therefore, it is crucial to detect neoplasia and other non-neoplastic lesions to determine risk and guide future treatment. Technology for detection needs to enhance contrast of subtle tissue differences in the colorectum and track multiple biomarkers simultaneously. This work implements one …

Development And Validation Of A Three-Dimensional Optical Imaging System For Chest Wall Deformity Measurement, Nahom Kidane

Electrical & Computer Engineering Theses & Dissertations

Congenital chest wall deformities (CWD) are malformations of the thoracic cage that become more pronounced during early adolescence. Pectus excavatum (PE) is the most common CWD, characterized by an inward depression of the sternum and adjacent costal cartilage. A cross-sectional computed tomography (CT) image is mainly used to calculate the chest thoracic indices. Physicians use the indices to quantify PE deformity, prescribe surgical or non-surgical therapies, and evaluate treatment outcomes. However, the use of CT is increasingly causing physicians to be concerned about the radiation doses administered to young patients. Furthermore, radiographic indices are an unsafe and expensive method of …

Image-Based Cancer Diagnosis Using Novel Deep Neural Networks, Hosein Barzekar

Theses and Dissertations

Cancer is the major cause of death in many nations. This serious illness can only be effectivelytreated if it is diagnosed early. In contrast, biomedical imaging presents challenges to both clinical institutions and researchers. Physiological anomalies are often characterized by modest modifications in individual cells or tissues, making them difficult to detect visually. Physiological anomalies are often characterized by slight abnormalities in individual cells or tissues, making them difficult to detect visually. Traditionally, anomalies are diagnosed by radiologists and pathologists with extensive training. This procedure, however, demands the participation of professionals and incurs a substantial expense, making the classification of …

Neroimaging Of Brain Activaion Using Diffuse Optical Tomography, Jingyu Huang

USF Tampa Graduate Theses and Dissertations

This research has two parts. The first part focuses on the use of non-invasive imaging technique, diffuse optical tomography (DOT), to study the brain activation during the stimulation in the clinical room. It further extends the application of DOT by using it to monitor the hemodynamic response during the TMS stimulation in different parameters. Diffuse optical tomography (DOT) is based on NIR light that exploits the relative transparency of biological tissue. The part two and three extends the application in the hospital for delirium patient study and arm muscle dystrophy by adding the sources and detectors to monitor the brain …