Engineering Commons^™

Frequency Sensitive Mechanism In Low-Intensity Ultrasound Enhanced Bioeffects, April D. Miller, Abdoulkadri Chama, Tobias M. Louw, Anuradha Subramanian, Hendrik J. Viljoen

Department of Chemical and Biomolecular Engineering: Faculty Publications

This study presents two novel theoretical models to elucidate frequency sensitive nuclear mechanisms in low-intensity ultrasound enhanced bioeffects. In contrast to the typical 1.5 MHz pulsed ultrasound regime, our group previously experimentally confirmed that ultrasound stimulation of anchored chondrocytes at resonant frequency maximized gene expression of load inducible genes which are regulatory markers for cellular response to external stimuli. However, ERK phosphorylation displayed no frequency dependency, suggesting that the biochemical mechanisms involved in enhanced gene expression is downstream of ERK phosphorylation. To elucidate such underlying mechanisms, this study presents a theoretical model of an anchored cell, representing an in vitro …

The Effect Of Antigen Polymorphisms On Serological Antibody Detection Assays Based Upon The, Kristi M. Miley

USF Tampa Graduate Theses and Dissertations

Onchocerca volvulus is a filarial parasite transmitted to humans by female Simulium spp. black flies. Infection with this parasite can cause blindness and severe skin disease among humans in Africa and the Americas. Enzyme-linked Immunosorbent Assay serological testing of OV-16 antigen is a diagnostic tool for determining effective elimination of the parasite. Programs typically rely on OV–16 ELISA to evaluate the progress towards interruption and/or elimination of disease by mass drug distribution of ivermectin and vector larvicidal control efforts. As elimination grows closer, monoclonal antibody positive controls for OV-16 ELISA become important to develop for Onchocerca testing due to the …

Pairing Of Anaerobic And Aerobic Treatment Of Petroleum Wastewater, Zachary Fica

Undergraduate Honors Capstone Projects

The objective of this project was to treat petroleum refinery wastewater using a combination of anaerobic and aerobic processes, namely an Up-flow Anaerobic Sludge Blanket (UASB) reactor paired with a Rotation Algae Biofilm Reactor (RABR), respectively, to produce a treated effluent. The treatment method developed needed to produce a cost-effective and efficient way to decrease nitrogen, phosphorous, total suspended solids (TSS), and COD concentrations to below State of Utah limitations. It was demonstrated that RABR treatment was capable of reducing effluent concentrations of nitrogen, phosphorus, and TSS to State of Utah limitations. RABR treatment did not significantly reduce COD from …

Department Of Biological Systems Engineering Newsletter, Spring 2017

BSE Department Magazine

No abstract provided.

Dysregulation Of Phospholipase D (Pld) Isoforms Increases Breast Cancer Cell Invasion, Kristen Fite

Browse all Theses and Dissertations

Breast cancer remains the second most prevalent cancer among women in the U.S. with metastatic breast cancer having the worst prognosis. A rapidly proliferating tumor under various stressors will promote phenotypic cellular changes, known as epithelial-to-mesenchymal transition (EMT), which allows cells to begin to invade surrounding tissue, enter the circulatory system, and eventually seed a distant metastatic site. The phospholipase D (PLD) enzymes are critical regulators of cell signaling pathways necessary for cell migration. While the importance of PLD enzymes in cancer cell invasion is well known, clinically applicable methods of PLD inhibition are not yet available. The best-studied isoforms …

Biomanufacturing Through Igem-An International Student Competition, Asif Rahman, Ryan J. Putman, Neal Hengge, Charles D. Miller

Biological Engineering Faculty Publications

The foundations of synthetic biology are built on molecular biology and genetic engineering. One of the purposes of synthetic biology is to make biology easier to engineer by the creation of standardized biological parts and devices. There are a wide range of potential applications for synthetic biology and a variety of approaches to constructing parts and systems. Undergraduate Science, Technology, Engineering, and Mathematics (STEM) students from around the world apply synthetic biology principles at the annual International Genetically Engineered Machine (iGEM) competition to demonstrate functioning biological systems created from standardized parts. The iGEM competition will continue to add to the …

Functional 3-D Cellulose And Nitrocellulose Paper-Based, Microfluidic Device Utilizing Elisa Technology For The Detection/Distinction Between Hemorrhagic And Ischemic Strokes, Alicia Leanne Holler

