Life Sciences Commons^™

Bridging Biological Systems With Social Behavior, Conservation, Decision Making, And Well-Being Through Hybrid Mathematical Modeling, Maggie Renee Sullens

Faculty Publications and Other Works -- Mathematics

This dissertation defense presentation highlights the power of hybrid mathematical modeling and addresses crucial issues such as:

1️. The Impact of Industry Collapse on Community Mental Health: A Complex Contagion ODE Model.

2️. Budget Allocation and Illegal Fishing: A Game Theoretic Model.

3️. Reactive Scope Model with an Energy Budget and Multiple Mediators: An ODE Model

The overarching theme of Hybrid Mathematical Modeling beautifully captures the essence of this work, demonstrating its potential to unravel ecological issues while addressing the intricate interactions between humans and the environment.

Shedding In The Timber Rattlesnake: Natural Patterns, Endocrinological Underpinnings, Temporal And Energetic Effort, And Integration As A Reptilian Life History Trait, Maxwell D. Carnes-Mason

Graduate Theses and Dissertations

The semi-frequent replacement of the epidermis (ecdysis) is a characteristic trait of reptiles. Whereas all reptiles regularly engage in some degree of skin shedding, skin morphology in snakes necessitates the synchronous replacement of the entire epidermis and facilitates the subsequent removal of the old layer as a single sheet. To date, the ubiquitous process has garnered little attention from researchers because snakes shed with unpredictable timing and frequency and are exceedingly cryptic during ecdytic cycles; previously impeding detailed physiological or ecological investigations of the process in the clade. Because of the lack of study, ecdysis is often viewed as a …

Biomechanics Of Mantis Prey Capture, Danielle S. Taylor

Honors Theses

Mantis species have a variety of different morphologies, so do the extreme forms of mantis limbs trade prey catching capability for camouflage? We hypothesize that some extreme forms of mantis limbs that are associated with cryptic species may be associated with a tradeoff of the capability of those limbs. Previous research has developed 2D morphologies of several hundred species of mantises. We are creating a 3D morphology by using micro dissection, micro CT imaging to construct our 3D biomechanical model. We found the attachment points of the ligaments and muscles from a Tenodera forearm and have constructed a 2D biomechanical …

High-Frequency Accelerometer Recording Of Key Predatory Behaviors In Vipers: Validation And Case Study With Timber Rattlesnakes (Crotalus Horridus), Morgan L. Thompson, Richard H. Adams, Anna Tipton, Dominic L. Desantis

Graduate Research Showcase

High-frequency accelerometer recording of key predatory behaviors in vipers: validation and case study with Timber Rattlesnakes (Crotalus horridus)

Morgan Thompson, Richard H. Adams, Anna F. Tipton, and Dominic L. DeSantis

Tri-axial accelerometers (ACTs) are becoming increasingly common in studies of animal behavior wherein direct observation of subjects in nature is constrained or impossible. ACTs are small (< 1 g) piezo-electric (spring-like) sensors that measure three-dimensional acceleration (upward, downward, and side-to-side) derived from subject motion. When leveraged with advanced machine learning techniques, these data can enable precise automated classification of a wide range of movement-mediated behaviors. Until recently, ACTs were largely reserved for larger-bodied organisms or those most amenable to the temporary external attachment of devices. Ongoing ACT miniaturization has now expanded the breadth of organisms amenable to these methods. This project aims to expand on a recently developed framework for ACT monitoring in wild-ranging snakes, a group that has been mostly overlooked in biologging applications. We are currently conducting extensive captive validation trials for robust model training and testing to enable classification of predatory behaviors, including striking and ingestion of prey items, in Timber Rattlesnakes (Crotalus horridus). Following captive validation, we will translate this method to the field with a population of C. horridus in the lower Piedmont of middle Georgia to evaluate the efficacy of externally attached ACTs for remote and continuous monitoring of …

Teaching Computation In Neuroscience: Notes On The 2019 Society For Neuroscience Professional Development Workshop On Teaching, William Grisham, Mathew Abrams, Walt E. Babiec, Adriene L. Fairhall, Robert E. Kass, Pascal Wallisch, Richard F. Olivo

Biological Sciences: Faculty Publications

The 2019 Society for Neuroscience Professional 1Development Workshop on Teaching reviewed current tools, approaches, and examples for teaching computation in neuroscience. Robert Kass described the statistical foundations that students need to properly analyze data. Pascal Wallisch compared MATLAB and Python as programming languages for teaching students. Adrienne Fairhall discussed computational methods, training opportunities, and curricular considerations. Walt Babiec provided a view from the trenches on practical aspects of teaching computational neuroscience. Mathew Abrams concluded the session with an overview of resources for teaching and learning computational modeling in neuroscience.

