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Batch Culture Models Of The Murine Gut Microbiome & The Impact Of Simple Dormancy On Dormancy-Capable Microorganisms Models, Ana C. Mendez

Mathematics Dissertations

The proposed mathematical biology research utilizes mathematical models to gain insight into biological systems. These systems of ordinary differential equations model diverse topics, ranging from gut microbiomes to harmful algal blooms. A complete stability analysis, supporting phase plane portraits, bifurcation diagrams, and numerical simulations will accompany the models presented. In Chapter 2, the murine gut microbiome is modeled to match laboratory experiments in the literature. In these experiments, mice eat plasmid-carrying “donor” bacteria and naturally carry plasmid-free “resident” bacteria in their gut. The models aim to capture the behavior of plasmids, donor bacteria, and resident bacteria. Chapter 3 explores dormancy …

Opensim-Based Musculoskeletal Modeling: Foundation For Interactive Obstetric Simulator, Bahador Dodge

Electrical & Computer Engineering Theses & Dissertations

The use of mathematical and computational models to understand complex biological systems, such as the human birth process, is a rapidly growing field in medicine. These models can be used to optimize and personalize medical treatments for individual patients, enhance training, and aid in educational efforts. While recent advancements in healthcare, particularly in obstetrics, have improved care for mothers and babies, studies and government reports indicate a rising rate of maternal mortality in the United States.

Despite this rising trend, there is a lack of detailed studies concerning the use of modeling and simulation to develop an interactive obstetrics simulator …

Modeling Vascular Diffusion Of Oxygen In Breast Cancer, Tina Giorgadze

Senior Projects Spring 2023

Oxygen is a vital nutrient necessary for tumor cells to survive and proliferate. Oxygen is diffused from our blood vessels into the tissue, where it is consumed by our cells. This process can be modeled by partial differential equations with sinks and sources. This project focuses on adding an oxygen diffusion module to an existing 3D agent-based model of breast cancer developed in Dr. Norton’s lab. The mathematical diffusion module added to an existing agent-based model (ABM) includes deriving the 1-dimensional and multi-dimensional diffusion equations, implementing 2D and 3D oxygen diffusion models into the ABM, and numerically evaluating those equations …

Accurate Simulation Of Reads And Improved Strategies For Abundance Estimation Supporting Reduced Representation Sequencing For Metagenomics, Ryan Kuster

Doctoral Dissertations

Next generation sequencing has impacted all areas of biology by providing affordable investigations into some of the most complex processes underpinning life. With its ubiquitous application, there is still benefit in considering the nuances of the technology and its downstream analysis. Sequencing libraries produced by fragmenting DNA with restriction enzyme digests limit the scope of sequencing to a reduced set of genomic loci, allowing for deeper sequencing of those regions at a reduced cost per sample. These sequencing libraries have been used to determine genetic markers within populations of closely related individuals due to their sensitivity and preservation within populations. …

Simulating Polistes Dominulus Nest-Building Heuristics With Deterministic And Markovian Properties, Benjamin Pottinger

Undergraduate Honors Theses

European Paper Wasps (Polistes dominula) are social insects that build round, symmetrical nests. Current models indicate that these wasps develop colonies by following simple heuristics based on nest stimuli. Computer simulations can model wasp behavior to imitate natural nest building. This research investigated various building heuristics through a novel Markov-based simulation. The simulation used a hexagonal grid to build cells based on the building rule supplied to the agent. Nest data was compared with natural data and through visual inspection. Larger nests were found to be less compact for the rules simulated.

Defining Interactions Between Deformable Dna Origami And Lipid Bilayers Through Molecular Dynamics Simulation, Zachary A. Loyd

Chancellor’s Honors Program Projects

No abstract provided.

Variability In Rice Returns Using A Representative Farm Approach, Adriana Dimas

LSU Master's Theses

Agriculture is a major contributor to the U.S. economy and vital to the continued availability of a safe and inexpensive food supply. Representative farms are virtual farms that represent the production practices of a specific crop and region. Annually, growers face critical management decisions on what crop enterprise selection and combinations will maximize the net returns. Risk for growers comes from the variation in different factors such as yield, market price, production input costs, among others that are required to produce each enterprise. Nine representative farms were established within Louisiana, Mississippi, and Arkansas to evaluate net return variability among different …

Lgbtqia+ Care Simulation: Examining Participating Students’ Attitude And Comfort, Grezelro Gonzalez

College of Science and Health Theses and Dissertations

Background: The LGBTQIA+ communities face healthcare disparities that contribute to reduced overall health. One factor affecting LGBTQIA+ communities’ reduced overall health is poor health-promoting behaviors or avoidance of care due to healthcare providers’ lack of knowledge, poor attitude, and low comfort levels with LGBTQIA+ care. There are limited studies to date that address nursing students’ attitude and comfort with LGBTQIA+ affirming care interventions outside of lectures. Therefore, the purpose of this study was to evaluate the effect of a simulation intervention on the attitude and comfort of prelicensure nursing students towards providing care to members of the LGBTQIA+ community. Sample: …

