Biomedical Engineering and Bioengineering Commons^™

Toward The Application Of Natural Language Processing In Electronic Health Record Analysis For Taxonomy Development, Latoya Mcdonald

All Dissertations

Electronic health records (EHRs) are pivotal resources for nurse practice because they increase the timeliness and reliability of patient information at the point of care and support access by multiple healthcare providers and the individual patients themselves. However, it is widely recognized that data extraction from EHRs is challenging due to the variability in the language used in clinical care notes and the lack of standardized terminology across healthcare systems. The broad objective of this dissertation is to develop taxonomy-based classification models for nursing care by applying feature engineering approaches to EHRs that include nursing care of ostomy patients following …

Identifying Novel Molecular Targets To Induce Ferroptosis In Drug-Tolerant Cancer Cells Through Computational Modeling, Haris J. Rana

Biological Sciences Undergraduate Honors Theses

Ferroptosis is an iron-dependent, reactive oxygen species (ROS)-driven form of regulated cell death in which the cell membrane is degraded by lipid peroxidation. It is regulated by multiple enzymes, such as glutathione peroxidase 4 (GPX4), which prevents membrane degradation by reducing lipid peroxides and protecting cells from oxidative damage. When inhibitors like RSL3 target GPX4, lipid peroxides build up, and toxic ROS compromises membrane integrity. Traditional anticancer treatments, such as most chemotherapies, aim to eliminate tumor cells by damaging DNA and triggering apoptosis. However, resistance to apoptosis is a “hallmark of cancer,” often resulting in treatment failure. As a distinct …

Metabolic Responses Of Adipose-Derived Stem Cells In Collagen I Hydrogels, Caroline R. King

Biological Sciences Undergraduate Honors Theses

Peripheral nerve injury affects approximately 44 in 1 million people in the United States every year and can lead to incomplete nerve recovery and loss of motor and sensory function. A significant amount of energy is required for nerve injury repair. A lack of energy allocation to the injury site hinders repair. Current treatments include hollow nerve guidance conduits, decellularized nerve grafts, and autografts. However, they are limited by factors such as donor site morbidity and sustained immunosuppressive treatments. Using three-dimensional collagen I hydrogels laden with adipose-derived stem cells (ASCs) can assist in neural regeneration. Three-dimensional collagen scaffolds aim to …

Mechanistic Investigation Of Ring-Opening Polymerization Of Polycaprolactone Using Tin(Ii) Catalysts: Ligand Effects And Biomedical Applications, Eva-Larue M. Barber

Honors Scholar Theses

This research explores the mechanistic aspects of ring-opening polymerization (ROP) of ε-caprolactone (CL) to produce polycaprolactone (PCL), a biodegradable polymer widely used in biomedical applications. The study investigates how light exposure and catalyst concentration influence polymerization efficiency, using tin(II) 2-ethylhexanoate [Sn(Oct)₂] as the catalyst in a non-polar toluene solvent at 90 °C. Reactions were conducted under either ambient light or black light bulb (BLB) illumination, with monomer-to-catalyst ratios of 1:1 and 200:1.

Proton nuclear magnetic resonance (¹H NMR) spectroscopy was used to analyze conversion efficiency by tracking the disappearance of monomer signals and appearance of characteristic PCL peaks. Results revealed …

Impact Of Shear Flow On Marine Biofilms Using Hyperspectral Imaging, Shantanu Mahesh Kore

All Theses

Various microbial communities in marine biofilms cause biofouling on submerged surfaces, posing challenges to marine industries. Despite their ecological and economic importance, biofilms' biomechanical and biochemical responses to hydrodynamic shear stress are insufficiently understood, particularly in dynamic flow conditions. To fill this gap, our study uses an innovative fiber-optic hyperspectral imaging (HSI) system and a supercontinuum laser source to examine marine biofilms' structure, composition, and detachment behavior at different shear stress levels.

To detect spectral and spatial heterogeneity in live biofilms without labeling, we created a custom imaging pipeline that captures reflectance spectra in the 600-850 nm range, targeting microbial …

Exploring Veto Activity: Dnam-1-Cd155 Axis In Overcoming Nk Cell-Mediated Allo-Rejection And Applications For Car-T Cell Therapy, Wei-Hsin Liu

Dissertations and Theses (Open Access)

As Miller et al. defined veto activity, it enables cells to target host cytotoxic T lymphocyte (CTL) precursors specific to veto cells' antigens, selectively eliminating anti- donor T cell clones without inducing rejection. By leveraging this unique immune property, two key research aims were proposed: “Exploration of the Impact of Veto Activity on Natural Killer (NK) Cell-Mediated Allo-rejection” and “Development of Off-the- shelf Chimeric Antigen Receptor (CAR)-T Therapy: Engineering Anti-Viral Veto CD8+ T Cells”. As demonstrated in our previous research, in a murine model with mild conditioning, anti-third-party central memory CD8+ veto T cells (veto Tcm) can prevent T cell- …

