Biomedical Engineering and Bioengineering Commons^™

Dynamic, Reconfigurable, And Hierarchical Biosynthetic Composites Via Collagen Self-Assembly Within Highly Crowded Microgel Pastes, Elif Narbay, Abbygail Caine, Sanika Pandit, Gabrielle Montgomery, Marion Harper, E. Daniel Cárdenas-Vásquez, Hatte Hamilton, Megan Hicks, Daniel Mattar, Kyle Choy, Marco Bisoffi, L. Andrew Lyon

Engineering Faculty Articles and Research

The fabrication of a new class of biomimetic biomaterials is reported using nanostructured microgel pastes formed from “overpacked” assemblies of ultrasoft poly(N-isopropyl acrylamide-co-acrylic acid) microgels and their composites with collagen. Despite the solid-like nature of microgel pastes, collagen fibrillogenesis is robust and rapid, with a 3D collagen network forming throughout the paste volume. Structural organization within the composite is interrogated via a suite of microscopy methods, while rheological characterization provides insight into the static and dynamic mechanical properties of the materials. Long-range fibrillogenesis is enabled by local crowding, dynamics, and spatial reconfigurability of pastes at the …

Strategies For Prolonging Ventricular Action Potential Duration Without Increasing Transmural Dispersion Of Repolarization, Candido Cabo

Publications and Research

Dispersion of repolarization results from a non-homogeneous recovery of excitability in cardiac tissue, and it is an important factor in arrhythmogenesis because it could lead to the initiation and maintenance of a variety of arrhythmias. Antiarrhythmic agents that prolong action potential duration (APD) by selectively blocking specific ion channels (like IKr) often increase dispersion of repolarization, which could result in a pro-arrhythmic risk. In this report, using computer models of the action potential of human epicardial, mid-myocardial, and endocardial myocytes, we have identified strategies to prolong APD without increasing transmural dispersion of repolarization. The first strategy, which involves blocking several …

Unsaturated Fatty Acid Oil-Based Microdroplets: A Promising Novel Class Of Microdroplets, Ramiz S. Alejilat

Seton Hall University Dissertations and Theses (ETDs)

Droplet-based microfluidics has rapidly advanced numerous fields, including chemistry, biology, materials science, medicine, food science, and cosmetics. In these systems, fluorocarbon oil combined with fluorinated surfactants is the preferred medium for fluid encapsulation, offering exceptional stability and biocompatibility essential for sensitive biological and chemical processes. However, growing concerns about the environmental and biological risks associated with fluorinated chemicals have prompted a search for alternatives.

This study is the first to explore the use of unsaturated fatty acids derived from emu oil for microdroplet formation. We characterized droplet formation based on flow rates and the presence non-fluorinated surfactant at a certain …

Fully Integrated Slippage Detection System For Lower Limb Amputees, Christopher E. Miglio

Master's Theses

Lower limb amputees face significant challenges in maintaining a proper prosthetic fit, as improper fit can lead to slippage at the limb-socket interface, resulting in discomfort, pressure sores, and long-term musculoskeletal complications. To address this issue, a fully integrated slippage detection system was developed to monitor an amputee’s daily activities and slippage occurrences to understand their prosthetic fit over time. The system consists of a prosthetic sock embedded with Interlink 406 flexible piezoresistive force-sensing resistors (FSRs). The sock, worn directly on the residual limb, continuously measures pressure at the limb-socket interface. Sensor data from six FSRs is sampled at approximately …

A Novel Microfluidic Device For Preclinical Testing Of Chemotherapeutics, Kaija Saleh Ogan

Master's Theses

This work demonstrates the feasibility of a novel microfluidic tumor model that reproduces physiologically relevant nutrient gradients and endothelium–tumor interactions, validating its potential as a preclinical test platform. Finite element simulations of glutamine diffusion and fluid dynamics aligned with experimental tracer studies, and co-cultures supported directed endothelial migration toward tumor spheroids, confirming the device’s ability to mimic in vivo–like behavior.

