Biomedical Engineering and Bioengineering Commons^™

Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid

Computational Modeling & Simulation Engineering Theses & Dissertations

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to …

Insights Into The Binding Mode Of Mek Type-Iii Inhibitors. A Step Towards Discovering And Designing Allosteric Kinase Inhibitors Across The Human Kinome, Zheng Zhao, Lei Xie, Philip E. Bourne

Publications and Research

Protein kinases are critical drug targets for treating a large variety of human diseases. Type- III kinase inhibitors have attracted increasing attention as highly selective therapeutics. Thus, understanding the binding mechanism of existing type-III kinase inhibitors provides useful insights into designing new type-III kinase inhibitors. In this work, we have systematically studied the binding mode of MEK-targeted type-III inhibitors using structural systems pharmacology and molecular dynamics simulation. Our studies provide detailed sequence, structure, interaction-fingerprint, pharmacophore and binding-site information on the binding characteristics of MEK type-III kinase inhibitors. We hypothesize that the helix-folding activation loop is a hallmark allosteric binding site …

A Deterministic Model Of The Effect Of Electric Field On Chemotherapeutics Delivery Into A Tumor, Maryam Moarefian, Luke Achenie

Biology and Medicine Through Mathematics Conference

No abstract provided.

Toward Measuring Network Aesthetics Based On Symmetry, Zengqiang Chen, Matthias Dehmer, Frank Emmert-Streib, Abbe Mowshowitz, Yongtang Shi

Publications and Research

In this exploratory paper, we discuss quantitative graph-theoretical measures of network aesthetics. Related work in this area has typically focused on geometrical features (e.g., line crossings or edge bendiness) of drawings or visual representations of graphs which purportedly affect an observer’s perception. Here we take a very different approach, abandoning reliance on geometrical properties, and apply information-theoretic measures to abstract graphs and networks directly (rather than to their visual representaions) as a means of capturing classical appreciation of structural symmetry. Examples are used solely to motivate the approach to measurement, and to elucidate our symmetry-based mathematical theory of network aesthetics.

Shear Driven Micro-Fluidic Pump For Cardiovascular Applications, Nihad E. Daidzic

Aviation Department Publications

A valveless shear-driven micro-fluidic pump design (SDMFP) for hemodynamic applications is presented in this work. One of the possible medical and biomedical applications is in-vivo hemodynamic (human blood circulation) support/assist. One or more SDMFPs can be inserted/implanted into vascular lumens in a form of a stent/duct in series and/or in parallel (bypass duct) to support blood circulation in-vivo. A comprehensive review of various micro-pump designs up to about mid 2000’s is given in [1,2]. Many of micropump designs considered are not suitable for in-vivo or even in-vitro medical/biomedical applications.

Operating principles, design, and SDMFP features are given in [3]. A …

Low Temperature Plasma For The Treatment Of Epithelial Cancer Cells, Soheila Mohades

Electrical & Computer Engineering Theses & Dissertations

Biomedical applications of low temperature plasmas (LTP) may lead to a paradigm shift in treating various diseases by conducting fundamental research on the effects of LTP on cells, tissues, organisms (plants, insects, and microorganisms). This is a rapidly growing interdisciplinary research field that involves engineering, physics, life sciences, and chemistry to find novel solutions for urgent medical needs. Effects of different LTP sources have shown the anti-tumor properties of plasma exposure; however, there are still many unknowns about the interaction of plasma with eukaryotic cells which must be elucidated in order to evaluate the practical potential of plasma in cancer …

Using A Respiratory Navigator Significantly Reduces Variability When Quantifying Left Ventricular Torsion With Cardiovascular Magnetic Resonance, Sean M. Hamlet, Christopher M. Haggerty, Jonathan D. Suever, Gregory J. Wehner, Kristin N. Andres, David K. Powell, Richard J. Charnigo, Brandon K. Fornwalt

Electrical and Computer Engineering Faculty Publications

Background: Left ventricular (LV) torsion is an important indicator of cardiac function that is limited by high inter-test variability (50% of the mean value). We hypothesized that this high inter-test variability is partly due to inconsistent breath-hold positions during serial image acquisitions, which could be significantly improved by using a respiratory navigator for cardiovascular magnetic resonance (CMR) based quantification of LV torsion.