Master's Theses

The purpose of this thesis project is to demonstrate and evaluate an enzyme-linked immunosorbent assay (ELISA) on a paper microfluidic device platform. The integration of ELISA technology onto paper microfluidic chips allows for a quantitative detection of stroke biomarkers, such as glial fibrillary acidic protein (GFAP). Dye experiments were performed to confirm fluid connectivity throughout the 3D chips. Several chip and housing designs were fabricated to determine an optimal design for the microfluidic device. Once this design was finalized, development time testing was performed. The results confirmed that the paper microfluidic device could successfully route fluid throughout its channels at …

How Do The Social Benefits And Costs Of The Patent System Stack Up In Pharmaceuticals?, Daniel J. Gifford

Journal of Intellectual Property Law

This paper explores the workings of the patent system in the context of the generation of new pharmaceutical products. First it identifies the relevant characteristics of the patent system and its relation to the market. The paper concedes that, in general, the patent system is probably the best way of generating new technology, in substantial part because that system uses the market to provide both incentives and rewards. The paper also identifies downsides of this patent/market system: deadweight loss and the unresponsiveness of that patent/market system to the needs of the poor. The paper then explores the social costs and …

Microfluidic E. Coli Detection, Kyle Pietrzyk, Scott Fukuoka, Andres Maldonado-Liu, Andy Ly

Interdisciplinary Design Senior Theses

In both developed and developing countries, there is a need for a fast diagnostic system to detect pathogens within a fluid sample. In developing a microfluidic platform, which utilizes a microfluidic chip and an optical detection method, doors may be opened for new methods of determining pathogen concentration in fluid. Most biological reactions are not instantaneous. A flow-controlling mechanism with no power requirement may be implemented in the microfluidic platform. As a proof-of-concept, our device uses a microfluidic chip, smartphone, and microlens to detect E. coli concentrations in water. The detection method is based on the latex agglutination assay which …

Calcium Phosphate As A Key Material For Socially Responsible Tissue Engineering, Vuk Uskoković, Victoria M. Wu

Pharmacy Faculty Articles and Research

Socially responsible technologies are designed while taking into consideration the socioeconomic, geopolitical and environmental limitations of regions in which they will be implemented. In the medical context, this involves making therapeutic platforms more accessible and affordable to patients in poor regions of the world wherein a given disease is endemic. This often necessitates going against the reigning trend of making therapeutic nanoparticles ever more structurally complex and expensive. However, studies aimed at simplifying materials and formulations while maintaining the functionality and therapeutic response of their more complex counterparts seldom provoke a significant interest in the scientific community. In this review …

Chitosan As An Antiviral, Tayler Pauls

Biomedical Engineering Undergraduate Honors Theses

There is no broad-based antiviral medication available today; there are specific antivirals, for example, the antiretroviral for HIV. However, these specific antivirals are not available in each country and can be problematic for specific patients. Chitosan is proposed as a possible broad-based antiviral, which has already demonstrated antibacterial properties, antiviral properties in plants, is used for wound healing and as a hydrogel among other medical applications. The methods used are transfection of NIH-3T3 cells with GFP-adenovirus with 0.1%, 0.5%, and 1% chitosan added to virus prior to transfection. Fluorescence microscopy and flow cytometry data has validated that the use of …

A Roadmap To Safe And Reliable Engineered Biological Nano-Communication Networks, Justin W. Firestone

School of Computing: Dissertations, Theses, and Student Research

Synthetic biology has the potential to benefit society with novel applications that can improve soil quality, produce biofuels, grow customized biological tissue, and perform intelligent drug delivery, among many other possibilities. Engineers are creating techniques to program living cells, inserting new logic, and leveraging cell-to-cell communication, which result in changes to a cell's core functionality. Using these techniques, we can now create synthetic biological organisms (SBOs) with entirely new (potentially unseen) behaviors, which, similar to silicon devices, can sense, actuate, perform computation, and interconnect with other networks at the nanoscale level. SBOs are programmable evolving entities, and can be likened …

The Use Of Microfluidics And Dielectrophoresis For Separation, Concentration, And Identification Of Bacteria, Cynthia Hanson, Michael Sieverts, Karen Tew, Annelise Dykes, Michaela Salisbury, Elizabeth Vargis

Biological Engineering Faculty Publications

Traditional bacterial identification methods take one to two days to complete, relying on large bacteria colonies for visual identification. In order to decrease this analysis time in a cost-effective manner, a method to sort and concentrate bacteria based on the bacteria's characteristics itself is needed. One example of such a method is dielectrophoresis, which has been used by researchers to separate bacteria from sample debris and sort bacteria according to species. This work presents variations in which dielectrophoresis can be performed and their associated drawbacks and benefits specifically to bacterial identification. In addition, a potential microfluidic design will be discussed.

