Biomedical Engineering and Bioengineering Commons^™

Enhancing Human Key Point Identification: A Comparative Study Of High-Resolution Vicon Dataset And Coco Dataset Using Bpnet, Bibash Lama

Masters Theses

Accurately identifying human key points is crucial for various applications, including activity recognition, pose estimation, and gait analysis. This study presents a high-resolution dataset created using the VICON motion capture system and three differently oriented 2D cameras, that can be used to train different neural networks for estimating the 2D key joint positions of the person from the 2D images or videos. The participants in the study included 25 healthy adults (17 males and 8 females) performing normal gait movements for about 2 to 3 seconds. The VICON system captured 3D ground truth data, while the three 2D cameras collected …

Hierarchical Based Classifcation Method Based On Fusion Ofgaussian Map Descriptors Foralzheimer Diagnosis Using T1‑Weighted Magnetic Resonance Imaging, Nourhan Zayed, Shereen E. Morsy, Inas A. Yassine

Mechanical Engineering

Alzheimer’s disease (AD) is considered one of the most spouting elderly diseases. In 2015, AD is reported the US’s sixth cause of death. Substantially, non-invasive imaging is widely employed to provide biomarkers supporting AD screening, diagnosis, and progression. In this study, Gaussian descriptors-based features are proposed to be efcient new biomarkers using Magnetic Resonance Imaging (MRI) T1-weighted images to diferentiate between Alzheimer’s disease (AD), Mild Cognitive Impairment (MCI), and Normal controls (NC). Several Gaussian map-based features are extracted such as Gaussian shape operator, Gaussian curvature, and mean curvature. The aforementioned features are then introduced to the Support Vector Machine (SVM). …

Engineering Multifunctional Adhesive Hydrogel Patches For Biomedical Applications, Aishik Chakraborty, Shana Alexander, Wei Luo, Narisse Al-Salam, Mia Van Oirschot, Sudhir H. Ranganath, Subrata Chakrabarti, Arghya Paul

Chemical and Biochemical Engineering Publications

Traditional patches, such as sticking plaster or acrylic adhesives used for over a hundred years, lack functionality. To address this issue of poor functionality, adhesive hydrogel patches have emerged as an efficient bioactive multifunctional alternative. Hydrogels are three-dimensional, water-swellable, and polymeric materials closely resembling the native tissue architecture. The physicochemical properties of hydrogels can be modified easily, allowing them to be suitable for various biomedical applications. Moreover, adhesive properties can be imparted to hydrogels through physicochemical manipulations, making them ideal candidates for supplementing or replacing traditional sticking plaster. As a result, sticky hydrogel patches are widely used for transdermal drug …

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

A Novel Approach To Detect Modified Cytosines In A Nanopore Sequencer, Benjamin Davidorf

McKelvey School of Engineering Graduate Student Theses & Dissertations

Epigenetic changes, such as DNA methylation, have been seen in various types of cancers, diseases, and neurological disorders. A common form of methylation occurs when a methyl group is added to the C-5 position of a cytosine, which is called 5-methyl-cyosine (5- mC). Hydroxymethylated is a type of methylation where 5mC is oxidized to 5-hydroxy-methyl- cytosine (5hmC), which has been linked to normal brain development. Current methods to sequence DNA methylation patterns (5-mC and 5-hmC) at a genome-wide level have several limitations, so there remains a need for a method to efficiently map DNA methylation. The state- of-the-art method for …

Understanding The Mechanisms By Which Cable Sway Produces Motion Artifact In Mobile Electroencephalography, David Rojas

Electronic Theses and Dissertations, 2020-2023

Mobile brain/body imaging utilizes electroencephalography (EEG) to record brain activity during human walking in dynamic environments. Motion artifact from cable sway affects the quality of EEG signals collected from the scalp, masking contributions of synchronously firing neurons. Previous studies have explored cable sway-induced motion artifact, but only during vigorous exercise or controlled sinusoidal motion. Therefore, a need remains to further understand the underlying mechanisms of this artifact, as it may help with developing real-time mitigation methods, reducing reliance on offline signal processing. In this thesis, I aimed to show that controlled cable sway could produce specific motion artifact waveforms in …