Methods: We assessed respiratory-related variability in measured LV torsion with two distinct experimental protocols. First, 17 volunteers were recruited for CMR with cine displacement encoding with stimulated echoes (DENSE) in which a respiratory navigator was used to measure …

Directed Acyclic Graph Continuous Max-Flow Image Segmentation For Unconstrained Label Orderings, John Sh Baxter, Martin Rajchl, A. Jonathan Mcleod, Jing Yuan, Terry M. Peters

Robarts Imaging Publications

Label ordering, the specification of subset–superset relationships for segmentation labels, has been of increasing interest in image segmentation as they allow for complex regions to be represented as a collection of simple parts. Recent advances in continuous max-flow segmentation have widely expanded the possible label orderings from binary background/foreground problems to extendable frameworks in which the label ordering can be specified. This article presents Directed Acyclic Graph Max-Flow image segmentation which is flexible enough to incorporate any label ordering without constraints. This framework uses augmented Lagrangian multipliers and primal–dual optimization to develop a highly parallelized solver implemented using GPGPU. This …

Engineering Fret Biosensors For Microrna Presence/Absence Analysis, Nicholas E. Larkey, Sean M. Burrows

Biomedical Engineering Western Regional Conference

No abstract provided.

Studying The Optimal Scheduling For Controlling Prostate Cancer Under Intermittent Androgen Suppression, Sunil K. Dhar, Hans R. Chaudhry, Bruce G. Bukiet, Zhiming Ji, Nan Gao, Thomas W. Findley

Harvard University Biostatistics Working Paper Series

This retrospective study shows that the majority of patients’ correlations between PSA and Testosterone during the on-treatment period is at least 0.90. Model-based duration calculations to control PSA levels during off-treatment are provided. There are two pairs of models. In one pair, the Generalized Linear Model and Mixed Model are both used to analyze the variability of PSA at the individual patient level by using the variable “Patient ID” as a repeated measure. In the second pair, Patient ID is not used as a repeated measure but additional baseline variables are included to analyze the variability of PSA.

P1: Using Modified Dean Flow Designs To Increase Mixing Performance, Joshua Clark

Undergraduate Research Posters 2017

We are using numerical solutions for the Navier-Stokes equations and the concentration - diffusion equation to model fluid flow and reactant distribution in serpentine type channels for micromixers/microreactors development. These mixers exploit centripetal forces on the fluid to induce cross-sectional fluid mixing, aka Dean flows. Various modifications are used to increase the mixing character of these crosssectional flows. We found that the performance of these mixers exceeds that of unmodified channels and we currently assess their performance relative to other state of the art methodologies used to induce mixing on the microscale.

P2: Implementation Of Groove Based Designs For Engineering Fluid Flow In Micromixers, Tahir Butt

Undergraduate Research Posters 2017

Mixing on microscale is important for the development of miniaturized chemical reactors that use small quantities of reactants and allow better control over the reaction conditions and products. Nevertheless, achieving rapid mixing in this type of micro-reactors is challenging due to the lack of turbulence and slow diffusion on the microscale. In this work we implement micromixers designs based on surface groove/ridge patterns targeted at inducing cross-sectional flows that both extend the interface between the different reactants, as well as induce chaotic advection. We discuss the fabrication of these structures using soft-lithography in PDMS employing a mold and their optical …

Going Green: Experimental Adaptation Of Scenedesmus Dimorphus To Marine Conditions, Mohammed Khalil