Low-Cost, Wireless Optical Oximeter For Monitoring Of Brain Function In High-Risk Pediatric Population, Zahra Meghjani

Browse all Theses and Dissertations

Nearly 4 million neonates die every year due to brain injuries, most caused by hypoxia. Neonatal ICU requires newborns with critical health conditions to be monitored continuously calling for the need of a non-invasive, compact and portable device. However, commercial devices are mostly bulky and/or expensive. The neonatal mortality is higher in under-developed countries, where such expensive and large devices are not affordable. Hence, my thesis focuses on building first generation compact, inexpensive, and wireless device that can monitor and provide feedback to clinicians during intervention. This approach is based on light absorption by oxy- and deoxy-hemoglobin chromophores. The total …

Modeling Effects Of Diet On Human Gut Microbiota, Richard Thomas Agans

Browse all Theses and Dissertations

The human gut microbiota is integrally involved in the metabolism of nutrients contained within the human diet. Studies into human nutrition have primarily been carried out using human and animal models. These studies are extremely important in our understanding of human nutrition, however, suffer from inherent limitations including unique microbial compositions between individuals, compliance in human studies, inability to carry out mechanistic studies, and inability to interrogate proximal regions of the gut without applying invasive techniques. In vitro gut simulator systems circumvent many of these limitations in animal and human models by allowing control of gut environmental conditions, decreasing variability …

A Scalable Low-Cost Cgmp Process For Clinical Grade Production Of The Hiv Inhibitor 5p12-Rantes In Pichia Pastoris, Fabrice Cerini, Hubert Gaertner, Knut Madden, Ilya Tolstorukov, Scott Brown, Bram Laukens, Nico Callewaert, Jay C. Harner, Anna M. Oommen, John T. Harms, Anthony R. Sump, Robert C. Sealock, Dustin J. Peterson, Scott K. Johnson, Stephan B. Abramson, Michael M. Meagher, Robin Offord, Oliver Hartley

Department of Chemical and Biomolecular Engineering: Faculty Publications

In the continued absence of an effective anti-HIV vaccine, approximately 2 million new HIV infections occur every year, with over 95% of these in developing countries. Calls have been made for the development of anti-HIV drugs that can be formulated for topical use to prevent HIV transmission during sexual intercourse. Because these drugs are principally destined for use in low-resource regions, achieving production costs that are as low as possible is an absolute requirement. 5P12-RANTES, an analog of the human chemokine protein RANTES/CCL5, is a highly potent HIV entry inhibitor which acts by achieving potent blockade of the principal HIV …

Assessing The Spatial Relationship Between Fixation And Foveal Specializations, Melissa A. Wilk, Adam M. Dubis, Robert F. Cooper, Phyllis Summerfelt, Alfredo Dubra, Joseph Carroll

Biomedical Engineering Faculty Research and Publications

Increased cone photoreceptor density, an avascular zone (FAZ), and the displacement of inner retinal neurons to form a pit are distinct features of the human fovea. As the fovea provides the majority of our vision, appreciating how these anatomical specializations are related is important for understanding foveal development, normal visual function, and retinal disease. Here we evaluated the relationship between these specializations and their location relative to the preferred retinal locus of fixation (PRL). We measured foveal pit volume, FAZ area, peak cone density, and location of the PRL in 22 subjects with normal vision using optical coherence tomography and …

When 1 + 1 > 2: Nanostructured Composites For Hard Tissue Engineering Applications, Vuk Uskoković

Pharmacy Faculty Articles and Research

Multicomponent, synergistic and multifunctional nanostructures have taken over the spotlight in the realm of biomedical nanotechnologies. The most prospective materials for bone regeneration today are almost exclusively composites comprising two or more components that compensate for the shortcomings of each one of them alone. This is quite natural in view of the fact that all hard tissues in the human body, except perhaps the tooth enamel, are composite nanostructures. This review article highlights some of the most prospective breakthroughs made in this research direction, with the hard tissues in main focus being those comprising bone, tooth cementum, dentin and enamel. …

