Biomedical Engineering and Bioengineering Commons^™

Mechanisms Of Correlated Neuronal Activity In The Globus Pallidus, Hamza Albawaliz

Electronic Theses and Dissertations

This thesis investigates the mechanisms of correlated neuronal activity in the globus pallidus externus (GPe), a key structure in the basal ganglia. Neuronal activity in the GPe is reportedly decorrelated in healthy subjects but can become highly correlated in Parkinson’s disease. However, high-density neuronal recordings in the GPe of healthy rats reveal a surprising degree of correlated activity. This raises the question of whether intrinsic properties or network connectivity alone can account for such patterns. To explore this, a computational model was developed in which GPe neurons are represented as coupled phase oscillators influenced by experimentally derived phase-response curves and …

Development Of A Non-Faradaic Impedimetric Biosensor Based On Reduced Graphene Oxide For The Detection Of Brain-Derived Neurotrophic Factor (Bdnf), Mariana N. Martins

Electronic Theses and Dissertations

Neurological disorders affect millions of people worldwide. In the case of Alzheimer’s disease (AD), the rising number of cases significantly increases global healthcare costs. Therefore, early detection of biomarkers at the onset of the disease is essential for early diagnosis. This study presents an electrochemical biosensor designed for the detection of Brain-Derived Neurotrophic Factor (BDNF) in human plasma, incorporating reduced graphene oxide (rGO) to enhance signal sensitivity. Dielectrophoresis (DEP) was employed to deposit rGO flakes on the electrode surface, improving conductivity and sensor performance. Electrochemical impedance spectroscopy (EIS) was used to monitor changes in impedance associated with BDNF binding events, …

Reproducibility In Modeling Of Knee Joint Mechanics, Maryam Nazem

Electronic Theses and Dissertations

Computational modeling of knee joint biomechanics can provide valuable insights into joint function, injury mechanisms, and patient outcomes, and can support surgical planning and informed clinical decision-making. However, achieving consistent and repeatable results, or reproducibility, is a significant challenge that affects the credibility of these models. This thesis addresses reproducibility through two studies related to the KneeHub Project, which is a multi-institutional collaboration designed to investigate reproducibility in finite-element modeling of the knee.

The first study involved model benchmarking, where predicted results of the calibrated models were compared with the experimental data to evaluate model reproducibility. While all models replicated …

Bending Energy Schemes For Discrete-Spring-Network Structural Modelling Of Red Blood Cells, Osayomwanbor Ehi-Egharevba, Mingzhu Chen, Fergal Boyle

Articles

Red blood cells (RBCs) undergo large structural deformation, including bending, when passing through capillaries. They also exhibit a range of complex shapes such as stomatocytes, discocytes and echinocytes that form due to altered blood pH and salt levels, ingested drugs and adenosine triphosphate depletion. Discrete-spring-network structural models of RBCs employ different numerical treatments of the continuum bending energy. This affects bending accuracy and the prediction of accurate RBC shapes. This research compares three representations called bending energy scheme (BES) A, B and C to evaluate their accuracy in shape predictions. BES A, seen throughout the literature, is based on the …

Advanced Plant Growth Using Halloysite Nanotubes (Hnts) And Waste Extraction For Medical Applications, Zeinab Jabbari Velisdeh

Doctoral Dissertations

This dissertation presents an integrated research framework that bridges nanotechnology, green chemistry, and sustainable agriculture, aiming to address two critical global challenges: enhancing plant growth under resource-limited conditions and valorizing agricultural waste for bioactive compound extraction. The study is divided into three major projects that together highlight the innovative application of magnesium oxide-coated halloysite nanotubes (MgO-HNTs) and the development of environmentally conscious extraction methods for high-value phytochemicals. The first component of this work investigates the design, fabrication, and functional evaluation of MgO-HNTs as advanced nanocarriers for promoting seed germination and early root development in tomato plants. MgO-HNTs were synthesized via …

Exploring The Effectiveness Of Virtual Reality Learning Through Use Of Visual Eye-Tracking Analytics (Veta) And Biological Measurements, Mckinley Anne Sherman