Undergraduate Research Posters 2017

Algae has gained some interest as the need for alternative fuels becomes more pressing. Reliance on fossil fuels is causing our environment and economy harm, and is not sustainable moving forward. Lipid rich algae strains can be used in the production of biofuels, and provide an alternative fuel source. One challenge facing the prospect of algae as a fuel source is that lipid rich algae grows exclusively in freshwater. Considering the scarcity and cost to use freshwater for algae growth, interest has grown in the possibility of adapting lipid rich, freshwater algae to a seawater environment. Seawater can have up …

The Viability Of Advantg Deterministic Method For Synthetic Radiography Generation, Andrew Albert Bingham

Masters Theses

"Time sensitive and high resolution image simulations are needed for synthetic radiography generation. The standard stochastic approach requires lengthy run times with poor statistics at higher resolutions. The investigation of the viability of a deterministic approach to synthetic radiography image generation was explored. The aim was to analyze a computational time decrease over the stochastic method. ADVANTG was compared to MCNP in multiple scenarios including a Benchtop CT prototype, to simulate high resolution radiography images. By using ADVANTG deterministic code to simulate radiography images the computational time was found to decrease over 10 times compared to the MCNP stochastic approach"--Abstract, …

Sugar Versus Lipid For Sustainable Biofuels, Yaşar Demirel

Yaşar Demirel Publications

Introduction

First‐generation biofuels, namely, ethanol and biodiesel, have led to far reaching impact on the peoples’ life world‐wide.[1] However, they inter-fere with the food supply chain and may not be sustainable although some of the biomass are converted to biofuels after those biomasses have met the human needs. Still, the first‐generation–based biofuels have proved that sugar and lipid platforms can be an answer to energy security and global warming concerns without the need for new infrastructure for feedstock delivery as well as for biomass‐to‐biofuel conversion tech-nologies. At the same time, we are discovering and assessing the long‐term environmental im-plications on …

Mathematical Analysis Of Feedback Targets Of Bmp Signaling In Drosophila Embryonic Development, Yan Luo

Open Access Theses

Bone morphogenetic proteins (BMPs) drive a range of cellular processes especially in the early stages of embryonic development. This family of proteins acts as one of the most important extracellular signals in development pattern formation across the animal kingdom. Cells in embryos differentiate into different cell types in response to the concentration level of BMP. This complex process is regulated by multiple regulators that serve to tune the signal response.

Extensive experimental and computational research has been performed to analyze BMP regulation in Drosophila, a widely studied model organism, and has advanced our understanding of animal development. Because of …

Dynamic Holography In Semiconductors And Biomedical Optics, Hao Sun

Open Access Dissertations

Three-dimensional scanning and display are rapidly-advancing new technologies with important commercial drivers such as 3D printing and remote imaging for big data applications. Holography is a natural approach to recording and displaying three-dimensional information because it uses phase-sensitive interferometry to record interference patterns when a reference beam encounters coherent light arriving from an object. The 3D information is contained in the values of wave optics. Holography is a broad field that goes beyond recording and displaying. For instance, holographic optical elements, which take advantage of holographic imaging principles, perform the functions of lenses, gratings or mirrors. Holographic interferometry is also …

Characterizing The Effects Of Repetitive Head Trauma In Female Soccer Athletes For Prevention Of Mild Traumatic Brain Injury, Diana Otero Svaldi

Open Access Dissertations

As participation in women’s soccer continues to grow and the longevity of female athletes’ careers continues to increase, prevention of mTBI in women’s soccer has become a major concern for female athletes as the long-term risks associated with a history of mTBI are well documented. Among women’s sports, soccer exhibits the highest concussion rates, on par with those of men’s football at the collegiate level. Head impact monitoring technology has revealed that “concussive hits” occurring directly before symptomatic injury are not predictive of mTBI, suggesting that the cumulative effect of repetitive head impacts experienced by collision sport athletes should be …

Development Of In Vivo Systems For Detecting And Studying Ribosome Inhibition By Small Molecules, Shijie Huang

Chemistry and Chemical Biology ETDs

The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome controlled green fluorescent protein reporter that produce fluorescent signal when the O-ribosome is inhibited. As a proof …