Current preclinical models often fail to capture the complexity of the tumor microenvironment (TME), limiting their predictive value for therapeutic testing. Nutrient availability and angiogenic signaling are critical drivers of tumor progression, yet they are poorly represented in traditional …

Muscle Impulse Transducer: Research, Pre-Pilot Experiments, And The Design Of A Pilot Study For Quadriplegic Spinal Cord Injured Subjects For The Development Of A Novel Device, Marta Oreglia

Master's Theses

Paralysis due to spinal cord injury is a challenging condition that affects millions of people around the world. The Muscle Impulse Transducer (MIT) is a novel, wearable device that can be used to improve grip strength in the hand by using functional muscle impulses as a trigger for stimulus delivery to weakened or paralyzed nerves, to induce contraction of a paralyzed or paretic muscle. The MIT is still in development, with proof of concept [1], and functional prototypes [2] achieved. In this thesis, research was conducted on the best methods for functional electrical stimulation, EMG data collection, and nerve stimulus …

Using Noninvasive Calibrated Cuff Plethysmography To Observe The Effects Of Lifestyle Habits On Arterial Compliance, Joshua M. Whitaker

Master's Theses

Cardiovascular disease remains as a leading cause of death for both sexes and across all racial backgrounds. Continuing to research causes, early predictors, and preventative actions are paramount to ensuring that cardiovascular disease starts to decrease in its activity. Endothelial dysfunction is the earliest known predictor of cardiovascular disease, therefore investigating early detection methods of endothelial dysfunction can improve health outcomes. This study revolves around a non-invasive calibrated cuff device that uses the principles of segmental plethysmography and oscilliometry to measure arterial compliance of baseline and induced hyperemic conditions in human subjects to determine how well arteries vasodilate in response …

Mechanics Post-Tavr For Trileaflet Vs Bicuspid Aortic Valves: Insights From Computational Simulation, Breandan B. Yeats, Aniket Venkatesh, Sri Krishna Sivakumar, Hoda Hatoum, Milad Samaee, Venkateshwar Polsani, Et. Al.

Michigan Tech Publications

Background: Bicuspid aortic valve (BAV) disease is the most common congenital heart defect and is associated with elliptical openings and excess calcification. Limited data are available on long-term efficacy of transcatheter aortic valve replacement (TAVR) for BAV patients.

Objectives: The purpose of this study was to compare simulated mechanical metrics post-TAVR between BAV and trileaflet patients with calcific aortic stenosis.

Methods: Pre-TAVR computed tomography scans of trileaflet (n = 22) and BAV (n = 25) were used to segment the aortic valve. Simulated balloon-expandable stent deployment was performed from a previously developed protocol. The bioprosthetic leaflets were then pressurized under …

Dendrimer Gel Nanoparticles With Dual-Targeting Of Upar And Ribonucleotide Reductase R2 Influence Necrosis, Apoptosis, And Cell Cycle Arrest In Triple-Negative Breast Cancer, Hsin Yin Chuang, Yue-Wern Huang, Hu Yang

Biological Sciences Faculty Research & Creative Works

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype with limited treatment options due to the absence of estrogen (ER), progesterone (PR), and human epidermal growth factor receptor 2 (HER2) receptors. We previously developed highly adaptable polyamidoamine (PAMAM) dendrimer-based gel nanoparticles (GDP-uPA/GTI) with dual-targeting capabilities against urokinase-type plasminogen activator receptor (uPAR) and ribonucleotide reductase R2 (R2) to achieve selective antitumor effects. In this study, we investigated the underlying mechanisms of GDP-uPA/GTI-induced tumor inhibition. In vivo, GDP-uPA/GTI significantly downregulated R2 expression and activated caspase 8 and caspase 3, indicating caspase-dependent apoptosis. Histological evaluation of major organs revealed no observable toxicity. …

Optimal Control Of Human Exercise Using An Individualized Physiological Three-Tank Model And Dynamic Programming, Asal Lotfi

