Engineering Commons^™

Enabling Novel Nanopore Sensing Approaches For Personalized Medicine Through Chemical Modifications To Analytes, Zehui Zhang

Theses and Dissertations

Nanopore sensors have garnered significant attention recently, not only for their groundbreaking advancements in single-molecule DNA sequencing but also for their diverse applications in stochastic sensing, single-molecule chemistry, and protein unfolding. The interaction of single molecules with the nanopore sensing interface leads to characteristic ionic current modulations, reflecting the composition, charge, distribution, structure, and sequence of the translocating molecule. With the electrical resistive pulse nanopore sensing, its single-molecule sensitivity and specificity have opened doors to numerous potential applications in personalized medicine. I will discuss recent advancements in the sensitivity and specificity of personalized medicine using nanopore sensors, focusing on proteomic …

Patient-Specific Hemodynamic Modeling For Optimizing Left Ventricular Assist Device And Right Heart Health, Holly Felice Grant

Theses and Dissertations

LVAD speed optimization is essential for efficient LVAD therapy and to minimize complications. However, the ideal LVAD speed is unknown and must be tailored for each patient. The interplay between the LVAD, systemic, and pulmonary circulations is critical and should be considered during optimization. A computational hemodynamic model that can be tailored for each patient may provide clinicians with useful guidance and reduce the need for repeated invasive studies. This study sought to customize and evaluate a patient-specific LVAD hemodynamic optimization model.

We conducted a retrospective analysis on 25 patients implanted with HM3 and who underwent right heart catheterization (RHC) …

Title: List Of 132 Papers Citing One Or More Skin Lesion Image Datasets, Neda Alipour, Ted Butke, Jane Courtney

Other resources

This document is provided as a supplementary digital resource to accompany the article Skin Type Diversity in Skin Lesion Datasets: A Review. The following list contains 132 papers that were identified during a systematic review of papers that use one or more skin lesion image datasets. A partial list of these papers appears in Table 1 of the aforementioned article. The full list is provided here for reference.

Wearable Alcohol Monitoring Device For The Data-Driven Transcutaneous Alcohol Diffusion Model, Ahmed Hasnain Jalal, Sepehr Arbabi, Mohammad A. Ahad, Fahmida Alam, Md. Ashfaq Ahmed

Electrical and Computer Engineering Faculty Publications

Wearable alcohol monitoring devices demand noninvasive, real-time measurement of blood alcohol content (BAC) reliably and continuously. A few commercial devices are available to determine BAC noninvasively by detecting transcutaneous diffused alcohol. However, they suffer from a lack of accuracy and reliability in the determination of BAC in real time due to the complex scenario of the human skin for transcutaneous alcohol diffusion and numerous factors (e.g., skin thickness, kinetics of alcohol, body weight, age, sex, metabolism rate, etc.). In this work, a transcutaneous alcohol diffusion model has been developed from real-time captured data from human wrists to better understand the …

Chemotherapy Drug Release From Hollow Core Polyethyleneimine Nanoparticles, Brian Boyle

Theses and Dissertations

Novel anticancer delivery vehicles are arising from engineered nanostructured materials. This work involved the synthesis, characterization, and release of novel hollow core polymeric nanoparticles (HCPNPs) for controlled drug delivery. Polyethyleneimine (PEI) was bound to AuNPs, forming polymer-shell nanoparticles with dissolution of the gold core via iodine forming HCPNPs with drug intercalated DNA bound to the surface. A high density (85 molecules/particle) of DNA intercalated with daunorubicin was conjugated. Particles were spherical with an average diameter of 105.7 ± 17.3 nm and zeta potential of 20.4 ± 3.54 mV. We hypothesize the DNA backbone electrostatically condensed to the primary amines on …

The Role Of Spontaneous Activity In Maturation Of The Calyx Of Held Nerve Terminal And Its Synaptic Target In The Medial Nucleus Of The Trapezoid Body, Daniel Tatsuo Heller

USF Tampa Graduate Theses and Dissertations

Neural circuit formation is a complex process involving synergistic roles between neurons and glial cells regulated by coordinated genetic and molecular cues and activity-dependent mechanisms. The canonical pathway for synapse formation begins with neurogenesis and migration followed by axonal outgrowth and dendritic arborization allowing for the capture and formation of nascent synapses. These initial synaptic contacts are exuberant in nature ensuring proper neural connectivity and undergo a period of pruning of superfluous inputs followed by maturation and strengthening of the remaining contacts. This maturation includes pre- and postsynaptic specialization of the active zone, localization and clustering of ion channels, and …

