Biomedical Engineering and Bioengineering Commons^™

A Practical Guide To An Fmri Experiment, Nasser H. Kashou

Biomedical, Industrial & Human Factors Engineering Faculty Publications

Functional Magnetic Resonance Imaging (fMRI) has been around for two decades and research in this field has been exponentially rising. Much of this research has been dominated by basic science. Recent trends have brought the clinical realm into play in which valuable contributions can still be made. Helping the clinician understand the basic concepts behind an fMRI experiment is crucial to further developing and evaluating functional paradigms and research. Critical to designing an fMRI experiment is understanding the related physics and how fine tuning scanning parameters affects the image quality, which in turn affect the findings of an fMRI study. …

Optimizing Alginate-Chitosan Microcapsules Using Co-Axial Air Flow Method As 3d Stem Cell Microenvironment, Noel Alfonso

Theses

Microencapsulation of cells is gaining popular interest in the field of biomedical engineering because it provides a more effective 3D scaffold that can mimic the cell microenvironment. The benefits of using microcapsules are biocompatibility, biodegradability, nontoxicity, and formation under mild gelation conditions. In this study, the ability of the alginate microcapsules to control the proliferation and differentiation of mouse OCT4-GFP embryonic stem cells is investigated. Microcapsules are produced by extrusion of alginate into a calcium chloride gelation bath with the aid of a co-axial air flow. It is shown that the size of the spheres is controlled based on needle …

Evaluation Of Methods To Account For Release From Nanofiber Scaffolds, Jennifer Moy

Theses

Electrospinning is a common technique utilized to form fibers from the micro- to nanometer range. Nanofibers form through electrospinning can be utilized as scaffolds since the fiber structures are similar to the structures within the extracellular matrix. Researchers use additives, such as growth factors, to help facilitate cell proliferation and function. Also, researchers are attempting to use electrospun fibers for drug delivery and as wound dressings since the electrospun fibers have high surface area to volume ratio. In both situations, the release of either the additive or the drug needs to be controlled so that the fibers would release the …

The Effect Of Vergence Vision Training On Binocularly Normal Subjects, Henry Talasan

Theses

Vergence is the disjunctive (inward or outward) movement of the eyes that is stimulated by retinal disparity (difference of where an image is projected to the retina and the fovea). A recent randomized clinical trial showed the efficacy of vision therapy for children with the binocular dysfunction known as convergence insufficiency is 73%. However, it is unknown whether binocularly normal persons will have any significant change to their vergence ocular motor system if they participate in vision training sessions. A total of ten (n = 10) binocularly normal persons participated in this study (18 to 28 years of age). A …

Short Term Modification Of Vergence Ramp Eye Movements In The Convergent Direction, Chang Yaramothu

Theses

Prior oculomotor studies have investigated the various effects of short-term modification on vergence, saccadic and smooth pursuit eye movements. Previous vergence studies have concentrated on step modification stimuli. Few have investigated the effects of short-term modification on vergence ramp movements. Thus, this study explores the trends observed within a short-term modification experiment studying smoothly tracking vergence eye movements responses elicited from convergent ramp stimuli. A short-term modification experiment is composed of three phases: baseline, modification and recovery. Baseline and recovery phases contain only test stimuli; whereas, during modification, the subject is presented test and conditioning stimuli in a ratio of …

Automated Localization And Segmentation Of Pelvic Floor Structures On Mri To Predict Pelvic Organ Prolapse, Sinan Onal

USF Tampa Graduate Theses and Dissertations

Pelvic organ prolapse (POP) is a major health problem that affects women. POP is a herniation of the female pelvic floor organs (bladder, uterus, small bowel, and rectum) into the vagina. This condition can cause significant problems such as urinary and fecal incontinence, bothersome vaginal bulge, incomplete bowel and bladder emptying, and pain/discomfort. POP is normally diagnosed through clinical examination since there are few associated symptoms. However, clinical examination has been found to be inadequate and in disagreement with surgical findings. This makes POP a common but poorly understood condition. Dynamic magnetic resonance imaging (MRI) of the pelvic floor has …

Averaging Improves Strain Images Of The Biceps Brachii Using Quasi-Static Ultrasound Elastography, Matthew Leineweber, J Westborn, A Cochran, Y Gao, J Choi

Faculty Publications

OBJECTIVE:Quasi-static ultrasound elastography is a technique for measuring tissue deformation (strain) under externally applied loading and can be used to identify the presence of abnormalities. The objective of this study was to demonstrate the efficacy of averaging strain images from repeated compression cycles in mitigating user-induced error using quasi-static ultrasound elastography.METHODS:Freehand compressions were performed with an ultrasound transducer on the biceps brachii of nine participants (five males and four females), as well as with a custom automated compression system. Sets of strain images from the freehand techniques were averaged to create single representative images and compared against strain images from …

