Biomedical Applications And Syntheses Of Selected Anthraquinone Dyes, Richard Sirard

Senior Honors Theses

Anthraquinones are aromatic organic compounds that have multiple applications in the biomedical field. Some anthraquinone-based compounds are used as fluorophores to contrast cell nuclei while others act as chemotherapeutic agents. However, there are not many fluorescent anthraquinone cell stains currently available. In this study, commercially available anthraquinone dyes, in addition to other dye families and compounds, were reviewed for their unique properties, advantages, and drawbacks. The development and characterization of three novel anthraquinone fluorophores revealed promising photophysical characteristics, like large Stokes shifts. One of the compounds, RBS3, was chosen for fixed and live cell staining and exhibited desirable biomedical properties. …

A Brief Bibliometric Survey Of Explainable Ai In Medical Field, Nilkanth Mukund Deshpande, Shilpa Shailesh Gite

Library Philosophy and Practice (e-journal)

_{^{Background: This study aims to analyze the work done in the field of explainability related to artificial intelligence, especially in the medical field from 2004 onwards using the bibliometric methods.}}

_{^{Methods: different articles based on the topic leukemia detection were retrieved using one of the most popular database- Scopus. The articles are considered from 2004 onwards. Scopus analyzer is used for different types of analysis including documents by year, source, county and so on. There are other different analysis tools such as VOSviewer Version 1.6.15. This is used for the analysis of different units such as co-authorship, co-occurrences, citation analysis …}}

Differential White Blood Cell Counting, Gregory Austin

Honors Scholar Theses

This thesis was completed with the goal of developing a model for the detection and differentiation of 8 different classes of white blood cells. Manual differential counting can be a time consuming and laborious task that would greatly be improved by an automated system. The model created in this project was to be used to automatically determine the number of each cell type in a sample, greatly reducing the need for manual counting. The model was produced using a convolutional neural network that utilized transfer learning from MobileNet_V2, an image recognition network produced by Google. After 20 epochs of training …

Highly Branched Polymers Based On Poly(Amino Acid)S For Biomedical Application, Marisa Thompson, Carmen Scholz

PRC-Affiliated Research

Polymers consisting of amino acid building blocks continue to receive consideration for biomedical applications. Since poly(amino acid)s are built from natural amino acids, the same building blocks proteins are made of, they are biocompatible, biodegradable and their degradation products are metabolizable. Some amino acids display a unique asymmetrical AB2 structure, which facilitates their ability to form branched structures. This review compares the three forms of highly branched polymeric structures: structurally highly organized dendrimers, dendrigrafts and the less organized, but readily synthesizable hyperbranched polymers. Their syntheses are reviewed and compared, methods of synthesis modulations are considered and variations on their traditional …

Highly Branched Polymers Based On Poly(Amino Acid)S For Biomedical Application, Marisa Thompson, Carmen Scholz

PRC-Affiliated Research

Polymers consisting of amino acid building blocks continue to receive consideration for biomedical applications. Since poly(amino acid)s are built from natural amino acids, the same building blocks proteins are made of, they are biocompatible, biodegradable and their degradation products are metabolizable. Some amino acids display a unique asymmetrical AB2 structure, which facilitates their ability to form branched structures. This review compares the three forms of highly branched polymeric structures: structurally highly organized dendrimers, dendrigrafts and the less organized, but readily synthesizable hyperbranched polymers. Their syntheses are reviewed and compared, methods of synthesis modulations are considered and variations on their traditional …

Preclinical Development Of Single Walled Carbon Nanotube-Based Optical Biosensors, Eric M. Hofferber

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

High resolution, long-term monitoring of key biological analytes would improve patient outcomes by providing earlier detection of disease states and improved efficacy of treatment. One class of biosensors that have gained much attention in recent years are optical biosensors. Optical probes are attractive biosensors due to their noninvasive nature of detection, as certain light can pass through tissue, water, and blood. Single walled carbon nanotubes (SWNT) are a specific type of optical biosensor that fluoresce in the near infrared range of the electromagnetic spectrum and offer unparalleled spatial and temporal resolution. SWNT have been applied as biosensors in vitro, …