Expert Level Microscopy For Everyone : Optimizing Microscopy Parameters With Modeling And Simulation, Ethan Woo

Legacy Theses & Dissertations (2009 - 2024)

Multiplexed fluorescent imaging (MFI) has transformed biological investigation by providing spatial context to labeled analytes, such as DNA, RNA, and proteins. Multiplexed imaging techniques can track multiple analytes at once and thus has the potential to provide an unprecedented view into the complex relationships between various molecules, cells, and tissues. However, most researchers rarely use more than 3 fluorophores at a time due to the complex technological and procedural requirements for highly multiplexed imaging. Currently, a major obstacle in the field is the inability to quantify uncertainty in fluorescent images, making it difficult to draw quantitative conclusions from the images. …

Incorporating Demographic Structure And Variable Interaction Types Into Community Assembly Models, Akhil Reddy Alasandagutti, Nayan Chawla

Honors Theses

Theoretical studies of ecological food webs have allowed ecologists to remove the constraints of specific location and timescales from their study of ecological communities; food webs are generally complex and thus empirical study is difficult. Further, this theoretical approach allows ecologists to compare ecological processes and outcomes across any possible food web structures. However, these simulated communities are only as useful as the model from which they were constructed. Modifying existing considerations in these models, and generating new ones, are the jobs of theoretical ecologists that seek to achieve the shared goal of a majority of simulations: representation of real …

Computer Simulations Of Biological Systems: From Protein Dynamics To Drug Discovery, Rupesh Agarwal

Doctoral Dissertations

Computational biophysics methods such as molecular dynamics (MD) simulations are often used in combination with experimental techniques like neutron scattering, NMR, and FTIR to explore protein conformational landscapes. With the improvements in experimental techniques, there is also a need to continually optimize the MD forcefield parameters to make precise predictions that match experimental results. To complement many of these experiments, an accurate model of deuteration is frequently required, but has been elusive. In our work, we developed a novel method to capture isotope effects in classical MD simulations by re-parameterization of the bonded terms of the CHARMM forcefield using quantum …

Using Systems Archetypes And Generic Structures To Support Water Resource Management Studies : The Case Of Cropping Pattern Change In New Mexico State, Babak Bahaddin

Legacy Theses & Dissertations (2009 - 2024)

A wide range of managerial problems are similar in nature, and yet they continuously appear in different forms and in different geographical locations. Compared to other sciences, it seems that in the field of management, managers have a hard time facing these similar problems. Part of this issues is caused by the extreme complexity of the systems and another part is caused by the lack of a universal language with which managers can communicate their lessons. This dissertation offers a set of tools that have been previously manufactured in systems science, and more specifically in System Dynamics.

Assessing The Economic Viability Of Arkansas Farms Under The 2018 Farm Bill, Grant Wilson

Graduate Theses and Dissertations

For over a century, the American agricultural industry has relied on federal government support to aid in the maintenance and expansion of farming operations. Since 1933, a series of 18 farm bills have shaped agricultural policy into what is commonly known as the agricultural safety net. The 2018 farm bill was passed on December 20, 2018 and is the most recent update of the agricultural safety net. Commodity programs and federal crop insurance are two key components of today’s agricultural safety net, and many times, these programs may be the difference between a net loss and a positive net income …

A Simulation Tool For Evaluating The Environmental Impacts Of Management Scenarios For Modern Broiler Production Systems, Martin Andrew Christie

Graduate Theses and Dissertations

The purpose of this work is to provide a simulation tool that allows broiler production practitioners and researchers to simulate the effects of farm design and management practices on resource consumption and environmental impacts. This tool allows the user to design unique farms and simulates on farm processes required to raise broiler chicks to a marketable age. The use can input data such as farm location, broiler breed, flock size, ration type, barn dimensions, and climate control equipment specifications. The algorithms used to simulate broiler breed specific feed intake, broiler weight gain, and other on farm processes such as heating, …

Measuring Flowering Phenology And Its Consequences: A Systematic Review, Samantha M. Mangum

USF Tampa Graduate Theses and Dissertations

Despite growing interest in flowering phenology among ecologists, as reflected by an increase in the number of papers, there is little information on how studies typically measure and describe a plant’s flowering phenology. The focus of this study was the literature on flowering phenology and the approaches researchers have taken to quantify flowering phenology. Initially, a comprehensive description of the breath of literature on flowering phenology was produced. From there, I described the current research on flowering phenology: the year that the studies were published, the locations of the studies, and the particular biomes where the studies were performed. The …

