Biomedical Engineering and Bioengineering Commons^™

Development Of High-Speed Photoacoustic Imaging Technology And Its Applications In Biomedical Research, Yun He

McKelvey School of Engineering Theses & Dissertations

Photoacoustic (PA) tomography (PAT) is a novel imaging modality that combines the fine lateral resolution from optical imaging and the deep penetration from ultrasonic imaging, and provides rich optical-absorption–based images. PAT has been widely used in extracting structural and functional information from both ex vivo tissue samples to in vivo animals and humans with different length scales by imaging various endogenous and exogenous contrasts at the ultraviolet to infrared spectrum. For example, hemoglobin in red blood cells is of particular interest in PAT since it is one of the dominant absorbers in tissue at the visible wavelength.The main focus of …

Three-Dimensional Image Reconstruction In Transcranial Photoacoustic Computed Tomography, Joemini Poudel

McKelvey School of Engineering Theses & Dissertations

Photoacoustic computed tomography (PACT) is an emerging imaging modality that exploitsoptical contrast and ultrasonic detection principles to form images of the photoacousticallyinduced initial pressure distribution within tissue. The PACT reconstruction problemcorresponds to an inverse source problem in which the initial pressure distribution is recoveredfrom measurements of the radiated pressure wavefield. A major challenge in transcranialPACT brain imaging is compensation for aberrations in the measured data due to the presenceof the skull. Ultrasonic waves undergo absorption, scattering and longitudinal-to-shear wavemode conversion as they propagate through the skull. To properly account for these effects, awave-equation-based inversion method should be employed that can …

Rhodococcus Opacus Pd630 Genetic Tool Development To Enable The Conversion Of Biomass, Drew Michael Delorenzo

McKelvey School of Engineering Theses & Dissertations

The discovery of fossil fuels facilitated a new era in human history and allowed many firsts, such as the mass production of goods, the ability to travel and communicate long distances, the formation of population dense cities, and unprecedented improvements in quality of life. Alternative sources of energy and chemicals are needed, however, as hydrocarbon reserves continue to deplete and the effects of burning fossils on the planet become better understood. Lignocellulosic biomass is the most abundant raw material in the world and a viable alternative to petroleum-derived products. The pre-treatment of lignocellulose (e.g., thermocatalytic depolymerization, enzymatic hydrolysis, pyrolysis, etc.) …

Wheelchair Propulsion For Everyday Manual Wheelchair Users: Repetition Training And Machine Learning-Based Monitoring, Pin-Wei Chen

Arts & Sciences Electronic Theses and Dissertations

Upper limb pain and injuries are prevalent among manual wheelchair users and can restrict their participation and daily activities. Due to the high repetition and force in wheelchair propulsion, chronic wheelchair propulsion has been linked to the risk of upper limb pain and injury. Prevention of upper limb pain and injury is a high priority in wheelchair-related research. Decades of research in wheelchair propulsion biomechanics have led to clinical practice guidelines (CPG). Unfortunately, a decade after the publication of the CPG, CPG-recommended propulsion is still uncommon. Hence, for the first aim, a randomized controlled trial pilot study with two groups …

Ph-Sensitive Oxygen Release Microspheres To Enhance Cell Survival In Ischemic Condition, Zhongting Liu

McKelvey School of Engineering Theses & Dissertations

Ischemic diseases such as myocardial infarction, stroke and limb ischemia are severe cardiovascular diseases with high rate of death and millions of people suffered from these diseases. Under ischemic environment, cells die due to deficient supply of nutrient and oxygen. To regenerate ischemic tissues, stem cell therapy is a promising approach because stem cells can differentiate into cells necessary for the regeneration. However, stem cell therapy has limitations. For example, few cells can survive under harsh ischemic environment. To enhance stem cells survival, implantation of oxygen release microspheres to sustained supply cells with oxygen represents an effective strategy. Previously, our …

Multi-Dimensional Extension Of The Alternating Minimization Algorithm In X-Ray Computed Tomography, Jingwei Lu