Optimum Double Rhombic Flap Design For Z-Plasty, Abdullah Khan

Honors Theses

In the medical field, especially in plastic surgery, Rhombic flap and z-plasty are common methods in surgical procedures to treat and close complex wounds of different types of injuries/surgery. Each conventional surgical method has its own pros and cons. When both conventional methods join, it would complement each other weaknesses. This senior design project purpose is to investigate the magnitude of stresses build on skin due to transposing of skin in these methods when the wound is close after the surgical procedure is done. In this project a combination of rhombic flap and z-plasty is studied which is Double Rhombic …

Surface-Eroding Drug Delivery Films For Sequential And/Or Intermittent Release Of Psychoactive Drugs, Jason Price

Honors Theses

ABSTRACT JASON BLAKE PRICE: Surface-Eroding Drug Delivery Films for Sequential and/or

Intermittent Release of Psychoactive Drugs For patients with psychiatric diseases, adherence to medication schedules, medication

errors, and abuse are common issues. Promising new forms of therapy for these patients, such as micro-dosed lysergic acid diethylamide (LSD), where patients receive 10-20% of a full dose every third day, present further drug delivery challenges. Sequential or intermittent release of drugs from an implanted device could ensure long-term drug compliance, automate drug dosing during the life of the implant, and eliminate potential for abuse and medication errors. To this end, we generated …

Understanding The Effect Of Adaptive Mutations On The Three-Dimensional Structure Of Rna, Justin Cook

Undergraduate Research and Scholarship Symposium

Single-nucleotide polymorphisms (SNPs) are variations in the genome where one base pair can differ between individuals.¹ SNPs occur throughout the genome and can correlate to a disease-state if they occur in a functional region of DNA.¹According to the central dogma of molecular biology, any variation in the DNA sequence will have a direct effect on the RNA sequence and will potentially alter the identity or conformation of a protein product. A single RNA molecule, due to intramolecular base pairing, can acquire a plethora of 3-D conformations that are described by its structural ensemble. One SNP, rs12477830, which …

Project Alien, Rebecca Mccallin, Madelyn Hoying, Alex Evans, Matthew Nestler, Karli Rae Sutton, Garett Craig, Lucia Secaia Del Cid, Alexander Guy, Rachel Fernandez, Amanda Trusiak, Paige Aley, Ingabire Gakwerere, Nina Dorfner, Maria Mosbacher, Mary Flavin, Selvin Hernandez, Audrey Steen, Benjamin Kazimer

Undergraduate Research and Scholarship Symposium

Project ALIEN is a comprehensive plan to send humans to Mars to look for life on the Martian surface while exploring the viability and adaptability of terrestrial microbes in Martian atmospheric conditions. ALIEN will use a ballistic capture trajectory to get to Mars and stay in aerostationary orbit for a 30-day surface mission, during which two surface crewmembers will perform a variety of experiments to achieve the mission’s goals of Martian microbial discovery within brines of the Gale Crater and terrestrial microbe adaptability and viability to Martian conditions. Experimentation is based on the presumption that Martian microbes are metabolically similar …

Bioprinting Alginate Structures Using The Fresh Method, Amanda Pellegrino

Undergraduate Research and Scholarship Symposium

Three-dimensional bioprinting is a tissue engineering and regenerative medicine technique that utilizes biomaterials to print clinically relevant scaffolds. These scaffolds are used for tissue repair and to treat disease, such as end-organ failure. The main problem with 3D bioprinting is its inability to print soft biomaterials, which collapse due to gravitational forces. In addition, the materials that can be used do not mimic native tissue’s mechanical properties and texture. To combat this, Dr Feinberg’s laboratory at Carnegie Mellon University developed the freeform reversible embedding of suspended hydrogels (FRESH) method. The FRESH method allows for soft biomaterials to be supported in …

Développement D'Une Méthode De Mesure De L'Exposition Sonore Effective Intraauriculaire Pour Une Utilisation En Milieu De Travail, Hugues Nélisse, Fabien Bonnet, Marcos Nogarolli, Jérémie Voix

Rapports de recherche scientifique

De nombreux travailleurs sont exposés quotidiennement à des niveaux de bruit susceptibles d'endommager leur audition. De ce fait, la mesure de l'exposition sonore est essentielle afin d'identifier et d’évaluer des solutions correctives pour protéger adéquatement les travailleurs. Cependant, les méthodes et les technologies de mesure actuelles ne permettent généralement pas de déterminer avec précision l'exposition au bruit subie par un individu sur son lieu de travail. La dosimétrie intraauriculaire est une solution prometteuse pour pallier un certain nombre de problèmes liés aux méthodes de mesure conventionnelles, mais cette méthodologie est fragilisée de trois façons : 1) l'exposition sonore mesurée dans …