Paper Structure Formation Simulation, Tyler R. Seekins

Electronic Theses and Dissertations

On the surface, paper appears simple, but closer inspection yields a rich collection of chaotic dynamics and random variables. Predictive simulation of paper product properties is desirable for screening candidate experiments and optimizing recipes but existing models are inadequate for practical use. We present a novel structure simulation and generation system designed to narrow the gap between mathematical model and practical prediction. Realistic inputs to the system are preserved as randomly distributed variables. Rapid fiber placement (~1 second/fiber) is achieved with probabilistic approximation of chaotic fluid dynamics and minimization of potential energy to determine flexible fiber conformations. Resulting digital packed …

A Time- And State-Based Approach To Estimate Winter Movement And Survival Of Juvenile Coho Salmon (Oncorhynchus Kisutch) In Freshwater Creek, California, Nicholas Paul Van Vleet

Cal Poly Humboldt theses and projects

Accounting for life history diversity and overwinter survival of juvenile Coho Salmon is important to inform restoration and recovery efforts for this threatened species. Multiple seaward migration patterns of Coho Salmon have been identified, including spring fry migrants, fall and winter parr migrants, and spring smolt migrants. Previous studies have indicated that spring smolt migrants have low overwinter survival rates while they are rearing in upstream habitats, suggesting that freshwater overwinter survival may be one factor that limits smolt production. However, previous research did not account for the early emigration of fall and winter parr migrants from the study area, …

Combining Footprinting Mass Spectrometry And Molecular Dynamics Simulation For Structural Studies In Membrane Proteins, Fengbo Zhou

Arts & Sciences Electronic Theses and Dissertations

Membrane proteins are essential in many cellular processes and represent ~60% of all current drug targets. Due to technical limits, membrane proteins of various types were not studied extensively in the past and the biochemistry and functionality of them remain unclear. The structural biology methodologies require pure isolated protein samples for us to resolve their structure and study their biochemical functions. For such in vitro studies, however, membrane proteins often become unstable when isolated from their native lipid bilayer environment. To overcome the challenge, I employed a novel methodology of solubilizing membrane proteins in solution without detergent. I reconstituted ferroportin, …

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 by …

Evaluating And Reducing The Effects Of Misclassification In A Sequential Multiple Assignment Randomized Trial (Smart), Jun He

Theses and Dissertations

SMART designs tailor individual treatment by re-randomizing patients to subsequent therapies based on their response to initial treatment. However, the classification of patients being responders/non-responders could be inaccurate and thus lead to inappropriate treatment assignment. In a two-step SMART design, by assuming equal randomization, and equal variances of misclassified patients and correctly classified patients, we evaluated misclassification effects on mean, variance, and type I error/ power of single sequential treatment outcome (SST), dynamic treatment outcome (DTRs), and overall outcome. The results showed that misclassification could introduce bias to estimates of treatment effect in all types of outcome. Though the magnitude …

2-D Electrophoresis Modeling Of Multienzyme Cutting Of Polypeptides, Howard Mayes

Theses

2-Dimensional Electrophoresis is one of the tools in the identification of proteins by molecular weight and pH. The display of molecular weight allows the researcher to quickly identify whether a specific protein or peptide string is in the sample. The pH measurement allows even better resolution between different species in the sample. The MultiEnzyme ElectroPhoresis (MEEP) program tries to model that by providing a graph that displays separated protein strings by both molecular weight and pH. The ability to cleave the protein with 43 different enzyme variations allows the researcher to analyze appropriate enzymes to isolate a protein subsequence before …

A Simulation Of Anthropogenic Mammoth Extinction, Matthew Klapman

Undergraduate Honors Papers

There are multiple hypotheses as to why the Columbian Mammoth (Mammuthus columbi) and other megafauna in North America went extinct relatively recently and relatively quickly. The most popular of which are disease, climate change, meteorite strikes, and over hunting by humans [2, 9]. There is evidence to show that a combination of factors contributed to the megafaunal extinction, but ”overkill” explores the idea that early humans migrated onto the continent and then hunted the mammoths and other megafauna to extinction. The overkill hypothesis was first proposed by anthropologist Paul Martin in 1973 [8]. Evidence from radiocarbon dating shows that the …

Quantifying And Simulating Fine-Scale Spatial Patterns In Plant Populations, Darin Schulte

Electronic Theses and Dissertations

Plant ecology as a discipline has increasingly acknowledged the importance of fine-scale spatial patterns in developing our understanding of community/population dynamics. These spatial patterns are largely determined by direct and indirect interactions between plants and their immediate neighbors. Such interactions thus play an important role in the structure and function of plant communities. Study of these types of local interactions has greatly benefitted from simulation based approaches. one such simulation method, agent-based modeling, has increasingly been identified as a useful tool for simulating these fine-scale interactions, and for investigating theoretical descriptions of underlying processes. Similarly, statistical techniques aimed at quantifying …

