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Full-Text Articles in Biomedical Engineering and Bioengineering

Feedforward And Feedback Signals In The Olfactory System, Srimoy Chakraborty May 2019

Feedforward And Feedback Signals In The Olfactory System, Srimoy Chakraborty

Theses and Dissertations

The conglomeration of myriad activities in neural systems often results in prominent oscillations. The primary goal of the research presented in this thesis was to study effects of sensory stimulus on the olfactory system of rats, focusing on the olfactory bulb (OB) and the anterior piriform cortex (aPC). Extracellular electrophysiological measurements revealed distinct frequency bands of oscillations in OB and aPC. However, how these oscillatory fluctuations help the animal to process sensory input is not clearly understood. Here we show high frequency oscillations in olfactory bulb carry feedforward signals to anterior piriform cortex whereas feedback from the aPC is predominantly ...


Assessing Biofiltration Without Ozonation For Removal Of Trihalomethane Precursors In Drinking Water At The Beaver Water District Drinking Water Treatment Plant, Sana Ajaz Dec 2018

Assessing Biofiltration Without Ozonation For Removal Of Trihalomethane Precursors In Drinking Water At The Beaver Water District Drinking Water Treatment Plant, Sana Ajaz

Theses and Dissertations

Biofiltration without pre-ozonation has the capability to remove natural organic matter (NOM) fractions that serve as precursors of disinfection byproducts (DBPs), which include the four regulated trihalomethanes (THMs) and dichloroacetonitrile (DCAN). Rapid small-scale column tests (RSSCTs) and Pilot Plant filters operated at empty-bed contact times (EBCTs) of 4, 8, and 16 minutes were used to evaluate the performance of nutrient-amended (free ammonia and phosphorus) biofiltration for THM and DCAN precursor removal, as measured using formation potential (FP) tests. NOM surrogates – which include dissolved organic carbon (DOC), specific ultraviolet absorbance (SUVA254) and fluorescence-PARAFAC components – were measured weekly throughout the 30-week study ...


A Discrete-Event Simulation Approach For Modeling Human Body Glucose Metabolism, Buket Aydas Aug 2018

A Discrete-Event Simulation Approach For Modeling Human Body Glucose Metabolism, Buket Aydas

Theses and Dissertations

This dissertation describes CarbMetSim (Carbohydrate Metabolism Simulator), a discrete-event simulator that tracks the blood glucose level of a person in response to a timed sequence of diet and exercise activities. CarbMetSim implements broader aspects of carbohydrate metabolism in human beings with the objective of capturing the average impact of various diet/exercise activities on the blood glucose level. Key organs (stomach, intestine, portal vein, liver, kidney, muscles, adipose tissue, brain and heart) are implemented to the extent necessary to capture their impact on the production and consumption of glucose. Key metabolic pathways (glucose oxidation, glycolysis and gluconeogenesis) are accounted for ...


Characterization Of Bacteriorhodopsin And Halorhodopsin Reconstituted In Lipid Bilayer Membranes, Joel Domkam Kamwa Jan 2018

Characterization Of Bacteriorhodopsin And Halorhodopsin Reconstituted In Lipid Bilayer Membranes, Joel Domkam Kamwa

Theses and Dissertations

Motivated to produce electricity with photon activated ion pumps, the main purpose of this work was to characterize the photosynthetic membrane proteins bacteriorhodopsin (proton pump) and halorhodopsin (chloride pump). The proteins were re-suspended in lipid bilayers. For this work, an experimental set-up was built which included: chambers for lipid bilayer formation and characterization, lasers for ion pump activation, and an AxoPatch electrophysiology system for small photocurrent measurement. Lipid bilayer membranes were formed using mostly folding method: folding two monolayers together. The membranes were characterized by their resistance, capacitance, and generated photocurrent. Photocurrent was generated upon illumination of lipid-protein membranes with ...


Quantitative Optical Studies Of Oxidative Stress In Rodent Models Of Eye And Lung Injuries, Zahra Ghanian Dec 2016

Quantitative Optical Studies Of Oxidative Stress In Rodent Models Of Eye And Lung Injuries, Zahra Ghanian

Theses and Dissertations

Optical imaging techniques have emerged as essential tools for reliable assessment of organ structure, biochemistry, and metabolic function. The recognition of metabolic markers for disease diagnosis has rekindled significant interest in the development of optical methods to measure the metabolism of the organ.