Automatic Generation And Novel Validation Of Patient-Specific, Anatomically Inclusive Scoliosis Models For Biomechanics-Informed Surgical Planning, Austin Tapp, Michel Audette, James Bennett

College of Engineering & Technology (Batten) Posters

Scoliosis is an abnormal spinal curvature of greater than 10 degrees. Severe scoliotic deformities are addressed with highly invasive procedures: anterior or posterior spinal fusion approaches. This invasiveness is due, in part, to the constraints of current surgical planning, which utilizes computed tomography (CT) scans unable to discern spinal ligaments that are dissected to make the spine sufficiently compliant for correction. If localization of ligaments and soft tissues were achieved pre-operatively, corrective procedures could become safer and more efficient by using finite element (FE) biomechanical simulations to determine decreased incidences of ligament releases. This research aims to achieve ligament localization …

High Throughput And On-Chip Analysis Of Engineered Extracellular Nano-Vesicles And Their Functional Characterizations, Brendan Johnson, Jiayi Zhang

Bioengineering Senior Theses

In recent years, extracellular vesicles (EVs) have shown great promises as drug delivery vehicles to treat various diseases, including cancer and neurological diseases. EV surface engineering is a critical step to achieve targeted drug delivery. By engineering EVs with transmembrane scaffolds, targeting molecules can be displayed on the EV outer surface, and cargos can be loaded into the EV lumen. However, EV heterogeneity and inadequate EV purification and characterization methods impose great challenges on understanding engineered EVs and choosing appropriate transmembrane scaffolds. To this day, surface engineered EVs are still limited to lab research. In this thesis, we modify the …

Musculoskeletal Modeling Of The Pelvis And Lumbar Spine During Running, Ruth Higgins, Maryam Moeini, Hunter Bennett, Stacie Ringleb

College of Engineering & Technology (Batten) Posters

Musculoskeletal modeling provides an alternative to in-vivo characteristics that are difficult to directly measure for movements such as running, especially for trunk muscles and joints. The full-body-lumbar-spine (FBLS) model by Raabe and Chaudhari, 2016 is an OpenSim model created for simulations of jogging. The lifting full-body (LFB) model by Beaucage-Gauvreau et al., 2018 is an adaptation of the FBLS created for estimating spinal loads during lifting. PURPOSE: Determine validity of the FBLS and LFB models in simulating pelvis and lumbar spine kinematics during running. METHODS: Inverse Kinematics were executed using experimental data for the FBLS and LFB models. To …

3d Lidar Human Skeleton Estimation For Long Range Identification, Alexander Glandon, Lasitha Vidyaratne, Nasrin Sadeghzadehyazdi, Nibir Dhar, Jide Familoni, Scott Acton, Khan Iftekharuddin

College of Engineering & Technology (Batten) Posters

This research project is the continuation of an effort by the Vision Lab to understand human gait and motion using special-purpose imaging sensors and novel computer vision algorithms. The project began using a Motion Capture (MoCap) system which measures 3D human skeleton information in real-time by attaching markers to a human subject and viewing the human motion with a set of cameras at different angles. We developed an algorithm to determine the gender of a subject wearing these sensors. The current phase of this project extends this work using a state-of-the-art flash Lidar sensor. This sensor scans the surface of …

Cyclophilin D Is A Sensor Of Nano-Pulse Stimulation, Brittney Ruedlinger, Bani Hani Maisoun, Lucas Potter, Nicola Lai, Stephen J. Beebe

The Graduate School Posters

Nano-Pulse Stimulation (NPS), a pulsed power-derived technology, stimulates structural and functional changes in plasma membranes and cellular organelles. NPS induces a Ca²⁺ influx and opening of the mitochondrial permeability transition pore (mPTP) that dissipates the mitochondrial membrane potential (ΔΨ_m) and, when sustained, induces regulated cell death. Here we show that in rat cardiomyoblasts (H9C2) cyclophilin D (CypD) is a mitochondrial sensor for NPS as defined by observations that loss of ΔΨ_m is Ca²⁺ and mitochondrial reactive oxygen species (mROS) dependent and cyclosporin A (CsA)-sensitive, which are diagnostic qualities for effects on CypD and the mPTP. …

