Engineering Commons^™

Under-Oil Autonomously Regulated Oxygen Microenvironments: A Goldilocks Principle-Based Approach For Microscale Cell Culture, Chao Li, Mouhita Humayun, Glenn M. Walker, Keon Young Park, Bryce Connors, Jun Feng, Molly C. Pellitteri Hahn, Cameron O. Scarlett, Jiayi Li, Yanbo Feng, Ryan L. Clark, Hunter Hefti, Jonathan Schrope, Ophelia S. Venturelli, David J. Beebe

Faculty and Student Publications

Oxygen levels in vivo are autonomously regulated by a supply–demand balance, which can be altered in disease states. However, the oxygen levels of in vitro cell culture systems, particularly microscale cell culture, are typically dominated by either supply or demand. Further, the oxygen microenvironment in these systems is rarely monitored or reported. Here, a method to establish and dynamically monitor autonomously regulated oxygen microenvironments (AROM) using an oil overlay in an open microscale cell culture system is presented. Using this method, the oxygen microenvironment is dynamically regulated via the supply–demand balance of the system. Numerical simulation and experimental validation of …

Analysis Of An Existing Method In Refinement Of Protein Structure Predictions Using Cryo-Em Images, Maytha Alshammari, Jing He, Willy Wriggers, Jiangwen Sun

College of Sciences Posters

Protein structure prediction produces atomic models from its amino acid sequence. Three-dimensional structures are important for understanding the function mechanism of proteins. Knowing the structure of a given protein is crucial in drug development design of novel enzymes. AlphaFold2 is a protein structure prediction tool with good performance in recent CASP competitions. Phenix is a tool for determination of a protein structure from a high-resolution 3D molecular image. Recent development of Phenix shows that it is capable to refine predicted models from AlphaFold2, specifically the poorly predicted regions, by incorporating information from the 3D image of the protein. The goal …

Identification Of Messenger Molecule For Immuno-Antibacterial Infection Drug Discovery With The Usage Of Bio-Ai, Minqiao (Lisa) Jin

Bioengineering Master's Theses

Facing the danger of Gram-positive bacterial infection, mammalian cells have their defense line. A functional proteomics study aided with Deep Learning indicates the direct interaction between collagen V from mammalian cell membrane and Sortase A which catalyzes the display of virulence factors on the gram positive bacteria. And CHO cell proteomes conducted with the use artificial intelligence via Tensorflow and found that the identified anti collagen V binds to Sortase A of S. aureus and regulates its monomer-homodimer equilibrium, which is responsible for the bacterial cell wall sorting activity. Our results suggest that the collagen V plays an instrumental role …

Engineering Stealthy Exosomes For Drug Delivery, Chris Olson, Mika Domingo

Bioengineering Senior Theses

Exosomes, a class of extracellular vesicles (EVs) are emerging as a new scientific and therapeutic tool for imaging, disease diagnostics, and drug delivery. Exosomes' excellent biological properties make them a strong candidate for surface modification as well as exogenous drug loading. While exosomes have excellent natural biocompatibility properties as well as low immunogenicity, they are still eliminated in the patient’s body through the immune system, mainly through phagocytosis by macrophages. In this report, we aim to aid exosomes in avoiding this elimination method by modifying them through surface display with antiphagocytic factors. We will use CD24 and CD47 “don't eat …

Accelerating Peripheral Nerve Regeneration Using Electrical Stimulation Of Selected Power Spectral Densities, Wei-Ming Yu, Madelyn Mccullen, Vincent Chiun-Fan Chen

Engineering Science Faculty Publications

Peripheral nerve injuries are common consequences of extremity trauma or chronic compression with a prevalence of 43.8 per 1 million people (on average) reported in the United States annually, accompanied by a yearly increase in cost of care. Patients suffering from these injuries require surgical procedures and rehabilitative strategies to reinforce their extensive recovery. Several studies have found that the application of electrical stimulation can accelerate peripheral nerve regeneration, thus shortening the time of peripheral nerve growth and reducing the cost of care (Willand et al., 2016). The electrical stimulation paradigms that effectively enhanced functional recovery in most studies employed …

