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High Throughput Analysis Of The Penetration Of Iron Oxide/Polyethylene Glycol Nanoparticles Into Multicellular Breast Cancer Tumor Spheroids, Jonathan Robert Gabriel

Theses and Dissertations

The purpose of this study was to design and optimize a system for the high-throughput analysis of multicellular tumor spheroids (MCTS), and validate the system through the study of a complex biological model. The system was successfully created and optimized, allowing the histological recovery of MCTS at rates up to 90% for microarrays of 24-spheroids. Arrays of 96-spheroids were recovered at rates up to 86%. The system was used to study the penetration of 5k Da-polyethylene coated superparamagnetic iron-oxide nanoparticles (5k-PEG SPIONs) into HTB-126 breast cancer spheroids cultured to a mean diameter of 486 micrometer (± 25.2 micrometer). Results were …

Fast Estimation Model Of Pressure-Temperature Response For Planning Focused Ultrasound Surgery, Tariq Mohammad Arif

Dissertations

High Intensity Focused Ultrasound (HIFU) is becoming a widely accepted modality for extracorporeal non-invasive hyperthermia and surgical procedures. Since ultrasonic transducers need to operate in various challenging body locations, the arrangement of their array elements can be optimized to improve the capability of controlling focus intensity. In the first part of this dissertation, patterns of pressure field variations with several selected design variables (kerf, transducer element’s number and element’s width-height) are studied. These patterns indicate that there is a more suitable shape and arrangement of transducer elements in a specified area to achieve highest possible pressure. In order to obtain …

Droplet-Microfluidic Device For The Characterization Of Perfluorinated Emulsions, Daniel Horvath, Nam Ahn Tran

Bioengineering Senior Theses

Microfluidics is being used throughout academia and industry today to perform large numbers of experiments with extremely small volumes of fluids. By doing this, those that study microfluidics hope to raise through-put, lower cost and limit the environmental impact of scientific research.2 Complementing the increased use of microfluidics, the use of perfluorinated emulsions in the field of droplet-based microfluidics is also experiencing large growth.3 However, many of the products available today are either proprietary and/or poorly understood. While some chemical structures are known, some of the most scientifically intriguing perfluorinated oils and surfactants do not have their chemical structures or …

Surface-Modified Polyacrylonitrile Nanofibres As Supports, Chris Ademola Bode-Aluko, Omoniyi Pereao, Olanrewaju Fatoba, Leslie Petrik

Mining Engineering Faculty Research & Creative Works

Polyacrylonitrile nanofibers (PAN-nfs) are one of the most studied nanofibers because of their excellent characteristics, such as good mechanical strength, chemical resistance, and good thermal stability. Due to the easy dissolution in polar organic solvents, PAN-nfs are mostly produced via electrospinning technique. The electro spun PAN-nfs surfaces are relatively in-active and hydrophobic, and, therefore, hinder some potential applications; however, chemical surface modification reactions, such as amination, reduction, hydrolysis, and amidoximation, have been carried out on them. These reactions bring about functional groups, such as amine, hydroxyl, carboxylic, imine etc., to the surface PAN-nfs and invariably make their surfaces active and …

Quantitative Analysis Of High Pressure Hazards In Oil And Gas Field Operations, Giuseppe Feo

Honors Capstones

No abstract provided.

Inhibition Of Mammalian Glycoprotein Ykl-40 Identification Of The Physiological Ligand, Abhishek A. Kognole, Christina M. Payne

Chemical and Materials Engineering Faculty Publications

YKL-40 is a mammalian glycoprotein associated with progression, severity, and prognosis of chronic inflammatory diseases and a multitude of cancers. Despite this well documented association, identification of the lectin′s physiological ligand and, accordingly, biological function has proven experimentally difficult. YKL-40 has been shown to bind chito-oligosaccharides; however, the production of chitin by the human body has not yet been documented. Possible alternative ligands include proteoglycans, polysaccharides, and fibers like collagen, all of which makeup the extracellular matrix. It is likely that YKL-40 is interacting with these alternative polysaccharides or proteins within the body, extending its function to cell biological roles …

Human Liver Sinusoid On A Chip For Hepatitis B Virus Replication Study, Young Bok (Abraham) Kang, Siddhartha Rawat, Nicholas Duchemin, Michael Bouchard, Moses Noh