Investigating The Effects Of Hepatocyte Growth Factor On Primary Myoblast Proliferation, Grace Heller

Biomedical Engineering

Peripheral artery occlusive disease (PAOD) is a progressive vascular condition that affects over 200 million people worldwide and approximately 8 million in the United States. It is characterized by atherosclerotic narrowing of peripheral arteries, leading to reduced blood flow, ischemia, and, in severe cases, tissue loss and limb amputation. Although surgical revascularization is the gold standard, many patients—particularly those with comorbidities like diabetes— continue to experience poor outcomes, emphasizing the need for alternative therapies. One promising strategy is to enhance collateral arteriogenesis, the remodeling and enlargement of collateral arterioles that naturally bypass occluded vessels. Satellite cells (SCs), which give rise …

A Neuroimmune Circuit Mediates Chemo Brain Pathology, Daniel Ahmadi

McKelvey School of Engineering Graduate Student Theses & Dissertations

Chemotherapeutic agents, while effective in targeting malignant tumors, often reduce the patients’ quality of life by inducing fatigue, pain, and motivational deficits. These symptoms are collectively referred to as “chemo brain.” The mechanisms underlying these adverse effects, and specifically whether fatigue and motivational impairments share a common etiology, remain poorly understood. The neural–immune substrates of these symptoms remain obscure, in part because standard preclinical regimens either bypass key systemic signals or introduce local toxicity confounds. Here, I establish and validate a three‑day, low‑dose intravenous cisplatin protocol that avoids peritoneal inflammation and severe renal injury yet produces robust, reversible fatigue and …

Analyzing Microalgae-Bacteria Population Changes In Response To Environmental Parameters For Improved Wastewater Treatment, Amanda M. Moravek

All Graduate Theses and Dissertations, Fall 2023 to Present

Microalgae are incredible organisms that have a variety of uses such as wastewater treatment, fertilizer, livestock feed, and bio-compound production. Microalgae require a light source and minimal nutrients space to proliferate, making them an environmentally friendly and sustainable option for such processes. The Sustainable Wastes-to-Bioproducts Engineering Center at Utah State University is developing and implementing a Rotating Algae Biofilm Reactor (RABR) to remove total nitrogen and phosphorous from the Central Valley Wastewater Reclamation Facility wastewater effluent. Harmful compounds such as nitrates and phosphates are metabolized by the microalgae and converted into useful bioproducts, resulting in a circular economy. These RABRs …

Uv-A Light And Heat-Activated Antimicrobial And Biodegradable Materials For Food Packaging And Preservation, Michael J. Bodily

All Graduate Theses and Dissertations, Fall 2023 to Present

Current food packaging materials are often non-biodegradable and harmful for ingestion, which poses a threat to the environment and public health. Thus far, the dangers of microbial contamination of food on human health have outweighed the risks associated with using these conventional packaging plastics. A possible solution to these issues is to use a combination of innovative materials and microbial inactivation methods that can potentially both reduce plastic waste and combat harmful microorganisms. In this study, two antimicrobial, biodegradable composites were developed and tested for their ability to inactivate two types of bacterium, Escherichia coli K12 and Listeria innocua, …

Minimizing Secondary Spinal Cord Injuries With Hypertonic Saline., Francisco A. Cortez-Thomas

Master of Engineering Theses

Spinal cord injury (SCI) disrupts white matter, causing periaxonal swelling, axonal degeneration, and impaired function. To examine vascular edema’s role, we developed a 3Dprinted dual-compartment imaging chamber to mimic and manipulate interstitial and vascular fluid dynamics in real time. We hypothesized that hypertonic saline (HTS) in the "vascular" chamber would osmotically shift fluid from the periaxonal space and preserve myelinated fibers after SCI. Using two-photon excitation microscopy, we imaged myelin and axons ex vivo in Thy1^YFP+ transgenic mice following C5 contusive SCI and assessed three clinically relevant HTS concentrations versus normal saline for their effectiveness in mitigating periaxonal swelling …

Enhanced And Interpretable Prediction Of Multiple Cancer Types Using A Stacking Ensemble Approach With Shap Analysis, Shahid Mohammad Ganie, Pijush Kanti Dutta Pramanik, Zhongming Zhao

Faculty, Staff and Student Publications

Background: Cancer is a leading cause of death worldwide, and its early detection is crucial for improving patient outcomes. This study aimed to develop and evaluate ensemble learning models, specifically stacking, for the accurate prediction of lung, breast, and cervical cancers using lifestyle and clinical data.

