Structural Characterization Of Cardiomyocyte Microenvironment In Murine Myocardium By Multimodal Stimulated Emission Depletion Microscopy, Zhao Zhang

All Dissertations

Cardiomyopathy, a disease of the heart muscle, is characterized by structural and functional abnormalities of the myocardium, in the absence of coronary artery disease, hypertension, valvular disease or congenital heart disease. In 2020, there were approximately 6.11 million prevalent cases of cardiomyopathy and myocarditis, and 0.37 million related deaths worldwide. Many affected individuals are asymptomatic, and chronically treated patients are at risk of heart failure. Within the myocardium, cardiomyocytes reside in a complex and dynamic extracellular matrix (ECM), consisting of basement membrane and interstitial matrix. The interactions between cardiomyocytes and myocardial ECM play a critical role in maintaining cardiac geometry …

Assessing Chondrocyte Viability Of Articular Cartilage Using Label-Free Imaging Methods, Hongming Fan

All Dissertations

ABSTRACT

Articular cartilage covers the ends of bones, providing a protective layer that can endure forces during movement. Chondrocytes, the only cell type found in articular cartilage, produce collagen fibers and proteoglycans that maintain the extracellular matrix (ECM). Cartilage damage impairs chondrocytes and their ability to maintain tissue stability. There are various factors that can cause cell death, which can be broadly classified into two categories: programmed cell death (apoptosis) and non-programmed cell death (necrosis). The consequences of cell death can have significant impacts on the extracellular matrix (ECM). The ECM is a complex network of proteins and carbohydrates that …

An Improved Saliency Map With Trustworthiness For Localizing Abnormalities In Medical Imaging, Nolan C. Skelly

Theses and Dissertations

Saliency maps are a widely used methodology to make deep learning models more interpretable. They provide post-hoc explanations through identification of the most pertinent areas of an input medical image. These techniques have been assessed based on 1) localization utility, 2) sensitivity to model weight randomization, 3) repeatability, and 4) reproducibility. Ten saliency map techniques will be tested, Grad, Smooth Grad, Integrated Gradients, Smooth Integrated Gradients, XRAI, Grad-CAM, Guided Backpropagation, Guided GradCAM, GradCAM++, and ScoreCAM. The neural networks used to predict and read medical information require a reliable solution to provide medical practitioners intelligible results. Using the information of two, …

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 …

Characterizing Intervertebral Disc Strain Under Dynamic Loading Conditions Using Ultrasound Texture Analysis, Radhika Kulkarni

Discovery Undergraduate Interdisciplinary Research Internship

Herniated discs in the spine are a significant patient burden, with potential links to lower back and leg discomfort and a considerable impact on daily life. These discs, located between spinal vertebrae, are comprised of the annulus fibrosus (AF) and the nucleus pulposus (NP). Herniations happen when the NP protrudes through a full-thickness annular tear, possibly compressing spinal nerves. The mechanical factors underlying herniated discs are poorly understood, necessitating research into these mechanisms and accessible diagnostic techniques. Our study employs high-resolution ultrasound and texture correlation to quantify strain patterns in intervertebral discs during dynamic loading.

A motion segment from the …

Autofluorescence Imaging Of Endogenous Metabolic Cofactors In Response To Cytokine Stimulation Of Classically Activated Macrophages, Shelby N. Bess, Matthew J. Igoe, Abby C. Denison, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Background

Macrophages are one of the most prevalent subsets of immune cells within the tumor microenvironment and perform a range of functions depending on the cytokines and chemokines released by surrounding cells and tissues. Recent research has revealed that macrophages can exhibit a spectrum of phenotypes, making them highly plastic due to their ability to alter their physiology in response to environmental cues. Recent advances in examining heterogeneous macrophage populations include optical metabolic imaging, such as fluorescence lifetime imaging (FLIM), and multiphoton microscopy. However, the method of detection for these systems is reliant upon the coenzymes NAD(P)H and FAD, which …

Don't Fear The Artificial Intelligence: A Systematic Review Of Machine Learning For Prostate Cancer Detection In Pathology, Aaryn Frewing, Alexander B. Gibson, Richard Robertson, Paul Urie, Dennis Della Corte

Faculty Publications

The adoption of whole slide image (WSI) scanners in clinical practice was accelerated by US Food and Drug Administration approval in 2017, which allowed primary pathologic diagnoses to be made on scanned images. Images in the digital domain allow the application of pathology artificial intelligence (AI), including clinical decision support with algorithms performing specific diagnoses.1,2 These algorithms, if trained properly, could go beyond the ability of human observation to detect and quantify features that are not recognizable by human perception.1,3,4

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 …

Scanning Electron Microscopy Analysis Of Murine Renal, Aortic, And Cardiac Tissue, Sarah E. Grev, Luke E. Schepers, Jennifer Anderson, Craig J. Goergen