Master's Theses

Virtual Reality (VR) offers an immersive and interactive platform for experiential learning. The purpose of this thesis was to evaluate the relationship between physiological responses and cognitive workload within a VR learning environment and to explore VR as an effective instructional tool. This research compared participant engagement, stress, and learning performance within a 6th-grade science module developed in VR by incorporating biometric data collected via Polar H10 heart rate monitor and Varjo Areo VR headset eye-tracking. Thirty-three participants completed a pre-lesson demographic survey, post-lesson survey, VR sickness questionnaire, and the NASA Task Load Index (NASA-TLX). While completing the lesson, the …

Modeling Synaptic Dysfunction As Neural Contagion: A Graph-Based Sedr Framework For Simulating Signal Spread, Michelle Marfo, Dr. Padmanabhan Seshaiyer, Alonso Ogueda-Oliva

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Scientific Characterization Of Historic Mortars Dating From The 15th-Century Of A Historical Building In Algeria: A Case Study, M. E. Belgacem, N. Rabahi-Touloum, R. Neves, Y. Ouldkhaoua

Journal of Sustainable Construction Materials and Technologies

This research investigates the historic mortars (Aggregate/Binder (A/B) ratio) of a historical patrimony building, dating from the 15th century, in Algeria, for restoration purposes. It is well known that thorough characterization is essential for successful restoration. To this end, several techniques, including Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), and X-ray Fluorescence (XRF), optical microscope were used to characterize the historic mortars. A mechanical test was used to characterize the compressive strength of a historic mortar. For a comprehensive characterization, A/B ratios were estimated using both Digital Image Analyses (DIA) and chemical analyses. The results obtained provided clear information on …

Resonant Body Communication For Neurodivergent Contexts: A Multimodal, Temporally Elastic Blueprint For Inclusive Biometric Systems, Piper Hutson, James Hutson

Faculty Scholarship

Prevailing emotion-sensing systems privilege a facial-and-gaze paradigm that encodes neurotypical tempo, channel priority, and expression classes, thereby mischaracterizing or erasing neurodivergent communication. This article advances a design-oriented framework for biometric sensing that centers resonant body communication: temporally extended, multimodal, and environmentally situated patterns of posture, gesture, rhythm, and interoception that carry affective meaning. Through an integrative methodology that synthesizes cognitive neuroscience, embodied arts practices, and human–computer interaction, the study formalizes a theoretical model with four pillars: temporal elasticity, multimodal sensory hierarchies, resonant gestures and rhythmic entrainment, and environmental attunement. Building on this model, the article specifies technical requirements for next-generation …

A Convolutional Neural Network Approach To Breast Cancer Tumor Boundary Detection, James Leah Matlosz

Master's Theses

Breast cancer is the second most common form of cancer and often goes undetected in its initial stages due to its subtle symptoms. As the tumors grow, they become more difficult to surgically remove with clean borders. To minimize the chance of recurrence, a 2D convolutional neural network is developed in this work for delineating tumor boundaries. Specifically, the U-shaped network model is trained, validated, and tested with longitudinal MRI scans of patients diagnosed with breast cancer and undergoing neoadjuvant therapy. For training, image masks were generated as ground truths using signal enhancement ratio segmentation, thresholding, and contour detection. The …

Stress-Relaxation And Failure Properties Of Spinal Ligaments In Pigs With And Without Scoliosis-Like Deformity, Christian D'Andrea, Mattan Orbach, Dogerno Norceide, Madeline Boyes, Axel Moore, Jacob Jordan, Thomas Schaer, Anita Singh, Patrick Cahill, Edward Vresilovic, Brian Snyder, Sriram Balasubramanian

Student Papers, Posters & Projects

This study addresses the need for accurate tissue material properties in computational models of the spine. Fundamental to functional spinal unit (FSU) biomechanics are the stress-relaxation and failure properties of the interspinous and intertransverse ligaments (ISL and ITL, respectively). These were measured and compared in normative and scoliotic spines using a Yorkshire pig model. Skeletally immature female pig spines were posterolaterally tethered to induce scoliosis. 23 ISLs and 17 ITLs excised from normative and scoliotic spine segments underwent stress-relaxation and failure tests. Group comparisons tested the effects of scoliosis (magnitude, convexity versus concavity), spinal level (thoracic, lumbar), and pig age. …