Methods: 12 base learners were trained on datasets for lung, breast, and cervical cancer. Stacking ensemble models were then developed using these base learners. The models were evaluated for accuracy, precision, recall, F1-score, AUC-ROC, MCC, and kappa. An explainable AI technique, SHAP, was used to interpret model predictions.

Results: The stacking …

Analysis Of Differentially Expressed Genes (Deg) And Upstream Regulator Proteins Indicates That Inhibition Of Transforming Growth Factor Beta 1 (Tgfb1) Is A Potential Target For Acne Inversa, Weri Veranita, Siva Fauziah, Siti Nurbaya

Indonesian Journal of Medical Chemistry and Bioinformatics

Acne inversa (AI) is a chronic inflammatory skin disease characterized by painful nodules, abscesses, and scarring, primarily in intertriginous areas. This study aims to identify potential therapeutic targets for managing acne inversa based on the analysis of differentially expressed genes (DEG). The expression targets of these genes were then validated for their potential as biomarkers, and upstream regulator proteins (URPs) were identified from the resulting DEG. DEG analysis on the GEO dataset GSE122592 (acne inversa vs. healthy donor skin) revealed five DEG that can serve as biomarkers for acne inversa, with a sensitivity and specificity of (100%). These DEG—IL10, GZMB, …

Induction Of Diabetic Cardiomyopathy In A Three-Dimensional Myocardial Model, Maelyn Andreasen

Student Research Symposium

Diabetic cardiomyopathy: Impairs and damages heart tissue through chronic exposure to hyperglycemia, or high blood sugar, in diabetic individuals

Laparoscopic Articulating Arm: In Collaboration With The Xenocor Saberscope, Zac Hastings, Lizbeth Pugliese, Rebecca Sweeten, Dallin Thomas, Dallin Treasure-Areno

Student Research Symposium

• Laparoscopy a minimally invasive procedure performed through small incisions using a laparoscope, a camera-equipped instrument, along with specialized tools.

• Laparotomy or "open" surgery, requires a large incision to perform an abdominal operation.

Mathematical Modeling Of Color Perception Using Differential Equation, Siavash Pooretemad

Student Research Symposium

Color perception begins in the retina, where three cone types (L, M, S) detect light and initiate neural signals. These signals are processed by horizontal and bipolar cells to form opponent color channels: red-green (RG), yellow-blue (YB), and light-dark (LD). Perception is not solely based on physical input but also shaped by neural adaptation and context.

This project models color perception using a differential equation approach, simulating how color contrast and adaptation emerge from interactions between photoreceptors and lateral inhibition.

We hypothesize that a system of differential equations can model how retinal cone cells respond to and process light intensity, …

Metabolite Analysis To Understand Factors Limiting Microbial Fermentation At High Substrate Concentrations, Bishal D. Sharma

Dartmouth College Ph.D Dissertations

Clostridium thermocellum, a thermophilic anaerobic bacterium, holds promise as a biocatalyst for conversion of lignocellulosic biomass into biofuels. This microbe has been subjected to various metabolic engineering strategies, including the deletion of genes encoding secondary fermentation products such as H₂, formate, acetate, and lactate, as well as the expression of heterologous genes to redirect carbon flux toward ethanol production. Despite these efforts, achieving economically viable ethanol titers remains a challenge. We hypothesized that studying how intracellular metabolite concentrations change as fermentation stops could reveal metabolic bottlenecks or regulatory mechanisms limiting ethanol production at high titers. However, metabolomics studies at …

Development Of Flexible Lactate-Specific Molecularly Imprinted Polymers Based On Laser-Induced Graphene Electrochemical Biosensors For Disease Diagnosis, Christopher Animashaun

Biomedical Engineering Theses & Dissertations

Lactate is a critical biomarker linked to conditions such as sepsis, ischemia, cancer, and heart failure. Current lactate detection methods remain invasive, costly, and unsuitable for real-time, continuous monitoring. This study presents the development of a flexible, non-enzymatic electrochemical biosensor based on laser-induced graphene (LIG) electrodes modified with gold nanoparticles (AuNPs) and molecularly imprinted polymers (MIPs) for highly selective and sensitive lactate measurement. The integration of AuNPs enhanced surface conductivity and provided nanoscale heterogeneity, facilitating superior signal amplification. The optimized LIG/AuNP/MIP sensor achieved an extensive dynamic detection range from 0.1 μM to 1000 μM, with an outstanding detection limit of …