Designing A Microbial Cultivation Platform For Continuous Biopharmaceutical Production, Nicholas Mozdzierz, Kerry Love, Alan Stockdale, John Clark, Noelle Colant, Christopher Love

Integrated Continuous Biomanufacturing II

The existing biopharmaceutical manufacturing paradigm is poorly suited to produce biologic drugs on demand at a point-of-care. Generally, commercial-scale (~2,000 - 10,000 L) manufacturing using fed-batch cultivation and fixed stainless-steel infrastructure is concentrated in developed nations and results in process cycle times on the order of weeks to months.^1,2 Coupled with the complex logistical challenges associated with continuous “plant-to-patient” cold-chains, the geographically biased nature of therapeutic protein production today can limit access to biologic drugs in developing areas of the world.³ There is an opportunity to create technologies capable of rapidly generating biopharmaceuticals in situ in emergency situations, …

A Comprehensive Review Of The Food And Drug Administration, The 510(K) Application Process, And Fda Certification For A Diagnostic Device, Taylor Davis

Biomedical Engineering

The company G-Force CRC LLC is currently experiencing the dichotomy of the FDA's conflicting role right now as they begin to approach FDA approval. G-Force CRC LLC is a small medical device company headquartered in San Diego, CA. The owner of the company, Dr. Ian Purcell, is an Otoneurologist apart of Alvarado Hospital. His medical practice mainly deals with patients who have balance disorders and therefore the devices that he has developed over the last 6+ years are primarily used to assist in the diagnosis of those balance disorders. G-Force CRC LLC was officially created in the summer of 2013 …

Design Of A Simple Device For Accurate Measurement Of Human Blood Viscosity In Oxygenated And Deoxygenated Conditions, Catherine E. Oliver, Jessica Hockla, Divya Kamireddi

Honors Scholar Theses

The purpose of this research is to design, fabricate, and test a simple device that can accurately measure the viscosity of whole blood in both an oxygenated and a deoxygenated environment. The ideal device is easy to operate, inexpensive to fabricate, and is usable outside of a laboratory setting. The microfluidic rheometer presented here was fabricated using a wet chemical etching method. Using the channel dimensions, the known viscosity of a reference fluid, and the velocity of fluid flow of the sample and a reference fluid through the microchannels the unknown viscosity of a sample fluid is calculated.

Multiplexed Microfluidic Loop-Mediated Isothermal Amplification Of The 16s Rrna Gene For The Diagnosis Of Neonatal Sepsis In Resource-Limited Environments, Griffin Thomas Sonaty

Biomedical Engineering Undergraduate Honors Theses

Bacterial infection, or sepsis, places a disproportionately high burden on newborns in developing countries. This is due in part to a lack of diagnostic tools suitable for sustainable use in resource-limited nurseries. One potential vehicle for a new diagnostic assay is loop-mediated isothermal amplification (LAMP), a high-yield DNA amplification method. LAMP has been used to detect single genes from bacteria in blood serum samples to aid in sepsis diagnosis. While specific, this approach can only provide detection for one species at a time. LAMP could be adapted to detect a broader set of bacteria, while retaining a degree of specificity …

Catalytic Fast Pyrolysis Of Whole Field Pennycress Biomass, Yonas Afewerki Kidane

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

To satisfy the energy demand of the ever-increasing world population as well as to prevent environmental pollution arising from the use of fossil fuels, an alternate source of energy has to be developed. Biomass has the potential to provide a renewable energy source that is inexpensive and environmentally friendly. Field pennycress (Thlaspi arvense L.), previously considered as a weed, has now been found to be an ideal source of bio-fuel production. The focus of this research was to produce upgraded bio-oil by a process known as catalytic fast pyrolysis. A characterization and a temperature degradation profile study helped to …

The Application Of Biomedical Engineering Techniques To The Diagnosis And Management Of Tropical Diseases: A Review, Fatimah Ibrahim, Tzer Hwai Gilbert Thio, Tarig Faisal, Michael Neuman

Michigan Tech Publications, Part 1

This paper reviews a number of biomedical engineering approaches to help aid in the detection and treatment of tropical diseases such as dengue, malaria, cholera, schistosomiasis, lymphatic filariasis, ebola, leprosy, leishmaniasis, and American trypanosomiasis (Chagas). Many different forms of non-invasive approaches such as ultrasound, echocardiography and electrocardiography, bioelectrical impedance, optical detection, simplified and rapid serological tests such as lab-on-chip and micro-/nano-fluidic platforms and medical support systems such as artificial intelligence clinical support systems are discussed. The paper also reviewed the novel clinical diagnosis and management systems using artificial intelligence and bioelectrical impedance techniques for dengue clinical applications.