Robust Feedback Control Based On Low Order Models With Uncertainty Estimation For A Class Of Biomedical Problems, Hector Puebla, Miguel A. Gutierrez-Limon, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Recent Approaches In Designing Bioadhesive Materials Inspired By Mussel Adhesive Protein, Pegah Kord Forooshani, Bruce P. Lee

Department of Biomedical Engineering Publications

Marine mussels secret protein-based adhesives, which enable them to anchor to various surfaces in a saline, intertidal zone. Mussel foot proteins (Mfps) contain a large abundance of a unique, catecholic amino acid, Dopa, in their protein sequences. Catechol offers robust and durable adhe-sion to various substrate surfaces and contributes to the curing of the adhesive plaques. In this article, we review the unique features and the key functionalities of Mfps, catechol chemistry, and strategies for preparing catechol-functionalized poly- mers. Specifically, we reviewed recent findings on the contributions of various features of Mfps on interfacial binding, which include coacervate formation, surface …

Anxiolytic Effects Of Propranolol And Diphenoxylate On Mice And Automated Stretch-Attend Posture Analysis, Kevin Scott Holly

Doctoral Dissertations

The prevention of social anxiety, performance anxiety, and social phobia via the combination of two generic drugs, diphenoxylate HC1 (opioid) plus atropine sulfate (anticholinergic) and propranolol HCl (beta blocker) was evaluated in mice through behavioral studies. A patent published on a September 8, 2011 by Benjamin D. Holly, US 2011/0218215 Al, prompted the research. The drug combination of diphenoxylate and atropine plus propranolol could be an immediate treatment for patients suffering from acute phobic and social anxiety disorders. Demonstrating the anxiolytic effects of the treatment on mice would validate a mouse model for neuroscientist to be used to detect the …

Generalized Partial Directed Coherence And Centrality Measures In Brain Networks For Epileptogenic Focus Localization, Joshua Aaron Adkinson

Doctoral Dissertations

Accurate epileptogenic focus localization is required prior to surgical resection of brain tissue for treatment of patients with intractable temporal lobe epilepsy, a clinical need that is partially fulfilled to date through a subjective, and at times inconclusive, evaluation of the recorded electroencephalogram (EEG). Using brain connectivity analysis, patterns of causal interactions between brain regions were derived from multichannel EEG of 127 seizures in nine patients with focal, temporal lobe epilepsy (TLE). The statistically significant directed interactions in the reconstructed brain networks were estimated from three second intracranial multi-electrode EEG segments using the Generalized Partial Directed Coherence (GPDC) and validated …

99mtc-Hexamethylpropyleneamine Oxime Imaging For Early Detection Of Acute Lung Injury In Rats Exposed To Hyperoxia Or Lipopolysaccharide Treatment, Said H. Audi, Anne V. Clough, Steven T. Haworth, Meetha Medhora, Mahsa Ranji, John C. Densmore, Elizabeth R. Jacobs

Biomedical Engineering Faculty Research and Publications

^99mTc-Hexamethylpropyleneamine oxime (HMPAO) is a clinical single-photon emission computed tomography biomarker of tissue oxidoreductive state. Our objective was to investigate whether HMPAO lung uptake can serve as a preclinical marker of lung injury in two well-established rat models of human acute lung injury (ALI).

Rats were exposed to >95% O₂ (hyperoxia) or treated with intratracheal lipopolysaccharide (LPS), with first endpoints obtained 24 h later. HMPAO was administered intravenously before and after treatment with the glutathione-depleting agent diethyl maleate (DEM), scintigraphy images were acquired, and HMPAO lung uptake was quantified from the images. We also measured breathing rates, heart …

An Interactive Videogame Designed To Improve Respiratory Navigator Efficiency In Children Undergoing Cardiovascular Magnetic Resonance, Sean M. Hamlet, Christopher M. Haggerty, Jonathan D. Suever, Gregory J. Wehner, Jonathan D. Grabau, Kristin N. Andres, Moriel H. Vandsburger, David K. Powell, Vincent L. Sorrell, Brandon K. Fornwalt