Improving Peripheral Nerve Regeneration Through Rehabilitation And Biomaterial-Based Drug Delivery Strategies, Yunfan Kong

Theses & Dissertations

Peripheral nerve injury (PNI) is a common problem worldwide, with trauma being a common cause. PNI can lead to loss of sensory and motor functions, chronic neuropathic pain, and mental health issues, significantly impacting patients' family life, work, and social situation. Recent studies revealed that beyond the topical injury site at peripheral nerves, PNIs can also induce dysfunctions in the central nervous system (CNS) by causing maladaptive plasticity, which will result in exaggeration and exacerbation of the pathological condition caused by primary injuries. The common therapy strategies for PNI treatment are using sutures, nerve autografts or conduits in cases requiring …

The Effects Of Mechanical Strain On Vascular Calcification And The Canonical Wnt Pathway, Hannah E. Douglas

Theses and Dissertations

Cardiovascular disease is a significant health crisis, representing 32% of deaths worldwide in 2019. Vascular calcification (VC), a major contributor to cardiovascular disease, is a regulated biomineralization process whose exact mechanisms are unknown. Additionally, vascular smooth muscle cells (VSMCs) significantly contribute to VC by undergoing a phenotypic switch and differentiating into osteoblast-like cells. When factors like hypertension cause disturbed laminar flow in the body’s vasculature, the mechanical stress promotes the phenotypic switch and calcification of VSMCs via mechanotransduction. VC is also induced by the Wnt pathway, which is activated via mineral imbalance and mechanical stimulation. However, the exact mechanisms behind …

Nanoscale Modeling Of Membrane Systems Under Mechanical Deformation In Traumatic Brain Injury Using Molecular Dynamics, Anh Thi Ngoc Vo

Theses and Dissertations

Neuronal membrane disruption and mechanoporation are nanoscale damage mechanisms that critically affect brain cell viability during traumatic brain injury (TBI). These nanoscale cellular impairments are elusive in experiments and necessitate in silico approaches such as molecular dynamics (MD) simulations. Implementing MD, this research aims to investigate the effects of different key factors related to membrane deformation and damage, including force field resolutions, lipid compositions, and loading conditions.

To examine the impact of force field resolution, MD deformation simulations were conducted on 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) lipid bilayer membranes, using all-atom (AA), united-atom (UA), and coarse-grained Martini (CG-M) force fields. The mechanical responses …

Multi-Objective Design Optimization Of Two Configurations Of Ventricular Shunts For Hydrocephalus, Will Kirkpatrick

Theses and Dissertations

Hydrocephalus is developed when the flow of cerebrospinal fluid is obstructed in the ventricles and a pressure build-up is generated within the brain. Ventricular shunts are used to remove excess fluid from the brain, but these shunts have a common problem of failure due to the shunt being obstructed by the build-up of astrocytes. To address this, two sets of 27 designs of ventricular shunts were identified and analyzed with parameters that could potentially reduce obstruction risks. The performance of these designs was examined using fluid simulations on these two sets of 27 designs. One set explored close-tipped shunt designs, …

Polyethylene Glycol-Mediated Directional Conjugation Of Biological Molecules For Enhanced Immunoassays At The Point-Of-Care, Dheerendranath Battalapalli, Purbali Chakraborty, Disha Jain, Umut A. Gurkan, Robert A. Bonomo, Mohamed S. Draz