An Analysis Of Factors Impacting Hay Auction Prices And The Potential For Nap To Reduce Alfalfa Revenue Risk, Madeline L. Dant

Theses and Dissertations--Agricultural Economics

Hay auctions have generally been understudied due to their unique market structure. Therefore, the factors that influence the price of hay at auction markets are not well-known. The price of hay at auction markets reflects the various characteristics that differentiate each lot of hay sold. This study is aimed at analyzing the determinants of Central Kentucky hay prices. A hedonic price model is estimated using data collected from a Central Kentucky hay auction. Known hay attributes include forage species, form, bale weight, and nutritive value. An important aspect of this analysis is to determine whether the quality measures of the …

The Effects Of A Game Simulation On Muscle Activation And Knee Kinematics In Females, Geoffrey Collins

Theses and Dissertations

Intro: Female athletes experience non-contact ACL injuries at 5 times the rate of male athletes. These injuries occur more frequently at the end of halves and may be associated with exercise-induced fatigue causing knee instability. The purpose of this pilot study was to determine the effect of strenuous exercise on lateral knee movement during the landing phase of a jump. Methods: Ten subjects completed both the exercise and the control trial consisting of two 25-min game simulations on a treadmill or on a separate day the equivalent rest. Before, at half time, and immediately following the interventions subjects performed sets …

The Development Of A Prosthetic Training Software For Upper Limb Amputees, Tyler Kayne Sullins

USF Tampa Graduate Theses and Dissertations

The purpose of this study was to develop an intuitive software that aids in the field of prosthetic training and rehabilitation by creating an individualized visualization of joint angles. This software is titled “the prosthetic training software (PTS) for individualized joint angle representation”, and it enables the individualized portrayal of predicted or pre-recorded joint angles. The PTS is an intuitive program for clinicians and prosthesis users that produces an animation of a virtual avatar reflecting the user’s segment lengths and amputation for rehabilitation and training purposes.

The PTS consists of a graphical user interface (GUI) and a 3D visualization of …

A Simulation Platform For Accurate Prediction Of In-Bin Drying And Storage Of Rough Rice, Houmin Zhong

Graduate Theses and Dissertations

Natural air (NA), in-bin drying and storage of rough rice generally maintains high grain quality, but the associated slow movement and occasional stagnation of the drying front during the process may result in problems of rice quality reduction, mold growth, and mycotoxin development, especially for rough rice in the top layers of the bin. Using modeling techniques to simulate in-bin rough rice drying in typically-encountered field scenarios may provide a tool for rapidly predicting the grain condition as drying progresses. The objectives for this study were to (1) investigate accurate models for predicting equilibrium moisture content (EMC) of rough rice …

A Study Of A Simulated Infectious Disease On Healthcare Workers' Reaction, Knowledge, Attitudes, And Performance Towards Hand Hygiene, Lydia Wigglesworth-Ballard

Health Services Research Dissertations

Problem Statement. The high rate of healthcare worker-patient contact provides many opportunities for exposure to pathogens, which creates challenges in assessing healthcare workers' success at preventing healthcare associated infections caused by these dangerous pathogens.

Methods. This study explored the effects of a simulated infectious disease on healthcare workers' hand hygiene knowledge, attitudes, performance, and reactions using Kirkpatrick's Four levels of Evaluation. The study utilized a mixed method pre-test – 2 post-test design. The dependent variables were hand hygiene knowledge, attitudes toward hand hygiene guidelines, hand hygiene performance, and reaction to the overall experience. Data was collected three times over a …

Addressing Genetic Pollution From Pollen Drift On A Heterogeneous Landscape, Mattia Ciro Mancini

Graduate Theses and Dissertations

Genetically modified (GM) crops are crops in which single or multiple genes have been introduced artificially in order to obtain certain characteristics that are difficult to obtain through conventional breeding. Even though farmers have the right to freely choose what types of crops to grow, pollen mediated gene flow from GM crops to non-GM crops can limit the possibility for crops to coexist on a same landscape, resulting in economic losses that depend on the institutional arrangements and the type of property rights in place. Although it is well known that spatial variability affects the degree of cross-contamination between GM …

Facilitating And Enhancing Biomedical Knowledge Translation: An In Silico Approach To Patient-Centered Pharmacogenomic Outcomes Research, Kourosh Ravvaz

Theses and Dissertations

Current research paradigms such as traditional randomized control trials mostly rely on relatively narrow efficacy data which results in high internal validity and low external validity. Given this fact and the need to address many complex real-world healthcare questions in short periods of time, alternative research designs and approaches should be considered in translational research. In silico modeling studies, along with longitudinal observational studies, are considered as appropriate feasible means to address the slow pace of translational research. Taking into consideration this fact, there is a need for an approach that tests newly discovered genetic tests, via an in silico …