Saha Cardiovascular Research Center Faculty Publications

Background: Advanced cardiovascular magnetic resonance (CMR) acquisitions often require long scan durations that necessitate respiratory navigator gating. The tradeoff of navigator gating is reduced scan efficiency, particularly when the patient’s breathing patterns are inconsistent, as is commonly seen in children. We hypothesized that engaging pediatric participants with a navigator-controlled videogame to help control breathing patterns would improve navigator efficiency and maintain image quality.

Methods: We developed custom software that processed the Siemens respiratory navigator image in real-time during CMR and represented diaphragm position using a cartoon avatar, which was projected to the participant in the scanner as visual feedback. The …

Diffuse Optical Measurements Of Head And Neck Tumor Hemodynamics For Early Prediction Of Chemoradiation Therapy Outcomes, Lixin Dong, Mahesh Kudrimoti, Daniel Irwin, Li Chen, Sameera Kumar, Yu Shang, Chong Huang, Ellis L. Johnson, Scott D. Stevens, Brent J. Shelton, Guoqiang Yu

Biomedical Engineering Faculty Publications

This study used a hybrid near-infrared diffuse optical instrument to monitor tumor hemodynamic responses to chemoradiation therapy for early prediction of treatment outcomes in patients with head and neck cancer. Forty-seven patients were measured once per week to evaluate the hemodynamic status of clinically involved cervical lymph nodes as surrogates for the primary tumor response. Patients were classified into two groups: complete response (CR) (n = 29) and incomplete response (IR) (n = 18). Tumor hemodynamic responses were found to be associated with clinical outcomes (CR/IR), wherein the associations differed depending on human papillomavirus (HPV-16) status. In HPV-16 …

Chlorine Demand Shows Thresholds And Hierarchy With Source Water Quality At Beaver Lake, Arkansas, Jaime M. Gile

Graduate Theses and Dissertations

This study investigated the effects of source water quality in Beaver Lake on the amount of chlorine (Cl) needed to develop decision support system to help guide chlorination practices in pre-treatment of source water. Chlorine demand assays were performed on water samples from Beaver Lake collected from the intake structure at Beaver Water District from March 2014 through August 2015, and using data from these assays, the two points of interest in this study were the Cl dose at which Cl residuals began to accumulate and the mean Cl demand occurring after that dose. Three methods of analysis were used …

Automated Microscopy Platform For High-Throughput Analysis Of Cellular Characteristics, Hussam Ibrahim

Physics: Student Scholarship & Creative Works

Existing microscopy platforms allow analysis post-hoc, but not in real time. This is an issue in the world of Bioengineering because you are limited to performing further analysis on specimen. The aim of my research was to design a sophisticated system whereby information can be exchanged between the software which acquires images and software that analyzes the images immediately after acquisition. In this system, images would be acquired by the microscope and analyzed by customized scripts (MATLAB, Mathworks) in real time. Specifically, MATLAB would wait for new images to be saved on the hard drive, import these images, and perform …

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries …

Nano-Photonic Waveguides For Chemical And Biomedical Sensing, Surya Venkatasekhar Cheemalapati

USF Tampa Graduate Theses and Dissertations

In this dissertation, advances in the fields of Photonics, and Plasmonics, and specifically, single cell analysis and waveguide sensing will be addressed. The first part of the dissertation is on Finite Difference Time Domain (FDTD) optimization and experimental demonstration of a nano-scale instrument that allows sensing at the cellular and subcellular levels. A new design of plasmonic coupler into a nanoscale waveguide is proposed and optimized using FDTD simulations. Following this, a subcellular nanoendoscope that can locally excite fluorescence in labelled cell organelles and collect the emitted fluorescent light for detailed spectrum analysis is fabricated and tested. The nanoendoscope has …