All Theses

This thesis develops a physiologically inspired three-tank model of human bioenergetics to describe and optimize fatigue and recovery during exercise. The aerobic, phosphagen, and glycogen systems are modeled as coupled reservoirs whose states constrain instantaneous power output. Building on this representation, dynamic programming is used to compute pacing strategies that respect physiological limits while maximizing task-specific goals such as peak power or total work over a fixed duration, enabling individualized, goal-driven exercise prescriptions. The three-tank dynamics are formulated in continuous time and then discretized under a zero-order-hold assumption for simulation and optimal control. Model parameters are linked to standard field …

Comparative Assessment Of Lower Limb Neuromusculoskeletal Activation And Joint Kinematics In Normal And Impaired Gait, Jack Ryan Schule

Theses and Dissertations

This thesis evaluates whether accessible and affordable technologies can provide clinically significant, quantifiable gait analysis comparable to traditional marker-based motion capture systems. Modern high-end systems offer excellent accuracy but remain financially and logistically inaccessible to many clinicians and researchers. To address this gap, a framework was developed using markerless pose estimation using the model, MediaPipe, inertial measurement units (IMUs) processed through an Extended Kalman Filter (EKF), and surface electromyography (sEMG) to measure joint kinematics and neuromuscular activity during gait. An experiment was performed where data was collected from participants with both normal gait and pathologies including: Osgood–Schlatter disease, Plica Band …

Establishing Procedures For Primary Human Myoblast Cell Culture, Erica Duffy

Biomedical Engineering

Peripheral Artery Disease (PAD) affects an estimated 200 million people worldwide and is the leading cause of amputation in the United States. PAD is characterized by atherosclerotic narrowing of arteries, resulting in ischemia from reduced blood flow to distal tissues. Although surgical and percutaneous interventions can restore perfusion, fewer than 50% of patients experience sustained benefit, highlighting the need for alternative therapeutic strategies. One promising approach is promoting arteriogenesis, the growth and outward remodeling of pre-existing collateral vessels that improve blood flow around the occluded arteries. Arteriogenesis is regulated by regenerative, M2-polarized macrophages, making macrophage polarization a key therapeutic target. …

G2pdeep-V2: A Web-Based Deep-Learning Framework For Phenotype Prediction And Biomarker Discovery For All Organisms Using Multi-Omics Data, Shuai Zeng, Trinath Adusumilli, Sania Zafar Awan, Manish Sridhar Immadi, Dong Xu, Trupti Joshi

Biomedical Sciences

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm …

Teachers Of Students With Visual Impairments (Tsvis) Assistive Technology (At) Competencies: An Update Study, Benjamin Kendall Lytle

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Assistive technology (AT) is essential for supporting access, independence, and learning among students with visual impairments. Teachers of students with visual impairments (TSVIs) are expected to integrate AT into instruction and ensure their students are prepared for academic, social, and workforce demands. The original list of 111 AT competencies for preservice TSVIs, developed by Smith et al. (2009), provided an important foundation but has not been revised despite significant technological advances over the past decade. Outdated competencies risk limiting teacher preparation programs and leaving educators underprepared to address the realities of today’s classrooms. A revised and streamlined competency framework is …

Developing A Metabolic Engineering Chassis From A Metabolically Versatile Organism, Rhodopseudomonas Palustris Cga009, Mark William Kathol

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Metabolic engineering has made it possible to develop biological processes that were once considered economically unfeasible or uncompetitive. This field has enabled both a robust niche market, whereby products, such as pharmaceutical substances like monoclonal antibodies, are produced exclusively through biological means, as well as an emerging commodity production market. Nonetheless, significant challenges remain in harnessing the unique metabolic capabilities of genetically non-tractable organisms. This dissertation focuses on Rhodopseudomonas palustris CGA009 as a potential chassis for metabolic engineering. To address the issue of genetic intractability, a synthetic biology toolkit was developed to facilitate the expression of heterologous proteins in R …