Trials And Tribulations Of Humanizing Mice For Cancer Research, Brittney Ruedlinger, Steven Warsof, Eric Feliberti, Mary Beth Hughes, Ayobami ‘Edwin’ Oshin, Chunqi Jiang, Brittany P. Lassiter, Siqi Guo, Stephen J. Beebe

The Graduate School Posters

Cancers are aggressive, evasive, and ruthless killers, claiming millions of lives every year. Cancers are heterogeneous and there is often no single, clearly defined problem as they harness and manipulate a multitude of fundamental mechanisms at the very essence of life. To investigate these mechanisms and vet potential interventive therapies, humanized mice offer a unique model as a prelude to the use of nanosecond pulse stimulation (NPS), a pulse power technology applying nanosecond duration, high electric field pulses, to ablate human tumors. Immunodeficient mouse strains, NSG and NSG-SGM3, were engrafted with human immune cells and human tumors, which would allow …

Artificial Lumbar Spinal Disc Implant For Treating Degenerative Disc Disease, Sara Layton, Nikhil Pai, Michael Rueckert

Bioengineering Senior Theses

Degenerative disc disease has been one of the leading causes of debilitating back pain, affecting more than 400 million people yearly worldwide. This disease is so common that top neurosurgeons around the world are performing multiple surgeries every day to help relieve their patients of constant pain. The recovery time after an intense lumbar replacement surgery could vary from patient to patient but something most patients have in common is they do not want to do it again because they need to replace the disc after a few years. This is why our team is led by a top Neurosurgeon, …

Skin Phantom For Biowearable Device Testing, Ruby Karimjee, Brooke Fitzwilson, Jordan Spice

Bioengineering Senior Theses

The biowearable industry currently utilizes animals, humans, and cadavers for testing skin mounted bio-devices. There is a need for a sustainable skin phantom that is capable of simulating the properties of skin. We proposed a skin phantom educational kit that emulates the perspiration and electrical properties (i.e. impedance spectrum) of skin. This kit can mimic the effects of different sweat concentrations and geometrical structures and allows students to visualize how these properties change electrical measurements. We designed a three-layered model composed of silicone rubber sandwiched between agar, which is similar to the skin's elastomeric and porous texture. We used simple …

Classification Of Breast Cancer Using Deep Learning And Mammogram Images, Travis Kay, Derrick Dang Nguyen, Lashan Wijayawickrama

Bioengineering Senior Theses

Breast cancer is the second leading cause of cancer deaths among US women. Thus, it is important for doctors to detect and diagnose breast cancer as early as possible. Mammography has been used for about 30 years, but there have been rapid developments using digital mammography technology and computer aided systems to help improve breast imaging. Deep learning techniques are being developed to provide a more effective tool for the classification of breast cancer. We adopt a transfer learning approach and fine-tune a pre-trained convolutional neural network model for accurate classification of breast masses based on screening mammograms. The model …

G-Map: Gastrointestinal Myoelectric Activity Phantom, Kei Castleberry, Sarah King, Edie O’Connor

Bioengineering Senior Theses

In the biowearable industry, there is a need for benchtop testing methods that present cost-effective, consistent, and ethical alternatives to current preclinical testing. Artificial phantoms serve to meet this need by mimicking the clinically relevant elements that biowearables monitor. They act as a tool for demonstrating a medical device’s safety and efficacy. The objective of this project is to create a gastrointestinal (GI) phantom that emulates the electrical and material properties of the stomach, small intestine, and colon in order to test diagnostic GI biowearables. Our team also aimed to create a computer-simulated model of the phantom in order to …

Tissue Engineering Pre-Reads, Ryan M. Williams

Open Educational Resources

This material provides an introduction to a tissue engineering module in an experimental methods in biomedical engineering course. Students are expected to be familiar with this material prior to a pre-assessment taken at the beginning of class as we have condense lecture time this semester.