The objective of my research was to employ optical imaging tools and to implement signal and image processing techniques capable of quantifying cellular metabolism for the diagnosis of diseases in human organs such as eyes and lungs. To accomplish this goal, three different tools, cryoimager, fluorescent microscope, and optical coherence tomography system were utilized to study the ...


Design And Basic Verification Of A Discrete Event Simulator For Glucose Metabolism In Human Beings, Elizabeth Andrews Dec 2016

Design And Basic Verification Of A Discrete Event Simulator For Glucose Metabolism In Human Beings, Elizabeth Andrews

Theses and Dissertations

This thesis describes the design and basic verification of a discrete event simulator for glucose metabolism in human beings. The simulator implements the glucose metabolism related behavior of various organs in the human body and tracks the blood plasma glucose level as the human body goes through a sequence of diet and exercise events. The simulator can mimic insulin resistance in various organs as well as the loss of insulin production in the pancreas and the adverse impact of these changes on the metabolic behavior of various organs. Thus, the simulator can serve as a model for people with diabetes ...


Chlorine Demand Shows Thresholds And Hierarchy With Source Water Quality At Beaver Lake, Arkansas, Jaime M. Gile Aug 2016

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

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 ...


Compounds Released From Biomass Deconstruction: Understanding Their Effect On Cellulose Enzyme Hydrolysis And Their Biological Activity, Angele Djioleu Dec 2015

Compounds Released From Biomass Deconstruction: Understanding Their Effect On Cellulose Enzyme Hydrolysis And Their Biological Activity, Angele Djioleu

Theses and Dissertations

The effect of compounds produced during biomass pretreatment on cellulolytic enzyme was investigated. Liquid prehydrolyzates were prepared by pretreating switchgrass using 24 combinations of temperature, time, and sulfuric acid concentration based on a full factorial design. Temperature was varied from 140°C to 180°C; time ranged from 10 to 40 min; and the sulfuric acid concentrations were 0.5% or 1% (v/v). Identified products in the prehydrolyzates included xylose, glucose, hydroxymethylfurfural (HMF), furfural, acetic acid, formic acid, and phenolic compounds at concentration ranging from 0 to 21.4 g/L. Pretreatment conditions significantly affected the concentrations of compounds ...


Simulating The Impact Of Diet And Exercise On Blood Glucose Level For People With Type 2 Diabetes, Md Abdul Halim Sarkar Aug 2015

Simulating The Impact Of Diet And Exercise On Blood Glucose Level For People With Type 2 Diabetes, Md Abdul Halim Sarkar

Theses and Dissertations

This thesis describes the design of a discrete-event simulator that tracks the blood glucose level and glycated hemoglobin level as a person goes through her daily diet and exercise activities. This thesis also reports results of simulations performed using the simulator that show the changes in blood glucose level and glycated hemoglobin level as a diabetic person makes specific changes to her diet/exercise routine.


Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz May 2015

Scattering Correction Methods Of Infrared Spectra Using Graphics Processing Units, Asher Imtiaz

Theses and Dissertations

Fourier transform infrared (FTIR) microspectroscopy has been used for many years as a technique that provides distinctive structure-specific infrared spectra for a wide range of materials (e.g., biological (tissues, cells, bacteria, viruses), polymers, energy related, composites, minerals). The mid-infrared radiation can strongly scatter from distinct particles, with diameters ranging between 2-20 micrometer. Transmission measurements of samples (approximately 100 micrometers x 100 micrometers x 10 micrometers) with distinct particles. will be dominated by this scattering (Mie scattering). The scattering distorts the measured spectra, and the absorption spectra appear different from pure absorbance spectra. This thesis presents development and implementation of ...


A Pump Monitoring Approach To Irrigation Pumping Plant Performance Testing, William Merritt Mcdougall May 2015

A Pump Monitoring Approach To Irrigation Pumping Plant Performance Testing, William Merritt Mcdougall

Theses and Dissertations

Traditionally, irrigation pumping plants have been tested using an instantaneous appraoch, which tests performance parameters over a very short time interval. Using this method, the tester measures the necessary work and energy use parameters to calculate the desired pumping plant performance values. The primary limitation of this approach is its inability to determine the season long efficiency of an irrigation pumping plant.

A new approach to evaluating irrigation pumping plant performance is the use of pump monitoring systems which use high frequency, real-time data collection and telemetry to relay information directly from the pump to the user. This method of ...