Synthesis And Study Of Stable Organic Radicals For Mri Contrast Agents And New Materials, Sabina Dhakal

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The first part of this dissertation focuses on the design, synthesis, and characterization of a thermally robust S =1/2 phototetrazolinyl monoradical and the development of synthetic methodologies for a high-spin (S = 1) phototetrazolinyl diradical. Electrochemical studies of the phototetrazolium cation (precursor to the monoradical) revealed a remarkably narrow electrochemical band gap (Ecell ≈ 0.82 V), suggesting promising electrical conductivity. Thermal analysis of the monoradical demonstrated excellent stability, with the onset of decomposition at 232 °C. Building on the excellent thermal stability and promising properties for electrical conductivity of the monoradical, we developed two condensation-based synthetic routes that provide viable …

Degradation Of Cobalt Chrome Molybdenum Hip And Knee Implants In Vivo And In Vitro, Peter William Kurtz

All Dissertations

Cobalt Chrome Molybdenum (CoCrMo) remains a popular material choice for femoral condyles in total knee arthroplasty and for acetabular liners in dual mobility total hip designs. CoCrMo has been phased out of conventional THA designs due to its correlation with adverse effects such as ALTR and ALVAL. It is less understood if the mechanisms (i.e. abrasive wear to the surface of the implant) that release metal ions into the surrounding tissue occur at similar rates as seen in conventional THA. Additionally, it is unknown what effect the secondary damage modes such as electrocautery damage and adhesive wear have on these …

Separating The Control Of Moving And Holding In Human Post-Stroke Arm Paresis, Alkis M. Hadjiosif, Kahori Kita, Scott T. Albert, Robert A. Scheidt, Reza Shadmehr, John W. Krakauer

Biomedical Engineering Faculty Research and Publications

Moving and holding-still (holding) have been posited to be separately controlled. The paretic arm after stroke exhibits different abnormalities during rest vs. movement, providing an opportunity to ask whether control of these behaviors is independently affected in stroke. We quantified resting postural abnormalities in human stroke patients by measuring their biases in force production as they held their hand still in various locations in a planar workspace and then assessed whether these resting force biases influenced reaching in the same workspace. Patients displayed marked resting force biases at each location, even when the arm was supported. However, these …

Effective Transfer Of Tumor Annotations From Hematoxylin And Eosin To Fluorescence Images Of Breast And Lung Tissues, Tianling Niu, Emi Ampo, Julie M. Jorns, Mollie Patton, Tongtong Lu, Dong Hye Ye, Tina Yen, Bing Yu

Biomedical Engineering Faculty Research and Publications

Significance: Accurate transfer of annotations from histological images to fluorescence images is essential in developing deep learning (DL)-based optical imaging systems for intraoperative assessment of tumor margins. Manual annotation is time-consuming, prone to interobserver variability, and impractical for large-scale datasets.

Aim: We present a semi-automated method that can effectively transfer tumor annotations from pathologist-annotated hematoxylin and eosin (H&E) images to fluorescence images captured using microscopy with ultraviolet surface excitation (MUSE). This method is not intended for intraoperative use but rather to facilitate the creation of annotated datasets for DL model development.

Approach: Our semi-automated method consists of nonrigid image registration, …

Reverse (Bio)Engineering: A Machine Learning Approach To Optimize Baseball Pitcher Health And Performance, Robert C. Moore

All Dissertations

Ball tracking systems are becoming ubiquitous in sport, creating an unprecedented opportunity for big data applications to optimize human health and performance. These applications are especially common in baseball, a sport known for analyzing ball flight data to quantify performance. Analysts routinely use ball flight data to identify the attributes of top performing pitchers, finding that the best pitchers throw with optimal combinations of release speed and spin to precise locations. However, for certain pitchers, the throwing motion required to produce optimal ball flight places exceedingly high biomechanical load on the elbow, and consequently injury rates continue to rise. This …