Biomedical Engineering and Bioengineering Commons^™

Using Computer Vision To Track Anatomical Structures During Cochlear Implant Surgery, Nicholas Bach

McKelvey School of Engineering Graduate Student Theses & Dissertations

There is a steep learning curve for surgeons performing cochlear implant surgeries. We aimed to use computer vision to track anatomical features with the goal of helping surgeons perform cochlear implant surgery without damaging the cochlea. We compared nine algorithms in total, seven object tracking algorithms and two optical flow algorithms utilizing the LucasKanade method, on manually created cochlear implant surgery videos to determine the accuracy associated with each. Compared with eight other algorithms, we observed that an iterative pyramidal implementation of the Lucas-Kanade (IPLK) method, implemented through OpenCV, performed the best. The IPLK method had the lowest error rate …

High-Spatial-Resolution Transcriptomic Map Of The Mouse Lymph Node Microenvironment Using Deterministic Barcoding, Archibald Enninful, Yang Liu, Rong Fan

The Yale Undergraduate Research Journal

Spatial transcriptomics is an emerging approach which characterizes gene expression profiles for a more nuanced understanding of biological processes at a tissue level. This offers significant advantages over traditional omics which require the digestion of tissues and subsequent isolation of cells, during which the spatial information is completely lost. Lymph nodes are an integral part of the immune system and an in-depth analysis of its spatial organization will provide useful insights which can be applicable in the development of novel immunotherapies. In this study, the mouse lymph node is characterized using the newly developed microfluidic-based approach, Deterministic Barcoding in Tissue …

Continuous Myoelectric Prediction Of Future Ankle Angle And Moment Across Ambulation Conditions And Their Transitions, Erika V. Zabre-Gonzalez, Lara I. Riem, Philip A. Voglewede, Barbara Silver-Thorn, Sara R. Koehler-Mcnichols, Scott A. Beardsley

Biomedical Engineering Faculty Research and Publications

A hallmark of human locomotion is that it continuously adapts to changes in the environment and predictively adjusts to changes in the terrain, both of which are major challenges to lower limb amputees due to the limitations in prostheses and control algorithms. Here, the ability of a single-network nonlinear autoregressive model to continuously predict future ankle kinematics and kinetics simultaneously across ambulation conditions using lower limb surface electromyography (EMG) signals was examined. Ankle plantarflexor and dorsiflexor EMG from ten healthy young adults were mapped to normal ranges of ankle angle and ankle moment during level overground walking, stair ascent, and …

Characterization Of Application-Driven Sol-Gel Coated Meshes And Composites, Armaghan Naderi

LSU Doctoral Dissertations

Surface engineering is a multi-disciplinary research area that encompasses disciplines such as materials science, chemistry, mechanical engineering, and electrical engineering. Coating is a surface modification technique in surface engineering, applied on the surface of a substrate (i.e., bulk material), to cover/protect it from environmental degradation or to modify/improve surface properties for specific applications. This PhD research presents an in-depth investigation of sol-gel ceramic coatings to modify surface characteristics of bulk materials for two specific applications: 1) antistatic/antidust applications, and 2) biomaterial implant applications.

First, zirconia antistatic thin films on glass substrates, and their application to polymer-based composites, was studied. Zirconia …

Dimensionality Reduction For Classification Of Object Weight From Electromyography, Elnaz Lashgari, Uri Maoz

Psychology Faculty Articles and Research

Electromyography (EMG) is a simple, non-invasive, and cost-effective technology for measuring muscle activity. However, multi-muscle EMG is also a noisy, complex, and high-dimensional signal. It has nevertheless been widely used in a host of human-machine-interface applications (electrical wheelchairs, virtual computer mice, prosthesis, robotic fingers, etc.) and, in particular, to measure the reach-and-grasp motions of the human hand. Here, we developed an automated pipeline to predict object weight in a reach-grasp-lift task from an open dataset, relying only on EMG data. In doing so, we shifted the focus from manual feature-engineering to automated feature-extraction by using pre-processed EMG signals and thus …

Photoacoustic Imaging, Feature Extraction, And Machine Learning Implementation For Ovarian And Colorectal Cancer Diagnosis, Eghbal Amidi

McKelvey School of Engineering Graduate Student Theses & Dissertations

Among all cancers related to women’s reproductive systems, ovarian cancer has the highest mortality rate. Pelvic examination, transvaginal ultrasound (TVUS), and blood testing for cancer antigen 125 (CA-125), are the conventional screening tools for ovarian cancer, but they offer very low specificity. Other tools, such as magnetic resonance imaging (MRI), computed tomography (CT), and positron emission tomography (PET), also have limitations in detecting small lesions. In the USA, considering men and women separately, colorectal cancer is the third most common cause of death related to cancer; for men and women combined, it is the second leading cause of cancer deaths. …

Towards The Discovery Of Prognostic Biomarkers For Glioblastoma Using Resting-State Functional Connectivity, Andy G. S. Daniel