Transformation Of Swine Manure And Algal Consortia To Value-Added Products, Mahmoud A. Sharara May 2015

Transformation Of Swine Manure And Algal Consortia To Value-Added Products, Mahmoud A. Sharara

Theses and Dissertations

The swine production sector is projected to grow globally. In the past, this growth manifested itself in increased herd sizes and geographically concentrated production. Although economically sound, these trends had negative consequences on surrounding ecosystems. Over-application of manure resulted in water quality degradation, while long-term storage of manure slurries was found to promote release of potent GHG emissions. There is a need for innovative approaches for swine manure management that are compatible with current scales of production, and increasingly strict environmental regulations.

This study aims to investigate the potential for incorporating gasification as part of a novel swine manure management ...


Femtosecond Laser Beam Propagation Through Corneal Tissue: Evaluation Of Therapeutic Laser-Stimulated Second And Third-Harmonic Generation, William R. Calhoun Iii Jan 2015

Femtosecond Laser Beam Propagation Through Corneal Tissue: Evaluation Of Therapeutic Laser-Stimulated Second And Third-Harmonic Generation, William R. Calhoun Iii

Theses and Dissertations

One of the most recent advancements in laser technology is the development of ultrashort pulsed femtosecond lasers (FSLs). FSLs are improving many fields due to their unique extreme precision, low energy and ablation characteristics. In the area of laser medicine, ophthalmic surgeries have seen very promising developments. Some of the most commonly performed surgical operations in the world, including laser-assisted in-situ keratomileusis (LASIK), lens replacement (cataract surgery), and keratoplasty (cornea transplant), now employ FSLs for their unique abilities that lead to improved clinical outcome and patient satisfaction.

The application of FSLs in medical therapeutics is a recent development, and although ...


Self-Assembly Of Gold Nanosphere Dimers By Inertial Force, George Andrew Christopher Sakhel Aug 2014

Self-Assembly Of Gold Nanosphere Dimers By Inertial Force, George Andrew Christopher Sakhel

Theses and Dissertations

The morphology and composition of a nanoparticle (NP) play a critical role in determining the NP's properties and function. To date, researchers have created a myriad of NPs of different shapes, sizes, and compositions with interesting attributes and applications ushering a revolution in medicine, electronics, microscopy, and microfluidics.

In this study, gold (Au) nanosphere dimers (NSDs) have been synthesized through a novel self-assembly method. These particles were created from Au NPs mono-dispersed in aqueous solution via a process of centrifugation and capping agent replacement. Au NSDs consist of two Au NPs combined together with minimal gaps between them. Optical ...


Citefinder: A System To Find And Rank Medical Citations, Seyed Soheil Moosavinasab May 2014

Citefinder: A System To Find And Rank Medical Citations, Seyed Soheil Moosavinasab

Theses and Dissertations

This thesis presents CiteFinder, a system to find relevant citations for clinicians' written content. Inclusion of citations for clinical information content makes the content more reliable through the provision of scientific articles as references, and enables clinicians to easily update their written content using new information. The proposed approach splits the content into sentences, identifies the sentences that need to be supported with citations by applying classification algorithms, and uses information retrieval and ranking techniques to extract and rank relevant citations from MEDLINE for any given sentence. Additionally, this system extracts snippets from the retrieved articles. We assessed our approach ...


Monitoring Changes In Hemodynamics Following Optogenetic Stimulation, Seth Thomas Frye May 2014

Monitoring Changes In Hemodynamics Following Optogenetic Stimulation, Seth Thomas Frye

Theses and Dissertations

The brain is composed of billions of neurons, all of which connected through a vast network. After years of study and applications of different technologies and techniques, there are still more questions than answers when it comes to the fundamental functions of the brain. This project aims to provide a new tool which can be used to gain a better understanding of the fundamental mechanisms that govern neurological processes inside the brain. In order for neural networks to operate, blood has to be supplied through neighboring blood vessels. As such, the increase or decrease in the blood supply has been ...


Extraction And Classification Of Drug-Drug Interaction From Biomedical Text Using A Two-Stage Classifier, Majid Rastegar-Mojarad Dec 2013

Extraction And Classification Of Drug-Drug Interaction From Biomedical Text Using A Two-Stage Classifier, Majid Rastegar-Mojarad

Theses and Dissertations

One of the critical causes of medical errors is Drug-Drug interaction (DDI), which occurs when one drug increases or decreases the effect of another drug. We propose a machine learning system to extract and classify drug-drug interactions from the biomedical literature, using the annotated corpus from the DDIExtraction-2013 shared task challenge. Our approach applies a two-stage classifier to handle the highly unbalanced class distribution in the corpus. The first stage is designed for binary classification of drug pairs as interacting or non-interacting, and the second stage for further classification of interacting pairs into one of four interacting types: advise, effect ...