Feasibility Of Eeg Based Detection Of Ischemic Stroke: Studies In A Simple Computational Model, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

Objective: To explore quantitatively, using streamlined mathematics, how transmembrane potential differences across cell bodies of individual cortical neurons could act to produce the skin surface potentials of the electroencephalogram (EEG), and how ischemic stroke might be detected using EEGs in prehospital settings. Methods: From fundamental principles of electrostatics, anatomy, and physiology, one can characterize the strength of apparent dipoles created during activation of the cell bodies of individual cortical neurons. The transient dipole strength in a cortical neuron depends upon the size and surface area of its cell body, its capacitance, and the difference in transmembrane electrical potentials appearing across …

Deep Learning Framework For Graph-Based Molecular Drug Discovery, Daniel Manu

Electrical and Computer Engineering ETDs

This dissertation proposes the GraphGANFed framework, which combines Graph Convolutional Networks (GCN), Generative Adversarial Networks (GAN), and Federated Learning (FL) to generate novel molecules while preserving data privacy. FL allows learning from distributed clients without sharing local datasets, GCN extracts molecular structural properties, and GAN generates new molecules retaining the learned properties. Extensive simulations on three benchmark datasets show GraphGANFed's effectiveness, producing molecules with high novelty (≈ 100) and diversity (> 0.9). Results indicate a trade-off among evaluation metrics, and the right dropout ratio avoids mode collapse. Additionally, Conditional GraphGANFed (cGraphGANFed) incorporates a critic network from Reinforcement Learning (RL) to …

Creative Insights Into Motion: Enhancing Human Activity Understanding With 3d Data Visualization And Annotation, Isaac Browen, Hector M. Camarillo-Abad, Franceli L. Cibrian, Trudi Di Qi

Engineering Faculty Articles and Research

This paper presents a novel 3D system for human motion analysis - Motion Data Visualization and Annotation (MoViAn). Designed to provide a comprehensive visual representation of 3D human motion data, MoViAn incorporates detailed visualization of gaze direction, hand movements, and object interactions, alongside an interactive interface for efficient data annotation. A user study involving eight participants indicates that MoViAn enables users to thoroughly explore and annotate human motion data, with System Usability Scale (SUS) results demonstrating a satisfactory usability level. The contribution of this paper lies in the development of an interactive and usable data analytics tool aimed at deepening …

Protocol For Recording Neural Activity Evoked By Electrical Stimulation In Mice Using Two-Photon Calcium Imaging, Seungbin Park, Megan Lipton, Yujiao J. Sun, Maria Dadarlat

Purdue University Libraries Open Access Publishing Fund

Electrical stimulation provides a clinically viable approach for treating neurological disorders. Here, we present a protocol for recording neural activity evoked by electrical stimulation in mice using two-photon calcium imaging. We detail steps for chronically implanting a head fixation bar, a stimulating electrode, and a glass imaging window.We additionally describe the procedures for viral injections and awake head-fixed recordings.

Cellular Energy Cycle Mediates An Advection-Like Forward Cell Flow To Support Collective Invasion, Jian Zhang, Jenna Mosier, Yusheng Wu, Logan Waddle, Paul V. Taufelele, Wenjun Wang, Heng Sun, Cynthia A. Reinhart-King

Biomedical Engineering Faculty Publications and Presentations

Collective cell migration is a model for nonequilibrium biological dynamics, which is important for morphogenesis, pattern formation, and cancer metastasis. The current understanding of cellular collective dynamics is based primarily on cells moving within a 2D epithelial monolayer. However, solid tumors often invade surrounding tissues in the form of a stream-like 3D structure, and how biophysical cues are integrated at the cellular level to give rise to this collective streaming remains unclear. Here, it is shown that cell cycle-mediated bioenergetics drive a forward advective flow of cells and energy to the front to support 3D collective invasion. The cell division …

Stretching The Limits Of Mri—Stretchable And Modular Coil Array Using Conductive Thread Technology, Folk W. Narongrit, Thejas Vishnu Ramesh, Joseph V. Rispoli

Purdue University Libraries Open Access Publishing Fund

Objective: We propose a modular stretchable coil design using conductive threads and commercially available embroidery machines. The coil design increases customizability of coil arrays for individual patients and each body part. Methods: Eight rectangular coils were constructed with custom-fabricated stretchable tinsel copper threads incorporated onto textile. Tune, match, and detune circuits were incorporated on the coil. A hook-and-loop mechanism was used to attach and decouple the modular coils. Phantom and in vivo scans at various anatomical flexion angles were acquired to highlight performance, and a temperature test was performed to verify safety. Results: In vivo MRI experiments demonstrate high sensitivity …

Editorial: Mitral Valve Disease: Mechanisms To Therapies, Maria Carmo Nunes, Hoda Hatoum, Alison M. Pouch, Muralidhar Padala

Michigan Tech Publications

No abstract provided.