The Effects Of Elevation On Foraging Behavior Of Bats In Southern Appalachia, Victoria Long

Electronic Theses and Dissertations

There are limited studies on bat activity in higher elevations in the Appalachian region. Levels of bat activity were compared in south central Appalachia at low (< 914.4 m) and high (> 1, 524 m) elevations in open, forest edge, and riparian habitats. Additionally, habitat suitability was modeled for a common species, big brown bat (Eptesicus fuscus). The study started May 27^th 2019, and sites were monitored biweekly until October 2^nd 2019. Six species and one genus were recorded during the study. Species from the Myotis genus were grouped together because of similar call characteristics. Results show that species were significantly more …

Historical And Contemporary Variables Affecting The Range And Distribution Of Aedes Aegypti, The Yellow Fever Mosquito, In The United States, Nicole Mackey

Master's Theses

Aedes aegypti, the primary mosquito vector of the yellow fever virus, threatens global health by passing on this virus, as well as chikungunya, dengue, and Zika viruses. Through its natural tendency to live in highly urban areas and bite human hosts; understanding the factors that affect the historical and current range of the pest is invaluable (Gubler, 1998). Although these viruses are not normally found in the United States, lack of vaccinations and wide-spread presence of the mosquito could lead to these diseases being reintroduced with potentially devastating effects (Monath, 2001). To determine a partial historical range of A. aegypti …

Multivariate Habitat-Based Predictive Modeling Of Three Demersal Rockfish Species In Central California, Georgia R. Martel

Cal Poly Humboldt theses and projects

Accurate, spatially explicit models of rockfish abundance are critical in implementing ecosystem-based management strategies and designating essential fish habitats and marine protected areas. Multibeam bathymetry methods and visual, non-extractive submersible transect surveys were combined to collect environmental variables and fish abundance data at three distinct sites within the study region. Zero-adjusted models were developed using habitat classification analyses of high-resolution (5 m) digital elevation models. Model accuracies were assessed by using a reserved subset of the original datasets. To demonstrate that a model’s predictive power was linked to its spatial origins, Mean Absolute Error and coefficient of determination values were …

Sonification Of Epigenetic Processes, Joelle Strom

Senior Theses

Sonification is the process of creating sound or music from data for investigative or aesthetic purposes. Data sonification has been used in multiple fields to provide an additional layer of analysis to datasets, engage general audiences in a scientific topic, or create an evocative musical piece. Sonification has been extended to biological subjects, including macromolecules such as protein and DNA. Epigenetics, the processes by which gene expression is regulated, is a burgeoning field of molecular biology research. Epigenetic processes have been scarcely sonified, and the process of sonifying DNA base methylation has never been published. DNA methylation is an integral …

The Correlation Between Sleep And Lifespan In Drosophila Melanogaster, Joshua Randall Lisse

Masters Theses

”Adequate sleep is associated with an individual’s health. Too little sleep is associated with many health problems, including cardiovascular disease, obesity, and a general increase in all-cause mortality. Yet the molecular changes that link poor sleep and changes in health are still not well understood. Individuals have a unique daily need for sleep, and deviations from the animal’s regular sleeping patterns can be indicative of, or result in, underlying changes in its health. Therefore, we hypothesize that changes in the sleep architecture in Drosophila melanogaster reflect changes in the fly’s health.