Extracting The Structure And Conformations Of Biological Entities From Large Datasets, Ali Dashti Dec 2013

Extracting The Structure And Conformations Of Biological Entities From Large Datasets, Ali Dashti

Theses and Dissertations

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging "diffract & destroy" X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of "unsorted" snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive.

It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms able to extract ...


Efficient Computation Of K-Nearest Neighbor Graphs For Large High-Dimensional Data Sets On Gpu Clusters, Ali Dashti Aug 2013

Efficient Computation Of K-Nearest Neighbor Graphs For Large High-Dimensional Data Sets On Gpu Clusters, Ali Dashti

Theses and Dissertations

The k-Nearest Neighbor Graph (k-NNG) and the related k-Nearest Neighbor (k-NN) methods have a wide variety of applications in areas such as bioinformatics, machine learning, data mining, clustering analysis, and pattern recognition. Our application of interest is manifold embedding. Due to the large dimensionality of the input data (<15k), spatial subdivision based techniques such OBBs, k-d tree, BSP etc., are not viable. The only alternative is the brute-force search, which has two distinct parts. The first finds distances between individual vectors in the corpus based on a pre-defined metric. Given the distance matrix, the second step selects k nearest neighbors for each member of the query data set.

This thesis presents the development and implementation of a distributed exact k-Nearest Neighbor Graph (k-NNG) construction method. The proposed method uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism for distributed computational systems using GPUs. It is scalable for different cluster sizes, with each compute node in the cluster containing ...


Design Of A Pretreatment And Enzymatic Saccharification Scheme Of Understory From Managed Pine Forest For A Biochemical-Refinery Platform: The Example Of The Sweetgum Tree, Angele Djioleu Dec 2012

Design Of A Pretreatment And Enzymatic Saccharification Scheme Of Understory From Managed Pine Forest For A Biochemical-Refinery Platform: The Example Of The Sweetgum Tree, Angele Djioleu

Theses and Dissertations

The possibility of using sweetgum from southern pine dominated forests as a biobased refinery feedstock was investigated. First, a baseline hydrolysis scheme for sweetgum wood and bark was designed. Sweetgum wood and bark were pretreated with 0.98% (v/v) sulfuric acid at 140°C for 30, 40, 50, 60 or 70 min and at 160°C for 30, 40, 50 or 60 min. The water insoluble solid (WIS) fraction was hydrolyzed with a cellulase enzyme cocktail. Results showed that maximum xylose and glucose yields from the wood were 82 and 86%, respectively. Similarly, the respective maximum yields of xylose ...


A Watershed Scale Evaluation Of Selected Second Generation Biofeedstocks On Water Quality, Gurdeep Singh Dec 2012

A Watershed Scale Evaluation Of Selected Second Generation Biofeedstocks On Water Quality, Gurdeep Singh

Theses and Dissertations

This study compares a novel simulation approach to the conventional Soil and Water Assessment Tool (SWAT) modeler's approach for targeting biofuel crop production on marginal lands. In conventional SWAT modeling approach, non-spatial definition of hydrological response units (HRUs) results in the simulation of biofuel crops on both marginal and non-marginal land. This study provides an alternative approach in which a marginal-land raster was integrated into the land use and land cover (LULC) raster in such a way that the land uses were divided into marginal and non-marginal components. This modified LULC was used for model setup which resulted in ...


Optical Cryoimaging Of Celular Redox In Kidneys From Diabetic Mice, Sepideh Maleki Aug 2012

Optical Cryoimaging Of Celular Redox In Kidneys From Diabetic Mice, Sepideh Maleki

Theses and Dissertations

Diabetic Nephropathy (DN) is the major single cause of end stage renal diseases (ESRD) in the United States. Diabetes is the third leading fatal disorder after cancer and heart disease. It is affecting 8.3% of the residents of the United States, with a total healthcare cost of $174 billion/yr by 2010.

There currently exists a need for a sensitive and specific diagnosis for temporal detection of oxidative stress (OS) in cellular metabolic levels, which plays an early role in the development of DN. The objective of this research is to use a fluorescence optical imaging technique in order ...