Faculty Publications - Biomedical, Mechanical, and Civil Engineering

We have developed a miniature human liver (liver-sinusoid-on-a-chip) model using a dual microchannel separated by a porous membrane. Primary human hepatocytes and immortalized bovine aortic endothelial cells were co-cultured on opposite sides of a microporous membrane in a dual microchannel with continuous perfusion. Primary human hepatocytes in this system retained their polygonal morphology for up to 26 days, while hepatocytes cultured in the absence of bovine aortic endothelial cells lost their morphology within a week. In order to demonstrate the utility of our human-liver-sinusoid-on-a-chip, human hepatocytes in this system were directly infected by Hepatitis B Virus (HBV). Expression of the …

Expanding The Applications Of Poly(Dimethylsiloxane) In Biomicrofluidics, Sawyer D. Stone

Doctoral Dissertations

This work aims to create novel applications for poly(dimethylsiloxane) (PDMS) in the field of biomicrofluidics through oxidative stress detection, doping of the polymer for intentional leaching into microdevices, and the development of low-cost implements for fabricating PDMS microfluidic devices. PDMS has become the polymer of choice for research in microfluidics due to its optical clarity, ease of fabrication, flexibility in design, good mechanical properties, and the ability to chemically modify the surface.

Biomicrofluidics enables the rapid throughput and analysis of small biological samples requiring less time investment and reagent use than traditional macroscale laboratory techniques. Polymer devices are inexpensive, easily …

An Investigation Into Spike-Based Neuromorphic Approaches For Artificial Olfactory Systems, Anup Vanarse, Adam Osseiran, Alexander Rassau

Research outputs 2014 to 2021

The implementation of neuromorphic methods has delivered promising results for vision and auditory sensors. These methods focus on mimicking the neuro-biological architecture to generate and process spike-based information with minimal power consumption. With increasing interest in developing low-power and robust chemical sensors, the application of neuromorphic engineering concepts for electronic noses has provided an impetus for research focusing on improving these instruments. While conventional e-noses apply computationally expensive and power-consuming data-processing strategies, neuromorphic olfactory sensors implement the biological olfaction principles found in humans and insects to simplify the handling of multivariate sensory data by generating and processing spike-based information. Over …

Integrative Pathway Analysis Pipeline For Mirna And Mrna Data, Diana Mabel Diaz Herrera

Wayne State University Theses

The identification of pathways that are involved in a particular phenotype helps us understand the underlying biological processes. Traditional pathway analysis techniques aim to infer the impact on individual pathways using only mRNA levels. However, recent studies showed that gene expression alone is unable to capture the whole picture of biological phenomena. At the same time, MicroRNAs (miRNAs) are newly discovered gene regulators that have shown to play an important role in diagnosis, and prognosis for different types of diseases. Current pathway analysis techniques do not take miRNAs into consideration. In this project, we investigate the effect of integrating miRNA …

Improving Peptide Identification By Considering Ordered Amino Acid Usage, Ahmed Al-Qurri

Theses and Dissertations

Proteomics has made major progress in recent years after the sequencing of the genomes of a substantial number of organisms. A typical method for identifying peptides uses a database of peptides identified using tandem mass spectrometry (MS/MS). The profile of accurate mass and elution time (AMT) for peptides that need to be identified will be compared with this database. Restricting the search to those peptides detectable by MS will reduce processing time and more importantly increase accuracy. In addition, there are significant impacts for clinical studies. Proteotypic peptides are those peptides in a protein sequence that are most likely to …

Investigate Genomic 3d Structure Using Deep Neural Network, Yan Zhang

Theses and Dissertations

The 3D structures of the chromosomes play fundamental roles in essential cellular functions, e.g., gene regulation, gene expression, evolution and Hi-C technique provides the interaction density between loci on chromosomes. In this dissertation, we developed multiple algorithms, focusing the deep learning approach, to study the Hi-C datasets and the genomic 3D structures.

Building 3D structure of the genome one of the most critical purpose of the Hi-C technique. Recently, several approaches have been developed to reconstruct the 3D model of the chromosomes from HiC data. However, all of the methods are based on a particular mathematical model and lack of …

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …

Process-Structure-Property Relationship In Magnesium-Based Biodegradable Alloy For Biomedical Applications, Pramanshu Trivedi

Open Access Theses & Dissertations

Magnesium alloys are considered to be the next generation of biomaterials because of their ability to degrade in the physiological environment. We elucidate here the impact of multiaxial forging of Mg-2Zn-2Gd alloy on grain refinement to sub-micron regime and relate the structure to mechanical properties and biological functionality. As-cast and annealed samples were multiaxial forged (MAF) for a total number of two passes with a true strain of ~2/pass. Considering that the microstructure governs the biological response of materials, we studied the constituents of the microstructure in conjunction with the mechanical behavior. The antimicrobial behavior in a Mg-2Zn-2Gd alloy with …