Faculty Scholarship

Rapid and reliable point-of-care (POC) diagnostic tests can have a significant impact on global health. One of the most common approaches for developing POC systems is the use of target-specific biomolecules. However, the conjugation of biomolecules can result in decreased activity, which may compromise the analytical performance and accuracy of the developed systems. To overcome this challenge, we present a polymer-based cross-linking protocol for controlled and directed conjugation of biological molecules. Our protocol utilizes a bifunctional thiol-polyethylene glycol (PEG)-hydrazide polymer to enable site-directed conjugation of IgG antibodies to the surface of screen-printed metal electrodes. The metal surface of the electrodes …

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 …

Development Of Air-Jetting System For Bioprinting Of Alginate Micro-Droplets, Nathan Lingenfelter

Electronic Theses and Dissertations

Transplantation of organoids has been demonstrated to be a promising cure to many diseases including Type-1 diabetes. However, achieving consistent and robust derivations of mature organoids from human pluripotent stem cells (hPSCs) is challenging. Cellular mechano-transduction, where mechanical stimuli is sensed and converted to biochemical signaling, has been proposed to overcome this challenge. This pathway relies on encapsulating hPSCs in a small volume of a biomaterial such as alginate, which has been widely used as cell encapsulation materials due to its biocompatibility and selective permeability. In this project, we focused on developing an air-jetting based technique to generate small and …

Efficient Scopeformer: Toward Scalable And Rich Feature Extraction For Intracranial Hemorrhage Detection, Yassine Barhoumi, Nidhal Carla Bouaynaya, Ghulam Rasool

Henry M. Rowan College of Engineering Departmental Research

The quality and richness of feature maps extracted by convolution neural networks (CNNs) and vision Transformers (ViTs) directly relate to the robust model performance. In medical computer vision, these information-rich features are crucial for detecting rare cases within large datasets. This work presents the “Scopeformer,” a novel multi-CNN-ViT model for intracranial hemorrhage classification in computed tomography (CT) images. The Scopeformer architecture is scalable and modular, which allows utilizing various CNN architectures as the backbone with diversified output features and pre-training strategies. We propose effective feature projection methods to reduce redundancies among CNN-generated features and to control the input size of …

Hemodynamic Assessment Of Y-Incision Aortic Root Enlargement Using Computational Simulations, Astitwa Ghimire

Electronic Theses and Dissertations

The Yang procedure is a new aortic root enlargement technique used to enlarge the aortic annulus by multiple valve sizes. The procedure prevents patient prosthesis mismatch and establishes a viable platform for future valve-in-valve implantation. This study used the Yang procedure to investigate the hemodynamics in the aortic root and bioprosthetic valve regions after aortic root enlargement. Results indicate the velocity magnitude at the sinus regions of a patient who underwent the Yang procedure was slower, indicating risks of flow stasis and thrombosis. Simulation results denote computational models can be created for optimization of surgical procedures.

Site-Specific Glyco-Engineering Of Recombinant Thrombomodulin, Joseph M. Keil

ETD Archive

Thrombomodulin (TM), a membrane glycoprotein predominately expressed on endothelium, plays essential roles in regulating local hemostatic balance. Particularly, TM modulates the activity of thrombin from a procoagulant to an anticoagulant protease. When bound to TM, thrombin activates plasma protein C, which selectively inactivates coagulation factors Va and VIIIa. At the same time, TM-bound thrombin is unable to cleave fibrinogen or to activate platelets diminishing its procoagulant activity. recombinant TM456 is a promising anticoagulant candidate, but it has a very short half-life. TM is a proteoglycan and its O-linked glycosaminoglycan (GAG), chondroitin sulfate (CS), on the D3 domain contributes to TM’s …

Quantification And Identification Of Neuro-Electrophysiological Markers And Brain Network For Biomedical Applications, Shu Kang

Bioengineering Dissertations - Archive

Electroencephalogram (EEG) can detect and monitor neuro-electrophysiological signals in the human brain, including assessing brain function in newborns at risk of neurological injury and healthy adults undergoing intervention with prefrontal transcranial photobiomodulation (tPBM). Moreover, EEG-based brain functional connectivity can be assessed in either resting-state or task-based measurements using graph-theoretical network modeling. However, the management of newborns with mild hypoxic ischemic encephalopathy (HIE) is controversial, and no study has investigated the EEG-based brain network and information flow resulting from HIE. Also, the underlying electrophysiological mechanism of tPBM is still unclear, and further research is needed to determine optimal parameters for tPBM …