We determined sleep architecture in wild-type male flies over …

Modeling The Effect Of Post-Dispersal Seed Predation On Tropical Tree Species In Panama, Justin Tirrell

Fall Student Research Symposium 2018

Palm trees provide a unique opportunity to study what conditions optimize the probability that a seed will grow successfully. The seeds of palm trees, endocarps, are large and easy to locate. When they don't grow, predators leave marks on them that tell the story of their fate. The focus of my experiment is to determine how the current distribution pattern of parent palm trees in Panama Palm trees affects the the future distribution of seedlings. I have programmed a versatile model that takes the assumption that bruchid beetles are the sole predators acting on the seeds, and that these fall …

Review: Using Physiologically Based Models To Predict Population Responses To Phytochemicals By Wild Vertebrate Herbivores, J. S. Forbey, T. T. Caughlin

Biology Faculty Publications and Presentations

To understand how foraging decisions impact individual fitness of herbivores, nutritional ecologists must consider the complex in vivo dynamics of nutrient–nutrient interactions and nutrient–toxin interactions associated with foraging. Mathematical modeling has long been used to make foraging predictions (e.g. optimal foraging theory) but has largely been restricted to a single currency (e.g. energy) or using simple indices of nutrition (e.g. fecal nitrogen) without full consideration of physiologically based interactions among numerous co-ingested phytochemicals. Here, we describe a physiologically based model (PBM) that provides a mechanistic link between foraging decisions and demographic consequences. Including physiological mechanisms of absorption, digestion and metabolism …

Modeling Habitat Of Freshwater Mussels (Bivalvia:Unionidae) In The Lower Great Lakes 25 Years After The Dreissena Invasion, Jonathan M. Bossenbroek, Lyubov E. Burlakova, Todd C. Crail, Alexander Y. Karatayev, Robert A. Krebs, David T. Zanatta

Biological, Geological, and Environmental Faculty Publications

Finding remnant populations of species that are of conservation concern can be difficult, particularly in aquatic habitats. Models of ecological niches can aid in the discovery of refuges. Remnant populations of native freshwater mussels (unionids) have been found in Lakes Erie and St Clair. Our goals were to predict undiscovered refuges in Lake Ontario based on habitat analysis from Lake Erie and to conduct surveys to test those predictions. We built a presence-only model on environmental data including attributes of the benthic zone and shoreline where mussels occurred in Lake Erie. We found a link between small- and large-scale variables …

Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru

Hui Ye

Background Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a …

Effects Of Diabetes On Ovarian Cancer: Data Analysis And Modeling Study, Claire Belay

Theses and Dissertations

Ovarian cancer has one of the highest mortality rates of all gynecological cancers [13]. Further knowledge of risk factors for the growth of ovarian tumors would be beneficial in both the treatment and prevention of this type of cancer. Previous research has shown a positive correlation between diabetes and prostate tumor growth [22], The first aim of this study was to determine the effect of diabetes of ovarian tumor growth. The second aim was to develop a model to predict ovarian tumor growth based on the microenvironment within a patient’s body. The hypothesis was that there would be a positive …

Biophysical Mechanisms Of Frequency-Dependence And Its Neuromodulation In Neurons In Oscillatory Networks, David Michael Fox

Dissertations

In response to oscillatory input, many isolated neurons exhibit a preferred frequency response in their voltage amplitude and phase shift. Membrane potential resonance (MPR), a maximum amplitude in a neuron’s input impedance at a non-zero frequency, captures the essential subthreshold properties of a neuron, which may provide a coordinating mechanism for organizing the activity of oscillatory neuronal networks around a given frequency. In the pyloric central pattern generator network of the crab Cancer borealis, for example, the pacemaker group pyloric dilator neurons show MPR at a frequency that is correlated with the network frequency. This dissertation uses the crab …

Dengue Vaccination Modulates The Dengue-Zika Viral System Via Immunogenic Cross-Talk, Noah J. B. Silva

Biology ETDs

A vaccine for dengue, a viral disease which is a major driver of morbidity and mortality in tropical and subtropical regions, has recently been approved by eleven countries. While vaccination has the potential to reduce disease burden, the approved vaccine faces challenges due to the interactions between the four serotypes of dengue virus (DENV1-4) and the potential interactions with Zika virus (ZIKV), a related flavivirus. In this study, we propose a mathematical model incorporating both DENV and ZIKV in order to investigate the effects of viral competition on dengue vaccine performance, the potential for change in incidence of Zika due …

Session C-1: Modeling Stem Activities Into Classroom Practice, Sowmya Anjur

Professional Learning Day

Students understand concepts better when they have had a chance to work hands on with relevant material. Examples will be presented from my classroom where difficult concepts have been modeled into simple experiments with considerable success in enhancing student understanding. Special focus will be given to selected topics that students seem to have the most difficulty grasping. The objective is to enable students to transfer their understanding to solve complex problems with considerable ease and apply their understanding to real world scenarios on assessments. Suggestions will also be provided for implementation of various concepts into the high school classroom.