A New System For Human Microrna Functional Evaluation And Network, Jiachun Han

School of Computing: Dissertations, Theses, and Student Research

MicroRNAs are functionally important endogenous non-coding RNAs that silence host genes in animal and plant via destabilizing the mRNAs or preventing the translation. Given the far-reaching implication of microRNA regulation in human health, novel bioinformatics tools are desired to facilitate the mechanistic understanding of microRNA mediated gene regulation, their roles in biological processes, and the functional relevance among microRNAs. However, most state-of-the-art computational methods still focus on the functional study of microRNA targets and there is no e ective strategy to infer the functional similarity among microRNAs. In this study, we developed a new method to quantitatively measure the functional …

Studies Of Cell Motility And Differentiation In Complex 3d In Vitro Microenvironment, Jing Wang

Dissertations - ALL

Cell behaviors, such as motility and differentiation, which are highly regulated by the complex 3D in vivo microenvironment, have been extensively studied in the past decades to better understand the mechanisms of development, disease, and healing. Due to the highly complex nature of the in vivo environment and limited resources and access to study cell behaviors in vivo, great efforts have been made to develop in vitro systems to mimic the in vivo microenvironment for a better understanding of cell-microenvironment interactions. However, most of the commonly used in vitro systems are static, which cannot mimic the dynamics of the microenvironment …

Developing The Three Dimensional Tumor Model For Melanoma Drug Screening, Guochang Ye

Theses and Dissertations

Two-dimensional (2D) Tissue Culture Treated Plastic (TCTP) is widely used for cancer drug screening and has dominated the field for a long time. Compared with traditional two dimensional cell culture, a three dimensional tumor model may able to provide more reliable experimental results related to drug screening and discovery. With the development of nanoparticle chemotherapies, there is a need for ways to better investigate and characterize the effect of the 3D tumor environment. Cerium oxide nanoparticles, Nanoceria, is one of the potential solutions being explored for treating melanoma in the future in combination with conventional chemotherapies. This is attributed to …

Lab-On-A-Chip Nucleic-Acid Analysis Towards Point-Of-Care Applications, Varun Lingaiah Kopparthy

Doctoral Dissertations

Recent infectious disease outbreaks, such as Ebola in 2013, highlight the need for fast and accurate diagnostic tools to combat the global spread of the disease. Detection and identification of the disease-causing viruses and bacteria at the genetic level is required for accurate diagnosis of the disease. Nucleic acid analysis systems have shown promise in identifying diseases such as HIV, anthrax, and Ebola in the past. Conventional nucleic acid analysis systems are still time consuming, and are not suitable for point-ofcare applications. Miniaturized nucleic acid systems has shown great promise for rapid analysis, but they have not been commercialized due …

Optimization Of The Bowtie Gap Geometry For A Maximum Electric Field Enhancement, Tsenguun Byambadorj

Master's Theses (2009 -)

Optimization of the geometry of a metallic bowtie gap at radio frequency is presented in this thesis. Since the design and fabrication of a plasmonic device (nanogap) at nanoscale is challenging, the results of this study can be used to estimate the best design parameters for nanogap structure. The geometry of the bowtie gap including gap size, tip width, metal thickness, and tip angle are investigated at macroscale to find the maximum electric field enhancement across the gap. This thesis focuses on the simulation portion of a work that consists of experimental and simulation platforms. The simulation platform is created …

Sugarcane Bagasse As A Carrier For The Immobilization Of Saccharomyces Cerevisiaein Bioethanol Production, Sita Heris Anita, Wibowo Mangunwardoyo, Yopi Yopi

Makara Journal of Technology

Sugarcane bagasse was used as a carrier to immobilize Saccharomyces cerevisiae in bioethanol production. This research aims to study the potential use of sugarcane bagasse as an alternative carrier for cell immobilization and improvement in the production process of cell immobilization in bagasse. The results showed that the physical characteristics of sugarcane bagasse as a carrier were water content (7.77 ± 0.35%), water retention (4.80 ± 0.44 g/g), water absorption index (8.58 ± 0.22 g/g), and lignin content (24.40 ± 1.52 %). Determination of cell retention was performed in an inoculum volume of 50 mL yeast suspension with various carrier …

Error Resilient Video Coding Using Bitstream Syntax And Iterative Microscopy Image Segmentation, Neeraj Jayant Gadgil