Skin Phantom For Wearable Device Benchtop Testing, Laura Apolloni, Vindhya Mullapudi, Takumi Simon

Bioengineering Senior Theses

The biowerables constitute one of the fastests growing sectors of the medical device industry. Novel approaches for rapid prototyping have increased design and development speeds. However, in vivo testing that is currently used for many medical devices makes testing time-consuming, costly, and presents ethical issues. As an alternative, benchtop testing tools promise to alleviate these concerns. Artificial tissue phantoms that are capable of mimicking the characteristics of human tissues are required for demonstrating a medical device’s safety and efficacy in benchtop tests. While there are many hydrogels that are able to mimic these relevant properties of human tissue, creating a …

Impulse, Spring 2022, University Marketing And Communications, Jerome J. Lohr College Of Engineering

Impulse (Jerome J. Lohr College of Engineering Publication)

2 | Ahmed Leads Construction and Operations Management
4 | Faculty News
8 | Kelley Steps Aside After 44 Years
12 | Boggs Retires From Mechanical Engineering
14 | Looking At Covid-19 Numbers
16 | Students Help College of Nursing
18 | Midwest Applied Materials Symposium Debuts
20 | Fourth Data Science Event Takes Place
24 | College Achievements
26 | Hard Work Pays Off
28 | Spotlight Shines on Students
30 | Mentoring Program Takes Off
32 | Robotics Club Busy With Activities
34 | The Numbers
36 | Brown, Sieve Honored
38 | Alumna Leads NASA Division
40 …

Modelling And Validation Of A Gas-Solid Fluidized Bed Using Advanced Measurement Techniques, Sebastián Uribe, Haidar Taofeeq, Muthanna H. Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

With a Euler-two-phase (E2P) approach, through computational fluid dynamics (CFD) techniques, a mathematical model for the prediction of the local hydrodynamic behavior of a gas-solid fluidized bed was implemented. Simulations are conducted for a fluidized bed of 0.14 m internal diameter packed with Gerdart B glass beads particles, with an average diameter of 365 μm, at dimensionless inlet velocities ranging from (Formula presented.). The implemented model considers the multiphase and multiscale interactions through the inclusion of three sub-models, which allows the model to have a broad range of applicability. Predictions were compared against experimental measurements reported on previous contributions for …

Integrated Direct Air Capture And Oxidative Dehydrogenation Of Propane With Co2 At Isothermal Conditions, Shane Lawson, Khaled Baamran, Kyle Newport, Turki Alghamadi, Gary Jacobs, Fateme Rezaei, Ali A. Rownaghi

Chemical and Biochemical Engineering Faculty Research & Creative Works

Developing routes of utilizing CO₂ emissions is important for long-term environmental preservation, as storing such emissions underground will eventually become unsustainable. One way of utilizing CO₂ emissions is as a light-oxidant feedstock for oxidative dehydrogenation of propane (ODHP) to propylene. However, the adsorption and reaction steps typically occur at widely different temperatures, meaning that the thermal gradients – and by extension process energy requirements – are often unreasonably high. In recent years, dual-functional materials (DFMs) – i.e., materials comprised of a high temperature adsorbent phase alongside a heterogeneous catalyst – have been employed for combined CO₂ adsorption …

Bioai For Anti-Infective Drug Discovery, Maria Esquivel, Johann Fernando, Anna Fisher, Cameron Leong, Adam Weaver

Interdisciplinary Design Senior Theses

Modern antibacterial drugs are quickly becoming insufficient for medical, agricultural and veterinary use, and the drug design techniques used to supplement the supply are not able to adequately and quickly produce enough effective candidates. We took a multi-pronged approach to remedying this problem, including shifting the target mechanism from antibiotic drugs in favor of anti-infective drugs, developing an AI which aimed to predict the interactions of small molecule fragments with the target protein, and refining wet lab testing protocols in order to make the drug design process holistically more efficient and effective. We have shown that there is potential in …