McKelvey School of Engineering Graduate Student Theses & Dissertations

Gliomas are highly diffusive, primary brain tumors. The most malignant form, glioblastoma, has a dismal survival rate: 14-17 months following the current standard of care, which consists of surgery, radiation, and chemotherapy. Insights into the molecular, cellular, and microenvironmental components of glioblastoma have revealed a vast array of factors utilized to support its proliferation, infiltration, and resistance to treatment. Recent advancements have also identified diagnostic and prognostic biomarkers that are now being used to guide treatment planning. However, survival has improved only marginally, thus emphasizing the continued need for novel biomarkers and treatment strategies. Given its delicate location in the …

Mechanisms For Osteoblast And Osteocyte Initiation And Sustainment Of Bone Formation In Young-Adult And Aged Mice, Taylor Lynn Harris

McKelvey School of Engineering Graduate Student Theses & Dissertations

The cellular mechanisms for loading-induced bone formation, from osteocyte mechano-sensation to osteoblast-directed bone formation, are not well understood. Elucidating these mechanisms and identifying any processes that are disrupted in aged mice can aide in the development of new anabolic drugs for treating diseases like osteoporosis. This thesis begins by investigating the genes expressed by osteocytes following loading at an early mechanosensitive (4-hr) timepoint, and later at a bone-forming (day 5) timepoint. We demonstrated increases in Ngf and Wnt1 in osteocyte-enriched intracortical bone by laser capture microdissection and microarray analysis. These results were important in demonstrating the presence of Ngf in …

Quantitative Flow Cytometry-Guided Protein Biomarker Characterization For Translational Proteomics And Precision Medicine, Yingye Fang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Angiogenesis, the growth of blood vessels from pre-existing vasculature, is primarily regulated by vascular endothelial growth factor receptors (VEGFRs). Dysregulated angiogenesis is associated with cancers, obesity, and over 70 vascular diseases. Upregulated VEGFR protein expressions in diseased vasculature are promising biomarkers for predicting clinical outcomes, as indicated by non-quantitative immunohistochemical studies in patients with impaired vascularization or tumor angiogenesis. While the quantitative characterization of VEGFRs is critical in identifying biomarkers for anti-angiogenic therapies, VEGFR biomarker development presents two particular challenges: (1) The invasive tissue biopsy needed limits the amount of VEGFR data that can be collected from both normal and …

Attachment Of Fibrous Materials In Nature And Surgical Repair, Ethan Daniel Hoppe

McKelvey School of Engineering Graduate Student Theses & Dissertations

Mother nature is the ultimate problem solver. Often by brute force and necessity for survival, the organism that has the best solution to a problem is the one to proliferate. One of these problems for which nature provides an elegant solution is the attachment of dissimilar materials. This dissertation explores the strengthening and relaxation of interactions between soft and hard materials, typically with one of the two being fibrous in character, with the goal of identifying strategies for improving the surgical reattachment of tendon to bone. The work begins with a study of the plant Harpagonella palmeri, which the dissertation …

Understanding And Improving Adult Stem Cells For Cartilage Tissue Engineering, Dakota Katz

McKelvey School of Engineering Graduate Student Theses & Dissertations

Articular cartilage allows for near frictionless joint movement; however, when damaged the tissue has very little capacity for self-repair. Tissue engineering can be used to both repair damaged articular cartilage and as an in vitro model for joint disease. Commonly used cell sources for tissue engineering are adipose-derived and bone marrow-derived mesenchymal stem cells (ASCs and MSCs) because they can be patient matched, expand rapidly in culture, and have multipotent differentiation potential. However, donor-to-donor variability of differentiation potential can mask the results of in vitro experiments and ASCs and MSCs only retain their multipotency for a limited number of passages. …

Human Ipsc Tissue-Engineered Cartilage For Disease Modeling Of Skeletal Dysplasia-Causing Trpv4 Mutations, Amanda R. Dicks

McKelvey School of Engineering Graduate Student Theses & Dissertations

Cartilage is essential to joint development and function. However, there is a variety of cartilage diseases, ranging from developmental (e.g., skeletal dysplasias) to degenerative (e.g., arthritis), in which treatments and therapeutics are lacking. For example, specific point mutations in the ion channel transient receptor potential vanilloid 4 (TRPV4) prevent proper joint development, leading to mild brachyolmia and severe, neonatally lethal metatropic dysplasia. Tissue-engineered cartilage offers an opportunity to elucidate the underlying mechanisms of these cartilage diseases for the development of treatments. Human induced pluripotent stem cells (hiPSCs) are an improved cell source option for cartilage tissue engineering given their minimal …

Long-Term Neural Activity Recorders Using Energy-Based Sensing, Compressive Computation And Data Logging, Darshit Mehta

McKelvey School of Engineering Graduate Student Theses & Dissertations

Insects are ideal candidates for developing bio-robotic systems owing to their ability to thrive in almost any environment. For example, neurons in their exquisite olfactory sensory systems can be tapped to create a sensing platform for standoff chemical monitoring. However, for enabling such cyborg systems, it is vital that the neural activity of a freely behaving organism can be measured for long periods of time. The current state-of-the-art neural recording techniques are power-intensive and they either need batteries, which make them too bulky for insects, or they have to maintain a continuous telemetry link to an external power source which …