Discovery Undergraduate Interdisciplinary Research Internship

Scanning electron microscopy (SEM) is a tool that provides detailed insight into objects invisible to the human eye. As the name suggests, an electron beam is used to create an image down to the nanometer scale. The beam focuses on the surface of a sample using lenses in the electron column. In this project, we use SEM to study three types of murine tissue. First, we examine the glomerulus, found in the kidney, that is primarily responsible for filtering blood. Following a left renal vein (LRV) stenosis, SEM is used to observe changes to the glomeruli. Differences in the left …

Prevention And Reversal Of Elastin-Associated And Phosphate-Dependent Arterial Calcification Using Targeted Nanotherapeutics In Pre-Clinical Models, Fatema Tuj Zohora

All Dissertations

Vascular calcification can be life-threatening, involving calcium phosphate crystal deposits in the blood vessels. The calcification in the intimal layer of the arterial wall is usually associated with atherosclerotic plaque build-up that, in the advanced stage, harbors ‘dispersed’ and ‘spotty’ deposits of calcium phosphate crystals in the necrotic core of the plaque. In contrast, medial arterial calcification (MAC) can form independently of atherosclerosis and appears as ‘Railroad-like’ calcific deposits along degraded elastin lamellae in the medial layer of arteries. The mechanisms of such elastin-associated medial arterial calcification and potential therapies are the key concerns of this dissertation. MAC is common …

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 …

List Of 121 Papers Citing One Or More Skin Lesion Image Datasets, Neda Alipour

Other resources

No abstract provided.

Mechanisms Of Theta Burst Transcranial Ultrasound Induced Plasticity In The Human Motor Cortex, Yazan Shamli Oghli, Talyta Grippe, Tarun Arora, Tasnuva Hoque, Ghazaleh Darmani, Robert Chen

Department of Medicine Faculty Papers

BACKGROUND: Transcranial ultrasound stimulation (TUS) is a novel non-invasive brain stimulation technique with high depth penetrance and spatial resolution. Theta-burst TUS (tbTUS) is a plasticity-inducing protocol which increases motor cortical excitability for up to 30 min following 80s of sonication. While this protocol may have therapeutic potential for the treatment of psychiatric and neurological disorders, the mechanisms of action of TUS remain unclear.

OBJECTIVE: We conducted the first pharmacological study to examine the mechanisms of TUS in human primary motor cortex. By administering brain-active drugs with known mechanisms of action, we aimed to elucidate the mechanisms of tbTUS.

METHODS: Fourteen …

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 …

Noninvasively Monitoring Of Cerebral Blood Flow In Piglet Models Of Graded Hemorrhage And Hypoxic Ischemic Brain Injury Using Diffuse Correlation Spectroscopy And Near-Infrared Spectroscopy, Randolph Sinahon, Danielle Shoshany, Shadi Malaeb, Mert Deniz Polat, Meltem Izzetoglu, Kurtulus Izzetoglu

St. Chris Research Day

No abstract provided.

Cerebral Blood Flow Measured By Diffuse Correlation Spectroscopy For Monitoring Depth Of Anesthesia In Piglets, Mert Deniz Polat, Kurtulus Izzetoglu, Randolph Sinahon, Meltem Izzetoglu, Shadi Malaeb

St. Chris Research Day

No abstract provided.

Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Geobacter sulfurreducens are anaerobic bacteria capable of making electrical contacts with other organisms and extracellular electron acceptors. The challenge of imaging live Geobacter bacteria is maintaining anaerobic conditions during the imaging process. In this thesis, we augment a single-molecule localization microscope (SMLM) with a home-built anaerobic imaging chamber and use constant argon bubbling to maintain oxygen-free imaging conditions. To validate the imaging protocol, we use the transient binding of Nile red to resolve the spherical morphology of lipid-coated glass spheres with nanoscale resolution. However, when imaging Geobacter, the distribution of Nile red localizations is non-uniform, both between different cells …

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

McKelvey School of Engineering Graduate Student 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 …

Development Of A Multispectral Vis-Swir Imaging Modality For Cutaneous Water Assessment, Quinlan Mcgrath

McKelvey School of Engineering Graduate Student Theses & Dissertations

Inflammatory skin diseases are estimated to impact 20% of the global population and are the fourth leading cause of nonfatal disability worldwide. Diagnosis and management are predominantly based on clinician visual assessment of disease related changes in skin morphology. The qualitative nature of this method can result in misdiagnosis and underdiagnoses of treatable diseases. There persists systematic undertreatment of skin of color patients given the more subtle presentation of erythema against pigmented skin. There exists a clinical need for a quantitative and objective inflammation assessment tool that meets the needs of a diverse patient population. The accumulation of interstitial fluid …

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 …

Light Sheet Microscopy Incubation Design And Control Scheme, Venkatanathan Kidambi

Honors Scholar Theses

The focus of the following paper is the development of a light sheet or selective plane illumination microscopy (LSM / SPIM) platform to support long duration three dimensional imaging of various cells and tissues. This paper describes the complete design and fabrication process behind the prototype, including a definition of light sheet microscopy and its differences from confocal microscopy, as well as existing open source selective plane microscopy literature and designs. The complete engineering design process as applied to the microscope design is described in detail. Specifically, this paper will focus on the development of an incubation chamber for light …