Biomechanical And Psychological Predictors Of Failure In The Air Force Physical Fitness Test, Jeffrey Turner, Brent T. Langhals, Torrey J. Wagner

Faculty Publications

Physical fitness is a pillar of U.S. Air Force (USAF) readiness and ensures that Airmen can fulfill their assigned mission and be fit to deploy in any environment. The USAF assesses the fitness of service members on a periodic basis, and discharge can result from failed assessments. In this study, a 21-feature dataset was analyzed related to 223 active-duty Airmen who participated in a comprehensive mental and social health survey, body composition assessment, and physical performance battery. Graphical analysis revealed pass/fail trends related to body composition and obesity. Logistic regression and limited-capacity neural network algorithms were then applied to predict …

Baseball Pitching Arm Three-Dimensional Inertial Parameter Calculations From Body Composition Imaging And A Novel Overweight Measure For Youth Pitching Arm Kinetics, Dalton J. Jennings, Scott K. Reaves, Jeffrey Sklar, Colin Brown, John Mcphee, Scott Hazelwood, Stephen M. Klisch

Biomedical Engineering

Many baseball pitching studies have used inverse dynamics to assess throwing arm kinetics as high and repetitive kinetics are thought to be linked to pitching injuries. However, prior studies have not used participant-specific body segment inertial parameters (BSIPs), which are thought to improve analysis of high-acceleration motions and overweight participants. This study's objectives were to (1) calculate participant-specific BSIPs using dual energy X-ray absorptiometry (DXA) measures, (2) compare inverse dynamic calculations of kinetics determined by DXA-calculated BSIPs (full DXA-driven inverse dynamics) against kinetics using the standard inverse dynamics approach with scaled BSIPs (scaled inverse dynamics), and (3) examine associations between …

A Meshless Approach To Computational Pharmacokinetics, Anthony Matthew Khoury

Doctoral Dissertations and Master's Theses

The meshless method is an incredibly powerful technique for solving a variety of problems with unparalleled accuracy and efficiency. The pharmacokinetic problem of transdermal drug delivery (TDDD) is one such topic and is of significant complexity. The locally collocated meshless method (LCMM) is developed in solution to this topic. First, the meshless method is formulated to model this transport phenomenon and is then validated against an analytical solution of a pharmacokinetic problem set, to demonstrate this accuracy and efficiency. The analytical solution provides a locus by which convergence behavior are evaluated, demonstrating the super convergence of the locally collocated meshless …

Neurogen: Eeg And Near-Infrared Light Stimulation Control System, Karina Sanchez, Sruthi Sakthivel, Michael Bose, Evan Jennings

Interdisciplinary Design Senior Theses

Neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease are widespread, affecting millions of people worldwide. These diseases occur when neurons in the brain or peripheral nervous system progressively lose function and deteriorate. Current pharmacological treatments manage some of the neurological symptoms, but there is no cure yet. Interventions that mitigate or restore loss of function can fill the void until that goal is met. Light stimulation, or transcranial photobiomodulation (tPBM) therapy, can help treat people with neurodegenerative diseases, as it has been shown to improve sleep, attention, memory, and cognitive function.

The objective of this project is to develop …

The Tin Man Needs A Heart: A Proposed Framework For The Regulation Of Bioprinted Organs, Linda Foit

Fordham Law Review

Each day, seventeen people die in the United States while waiting for an organ transplant. At least part of this need could be met by bioprinting, a technology that allows the on-demand production of custom-sized organs from a patient’s own cells. The field of bioprinting is progressing rapidly: the first bioprinted organs have already entered the clinic. Yet, developers of bioprinted organs face significant uncertainty as to how their potentially lifesaving products will be regulated—and by which government agency. Such regulatory uncertainty has the potential to decrease investment and stifle innovation in this promising technological field. This Note examines how …