McKelvey School of Engineering Theses & Dissertations

X-ray computed tomography (CT) is an important and effective tool in medical and industrial imaging applications. The state-of-the-art methods to reconstruct CT images have had great development but also face challenges. This dissertation derives novel algorithms to reduce bias and metal artifacts in a wide variety of imaging modalities and increase performance in low-dose scenarios. The most widely available CT systems still use the single-energy CT (SECT), which is good at showing the anatomic structure of the patient body. However, in SECT image reconstruction, energy-related information is lost. In applications like radiation treatment planning and dose prediction, accurate energy-related information …

Multi-Dimensional Extension Of The Alternating Minimization Algorithm In X-Ray Computed Tomography, Jingwei Lu

McKelvey School of Engineering Theses & Dissertations

X-ray computed tomography (CT) is an important and effective tool in medical and industrial

imaging applications. The state-of-the-art methods to reconstruct CT images have had

great development but also face challenges. This dissertation derives novel algorithms to

reduce bias and metal artifacts in a wide variety of imaging modalities and increase performance

in low-dose scenarios.

The most widely available CT systems still use the single-energy CT (SECT), which is

good at showing the anatomic structure of the patient body. However, in SECT image

reconstruction, energy-related information is lost. In applications like radiation treatment

planning and dose prediction, accurate energy-related information …

A Modular Approach For Modeling, Detecting, And Tracking Freezing Of Gait In Parkinson Disease Using Inertial Sensors, Prateek Gundannavar Vijay

McKelvey School of Engineering Theses & Dissertations

Parkinson disease, the second most common neurodegenerative disorder, is caused by the loss of dopaminergic subcortical neurons. Approximately 50% of people with Parkinson disease experience freezing of gait (FOG), a brief, episodic absence or marked reduction of forward progression of the feet despite the intention to walk. FOG causes falls and is resistant to medication in more than 50% of cases. FOG episodes can often be interrupted by mechanical interventions (e.g., a verbal reminder to march), but it is often not practical to apply these interventions on demand (e.g., there is not usually another person to detect an FOG episode …

Joint Reconstruction For Single-Shot Edge Illumination Phase-Contrast Tomography (Eixpct), Yujia Chen

McKelvey School of Engineering Theses & Dissertations

Edge illumination X-ray phase-contrast tomography (EIXPCT) is an emerging X-ray phasecontrast tomography technique for estimating the complex-valued X-ray refractive index distribution of an object with laboratory-based X-ray sources. Conventional image reconstruction approaches for EIXPCT require multiple images to be acquired at each tomographic view angle. This contributes to prolonged data-acquisition times and elevated radiation doses, which can hinder in vivo applications. In this dissertation, a new “single-shot” method without restrictive assumptions related to the object, imaging geometry or hardware is proposed for joint reconstruction (JR) of the real and imaginary-valued components of the refractive index distribution from a tomographic data …

Metabolic Engineering Of Cyanobacteria For Production Of Chemicals, Po-Cheng Lin

McKelvey School of Engineering Theses & Dissertations

Concerns over the impact of climate change caused by CO2 emission have driven the research and development of renewable energies. Microbial production of chemicals is being viewed as a feasible approach to reduce the use of fossil fuels and minimize the impact of climate change. With recent advances in synthetic biology, microorganisms can be engineered to synthesize petroleum-based chemicals and plant-derived compounds. Cyanobacteria are photosynthetic prokaryotes that use only sunlight, CO2, and trace minerals for growth. Compared to other microbial hosts, cyanobacteria are attractive platforms for sustainable bioproduction, because they can directly convert CO2 into products. However, the major challenge …

Understanding Excitation Energy Quenching In Isia, Hui-Yuan Steven Chen

McKelvey School of Engineering Theses & Dissertations

Cyanobacteria are photoautotrophic organisms that contribute a significant amount of global primary productivity. They are found in freshwater, marine and even some extremely severe environments. Among those environments, iron deficiency is one of the most common stress conditions in cyanobacterial habitats. To survive, cyanobacteria have evolved and developed several strategies to alleviate the damage caused by iron deficiency.