Next-Generation Biomedical Implants And Stimuli Responsive Soft Optical Arrays Via Surface Functionalized Elastomeric Materials, John M. Kapitan

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

The demands of emerging technologies, such as soft robotics, stretchable electronics, and next generation biomedical implants, has led to the development of diverse polymeric and hybrid organic/inorganic materials specifically tuned to meet these challenges. These materials typically have low Young’s moduli and are inert with high chemical stability. However, this has led to materials that are static in nature, lacking any meaningful way of responding to changes in their environment and adapting to these changes. This has driven a shift towards the design, manufacturing, and characterization of various stimuli responsive surfaces, relying on precise control of surface chemical coatings and …

Painting Rich Six-Dimensional Pictures Using Polarized Fluorescence Microscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

No abstract provided.

Development, Optimization, And Validation Of A High-Sensitivity Capillary Zone Electrophoresis System For Bioanalytical Applications, Aaron I. Mena

Electronic Theses and Dissertations

Capillary zone electrophoresis (CZE) is a powerful analytical technique widely used for biomolecular separation due to its high resolution, efficiency, and sensitivity. This report presents the development and validation of a novel CZE system designed to improve modularity, reproducibility, and operational efficiency. The system integrates a laser-induced fluorescence (LIF) detection method with a 488 nm laser, enhanced fluid control through a negative pressure system, and a user-friendly GUI for automated operation and data acquisition. Performance verification included pressure stability tests, fluorescence accuracy assessments, and electrophoretic reproducibility studies. Comparative analysis with a previous CZE iteration confirmed improved baseline stability, peak resolution, …

Advancing Tka Biomechanics: From Joint Simulator To Boundary Condition Development, Yashar Ali Behnam

Electronic Theses and Dissertations

This dissertation addresses four specific aims that collectively attempted to advance the experimental and computational analysis of total knee arthroplasty (TKA) components. The first study focused on the development of a novel whole knee joint simulator capable of simultaneous tibiofemoral and patellofemoral knee loading. This simulator employs custom fixturing to facilitate dynamic, unconstrained, muscle-driven PF articulation alongside controlled TF contact mechanics. Validation against experimental measurements showed strong agreement, demonstrating the simulator's potential as a valuable tool for future TKA design and surgical technique investigations.

The second study verified implant-specific physiological boundary conditions which accurately simulate activities of daily living using …

Treating Ground Water For Agricultural And Individual Consumption, Gabby Miller, Bronson Scott, Michael Clawson

Biomedical Engineering

This project, conducted in collaboration with Cal Poly seniors and Da Vinci High School students, aims to develop a solar-powered groundwater purification system. This system is designed to provide clean water for agricultural use and individual consumption, addressing the growing concerns of groundwater contamination and accessibility needs. The final prototype integrates a gravity filtration system combined with chemical purification, utilizing aluminum sulfate and chlorine to remove particulates, bacteria, and organic compounds.

The research phase involved an extensive review of groundwater contamination issues, existing filtration technologies, and market analysis. Key design constraints included cost-effectiveness, ease of maintenance, and minimal energy consumption, …

Overexpression And Biophysical And Functional Characterization Of A Recombinant Fgf21, Phuc Phan, Jason Hoang, Thallapuranam Krishnaswamy Suresh Kumar

Chemistry & Biochemistry Faculty Publications and Presentations

Fibroblast growth factor 21 (FGF21) is an endocrine FGF that plays a vital role in regulating essential metabolic pathways. FGF21 increases glucose uptake by cells, promotes fatty acid oxidation, reduces blood glucose levels, and alleviates metabolic diseases. However, detailed studies on its stability and biophysical characteristics have not been reported. Herein, we present the overexpression, biophysical characterization, and metabolic activity of a soluble recombinant FGF21 (rFGF21). The far-UV circular dichroism spectra of rFGF21 show a negative trough at 215 nm, indicating that the protein’s backbone predominantly adopts a β sheet conformation. rFGF21 shows intrinsic tyrosine fluorescence at 305 nm. Thermal …

Trpv4 Dominates High Shear-Induced Initial Traction Response And Long-Term Relaxation Over Piezo1, Mohanish Chandurkar, Manli Yang, Majid Rostami, Sangyoon J. Han

Michigan Tech Publications

Modulation of endothelial traction is critical for the responses of endothelial cells to fluid shear stress (FSS), which has profound implications for vascular health and atherosclerosis. Previously, we demonstrated that under high FSS, endothelial cells rapidly increase traction forces, followed by relaxation, with traction aligning in the flow direction. In contrast, low shear preconditioning induces a modest short-term increase in traction (min), followed by a secondary long-term (>14 hr) rise, with traction/cells aligning perpendicular to the flow. The upstream mechanosensors driving these responses, however, remain unknown. Here, we sought the roles of Piezo1 and TRPV4 ion channels in shear-induced …