Extraction Of Intrinsic Fluorescence From Single Fiber Fluorescence Measurements On A Turbid Medium: Experimental Validation, U. A. Gamm, C. L. Hoy, F. Van Leeuwen - Van Zaane, H. J. C. M. Sterenborg, S. C. Kanick, D J. Robinson, A. Amelink

Dartmouth Scholarship

Abstract

The detailed mechanisms associated with the influence of scattering and absorption properties on the fluorescence intensity sampled by a single optical fiber have recently been elucidated based on Monte Carlo simulated data. Here we develop an experimental single fiber fluorescence (SFF) spectroscopy setup and validate the Monte Carlo data and semi-empirical model equation that describes the SFF signal as a function of scattering. We present a calibration procedure that corrects the SFF signal for all system-related, wavelength dependent transmission efficiencies to yield an absolute value of intrinsic fluorescence. The validity of the Monte Carlo data and semi-empirical model is …

Fluid Flow-Induced Mesenchymal Stem Cell Migration: Role Of Fak And Rock Mechanosensors, Brandon D. Riehl

Department of Mechanical and Materials Engineering: Dissertations, Theses, and Student Research

The study of mesenchymal stem cell (MSC) migration under mechanical stimulation conditions with investigation of the underlying molecular mechanism could lead to a better understanding and outcomes in stem cell-based regenerative medicine. MSCs having multipotent regenerative capability exist in niches in the bone marrow, muscle, vasculature, and in other tissues throughout the body, and their migration through tissues and vasculature for the repair of damaged tissue is a key process of cell and tissue homeostasis, remodeling, and regeneration. While cell migration in response to cytokines and other chemo-attractants is relatively well understood, little is revealed in regard to the effect …

Comprehensive T Cell Antigen Discovery Using A Genomic Approach, Jessica Baker

Vaccine Technology IV

No abstract provided.

Modeling And Development Of Iterative Reconstruction Algorithms In Emerging X-Ray Imaging Technologies, Jiaofeng Xu

All Theses and Dissertations (ETDs)

Many new promising X-ray-based biomedical imaging technologies have emerged over the last two decades. Five different novel X-ray based imaging technologies are discussed in this dissertation: differential phase-contrast tomography (DPCT), grating-based phase-contrast tomography (GB-PCT), spectral-CT (K-edge imaging), cone-beam computed tomography (CBCT), and in-line X-ray phase contrast (XPC) tomosynthesis. For each imaging modality, one or more specific problems prevent them being effectively or efficiently employed in clinical applications have been discussed. Firstly, to mitigate the long data-acquisition times and large radiation doses associated with use of analytic reconstruction methods in DPCT, we analyze the numerical and statistical properties of two classes …

Reading And Wirelessly Sending Eeg Signals Using Arduinos And Xbee Radios To Control A Robot, Andrew Paul Simms

Electrical Engineering Undergraduate Honors Theses

The objective of this project is to develop an EEG device that can read brainwaves from an individual, analyze the data, and use the result to send a wireless signal using Arduinos and XBee Radios to a Boe-bot to perform an action. One of the goals of this project is to read EEG data with a higher sampling frequency than a previously manufactured EEG device. The second part of the project used the device developed to differentiate an individual’s thinking between right and left and then send a simple signal to a robot using an XBee radio to perform an …

In Vitro Validation Of Patient-Specific Hemodynamic Simulations In Coronary Aneurysms Caused By Kawasaki Disease, Ethan Kung, Andrew M. Kahn, Jane C. Burns, Alison Marsden

Publications

To perform experimental validation of computational fluid dynamics (CFD) applied to patient specific coronary aneurysm anatomy of Kawasaki disease. We quantified hemodynamics in a patient-specific coronary artery aneurysm physical phantom under physiologic rest and exercise flow conditions. Using phase contrast MRI (PCMRI), we acquired 3-component flow velocity at two slice locations in the aneurysms. We then performed numerical simulations with the same geometry and inflow conditions, and performed qualitative and quantitative comparisons of velocities between experimental measurements and simulation results. We observed excellent qualitative agreement in flow pattern features. The quantitative spatially and temporally varying differences in velocity between PCMRI …

A Study Of Ciliary Beating In Chlamydomonas, Xin Li

Renée Crown University Honors Thesis Projects - All

The goal of this research is to understand how a unicellular green alga, Chlamydomonas-reinhardtii, responds to red light (670nm) and sound waves, by monitoring the beating frequency of its two cilia, which control cell motility. Ciliary beating frequency (BF) is proportional to the production of ATP, mainly generated by photosynthesis. A photosynthesis inhibitor, 3-(3-, 4-dichlorophenyl)-1, 1-dimethylurea (DCMU) decreases ATP production by photosynthesis. I used DCMU as a tool to analyze the red light effect on BF.