Iron stress-inducible protein (IsiA) is a chlorophyll-binding membrane protein found in cyanobacteria grown in iron-deficient conditions. During the past decades, considerable effort has been put on understanding how IsiA functions to help cyanobacteria survive iron deficiency. It has been reported that IsiA …

Metabolic Engineering Of Cyanobacteria For Production Of Chemicals, Po-Cheng Lin

McKelvey School of Engineering Theses & Dissertations

Concerns over the impact of climate change caused by CO2 emission have driven the research and development of renewable energies. Microbial production of chemicals is being viewed as a feasible approach to reduce the use of fossil fuels and minimize the impact of climate change. With recent advances in synthetic biology, microorganisms can be engineered to synthesize petroleum-based chemicals and plant-derived compounds. Cyanobacteria are photosynthetic prokaryotes that use only sunlight, CO2, and trace minerals for growth. Compared to other microbial hosts, cyanobacteria are attractive platforms for sustainable bioproduction, because they can directly convert CO2 into products. However, the major challenge …

Mechanosensitive Epithelial Cell Scattering And Migration On Layered Matrices, Christopher Michael Walter

McKelvey School of Engineering Theses & Dissertations

Epithelial cells form multi-layered tissue scaffolding that makes up every organ in the body. Along with epithelial cells, the basement membrane (BM) and connective tissue are composed of various proteins that sculpt the organs and protect them from foreign macromolecules. Epithelial cells respond to various cues, both chemical and mechanical, from their surrounding matrices to aid in maintenance and repair of these layers through degradation and deposition of extracellular matrix (ECM) proteins. In cancer progression, epithelial cells lose their normal function of supporting tissue structure and instead adopt more aggressive behaviors through an epithelial-to-mesenchymal transition (EMT) of their cellular traits. …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available. Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …

Quantitatively Studying Tissue Damage In Multiple Sclerosis Using Gradient Recalled Echo Mri Sequences, Biao Xiang

Arts & Sciences Electronic Theses and Dissertations

Multiple Sclerosis (MS) is an unpredictable, often disabling disease of the central nervous system (CNS) that disrupts the flow of information within the brain, and between the brain the body. MS is the most common progressive neurologic disease of young adults, affecting approximately 2.3 million people worldwide. It is estimated that more than 700,000 individuals are affected by MS in United States. While MS has been studied for decades, the cause of it is still not definite and a fully effective treatment for MS is not yet available.

Magnetic resonance imaging (MRI) has been used extensively in MS diagnosis and …

Preclinical Imaging Of Multiple Myeloma Therapy Response, Deep Hathi

McKelvey School of Engineering Theses & Dissertations

Multiple myeloma (MM) is a debilitating hematologic malignancy of terminally differentiated plasma cells in the bone marrow (BM). Advances in therapeutic regimens and the use of autologous stem cell transplantation have significantly improved survival rates and quality of life in patients. However, the disease remains incurable, with shorter, successive remission cycles following relapse. To reduce systemic, off-target toxicity and improve quality of life, there is a need for improved stratification of responding patients. Identification of specific, noninvasive, imaging biomarkers that correlate to therapeutic efficacy is an attractive strategy for stratifying responding patients, since the use of positron emission tomography (PET), …

A High-Throughput Screening Platform For In Vitro Elastic Fiber Production And The Mass Transport Properties Of The Elastic Fiber Compromised Arterial Wall, Austin John Cocciolone

McKelvey School of Engineering Theses & Dissertations

Elastin comprises nearly 50% of the wall in large elastic arteries and has a broad variety of physiological roles. As a structural extracellular matrix protein, elastin is responsible for the reversible elasticity in large arties that dampens pulsatile flow and ultimately reduces the workload on the heart. Structural compromise to the elastic fiber network is apparent in the elastin genetic disorders, supravalvular aortic stenosis and autosomal dominant cutis laxa-1, and acquired elastin disorders including hypertension, atherosclerosis, artery calcification, aneurysms, diabetes, and obesity. All of these disorders lead to an increased incidence of cardiovascular related death and the compromised elastic fiber …

Approaches To Understanding The Function Of Intrinsic Activity And Its Relationship To Task-Evoked Activity In The Human Brain, Dohyun Kim