Nanoanalytical Analysis Of Bisphosphonate-Driven Alterations Of Microcalcifications Using A 3d Hydrogel System And In Vivo Mouse Model, Jessica L. Ruiz, Joshua D. Hutcheson, Luis Cardoso, Amirala Bakhshian Nik, Alexandra Condado De Abreu, Tan Pham, Fabrizio Buffolo, Sara Busatto, Stefania Frederici, Andrea Ridolfi, Masanori Aikawa, Sergio Bertazzo, Paolo Bergese, Sheldon Weinbaum, Elena Aikawa

Publications and Research

Vascular calcification predicts atherosclerotic plaque rupture and cardiovascular events. Retrospective studies of women taking bisphosphonates (BiPs), a proposed therapy for vascular calcification, showed that BiPs paradoxically increased morbidity in patients with prior acute cardiovascular events but decreased mortality in event-free patients. Calcifying extracellular vesicles (EVs), released by cells within atherosclerotic plaques, aggregate and nucleate calcification. We hypothesized that BiPs block EV aggregation and modify existing mineral growth, potentially altering microcalcification morphology and the risk of plaque rupture. Three-dimensional (3D) collagen hydrogels incubated with calcifying EVs were used to mimic fibrous cap calcification in vitro, while an ApoE−/− mouse was used …

An Automated Framework For Connected Speech Evaluation Of Neurodegenerative Disease: A Case Study In Parkinson's Disease, Sai Bharadwaj Appakaya

USF Tampa Graduate Theses and Dissertations

Neurodegenerative diseases affect millions of people around the world. The progressive degeneration worsens the symptoms, heavily impacting the quality of life of the patients as well as the caregivers. Speech production is one of the physiological processes affected by neurodegenerative diseases like Alzheimer’s disease, amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD). Speech is the most basic form of communication, and the effect of neurodegeneration degrades speech production, thereby reducing social interaction and mental well-being. PD is the second most common neurodegenerative disease affecting speech production in 90% of the diagnosed individuals. Speech analysis methods for PD in clinical methods …

Predictions Of Knee Joint Contact Forces Using Only Kinematic Inputs With A Recurrent Neural Network, Kaileigh Elisabeth Estler

Human Movement Studies & Special Education Theses & Dissertations

BACKGROUND: Knee joint contact (bone on bone) forces are commonly estimated using surrogate measures such as external knee adduction moments (with limited success) or musculoskeletal modeling (more successful). Despite its capabilities, modeling is not optimal for clinicians or persons with limited experience and knowledge. Therefore, the purpose of this study was to design a novel prediction method for knee joint contact forces that is equal or more accurate than modeling, yet simplistic in terms of required inputs. METHODS: This study included all six subjects’ (71.3±6.5kg, 1.7±0.1m) data from the opensource “Grand Challenge” datasets (simtk.org) and two subjects from the "CAMS" …

Drive Leg And Stride Leg Ground Reaction Forces Relationship To Medial Elbow Stress And Velocity In Collegiate Baseball Pitchers, Brett Smith

Biomedical Engineering Theses & Dissertations

This study examines several different kinetic variables in relation to pitch velocity and elbow varus torque in collegiate baseball pitchers using force plates, an inertial measurement unit, and a radar unit. The purpose of this study is to investigate the kinetic variables being measured and their relationship to pitch velocity and loads being placed on the medial elbow. Twelve collegiate baseball pitchers participated in this study, which was approved by the IRB. Impulse of the drive leg in the anterior-posterior direction, stride leg peak force in the anterior-posterior (AP) direction, elbow varus torque, and pitch velocity were all measured. Two …

Defining The Pathophysiology Of Gut Humoral Immunodeficiency, Ahmed Dawood Mohammed

Theses and Dissertations

Mucosal antibodies maintain gut homeostasis by promoting spatial segregation between host tissues and luminal microbes. Antibody-deficiency is the most common form of primary immunodeficiency observed in humans. In antibody-deficient humans, abnormal composition of the gut microbiota ('dysbiosis') is associated with chronic inflammatory responses and gastrointestinal complications. However, the mechanisms by which dysbiosis promotes inflammatory disease are poorly defined. In the studies described in this dissertation, we utilize CD19-/- mice as a model of antibody deficiency to test the hypothesis that antibody deficiency negatively impacts gut physiology under steady-state conditions. Chapter #1 is an overview of B cell development and how …

Development And Mechanical Characterization Of A Composite Biomaterial Made From Agricultural Waste Reinforcement In A Fungal Mycelium Matrix., John Adam Howe

Honors Capstones

No abstract provided.

Velocity Distribution And Stress Analysis In A Continuous Exchange Cell-Free Protein Synthesis System, Grace Nguyen

Honors Capstones

No abstract provided.