Multiscale 3d Whole Joint Cellular And Molecular Mapping Reveals Disease-Specific Neurovascular Plasticity Underlying The Structure-Pain Relationship, Peng Chen, Jiaxin Chai, Abirami Soundararajan, R. Glenn Hepfer, Benjamin Kheyfets, Jiaxin Hu, Ishraq Alshanqiti, Swarnalakshmi Raman, Ikue Tosa, Jun Tae Huh, Matthew Yee, Brooke J. Damon, Shangping Wang, Yu Shin Kim, Man-Kyo Chung, Mildred C. Embree, Janice S. Lee, Tong Ye, Hai Yao

Publications

Understanding musculoskeletal joints from a 3D multiscale perspective, from molecular to anatomical levels, is essential for resolving the confounding relationships between structure and pain, elucidating mechanisms regulating joint health and diseases, and developing new treatment strategies. Here, a musculoskeletal joint immunostaining and clearing (MUSIC) method specifically developed to overcome key challenges of immunostaining and optical clearing of intact joints are introduced. Coupled with large-field light sheet microscopy, this approach achieves 3D high-resolution, microscale neurovascular mapping within the context of whole-joint anatomy without the need for image coregistration across various joints, including temporomandibular joints, knees, and spines, and multiple species, including …

Fabrication Of Multimodal Anion Exchange Membrane For Chromatographic Purification Of Full Adeno-Associated Viral Capsids, Xiaolei Hao, Sumith Ranil Wickramasinghe, Xianghong Qian

Biomedical Engineering Faculty Publications and Presentations

A multi-modal anion exchange ligand 2-methyl-phenylimidazole has been successfully functionalized on highly porous electrospun regenerated cellulose membrane substrate for the separation of full and empty adeno-associated viral (AAV) capsids. The functionalized membrane has an average pore size of 0.5 mu m and exhibits both charge and hydrophobic functionality. The ligand is able to distinguish the subtle physio-chemical differences between the full and empty viral capsids. The multi-modal anion exchange membrane is able to separate the full capsids from affinity-captured mammalian AAV2 using both gradient and two-step elution methods with superior performance. A full capsid recovery of 72.9% at 85.3% purity …

Characterizing Piezoelectric-Blended Polydimethylsiloxane For Use As A Mechanoelectrical Responsive Cell Culture Substrate, Alexis P. Applequist, Lance D. Cordes, Lais A. Ferreira, Kartik Balachandran

Biomedical Engineering Faculty Publications and Presentations

In this study, we developed a piezoelectric-polydimethylsiloxane (pz-PDMS) composite by blending poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) with PDMS to create a biocompatible, mechanoelectrical responsive material. The pz-PDMS was synthesized with varying piezoelectric concentrations (0%, 1%, 3%, and 5%) and characterized for visual properties, mechanical properties, mechanoelectrical sensitivity, and biocompatibility. Compression testing showed no significant change in mechanical strength with the addition of piezoelectric particles, while mechanolectrical sensitivity testing revealed a non-linear increase in voltage response, with 5% pz-PDMS producing the highest sensitivity. Fatigue testing demonstrated no change in sensitivity after 7 days of cyclic displacement. Additionally, microcantilever experiments demonstrated the high fidelity …

Strategies For Increasing Methane Removal In Methanotroph Stirred-Tank Reactors For The Production Of Ectoine, Jaden Storrer, Tansley M. Mazurkiewicz, Bodee Hancock, Ronald C. Sims

Biological Engineering Student Research

Methane is a potent greenhouse gas that requires its emissions to be mitigated. A significant source for methane emissions is in the form of the biogas that is produced from anaerobic digestion in wastewater reclamation and landfill facilities. Biogas has a high valorization potential in the form of its bioconversion into ectoines, an active ingredient in skin care products, by halotolerant alkaliphilic methanotrophs. Cultures of Methylotuvimicrobium alcaliphilum 20Z were grown in bench scale stirred-tank reactors to determine factors to improve methane uptake and removal. Tangential flow filtration was also implemented for a bio-milking method to recover ectoine from culture media. …

Different Brain Network Connectomic Relationships Subserve Hand Dexterity During Task Versus Resting States In People With Brain Tumors, Timothy F. Boerger, Leon Taquet, Kaitlin Goetschel, Sarah Young, Jennifer Connelly, Jeffrey R. Binder, Brian Schmit, Max O. Krucoff

Biomedical Engineering Faculty Research and Publications

Purpose

The purpose of this study was to explore different brain network connectomic relationships subserving hand dexterity in patients with contrast-enhancing brain tumors during task and resting states.