Overcoming Supply Disruptions During Pandemics By Utilizing Found Hardware For Open Source Gentle Ventilation, S. Oberloier, N. Gallup, J. M. Pearce

Michigan Tech Publications, Part 1

This article details the design of an open source emergency gentle ventilator (gentle-vent) framework that can be used in periods of scarcity. Although it is not a medical device, the system utilizes a wide range of commonly-available components that are combined using basic electronics skills to achieve the desired performance. The main function of the gentle-vent is to generate a calibrated pressure wave at the pump to provide support to the patient's breathing. Each gentle-vent permutation was tested using a DIY manometer as it would be utilized in the field in low-resource settings and validated with an open source VentMon. …

Noninvasive In Vivo Optoacoustic Imaging Of Alcohol Use Disorder Using A Mouse Model Of Alcohol Use Disorder, Augustine Meombe Mbolle

USF Tampa Graduate Theses and Dissertations

This research has two parts. The first part focuses on the use of photoacoustic imaging (PAI) to study alcohol-induced effects in the cerebral vasculature of selectively bred alcohol-preferring mice. Part two extends the application of PAI by developing a novel Photoacoustic imaging guided system for repetitive low intensity focused ultrasound (PAI-LIFU) stimulation treatment for alcohol use disorder in crossed high alcohol preferring (cHAP) mice.

Photoacoustic imaging is an emerging hybrid non-invasive optical imaging modality which relies on optical absorption contrast to visualize deep tissue structures and function. It combines the high contrast associated with pure optical imaging and the high …

Biomechanical Analysis Of Athletes Sprinting With Varying Degrees Of Resistance, Michaela Ott

Honors Program: Senior Projects (Public)

Utilizing resistance methods for sprinters is a common approach to their training. In this study, six athletes from the University of Nebraska-Lincoln Women’s Track and Field Team ran a series of sprints using a resistance machine to collect data regarding the change in power output, stride length, level of trunk tilt with respect to the ground, and acceleration throughout a distance of ten meters when different amounts of resistant forces were applied to the athlete. It was hypothesized that as resistance increased, power output would increase, stride length would decrease, the runners would become more horizontal resulting in a larger …

Process- And Product-Related Foulants In Virus Filtration, Solomon Isu, Xianghong Qian, Andrew L. Zydney, S. Ranil Wickramasinghe

Biomedical Engineering Faculty Publications and Presentations

Regulatory authorities place stringent guidelines on the removal of contaminants during the manufacture of biopharmaceutical products. Monoclonal antibodies, Fc-fusion proteins, and other mammalian cell-derived biotherapeutics are heterogeneous molecules that are validated based on the production process and not on molecular homogeneity. Validation of clearance of potential contamination by viruses is a major challenge during the downstream purification of these therapeutics. Virus filtration is a single-use, size-based separation process in which the contaminating virus particles are retained while the therapeutic molecules pass through the membrane pores. Virus filtration is routinely used as part of the overall virus clearance strategy. Compromised performance …

The Submission Of A Section 513(G) Request For Information, Morgan Ashley Lano

Theses and Dissertations

The Food and Drug Administration designates all medical devices into one of three general classes contingent on their intended use, indications for use, and potential risk to the user. This classification dictates the further path the device must take to be approved for the commercial market. Section 513(g) of the Federal Food, Drug, and Cosmetic Act (21 U.S.C. 360c(g)) is submitted in order to gain the agency’s unofficial classification and suggested regulatory requirements. The Coagulation Companion (MicroVide) is a device designed to fluorescently quantify a key enzyme involved in the coagulation cascade, plasmin, in pediatric patients. clot formation and degradation …

Engineering And Optimization Of An Aav Based Viral Vector To Limit The In-Vitro Expression Of Sars-Cov-2 Spike-Protein, Ronald Anderson Smithwick