Comparing Game Simulation To Concept Models For Student-Centered Learning In Biology, Margaurete Romero

USF Tampa Graduate Theses and Dissertations

Science education research continues to demonstrate improved learning with active-learning techniques compared to lectures. However, the question of which active-learning methods are the most effective for learning complex scientific principles in various context still remains. Models are commonly used in activities that allow students to simplify complex systems and understand how components interact. I investigated the outcomes for student learning and engagement of two model-based activities - concept models and game simulations. The activities were conducted in an introductory biology course in sixteen discussion sections. Eight sections were assigned to the concept model activity and eight to the simulation activity. …

Interspecies Comparison Of Peptide Substrate Reporter Metabolism Using Compartment-Based Modeling [Post-Print], Allison Tierney, Nhat Pham, Kunwei Yang, Brooks Emerick, Michelle Kovarik

Faculty Scholarship

Peptide substrate reporters are fluorescently labeled peptides that can be acted upon by one or more enzymes of interest. Peptide substrates are readily synthesized and more easily separated than full-length protein substrates; however, they are often more rapidly degraded by peptidases. As a result, peptide reporters must be made resistant to proteolysis in order to study enzymes in intact cells and lysates. This is typically achieved by optimizing the reporter sequence in a single cell type or model organism, but studies of reporter stability in a variety of organisms are needed to establish the robustness and broader utility of these …

Upper, Lower Solutions And Analytic Semigroups For A Model With Diffusion, Yannick T. Kouakep

Applications and Applied Mathematics: An International Journal (AAM)

In this discussion we consider an autonomous parabolic epidemic 2-dimensional system modelling the dynamics of transmission of immunizing diseases for a closed population into bounded regular domain. Our model takes into account diffusion of population with external influx as well as one class of infected individuals. We study the well-posedness two-component diffusion equations including external supplies with Neumann conditions using upper/lower solutions and analytic semigroups. In case of constant population or not, with non-oscillatory solution and constant diffusion, this problem admits travelling wave solutions whose minimum wave speed is surveyed here.

Nonlinear Dynamics Of Filaments In Free Space And Fluids, Victoria Kelley

Senior Honors Projects, 2010-2019

The purpose of this paper is to study a straight rod, held at both ends, with a known twist and tension or compression. We study the stability of this steady state when the system is dominated either by inertia or drag. In order to do this, we first replicate the work of Goriely and Tabor to look at the case with inertia, without drag. After conducting the analysis for that case, we then apply their framework to perform a linear stability analysis of a model that is without inertia, but with hydrodynamic drag. Our motivation is the study of locomotion …

When The Leaves Fall: Modeling Seasonal Variation Of Litter Flux In An Urban Forest, Scott W. Oswald

Honors College Theses

I propose a statistical model to describe the seasonal variation in forest litter flux rates. To examine the effectiveness of the proposed model and to estimate the model parameters, a small set of litter flux data was collected. Data collection was continuous from November 2014 to January 2016. Model parameters were estimated from the data. Using the estimated parameters, the model was applied to an existing dataset to provide some evidence of the model's potential to predict future litter flux rates. While the model did reasonably fit the data, it only had some limited success at prediction. Future research is …

Forecasting Climate Change Impacts On The Distribution Of Wetland Habitat In The Midwestern United States, Heath Garris, Randall Mitchell, Lauchlan Fraser, Linda Barrett

Randall J. Mitchell

Shifting precipitation patterns brought on by climate change threaten to alter the future distribution of wetlands. We developed a set of models to understand the role climate plays in determining wetland formation on a landscape scale and to forecast changes in wetland distribution for the Midwestern United States. These models combined 35 climate variables with 21 geographic and anthropogenic factors thought to encapsulate other major drivers of wetland distribution for the Midwest. All models successfully recreated a majority of the variation in current wetland area within the Midwest, and showed that wetland area was significantly associated with climate, even when …

An Integrative, Cost-Benefit Analysis On Animal Perturbations: Autotomy And Life-History Related Weight Gain, Chi-Yun Kuo