Method

We measured hand dexterity, resting state functional connectivity, and task-based functional connectivity in 21 participants with newly diagnosed brain tumors. Hand dexterity was measured using the 9-hole peg test (9HPT), and patient-reported outcomes were assessed with the Duroz Hand Index (DHI).

Findings

We discovered the following: (1) The inability to complete dexterous tasks is most associated with low somatomotor-basal ganglia network connectivity during rest but high somatomotor-basal ganglia network connectivity during …

Patient-Informed Fluid-Structure Interaction Simulations Of Bicuspid Aortic Valve In Young Adults Reveal Regionalized Differences In Mechanical Stress, Hail B. Kazik, Harkamaljot S. Kandail, Joy Lincoln, John F. Ladisa

Biomedical Engineering Faculty Research and Publications

Bicuspid aortic valve (BAV) is a common congenital cardiovascular defect characterized by two, rather than three, cusps. Many BAV patients prematurely develop calcification and aortic stenosis by age 35, which is more severe with fusion of the right and noncoronary (RC/NC) cusps. The mechanisms underlying calcification observed within the coaptation, attachment, and fusion regions of BAV patients are unknown. While abnormal mechanical stimuli induced by the bicuspid anatomy likely plays a role, little is known about regionalized mechanical stimuli in these susceptible cusp regions of young patients prior to calcification. Strongly coupled fluid-structure interaction simulations were conducted using physiologic boundary …

Harvesting Aav By Tangential Flow Filtration Using Reverse Asymmetric Membranes, Xiaolei Hao, Ronny Horax, Xianghong Qian, April Wheeler, Hironobu Shirataki, Sumith Ranil Wickramasinghe

Chemical Engineering Faculty Publications and Presentations

Efficient bioreactor clarification for harvesting virus particles is often challenging. Tangential flow filtration is attractive as it can be easily adapted for batch and perfusion operations. Here the feasibility of using reverse asymmetric hollow fiber membranes, where the more open support structure faces the feed stream, has been investigated for harvesting adeno associated virus serotype 2. The open support structure of these membranes stabilizes a secondary membrane consisting of rejected particulate matter. It is essential that the stabilized secondary membrane remains highly permeable. Flux stepping experiments were conducted in total recycle mode in order to determine the critical flux. The …

Capacity Of Microbial Strains And Communities To Degrade Sewerage Fats, Oils, And Grease Clog Deposits, Allondra M. Woods, Catherine J. Pettinger, Catherine Harris, Tanya Soule, Garth Farley, Erica L.-W. Majumder

Biological Engineering Student Research

Fats, oils, and grease (FOG) deposits are hardened, sticky, insoluble solids that accumulate in sewage systems globally. These deposits contribute to pipe blockages and sanitary sewer overflows, releasing pathogens and pollutants into the environment, posing significant environmental and public health risks. Current removal methods are labor-intensive and costly, emphasizing the need for alternatives. While biological strategies offer a viable alternative, the microbial breakdown of FOG is poorly understood. In this study, we evaluated the potential of individual microbial strains and synthetic microbial communities to biodegrade wastewater-derived FOG deposit samples. These biological agents were applied to a range of FOG samples, …

Metabolic Insights Into Cyst Fluid Composition And The Role Of Taurine In Polycystic Kidney Disease, Vineetha Garimella

USF Tampa Graduate Theses and Dissertations

Polycystic kidney disease (PKD) is the most common genetic disorder affecting kidneys and the fourth leading cause of kidney failure. It occurs in two major forms, autosomal dominant PKD (ADPKD), and autosomal recessive PKD (ARPKD). ADPKD is typically adult-onset and caused by mutations in the PKD1 and PKD2 genes, and ARPKD generally manifests in utero and is caused by mutations in the PKHD1 gene. Despite the severity of the disease, only one FDA-approved drug, tolvaptan, is currently available for ADPKD and remains under clinical investigation for ARPKD. However, its use is limited by adverse side effects including polyuria, polydipsia, and …