Aging-Related Changes In The Mechanical Properties Of Single Cells, Amarnath Singam, Chandrabali Bhattacharya, Seungman Park

Mechanical Engineering Faculty Research

Mechanical properties, along with biochemical and molecular properties, play crucial roles in governing cellular function and homeostasis. Cellular mechanics are influenced by various factors, including physiological and pathological states, making them potential biomarkers for diseases and aging. While several methods such as AFM, particle-tracking microrheology, optical tweezers/stretching, magnetic tweezers/twisting cytometry, microfluidics, and micropipette aspiration have been widely utilized to measure the mechanical properties of single cells, our understanding of how aging affects these properties remains limited. To fill this knowledge gap, we provide a brief overview of the commonly used methods to measure single-cell mechanical properties. We then delve into …

Patient-Specific Musculoskeletal Modeling Of Total Shoulder Arthroplasty, Brendan M. Curran

Electronic Theses and Dissertations

Total shoulder arthroplasty (TSA) is often considered a surgery of last resort for patients with debilitating pathologies of the glenohumeral joint such as osteoarthritis, humeral head fracture, and advancing rotator cuff tears. TSA replaces the articulation between the humeral head and the glenoid fossa, with the goals of relieving pain and restoring function. Two types of total shoulder implants are available: Anatomic Total Shoulder Arthroplasty (aTSA) and Reverse Total Shoulder Arthroplasty (rTSA). TSA survivorship is lower than that of the survivorship seen in total knee and hip replacements [1]. Shoulder muscle moment arms and lines of action have been measured …

Statistical Modeling Of Knee Morphology And Material Properties Considering Diverse Populations, Gabrielle Jeannine Kindy

Electronic Theses and Dissertations

Total Knee Arthroplasty (TKA) is a widely performed surgical procedure aimed at alleviating pain and restoring function in patients with severe knee osteoarthritis. Despite its general success, disparities in postoperative outcomes have been observed across different racial and ethnic groups, with minority populations often experiencing less favorable results. One potential avenue for improving the generalizability of orthopaedic implants is using Statistical Shape and Intensity Models (SSIMs), which can be used to incorporate patient variability directly into the orthopaedic medical device development workflow through population-based finite element analysis.

This work aimed to construct an SSIM from a diverse subject set, incorporating …

Shape Memory Alloy Capsule Micropump For Drug Delivery Applications, Youssef Mohamed Kotb

Theses and Dissertations

Implantable drug delivery devices have many benefits over traditional drug administration techniques and have attracted a lot of attention in recent years. By delivering the medication directly to the tissue, they enable the use of larger localized concentrations, enhancing the efficacy of the treatment. Passive-release drug delivery systems, one of the various ways to provide medication, are great inventions. However, they cannot dispense the medication on demand since they are nonprogrammable. Therefore, active actuators are more advantageous in delivery applications. Smart material actuators, however, have greatly increased in popularity for manufacturing wearable and implantable micropumps due to their high energy …

Transforming Orthopedic Surgery: Autonomous Image-Guided Techniques For Femur Fracture Robotic Surgery, Marzieh Sadat Saeedi-Hosseiny

Theses and Dissertations

Long-bone fractures, particularly femur fractures, are prevalent and necessitate surgical intervention due to traumatic forces. Manual reduction procedures pose challenges, including excessive traction forces and reliance on limited X-ray imaging, resulting in malalignment-related complications and repeated surgeries. Current methods for femur fracture reduction are prone to inaccuracies, prolonged surgical times, and postoperative complications. This research introduces image-guided methods to automate a surgical robotic system, Robossis, to enhance femur alignment accuracy, reduce procedure times, and improve patient outcomes. To address these challenges, a marker-based approach utilizing a few X-ray images is developed to detect the spatial relative position of the femur …

Preclinical Examination Of A Nerve Specific Fluorophore Using Ex Vivo Human Tissues, Logan Michael Bateman