Open Access Dissertations

There has been a dramatic increase in the amount of video traffic over the Internet in past several years. For applications like real-time video streaming and video conferencing, retransmission of lost packets is often not permitted. Popular video coding standards such as H.26x and VPx make use of spatial-temporal correlations for compression, typically making compressed bitstreams vulnerable to errors. We propose several adaptive spatial-temporal error concealment approaches for subsampling-based multiple description video coding. These adaptive methods are based on motion and mode information extracted from the H.26x video bitstreams. We also present an error resilience method using data duplication in …

Centimeter-Deep Tissue Fluorescence Microscopic Imaging, Bingbing Cheng

Bioengineering Dissertations - Archive

Fluorescence microscopic imaging in centimeter-deep tissue has been highly sought-after for many years because much interesting in vivo micro-information—such as microcirculation, tumor angiogenesis, and cancer metastasis—may deeply locate in tissue. However, it is very challenging because of strong tissue light scattering. This includes: how to confine the fluorescence emission into a small volume to achieve high spatial resolution; how to increase fluorescence emission efficiency to compensate the signal attenuation caused by small emission volume and tissue scattering/absorption; and how to reduce background fluorescence noise and exclusively differentiate signal photons from background photons to increase signal-to-noise ratio (SNR) and sensitivity. Ultrasonic …

Microbubble Generation By Piezoelectric Transducers For Biomedical Studies, Mohammed Alkhazal

Electrical & Computer Engineering Theses & Dissertations

Bubbles induced by blast waves or shocks are speculated as the major cause of damage in biological cells in mild traumatic brain injuries (TBI). Microbubble collapse was found to induce noticeable cell detachment from the cell substrate, changes in focal adhesion, and biomechanics. To better understand the bubble mechanism, a system needs to be constructed which allows clear differentiation on the impact of bubbles from that of shocks. Such a generator needs to be low profile in order to place under a microscope. A piezoelectric transducer system was designed to meet the need. The system uses either a flat or …

Design And Validate A Synthetic Circuit For Detecting Pathway Signaling In Mammalian Cells, Darisha Jhutty, Nicholas Parker

Bioengineering Senior Theses

Synthetic circuits provide novel ways for scientists to program and probe mammalian cell behavior. This allows for enhanced research tools and chemical sensors. Our project works with an engineered synthetic circuit and monitors the output of the circuit using green fluorescent protein( GFP) and luciferase. Expression of GFP is both quantifiable and observable over a time period in living cells. Luciferase can be detected by an assay in lysed cells to give data on overall expression of the circuit. By measuring and comparing output of this circuit over time, we can create a model to demonstrate the lack of expression, …

Biodegradable Magnesium Alloys For Orthopaedic Applications: A Review On Corrosion, Biocompatibility And Surface Modifications., Sankalp Agarwal, James Curtin, Brendan Duffy, Swarna Jaiswal

Articles

Magnesium (Mg) and its alloys have been extensively explored as potential biodegradable implant materials for orthopaedic applications (e.g. Fracture fixation). However, the rapid corrosion of Mg based alloys in physiological conditions has delayed their introduction for therapeutic applications to date. The present review focuses on corrosion, biocompatibility and surface modifications of biodegradable Mg alloys for orthopaedic applications. Initially, the corrosion behaviour of Mg alloys and the effect of alloying elements on corrosion and biocompatibility is discussed. Furthermore, the influence of polymeric deposit coatings, namely sol-gel, synthetic aliphatic polyesters and natural polymers on corrosion and biological performance of Mg and its …

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 …

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

05. Chemistry, Northeastern State University

Oklahoma Research Day Abstracts

No abstract provided.

03. Biology, Northeastern State University

Oklahoma Research Day Abstracts

No abstract provided.

Ms-Reduce: An Ultrafast Technique For Reduction Of Big Mass Spectrometry Data For High-Throughput Processing, Muaaz Gul Awan, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Modern proteomics studies utilize high-throughput mass spectrometers which can produce data at an astonishing rate. These big Mass Spectrometry (MS) datasets can easily reach peta-scale level creating storage and analytic problems for large-scale systems biology studies. Each spectrum consists of thousands of peaks which have to be processed to deduce the peptide. However, only a small percentage of peaks in a spectrum are useful for peptide deduction as most of the peaks are either noise or not useful for a given spectrum. This redundant processing of non-useful peaks is a bottleneck for streaming high-throughput processing of big MS data. One …