Theses and Dissertations

Severe Acute Respiratory Syndrome Corona Virus-2, also known as SARS-CoV-2, is a newly emerged respiratory viral pathogen. The outbreak of SARS-CoV-2 started in Wuhan, China, in late 2019 and rapidly transformed into a pandemic. Several vaccines have been developed and are available to the public on an unprecedented timeline, protecting individuals from a severe infection and saving precious lives. However, none of the vaccines can provide a sterile immunity, and the SARS-CoV-2 transmission cycle continues. Additionally, because of the mutation-prone RNA genome and immunological selection pressure, SARS-CoV-2 is rapidly mutating, especially the Spike(S) protein, and new viral strains are arising …

Interrogating The Role Of Ing4 In Hematopoietic Stem Cells And Cancer, Zanshé Thompson

Theses and Dissertations

We recently identified the tumor suppressor, Ing4, as a critical regulator of hematopoietic stem cell (HSC) homeostasis. The mis-regulation of Ing4 in human cancers has also been shown to lend malignant cells specific advantages that support carcinogenesis and tumor progression. This activity is, in part, due to Ing4 mediated regulation of overlapping signaling pathways that regulate stem cell activity and cancer cells, including NF-B and c-Myc. In a two-part study, we have investigated the role of Ing4 in murine hematopoiesis and human malignancies. While the specific mechanisms of stem cell self-renewal, maintenance, and differentiation are poorly characterized, we have determined …

Macrophage-Targeted Anti-Ccl2 Immunotherapy Enhances Tumor Sensitivity To 5-Fluorouracil In A Balb/C-Ct26 Murine Colon Carcinoma Model Measured Using Diffuse Reflectance Spectroscopy, Shelby N. Bess, Gage J. Greening, Narasimhan Rajaram, Timothy J. Muldoon

Biomedical Engineering Faculty Publications and Presentations

Background

Immunotherapy in colorectal cancer (CRC) regulates specific immune checkpoints and, when used in combination with chemotherapy, can improve patient prognosis. One specific immune checkpoint is the recruitment of circulating monocytes that differentiate into tumor-associated macrophages (TAMs) and promote tumor angiogenesis. Changes in vascularization can be non-invasively assessed via diffuse reflectance spectroscopy using hemoglobin concentrations and oxygenation in a localized tumor volume. In this study, we examine whether blockade of monocyte recruitment via CCL2 (macrophage chemoattractant protein-1) leads to enhanced sensitivity of 5-fluorouracil (5-FU) in a CT26-Balb/c mouse model of CRC. It was hypothesized that the blockade of TAMs will …

Finding Signal In The Noise: High-Fidelity, Quantitative, Optical Blood Perfusion Imaging With Interference, Abdul Mohaimen Safi

USF Tampa Graduate Theses and Dissertations

For label-free, non-invasive, wide field-of-view (FOV) imaging/monitoring of blood flow, speckle-based approaches are gaining popularity. However, to obtain quantitative flow information, speckle techniques rely on the multi-exposure scheme which requires complex, bulky, and expensive instrumentation, limiting its application to preclinical studies. This dissertation directly addresses these issues. In the first part of this dissertation, we report a novel single shot synthetic multi-exposure speckle imaging (syMESI) method to synthetically produce multi-exposure images from one short single exposure speckle image using spatial binning/averaging. We demonstrate that syMESI can reimagine conventional hardware based MESI, with low-cost single exposure laser speckle imaging (LSCI) instrumentation. …

Volume Introduction, I. Glenn Cohen, Timo Minssen, W. Nicholson Price Ii, Christopher Robertson, Carmel Shachar

Other Publications

Medical devices have historically been less regulated than their drug and biologic counterparts. A benefit of this less demanding regulatory regime is facilitating innovation by making new devices available to consumers in a timely fashion. Nevertheless, there is increasing concern that this approach raises serious public health and safety concerns. The Institute of Medicine in 2011 published a critique of the American pathway allowing moderate-risk devices to be brought to the market through the less-rigorous 501(k) pathway,1 flagging a need for increased postmarket review and surveillance. High-profile recalls of medical devices, such as vaginal mesh products, along with reports globally …