Dartmouth College Master’s Theses

Fluorescence-guided surgery (FGS) is a nascent field which seeks to improve patient safety and surgical outcomes using fluorescent agents known as fluorophores. Fluorophores are molecules which upon excitation with a specific wavelength of light emit a photon of a specific wavelength which can be detected using a modified camera system. Creation and translation of a fluorophore for clinical use is a costly, laborious, and time intensive process. Only a handful of fluorophores have received FDA approval and they required multiple years of tightly regulated clinical trials. Prior to these first-in-human studies these agents are subject to a litany of preclinical …

Electrical Conductivity Of Subsurface Ocean Analogue Solutions From Molecular Dynamics Simulations, Catherine A. Psarakis, Timothy Tizhe Fidelis, Keith B. Chin, Baptiste Journaux, Abby Kavner, Pranb Sarker, Marshall J. Stycinski, Steven D. Vance, Tao Wei

Faculty Publications

Investigating the habitability of ocean worlds is a priority of current and future NASA missions. The Europa Clipper mission will conduct approximately 50 flybys of Jupiter’s moon Europa, returning a detailed portrait of its interior from the synthesis of data from its instrument suite. The magnetometer on board has the capability of decoupling Europa’s induced magnetic field to high precision, and when these data are inverted, the electrical conductivity profile from the electrically conducting subsurface salty ocean may be constrained. To optimize the interpretation of magnetic induction data near ocean worlds and constrain salinity from electrical conductivity, accurate laboratory electrical …

Quantifying Variation Across 16s Rrna Gene Sequencing Runs In Human Microbiome Studies, Andrew J. Hoisington, Christopher E. Stamper, Joseph C. Ellis, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Recent microbiome research has incorporated a higher number of samples through more participants in a study, longitudinal studies, and metanalysis between studies. Physical limitations in a sequencing machine can result in samples spread across sequencing runs. Here we present the results of sequencing nearly 1000 16S rRNA gene sequences in fecal (stabilized and swab) and oral (swab) samples from multiple human microbiome studies and positive controls that were conducted with identical standard operating procedures. Sequencing was performed in the same center across 18 different runs. The simplified mock community showed limitations in accuracy, while precision (e.g., technical variation) was robust …

A Pilot Study Comparing Muscle Activation And Kinematic Parameters Between Professional And Non-Professional Tennis Players, Anton S. Petrenko

Masters Theses

Tennis, a widely played sport across various age and skill groups, prompts continual skill improvement among competitive players seeking a competitive edge. This study explores two approaches for enhancing playing style: motion capture (MoCap) and surface electromyographic (sEMG) signals. The study addresses a gap in simultaneous examination of MoCap and entire dominant leg muscle activation, particularly concerning the influence of skill level and gender on various tennis strokes. To fill this void, the research records and analyzes MoCap and dominant leg sEMG data during serves and strokes on both court sides. The hypothesis posits differences in muscle activation and body …

Effects Of An Indole Derivative On Cell Proliferation, Transfection, And Alternative Splicing In Production Of Lentiviral Vectors By Transient Co-Transfection, Nataly Carolina Mier, Donald Keith Roper

Biological Engineering Faculty Publications

Lentiviral vectors derived from human immunodeficiency virus type I are widely used to deliver functional gene copies to mammalian cells for research and gene therapies. Post-transcriptional splicing of lentiviral vector transgene in transduced host and transfected producer cells presents barriers to widespread application of lentiviral vector-based therapies. The present study examined effects of indole derivative compound IDC16 on splicing of lentiviral vector transcripts in producer cells and corresponding yield of infectious lentiviral vectors. Indole IDC16 was shown previously to modify alternative splicing in human immunodeficiency virus type I. Human embryonic kidney 293T cells were transiently transfected by 3^rd generation …

Molecular Behavior Of Silicone Adhesive At Buried Polymer Interface Studied By Molecular Dynamics Simulation And Sum Frequency Generation Vibrational Spectroscopy, Yuchen Wu, Ting Lin, Elizabeth Santos, Dongchan Ahn, Ryan Marson, Pranab Sarker, Xiaoyun Chen, Frédéric Gubbels, Nick E. Shephard, Carol Mohler, Tao Wei, Tzu-Chi Kuoc, Zhan Chen