Automated Segmentation Of Autofluorescence Lifetime Images Using A Convolutional Neural Network, Nicole Hooten

Biomedical Engineering Undergraduate Honors Theses

Chronic wounds affect nearly 1 out of every 50 people in the United States, decreasing quality of life and putting people with potential comorbidities at high risk for obtaining an infection. Wound healing progress in clinical settings is measured by tracking wound size and there are currently no non-invasive, quantitative measurement techniques. Previous studies have proposed nicotinamide adenine dinucleotide (NADH) autofluorescence lifetime (FLIM) imaging of the wound edge as a method to quantify the wound healing process by connecting the role of NADH in cellular metabolism to wound healing stage. However, evaluation of FLIM images is heavily subjective, as a …

Correlation Of Intracellular Metabolites With Optical Metabolic Imaging In Polarized Macrophages As Indicators Of Metabolic Reprogramming, Abby Claire Denison, Shelby Bess

Biomedical Engineering Undergraduate Honors Theses

Macrophages are a type of immune cell that are characterized by their ability to differentiate into various active phenotypes based on environmental stimuli. They can generally be classified as one of two extremes: inflammatory/M1 or wound-healing/M2. Macrophage populations in vivo, however, are rarely homogenous, and since macrophages play vital roles in the immune response, particularly in the context of the tumor microenvironment (TME), it’s important to be able to investigate and understand heterogenous macrophage populations to develop more effective treatments. Recently, autofluorescence imaging such as multiphoton microscopy and fluorescence lifetime imaging microscopy (FLIM) of metabolic cofactors NADH and FAD have …

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

McKelvey School of Engineering Graduate Student 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 …

Portable Diffuse Reflectance Spectroscopy For Non-Invasive And Quantitative Assessment Of The Parathyroid Glands Viability During Surgery, Mark Romine, Linh Luong, Alex Moazzen, Katie Cho, Paul Lee

Symposium of Student Scholars

Portable Diffuse Reflectance Spectroscopy for Non-invasive and Quantitative Assessment of the Parathyroid Glands Viability During Surgery

Mark Romine, Linh Luong, Alex Moazzen, Katie Cho and Paul Lee

The parathyroid glands (PTGs) are responsible for the regulation of calcium levels in the blood by secreting a parathyroid hormone. This parathyroid hormone then regulates the body’s absorption, storage, and secretion of calcium, which can directly affect the way muscles and nerves operate. PTGs are often at risk of damage, or accidental removal during thyroid surgeries, because it is challenging to identify PTGs and to determine their viability. Current methods of visual inspections …

Wireless, Handheld Diffuse Reflectance Spectroscopy To Quantify Tissue Microvascular Hemodynamics, Linh Luong, Alex Moazzen, Mark Romine, Katie Cho, Paul Lee

Symposium of Student Scholars

Diffuse Reflectance Spectroscopy (DRS) is a non-invasive optical method to characterize tissue optical properties for disease diagnosis and health monitoring. Two optical fibers are often used in a DRS system: one to deliver light to the tissue and the other to gather diffuse reflectance spectra, which provide quantitative details about the structure and composition of the tissue. The conventional DRS system, however, is expensive, bulky, and composed of fragile optical fibers and multiple electrical connections. Here we propose to build a wireless, handheld, and fiber-less diffuse optical spectroscopy system. Unfortunately, the diffusion approximation utilized for data analysis of the conventional …

Enhancement Of Deep Learning Protein Structure Prediction, Ruoming Shen

Modeling, Simulation and Visualization Student Capstone Conference

Protein modeling is a rapidly expanding field with valuable applications in the pharmaceutical industry. Accurate protein structure prediction facilitates drug design, as extensive knowledge about the atomic structure of a given protein enables scientists to target that protein in the human body. However, protein structure identification in certain types of protein images remains challenging, with medium resolution cryogenic electron microscopy (cryo-EM) protein density maps particularly difficult to analyze. Recent advancements in computational methods, namely deep learning, have improved protein modeling. To maximize its accuracy, a deep learning model requires copious amounts of up-to-date training data.

This project explores DeepSSETracer, a …

Image Analysis Methodology For Evaluating Coating Uniformity Of Drug-Coated Angioplasty Balloons, Allison Dobson Zieschang

LSU Master's Theses

Percutaneous transluminal balloon angioplasty (PTA) is a surgical procedure to treat peripheral artery disease, but restenosis causes suboptimal outcomes in many patients. Drug-coated angioplasty balloons (DCBs) were developed to reduce the risk of restenosis by delivering anti-proliferative drugs to the lesion. The efficacy of DCBs depends on factors like drug loading and drug release rate, both of which are directly impacted by the coating uniformity. This thesis evaluates the uniformity of DBCs using fluorescence microscopy, scanning electron microscopy (SEM), qualitative analysis, and an image processing algorithm. Uniformity was quantified by three measurements: histogram standard deviation, histogram percentage of coverage, and …