In the process of studying the effect of red light, I unexpectedly discovered experimental conditions for unstable ciliary beating (as shown in the video). …

Modeling The Adaptive Immune Response To Mutation-Generated Antigens, Rory J. Geyer

University Scholar Projects

Somatic mutations may drive tumorigenesis or lead to new, immunogenic epitopes (neoantigens). The immune system is thought to represses neoplastic growths through the recognition of neoantigens presented only by tumor cells. To study mutations as well as the immune response to mutation-generated antigens, we have created a conditional knockin mouse line with a gene encoding, 5’ to 3’, yellow fluorescent protein (YFP), ovalbumin (which is processed to the immunologically recognizable peptide, SIINFEKL), and cyan fluorescent protein (CFP), or, YFP-ovalbumin-CFP. A frame shift mutation has been created at the 5’ end of the ovalbumin gene, hence YFP should always be expressed, …

Validation Of A Diffuse Reflectance Microendoscope With Polydimethylsiloxane Optical Phantoms And Monte Carlo Modeling, Gage Joseph Greening

Biomedical Engineering Undergraduate Honors Theses

We have introduced a method for creating thin-film PDMS optical phantoms that can be used to validate a bench-top optical device called a Diffuse Reflectance Microendoscope (DRME). The DRME is acquires data on cell surface morphology and sub-surface diffuse reflectance, which may provide clinicians with the tools to diagnose oral cancer at earlier stages. Phantoms were created with PDMS. Optical properties of the phantoms were controlled with the addition of nigrosin and titanium dioxide. Depth of phantoms was controlled by a spin coater. The DRME was built with a combination of filters and dichroic mirrors to separate electromagnetic radiation in …

Poly (Glycerol Sebacate) Nanofibers And Nanofilms For Tissue Engineering Application, Stephanie Grace Cone

Biomedical Engineering Undergraduate Honors Theses

In the field of tissue engineering, the development of biodegradable scaffolds that provide both structure and functionality is a major challenge. The use of biological implants, such as decellularized tissues, provides a complete matrix with full tissue functionality, however, problems with immunogenicity often arise when implants from other organisms are used in treatments. As such, there are many benefits to the use of polymeric constructs in tissue engineering. The ability to customize the material, design, and size of an implant provides opportunities for increased structural support and controlled rates of biodegradation. The selection of polymers for tissue engineering applications requires …

Prostate Cancer Detection Using Combined Autofluorescence And Light Reflectance Spectroscopy: Ex Vivo Study Of Human Prostates, Vikrant Sharma, Ephrem O. Olweny, Payal Kapur, Jeffrey A. Cadeddu, Claus G. Roehrborn, Hanli Liu

Bioengineering Faculty Publications - Archive

This study was conducted to evaluate the capability of detecting prostate cancer (PCa) using auto-fluorescence lifetime spectroscopy (AFLS) and light reflectance spectroscopy (LRS). AFLS used excitation at 447 nm with four emission wavelengths (532, 562, 632, and 684 nm), where their lifetimes and weights were analyzed using a double exponent model. LRS was measured between 500 and 840 nm and analyzed by a quantitative model to determine hemoglobin concentrations and light scattering. Both AFLS and LRS were taken on n = 724 distinct locations from both prostate capsular (nc = 185) and parenchymal (np = 539) tissues, including PCa tissue, …

Classification And Quantification Of Phenotypic Characteristics Of Normal And Dysplastic Oral Cells, Jackson W. Boice

Biomedical Engineering Undergraduate Honors Theses

Introduction Oral cancer accounts for 2.5% of all cancer cases in the United States. The 5 year survival rate or stage 1 or localized oral cancer is 82%, and the survival rate of unstaged oral cancer is only 50%; therefore, early diagnosis is key. Current clinical practices for determining malignancy of tissue include physical examination and surgical biopsy, which can be plagued by high variability between observers and are invasive for the patient. Proflavine intercalates between base pairs of nucleic acids and has excitation and emission peaks at 455 (+/- 20) nm and 515 nm respectively; therefore, it can be …

Optimizing In Vitro Extracellular Matrix Production Using Polymer Scaffolds With Targeted Pore Size, Addison M. Walker

Biomedical Engineering Undergraduate Honors Theses

Extracellular matrix (ECM) has been shown to provide the framework needed for healthy tissue to grow after experiencing an injury. The optimization of growing ECM is a pressing concern in the tissue regeneration field. From prior research, an in vitro approach for harvesting ECM has been created using polyurethane (PU) foams seeded with cells. Our approach aimed at discovering if the pore size of the foams increased the amount of recovered ECM. Scaffolds of targeted pore size were created by separating sugar granules using a sieve, packing the sugar into a cylindrical mold, then pouring PU over the sugar. Three …