Doctoral Dissertations

The variation in behavioral traits and the adaptive significance behind such variation has been a classic question in behavioral ecology. Traits that enhance while simultaneously impose high fitness costs are particularly suitable for addressing this fundamental question, as their expressions are likely under strong selection. In this dissertation, I investigate the variation in a costly antipredator behavior and the underlying cost-benefit mechanisms. The trait of interest is the voluntary shedding of the tail, or tail autotomy, in lizards. Tail autotomy allows lizards to survive close-range encounters with predators but also has severe fitness consequences, including increased energetic demand for regeneration …

Forecasting Climate Change Impacts On The Distribution Of Wetland Habitat In The Midwestern United States, Heath Garris, Randall Mitchell, Lauchlan Fraser, Linda Barrett

Linda R. Barrett

Shifting precipitation patterns brought on by climate change threaten to alter the future distribution of wetlands. We developed a set of models to understand the role climate plays in determining wetland formation on a landscape scale and to forecast changes in wetland distribution for the Midwestern United States. These models combined 35 climate variables with 21 geographic and anthropogenic factors thought to encapsulate other major drivers of wetland distribution for the Midwest. All models successfully recreated a majority of the variation in current wetland area within the Midwest, and showed that wetland area was significantly associated with climate, even when …

Vesicle Biomechanics In A Time-Varying Magnetic Field, Hui Ye, Austen Curcuru

Biology: Faculty Publications and Other Works

Background Cells exhibit distortion when exposed to a strong electric field, suggesting that the field imposes control over cellular biomechanics. Closed pure lipid bilayer membranes (vesicles) have been widely used for the experimental and theoretical studies of cellular biomechanics under this electrodeformation. An alternative method used to generate an electric field is by electromagnetic induction with a time-varying magnetic field. References reporting the magnetic control of cellular mechanics have recently emerged. However, theoretical analysis of the cellular mechanics under a time-varying magnetic field is inadequate. We developed an analytical theory to investigate the biomechanics of a modeled vesicle under a …

Modeling Atp-Binding Cassette G2 (Abcg2) Substrate Specificity, Raghav D. Acharya, Aurijit Sarkar, Glen E. Kellogg

Undergraduate Research Posters

How well can we predict efflux by ATP-binding cassette G2?

It is estimated that there will be about 1.6 million new cases of cancer and half a million cancer deaths in the US during 2015.ATP-binding cassette (ABC) efflux transporters such as ABCG2 are overexpressed in chemotherapy-resistant cancer cells. Anticancer drugs are prone to efflux by these transporters. Being able to identify drugs that are effluxed is of great interest in drug discovery.The current arsenal of methods used to detect efflux are not easily adaptable to high throughput formats and are limited in scope, making experimental analysis an expensive prospect. Hence, …

On The Challenges Of Modeling The Net Radiative Forcing Of Wetlands: Reconsidering Mitsch Et Al. 2013, Scott C. Neubauer

Biology Publications

Wetlands play a role in regulating global climate by removing carbon dioxide (CO2) from the atmosphere and sequestering it as soil carbon, and by emitting methane (CH4) and nitrous oxide (N2O) to the atmosphere. In a recent article in this journal (Mitsch et al. Landscape Ecol 28:583–597, 2013), CO2 sequestration and CH4 emissions were modeled for several freshwater wetlands that vary in vegetation type, climate, and hydrology. The authors of that study made significant errors that caused them to underestimate the importance of wetland CH4 emissions on climate dynamics. Here, I reanalyze the Mitsch et al. dataset and show that …

Methodological Advancements For Improving Performance And Generating Ensemble Ecological Niche Models, Robert Boria

Dissertations and Theses

This study employs spatial filtering of occurrence data with the aim of reducing overfitting to sampling bias in ecological niche models (ENMs). Sampling bias in geographic space leads to localities that may also be biased in environmental space. If so, the model can overfit to those biases. As a preliminary test addressing this issue, we used Maxent, bioclimatic variables, and occurrence localities of a broadly distributed Malagasy tenrec, Microgale cowani (Family Tenrecidae: Subfamily Oryzorictinae). We modeled the abiotically suitable area of this species using three distinct datasets: unfiltered, spatially filtered, and rarefied unfiltered localities. To quantify overfitting and model performance, …