Faculty Publications

Silicones have excellent material properties and are used extensively in many applications, ranging from adhesives and lubricants to electrical insulation. To ensure strong adhesion of silicone adhesives to a wide variety of substrates, silane-based adhesion promotors are typically blended into the silicone adhesive formulation. However, little is known at the molecular level about the true silane adhesion promotion mechanism, which limits the ability to develop even more effective adhesion promoters. To understand the adhesion promotion mechanism of silane molecules at the molecular level, this study has used sum frequency generation vibrational spectroscopy (SFG) to determine the behavior of (3-glycidoxypropyl)trimethoxy silane …

Single-Molecule Orientation Imaging Reveals The Nano-Architecture Of Amyloid Fibrils Undergoing Growth And Decay, Brian Sun, Tianben Ding, Weiyan Zhou, Tara S. Porter, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Amyloid-beta (Aβ42) aggregates are characteristic Alzheimer’s disease signatures, but probing how their nanoscale architectures influence their growth and decay remains challenging using current technologies. Here, we apply time-lapse single-molecule orientation-localization microscopy (SMOLM) to measure the orientations and rotational “wobble” of Nile blue (NB) molecules transiently binding to Aβ42 fibrils. We correlate fibril architectures measured by SMOLM with their growth and decay over the course of 5 to 20 min visualized by single-molecule localization microscopy (SMLM). We discover that stable Aβ42 fibrils tend to be well-ordered and signified by well-aligned NB orientations and small wobble. SMOLM also shows that increasing order …

A Study On The Effects Of Cementless Total Knee Arthroplasty Implants’ Surface Morphology Via Finite Element Analysis, Scott Hazelwood, Peter J. Hunt, Mohammad Noori, Naudereh B. Noori, Wael A. Altabey

Biomedical Engineering

Total knee arthroplasty (TKA) is one of the most commonly performed orthopedic surgeries, with nearly one million performed in 2020 in the United States alone. Changing patient demographics, predominately indicated by increases in younger, more active, and more obese patients undergoing TKA, poses a challenge to orthopedic surgeons as these factors present a greater risk of long-term complications. Historically, cemented TKA has been the gold standard for fixation, but long-term aseptic loosening continues to be a risk for cemented implants. Cementless TKA, which relies on the surface morphology of a porous coating for biologic fixation of implant to bone, may …

Noninvasive Technique For Measuring Cardiac Output, Grace E. Kolar, Rachel Simonton, Eli Strohecker

Williams Honors College, Honors Research Projects

NA

Evaluating Visual Dependence In Postural Stability Using Smartphone And Stroboscopic Glasses, Brent A. Harper, Michael Shiraishi, Rahul Soangra

Physical Therapy Faculty Articles and Research

This study explores the efficacy of integrating stroboscopic glasses with smartphone-based applications to evaluate postural control, offering a cost-effective alternative to traditional forceplate technology. Athletes, particularly those with visual and visuo-oculomotor enhancements due to sports, often suffer from injuries that necessitate reliance on visual inputs for balance—conditions that can be simulated and studied using visual perturbation methods such as stroboscopic glasses. These glasses intermittently occlude vision, mimicking visual impairments that are crucial in assessing dependency on visual information for postural stability. Participants performed these tasks under three visual conditions: full vision, partial vision occlusion via stroboscopic glasses, and no vision …

Development Of An Advanced Step Counting Algorithm With Integrated Activity Detection For Free Living Environments, Paige M. Dolan

Master's Theses

Physical activity plays a crucial role in maintaining overall health and reducing the risk of various chronic diseases. Step counting has emerged as a popular method for assessing physical activity levels, given its simplicity and ease of use. However, accurately measuring step counts in free-living environments presents significant challenges, with most activity trackers exhibiting a percent error above 20%. This study aims to address these challenges by creating a machine learning algorithm that leverages activity labels to improve step count accuracy in real-world conditions. Two approaches to balancing data were used: one employed a simpler oversampling technique, while the other …

Engineering An Injectable Hydrogel With Self-Assembling 3d Vasculature, Kendyl Cohn

Master's Theses

This research developed methods for culturing self-assembling capillaries in an injectable gel as a potential method for vascularizing tissue-on-a-chip models to mimic physiological drug delivery. Additionally, a mathematical model was developed as a tool for understanding nutrient delivery and comparison of potential delivery systems. Organs-on-a-chip provide novel platforms for studying biology and physiology in 3D, allow exploration of tissue engineering on a manageable scale, and serve as models for drug screening and drug-delivery testing.

Methods were first developed for co-culture of endothelial cells and fibroblasts (3T3s or HDFs) in 2D, evaluating culture time, seeding density and ratio of HUVECs and …