Synthesis Of Thiol-Acrylate Hydrogels For 3d Cell Culture And Microfluidic Applications, Anowar Hossain Khan

LSU Doctoral Dissertations

Globally cell culture is an $18.98 billion industry as of 2020, with an 11.6 percent annual growth rate. Drug discovery has an estimated worth of $69.8 billion in 2020 and is predicted to grow to $110.4 billion by 2025. Three-dimensional (3D) cell culture of cancer cells is one of the rapidly growing felids since it better recapitulates in vivo conditions compared to two-dimensional (2D) models. However, it is challenging to grow 3D tumor spheroids outside the body, and some of the existing technology can generate these spheroids outside the human body but poorly mimic in vivo tumor models. Therefore, there …

Two-Stage Transfer Learning For Facial Expression Classification In Children, Gregory Hubbard, Megan Witherow, Khan Iftekharuddin

Undergraduate Research Symposium

Studying facial expressions can provide insight into the development of social skills in children and provide support to individuals with developmental disorders. In afflicted individuals, such as children with Autism Spectrum Disorder (ASD), atypical interpretations of facial expressions are well-documented. In computer vision, many popular and state-of-the-art deep learning architectures (VGG16, EfficientNet, ResNet, etc.) are readily available with pre-trained weights for general object recognition. Transfer learning utilizes these pre-trained models to improve generalization on a new task. In this project, transfer learning is implemented to leverage the pretrained model (general object recognition) on facial expression classification. Though this method, the …

Bayesian Network-Based Diagnostic Support Tool With Limited Point-Of-Care Ultrasound For Work-Related Elbow Injuries, Cristina Maria Franceschini Sánchez

USF Tampa Graduate Theses and Dissertations

The upper extremity is commonly injured at the workplace, frequently involving the elbow. Currently, there are not many diagnostic support tools for elbow injuries. Developing a clinical decision support tool would allow for narrowing differential diagnoses and guide management steps in a timely and cost-effective manner. In a descriptive retrospective cohort study, 85 non-contrast elbow MRIs were obtained from a large Workers Compensation insurer database. MRIs were either (a) greater than 2 weeks after first clinic visit, or (b) more than 6 weeks after injury, but (c) not more than 3 months after injury. A Bayesian network-based diagnostic support tool …

Protocol To Engineer Nanofilms Embedded Lipid Nanoparticles For Controlled And Targeted Drug Delivery (Nectar), Rashi Porwal, Stephen L. Hayward, Srivatsan Kidambi

Department of Chemical and Biomolecular Engineering: Faculty Publications

We present a protocol to engineer a substrate-mediated delivery platform comprising hyaluronic acid-coated lipid nanoparticles (HALNPs) embedded into polyelectrolyte multilayer (PEM) films. This platform allows controlled spatiotemporal release of lipid nanoparticles (LNP) by embedding them within the polyelectrolyte multilayer films matrix. HALNP conjugate with antibodies also adds the ability for targeted delivery. The use of LNP enables this platform to encapsulate both hydrophobic and hydrophilic drugs. This platform can easily be reproduced and utilized for various biomedical drug delivery applications. For complete details on the use and execution of this protocol, please refer to Hayward et al. (2015, 2016a, 2016b), …

Deep Learning Approach For Chemistry And Processing History Prediction From Materials Microstructure, Amir Abbas Kazemzadeh Farizhandi, Omar Betancourt, Mahmood Mamivand

Mechanical and Biomedical Engineering Faculty Publications and Presentations

Finding the chemical composition and processing history from a microstructure morphology for heterogeneous materials is desired in many applications. While the simulation methods based on physical concepts such as the phase-field method can predict the spatio-temporal evolution of the materials’ microstructure, they are not efficient techniques for predicting processing and chemistry if a specific morphology is desired. In this study, we propose a framework based on a deep learning approach that enables us to predict the chemistry and processing history just by reading the morphological distribution of one element. As a case study, we used a dataset from spinodal decomposition …