Three-Dimensional Phase Field Modeling Of Fracture In Shape Memory Ceramics, Ehsan Moshkelgosha, Mahmood Mamivand

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Despite the vast applications of transformable ceramics, such as zirconia-based ceramics, in different areas from biomedical to aerospace, the fundamental knowledge about their mechanical degradation procedure is limited. The interaction of the phase transformation and crack growth is crucial as the essential underlying mechanism in fracture of these transformable ceramics, also known as shape memory ceramics. This study develops a three-dimensional (3D) multiphysics model that couples the variational formulation of brittle crack growth to the Ginzburg-Landau equations of martensitic transformation. We parameterized the model for the 3D single crystal zirconia, which experienced stress- and thermal-induced tetragonal to monoclinic transformation. The …

Developing An Induction Protocol And Generating A Selectable Cell Line To Obtain High-Purity V0v Interneuron Cultures From Mouse Embryonic Stem Cells, Jennifer Pardieck

McKelvey School of Engineering Graduate Student Theses & Dissertations

Spinal cord injury (SCI) leads to loss of motor function among other devastating impairments, with patients having a grim outlook on recovery as currently there are no widely efficacious treatment methods. The native regenerative capacity of the neurons in the central nervous system is limited, thus recovery of the axonal connections between the different components of the complex circuitry that enables motor function is minimal after SCI. Investigators aiming to improve motor function post-SCI approach the problem from different angles, including removing inhibitory elements to axonal regeneration and supporting regeneration through implantation of biomaterials, exposure to pro-regenerative factors, and transplantation …

Use Of Bioelectrochemical Systems For The Domestic Wastewater Treatment And Reuse, Gustavo Holz Bracher

International Programs

The goal of this study was to evaluate the potential of bioelectrochemical systems (BES) for domestic wastewater treatment and reuse.BES are systems capable of using microorganisms as catalyst on electrodes for power generation from water contaminants removal.

The BES are a promising sustainable technology that could be used for sewage treatment to allow its reuse, since studies verified the capacity of BES to produce energy, remove organic matter, nutrients and pathogens from sewage, and produce low waste quantities.

Thermal Properties Of 18f-Fdg Uptake And Imaging In Positron Emission Tomography Scans Of Cancerous Cells, Carleigh R. Eagle

PANDION: The Osprey Journal of Research and Ideas

Positron Emission Tomography (PET) scans can utilize a radioactive tracer, in this case 2-deoxy2-[fluorine-18] fluoro-D-glucose (¹⁸F-FDG), to visualize malignant tumors in cancer patients. The uptake was compared to glucose to understand the difference in thermal properties, which contribute to the ability to image the cancerous cells. The uptake of ¹⁸F-FDG by cancer cells and the imaging process of positron emission tomography were reviewed from a thermodynamic perspective. Gastrointestinal and neurological imaging techniques were reviewed to understand the role of PET imaging in different areas of the human body.

A Single Cell Pair Mechanical Interrogation Platform To Study Cell–Cell Adhesion Mechanics, Amir Monemianesfahani

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

Cell-cell adhesion complexes are macromolecular adhesive organelles that integrate cells into tissues. Perturbations of the cell-cell adhesion structure or relatedmechanotransduction pathways lead to pathological conditions such as skin and heart diseases, arthritis, and cancer. Mechanical stretching has been used to stimulate the mechanotransduction process originating from the cell-cell adhesion and cell-extracellular matrix (ECM) complexes. The current techniques, however, have limitations on their ability to measure the cell-cell adhesion force directly and quantitatively. These methods use a monolayer of cells, which makes it impossible to quantify the forces within a single cell-cell adhesion complex. Other methods using single cells or cell …

Development Of A Microfluidic Viscoelastic Hemostatic Assay For Real-Timeviscosity Measurements Of Blood, Shay Kent

Electronic Theses and Dissertations

Blood coagulation disorders are malfunctions in the body’s ability to control blood clotting. It can result in either insufficient clotting causing an increased risk of bleeding or excessive clotting obstructing blood flow. The rapid and accurate diagnosis of coagulopathies is an important, unmet need in the clinical setting. Rapidly identifying the source of bleeding, either acquired or inherited, is critical to reduce the risk of major blood loss and deliver personalized hemostatic therapies. Viscoelastic hemostatic assays, or VHAs, deliver an effective solution to the diagnosis of coagulopathies by evaluating global hemostatic function using whole blood rather than plasma. VHAs are …

Tracking The Amide I And Αcoo− Terminal Ν(C=O) Raman Bands In A Family Of L-Glutamic Acid-Containing Peptide Fragments: A Raman And Dft Study, Ashley E. Williams, Nathan I. Hammer, Ryan C. Fortenberry, Dana N. Reinemann

Faculty and Student Publications

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length …