Fast 3d Printing Of Fine, Continuous, And Soft Fibers Via Embedded Solvent Exchange, Wonsik Eom, Mohammad Tanver Hossain, Vidush Parasramka, Jeongmin Kim, Ryan W. Y. Siu, Kate A. Sanders, Dakota Piorkowski, Andrew Lowe, Hyun Gi Koh, Michael F. L. De Volder, Douglas S. Fudge, Randy H. Ewoldt, Sameh H. Tawfick

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Nature uses fibrous structures for sensing and structural functions as observed in hairs, whiskers, stereocilia, spider silks, and hagfish slime thread skeins. Here, we demonstrate multi-nozzle printing of 3D hair arrays having freeform trajectories at a very high rate, with fiber diameters as fine as 1.5 µm, continuous lengths reaching tens of centimeters, and a wide range of materials with elastic moduli from 5 MPa to 3500 MPa. This is achieved via 3D printing by rapid solvent exchange in high yield stress micro granular gel, leading to radial solidification of the extruded polymer filament at a rate of 2.33 μm/s. …

Associations Between Social Determinants Of Health And Mental Health Disorders Among U.S. Population: A Cross-Sectional Study, S. Tanarsuwongkul

Faculty Publications

Aims

The impact of social determinants of health (SDOH) on mental health is increasingly realized. A comprehensive study examining the associations of SDOH with mental health disorders has yet to be accomplished. This study evaluated the associations between five domains of SDOH and the SDOH summary score and mental health disorders in the United States.

Methods

We analyzed data from a diverse group of participants enrolled in the All of Us research programme, a research programme to gather data from one million people living in the United States, in a cross-sectional design. The primary exposure was SDOH based on Healthy …

Advancing Prosthetic Technology: 3d-Printed Robotic Arm With Micro Linear Actuators, Vu Tran, Nathan Reed, Mahdi Yazdanpour

Posters-at-the-Capitol

The increasing demand for affordable and accessible prosthetic solutions has driven innovation in the field of robotics. In this project, we present the design and development of a 3D-printed robotic prosthetic arm aimed at addressing the challenges faced by individuals with upper limb amputations. Our prosthetic arm utilizes five micro linear actuators to achieve precise and naturalistic movement. The design of the prosthetic arm prioritizes affordability and accessibility, with a focus on leveraging 3D printing technology to reduce manufacturing costs and enable customization. The use of micro linear actuators offers advantages in terms of compactness, lightweight construction, and efficient power …

Inactivation Of Zika Virus With Hydroxypropyl-Beta-Cyclodextrin, Cory R. Hewitt, Nicholas J. Wixon, Arthur Gallegos, You Zhou, Victor C. Huber, M. Scott. Killian

Nebraska Center for Biotechnology: Faculty and Staff Publications

Background/Objectives: Zika virus (ZIKV) infection is associated with life-threatening diseases in humans. To date, there are no available FDA-approved therapies or vaccines for the specific treatment or prevention of ZIKV infection. Variation in the ZIKV envelope protein (Env), along with its complex quaternary structure, presents challenges to synthetic approaches for developing an effective vaccine and broadly neutralizing antibodies (bnAbs). We hypothesized that beta-cyclodextrin (BCD) could be used to uniquely inactivate infectious ZIKV without disruption of Env.

Methods: ZIKV was propagated in Vero cells and admixed with BCD. The BCD-treated ZIKV was evaluated for infectivity using immunofluorescence and quantitative …

Characterization Of Multispecies Microbial Communities At Beef And Pork Processing Plants And Their Impact On Pathogen Stress Tolerance, Rong Wang, Sapna Chitlapilly Dass, Vignesh Palanisamy, You Zhou, Tatum Katz, Joseph M. Bosilevac

Nebraska Center for Biotechnology: Faculty and Staff Publications

Escherichia coli O157:H7 and Salmonella enterica are major foodborne pathogens. Biofilm formation may potentially contribute to product contamination by these pathogens at meat processing facilities. Further, pathogen stress tolerance may vary significantly due to the interactions with the multispecies microbial community at meat plants, which may be affected by processing activity, animal species, and the local selective pressure caused by sanitization practices.

We characterized natural microorganisms collected from floor drains at various areas at three beef plants and two pork plants and analyzed their impact on pathogen sanitizer tolerance.

The pathogen strains were able to integrate efficiently into the multispecies …