Multiplexed Loop-Mediated Isothermal Amplification Of The 16s Rrna Gene For The Diagnosis Of Neonatal Sepsis In Resource-Limited Environments, Griffin T. Sonaty

Inquiry: The University of Arkansas Undergraduate Research Journal

Sepsis, or dysregulated inflammation caused by bacterial infection, places a disproportionately high burden on newborns in developing countries. This is due in part to a lack of diagnostic tools suitable for sustainable use in resource-limited nurseries. One potential vehicle for a new diagnostic assay is loop-mediated isothermal amplification (LAMP), a high-yield DNA amplification method. LAMP has previously been used to detect genes from single species of bacteria in blood serum samples to aid in sepsis diagnosis. LAMP could be adapted to detect a broad set of bacteria, while retaining a degree of specificity that allows clinicians to begin directed antimicrobial …

Development Of A Heart Rate Variability Measurement System Using Embedded Electronics, Naresh Kumar Velmurugan

Graduate Theses and Dissertations

Recent advances in embedded electronics have a remarkable influence on the health care system. One of the most important applications is to monitor the health care of the patients at anytime and anyplace. In the last two decades, many researchers have focused mainly on heart rate variability (HRV) measurements. Patient's heart rate variability should be continuously monitored to help them in case of emergency. Under these circumstances, patients are required to have a HRV measuring kit for a constant observation.

The proposed project focuses on the development of a heart rate variability measurement system with the use of embedded electronics. …

Comparative Analysis Of Clavicular Tunnel Confìguration For Coracoclavicular Ligament Reconstruction, Mark Omwansa

Masters Theses

A number of coracoclavicular ligament reconstructions are carried out each year and post surgical fractures of the clavicle have been reported. The primary objective of this research is to develop a comparative metrics that compares clavicular tunnel configurations used in coracoclavicular reconstruction techniques. The goal of this comparison is to reduce post surgical failures due to clavicle fractures. The present analysis compared two techniques { a single 3 mm clavicular tunnel and the other double 6 mm tunnels { experimentally, using Four-point bending testing and Finite Element Analysis (FEA). A unique method, slicing, was used to create an FE clavicle …

A Collagen‐Glycosaminoglycan‐Fibrin Scaffold For Heart Valve Tissue Engineering Applications, Claire Brougham, Stefan Jockenhoevel, Thomas Flanagan, Fergal O'Brien

Conference Papers

The field of heart valve biology and tissue engineering a heart valve continue to expand. The presentatio ns at this meeting reflect the advances made in both areas due to the multi-disciplinary approach taken by many laboratories.

Development, Characterization, And Optimization Of Process For Minimal Functional Barrier And Channel Width In Nitrocellulose Paper Microfluidic Diagnostic Platforms, Ryan Daniel Silva

Biomedical Engineering

A central goal of diagnostic microfluidics is to reduce the cost of diagnostic medicine by reducing the equipment and reagents needed to perform diagnostic tests. The literature has demonstrated that a wax printer can be used to pattern nitrocellulose paper with hydrophobic barriers to direct a sample in a defined reaction path, eliminating the need for external pumps and controllers. However, manufacturing methods for minimizing sample volume (and thus reagent volume) in a paper-diagnostic chip have not been well defined. In this work, we experimentally determine manufacturing processes for creating functional features of minimal size—effectively reducing the sample size and …

Development Of An Efficient Human Hepatocyte Culture Platform For Assessing Novel Therapeutic Efficacy Against Plasmodium Liver Parasites, Steven Patrick Maher

USF Tampa Graduate Theses and Dissertations

Malaria is a critical and global public health problem, affecting over 200 million people every year, resulting in over 500,000 deaths. A vaccine is not currently available and only one drug, primaquine, is effective against the dormant stages of Plasmodium vivax. Preclinical assessment of novel therapeutic drugs and vaccines is hampered by the lack of an in vitro liver model for P. falciparum and P. vivax. To provide a stable human hepatocyte-based culture platform for parasite development, we engineered a microfluidic bilayer device capable of both simple and complex culture methods, including perfusion and co-culture, to better understand the requirements …