Development And Application Of A Microfluidic Platform For Quantifying Intra-Tumoral Compressive Stress., Zachary P. Fowler

Electronic Theses and Dissertations

Cancer progression is linked to the emergence of aberrant mechanical signaling in the tumor microenvironment. Modulation of extrinsic signals, such as ECM stiffness and composition, have been thoroughly explored. However, the development of solid stresses within the tumor remains poorly understood. To address this, we have developed a microfluidic platform that generates deformable alginate microbeads that allow for the quantification of compressive stresses generated within a growing glioblastoma (GBM) tumorsphere. PDMS microfluidic devices were fabricated via SU-8 mold with channels ranging from 10µm-40µm in diameter. Fluorescently labeled sodium alginate underwent a cross-linking reaction within the device to generate monodisperse beads …

Design And Evaluation Of A Multi-Functional Surgical Device For Microgravity Surgeries., Sienna Shacklette

Electronic Theses and Dissertations

No abstract provided.

Investigation Of Possible Inflammatory Response After Ultrasound And Microbubble Procedure In The Spinal Cord., Jenna Wilkerson

Electronic Theses and Dissertations

The purpose of this experiment is to explore the inflammatory effects of focused ultrasound paired with intravenously delivered microbubbles when used in the lumbar spinal cord. There are currently very few pharmaceuticals that can successfully enter the blood spinal cord barrier (BSCB). This technique used at the lumbar enlargement might allow targeted treatment of pathologies involving the spinal cord.

To test the possible inflammatory response of this technique, an animal experiment was performed. 15 animals were given a T12 laminectomy and allowed to fully recover. Once recovered, all animals received FUS+MB at L2 and were euthanized in groups of five …

Computational Comparison Of Medializing Tibial Tubercle Osteotomy And Trochleoplasty In Patients With Trochlear Dysplasia, Clare K. Fitzpatrick, Robert N. Steensen, Oliver Alvarez, Amy E. Holcomb, Paul J. Rullkoetter

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Medial patellofemoral ligament reconstruction (MPFLR) has emerged as the procedure of choice for recurrent patellar dislocation. This addresses soft tissue injury but does not address underlying anatomic factors, including trochlear dysplasia, that are commonly present and increase risk of dislocation. Quantification of the stability offered by other surgical interventions, namely, medializing tibial tubercle osteotomy (mTTO) and trochleoplasty, with and without MPFLR, may provide insight for surgical choices in patients with trochlear dysplasia. We developed subject-specific finite element models based on magnetic resonance scans from a cohort of 20 patients with trochlear dysplasia and recurrent patellar dislocation. The objectives of this …

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 …

A Novel Brain Computer Interface Design, Steven Vogan

Senior Honors Theses

A brain computer interface (BCI) is a system which connects neural signals to a computer system. They have been used for controlling systems including robotics, on-screen computer control such as mouse movement, typing, and synthesizing audio signals. Invasive, or implanted, systems are often long-term medical solutions, or used for research where very clear signal is required. Non-invasive systems usually rely on exterior signals gathered through a headset using one or more electrode sensors. These signals are composed of sums of neuron activation potentials from brain activity and can be used to determine particular aspects of brain function. All BCIs rely …

Photodynamic Therapy To Treat Triple Negative Breast Cancer In Vitro, Hunter S. Warren

All Theses

Triple negative breast cancer (TNBC) is the most resilient form of breast cancer, being one of the leading causes of death for women and making up 7% of all cancer deaths. Photodynamic therapy (PDT) offers a minimally invasive solution to TNBC as a passive-targeting treatment that reduces the need for other well established yet harsh treatments that can be taxing on the patient. PDT involves the use of a high-energy red light on the area of a tumor injected with photosensitizers (PS) that generate reactive oxygen species (ROS) in the tumor, triggering cell death. The PS tetra(hydroxyphenyl)chlorin (m-THPC) was used …