McKelvey School of Engineering Theses & Dissertations

Traditionally neuroscience research has focused on characterizing the topography and patterns of brain activation evoked by specific cognitive or behavioral tasks to understand human brain functions. This activation-based paradigm treated underlying spontaneous brain activity, a.k.a. intrinsic activity, as noise hence irrelevant to cognitive or behavioral functions. This view, however, has been profoundly modified by the discovery that intrinsic activity is not random, but temporally correlated at rest in widely distributed spatiotemporal patterns, so called resting state networks (RSN). Studies of temporal correlation of spontaneous activity among brain regions, or functional connectivity (FC), have yielded important insights into the network organization …

Improved Orthopaedic Repairs Through Mechanically Optimized, Adhesive Biomaterials, Stephen Wheeler Linderman

McKelvey School of Engineering Theses & Dissertations

Despite countless surgical advances over the last several decades refining surgical approaches, repair techniques, and tools to treat tendon and tendon-to-bone injuries, we are still left with repair solutions that rely on fairly crude underlying mechanical principles. Musculoskeletal soft tissues have evolved to transfer high loads by optimizing stress distribution profiles across the tissue at each length scale. However, instead of mimicking these natural load transfer mechanisms, conventional suture approaches are limited by high load transfer across only a small number of anchor points within tissue. This leads to stress concentrations at anchor points that often cause repair failure as …

Elucidating The Roles Of Astrocyte-Derived Factors In Recovery And Regeneration Following Spinal Cord Injury, Russell E. Thompson

McKelvey School of Engineering Theses & Dissertations

Central nervous system (CNS) injury often causes some level of long-term functional deficit, due to the limited regenerative potential of the CNS, that results in a decreased quality of life for patients. CNS regeneration is inhibited partly by the development of a glial scar following insult that is inhibitory to axonal growth. The major cell population responsible for the formation this glial scar are astrocytes, which has led to the belief that astrocytes are primarily inhibitory following injury. Recent work has challenged this conclusion, finding that astrocyte reactivity is heterogeneous and that some astrocytes are pro-regenerative following injury. Astrocyte transplantation …

Ultrasound-Guided Optical Techniques For Cancer Diagnosis: System And Algorithm Development, Atahar Kamal Mostafa

McKelvey School of Engineering Theses & Dissertations

Worldwide, breast cancer is the most common cancer among women. In the United States alone, the American cancer society has estimated there will be 271,270 new breast cancer cases in 2019, and 42,260 lives will be lost to the disease. Ultrasound (US), mammography, and magnetic resonance imaging (MRI) are regularly used for breast cancer diagnosis and therapy monitoring. However, they sometimes fail to diagnose breast cancer effectively. These shortcomings have motivated researchers to explore new modalities. One of these modalities, diffuse optical tomography (DOT), utilizes near-infrared (NIR) light to reveal the optical properties of tissue. NIR-based DOT images the contrast …

Regularized Fourier Ptychographic Microscopy, Shiqi Xu

McKelvey School of Engineering Theses & Dissertations

Quantitative phase image (QPI) is a popular microscopy technique for studying cell morphology. Recently, Fourier ptychographic microscopy (FPM) has emerged as a low-cost computational microscopy technique for forming high-resolution wide-field QPI images by taking multiple images from different illumination angles. However, the applicability of FPM to dynamic imaging is limited by its high data requirement. In this thesis, we propose new methods for highly compressive FPM imaging using a data-adaptive sparse coding and an online plug-and-play (PnP) method with non-local priors based on the fast iterative shrinkage/threshold algorithm (FISTA). We validate the proposed method on both simulated and experimental data …

Long-Term, Super-Resolution Imaging Of Amyloid Structures Using Transient Amyloid Binding Microscopy, Tianben Ding, Kevin Spehar, Jan Bieschke, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid fibrils and tangles are signatures of Alzheimer disease, but nanometer-sized aggregation intermediates are hypothesized to be the structures most toxic to neurons. The structures of these oligomers are too small to be resolved by conventional light microscopy. We have developed a simple and versatile method, called transient amyloid binding (TAB), to image amyloid structures with nanoscale resolution using amyloidophilic dyes, such as Thioflavin T, without the need for covalent labeling or immunostaining of the amyloid protein. Transient binding of ThT molecules to amyloid structures over time generates photon bursts that are used to localize single fluorophores with nanometer precision. …