The Effects Of Compression Wrapping Techniques And Primary Wound Dressings On Leg Skin Interface Pressure, James Cox

All Theses

Peripheral edema affects approximately 20% of people in the US over the age of 50 and is frequently encountered among individuals with conditions such as heart disease, prolonged immobility, and venous insufficiency.¹ Compression is an established therapeutic tool utilized for the management of several chronic edema presentations including lymphedema and venous leg ulcers.^2,3 Therapeutic efficacy of compressive applications can be evaluated by defining interface pressure (IP) and IP distributions associated with specific textile combinations.² During compressive applications where an open wound is present, primary wound dressings should be used in combination with compressive wraps. Primary wound dressings …

Tandem Peptides Targeting Her2 For Delivery Of Cd44 Sirna Into Her2+ Breast Cancer Cells In Vitro, James Kalogeros

All Theses

More than 300,000 women will be diagnosed with breast cancer, and approximately 48,000 women will die this year due to the disease in the United States. HER2+ breast cancer accounts for 20-25% of invasive breast cancer, and it has a worse prognosis and higher early-stage mortality rate than other breast cancer subtypes. Common treatments for HER2+ breast cancer involve surgical removal of the breast or systemic therapy with chemotherapeutic drugs, both of which cause damage to healthy tissue. Due to the lack of a natural ligand for the HER2 receptor, there is a need for improved targeting strategies for the …

Assessment Of Knee Flexion In Young Children With Prosthetic Knee Components Using Dynamic Time Warping, Mark Daniel Geil, Zahra Safaeepour

Faculty Articles

Introduction: Analysis of human locomotion is challenged by limitations in traditional numerical and statistical methods as applied to continuous timeseries data. This challenge particularly affects understanding of how close limb prostheses are to mimicking anatomical motion. This study was the first to apply a technique called Dynamic Time Warping to measure the biomimesis of prosthetic knee motion in young children and addressed the following research questions: Is a combined dynamic time warping/root mean square analysis feasible for analyzing pediatric lower limb kinematics? When provided at an earlier age than traditional protocols dictate, can children with limb loss utilize an articulating …

Approximate Entropy And Velocity Of Center Of Pressure To Determine Postural Stability: A Pilot Study, Natalie Tipton, Gordon Alderink, Samhita Rhodes

Open Access Publishing Support Funded Articles

The body’s postural control system is responsible for responding to perturbations of balance and keeping the body upright. During quiet standing, the center of pressure oscillates about the center of mass, counteracting imbalances. These oscillations can be analyzed to determine the degree of stability, which could be helpful in quantifying the effects of brain injuries. In this research, the center of pressure was recorded for stances with feet together and feet tandem, with eyes opened and eyes closed, in neurotypical participants. These signals were analyzed using indices of approximate entropy and velocity to determine how sensitive the measures were in …

Visual Complexity Of The Time-Frequency Image Pinpoints The Epileptogenic Zone: An Unsupervised Deep-Learning Tool To Analyze Interictal Intracranial Eeg, Sarvagya Gupta

Graduate Masters Theses

Epilepsy, a prevalent neurological disorder characterized by recurrent seizures, continues to pose significant challenges in diagnosis and treatment, particularly among children. Despite substantial advancements in medical technology and treatment modalities, localization of the part of brain that causes seizures (Epileptogenic Zone) remains a difficult task. Intracranial EEG (iEEG) is often used to estimate the epileptogenic zone (EZ) in children with drugresistant epilepsy (DRE) and target it during surgery. Conventionally, iEEG signals are inspected in the time domain by human experts aiming to locate epileptiform activity.

Visual scrutiny of the iEEG time-frequency (TF) images can be an alternative way to review …