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.

Modeling Of Individual Egg Weights Of Lohmann-Brown Layer Hens, Esra Yavuz, Samet Hasan Abaci, Kadi̇r Erensoy, Mustafa Şahi̇n

Turkish Journal of Veterinary & Animal Sciences

This study was carried out to determine the most suitable model for egg weights of the Cubic, Gompertz, Logistics, Gamma, Richard, Piecewise Quadratic, Orscov, and Sigmoaidal models, which are widely used in estimation. Lohmann-Brown Classic laying hens raised in Ondokuz Mayıs University Research and Application farm were used as animal material. In the modeling of egg weights of 351 layer hens raised in 3-storey cages, individual egg weight data measured at weekly intervals, 32 on the 1st floor, 17 on the 2nd floor, and 27 on the 3rd floor, were taken into account, and a total of 76 hens' individual …

Addressing Soil Carbon Sequestration Response From Multispecies Dairy Forage Systems And Modeling Rangeland Beef Cow Dry Matter Intake Using Precision Enteric Emissions Measurements, Lillian J. Mcfadden

Electronic Theses and Dissertations

Regenerative agriculture is a pressing matter for the dairy industry to address cropland sustainability and carbon sequestration. One regenerative management practice that has been identified to help with row crop sustainability for key metrics like soil organic carbon (SOC) is complex covers. When producers use complex covers one of the main challenges is that it takes time to detect a change in SOC. However, simulation models are a tool that can be used to help determine if a regenerative practice is a strategy that gives the best results (i.e., increased SOC) while aligning with long-term production goals. Therefore, our objectives …

Application Of Simulation Modelling In Broiler Integration: Is It A Necessary Nutritional Tool?, Peter Chrystal

Proceedings of the Arkansas Nutrition Conference

Modelling techniques have been used in many industries globally to illustrate to others an understanding of the way processes work. Also, engineers and scientists employ models to predict the consequences of various courses of action. Simple pictorial models, such as the diagram of the chicken digestive system, are useful in education and may be more suitable than a photograph for the purposes of explaining how the animal converts ingested feed into components that can be assimilated, leaving residue that is excreted. Complex, predictive models seek to quantify a specified outcome based on defined inputs. Many attempts have been made over …

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 …

A Deterministic Model For Understanding Nonlinear Viral Dynamics In Oysters, Qubin Qin, Jian Shen, Kimberly S. Reece

VIMS Articles

Contamination of oysters with a variety of viruses is one key pathway to trigger outbreaks of massive oyster mortality as well as human illnesses, including gastroenteritis and hepatitis. Much effort has gone into examining the fate of viruses in contaminated oysters, yet the current state of knowledge of nonlinear virus-oyster interactions is not comprehensive because most studies have focused on a limited number of processes under a narrow range of experimental conditions. A framework is needed for describing the complex nonlinear virus-oyster interactions. Here, we introduce a mathematical model that includes key processes for viral dynamics in oysters, such as …

Assessing Dietary Branched-Chain Amino Acids To Achieve Linear Programming Goals Through Model Extrapolation And Empirical Research, Craig W. Maynard, Ed E. Gbur, Vinh-Loi Ly, Minh-Duc Le, Thi H. Ngan Le Jr, Justina Caldas, Michael T. Kidd

Proceedings of the Arkansas Nutrition Conference

Renewed interest, especially in the United States, has sparked in assessing branched-chain amino acid interactions in practical diets for broilers. Indeed, as L-valine enters formulation bird nitrogen excesses are reduced as diet protein falls to the new first limiting amino acid (e.g., isoleucine, arginine, or tryptophan). For a United States based example, the result is less oilseeds and more gains, which typically result in increased inclusions in corn or corn by-products, coupled with a concomitant increase in dietary leucine. The proceedings outline the foundations of the branched-chain amino acid early research, antagonism studies, and a meta-analysis conducted on publications with …

Evaluating Moose Alces Alces Population Response To Infestation Level Of Winter Ticks Dermacentor Albipictus, Daniel D. Ellingwood, Peter J. Pekins, Henry Jones, Anthony R. Musante

USDA Wildlife Services: Staff Publications

Many wildlife populations are experiencing a variety of environmental pressures due to the direct and indirect consequences of a changing climate. In the northeast, USA, moose Alces alces are declining in large part because of the increasing parasitism by winter tick Dermacentor albipictus, facilitated by high host density and optimal environmental conditions. To test this hypothesis, and better understand the influence of this interaction on the stability of the regional population, we constructed a population viability model using data collected through comprehensive survival and productivity studies in 2002–2005 and 2014–2018 in northern New Hampshire. Years of heavy tick infestation (epizootics) …

Recolonization Potential For Coho Salmon (Oncorhynchus Kisutch) In Tributaries To The Klamath River After Dam Removal, Max M. Ramos

Cal Poly Humboldt theses and projects

Removal of four major dams on the Klamath River is scheduled to begin in 2023, restoring access to greater than 50 km of historic mainstem habitat for coho salmon. However, mainstem habitat may not be suitable for juvenile coho salmon due to elevated water temperatures and high concentrations of infectious myxospores in the summer and fast water velocities in the winter. Small, cooler tributaries can provide essential habitat for escape from deleterious conditions in the mainstem Klamath River. I used temperature and other physical features of six tributaries to the Klamath River above Iron Gate Dam to assess their capacity …

Contribution Of Juvenile Estuarine Residency In A Bar-Built Estuary To Recruitment Of Chinook Salmon (Oncorhynchus Tshawytscha), Emily Katherine Chen

Cal Poly Humboldt theses and projects

Estuaries are commonly touted as nurseries for out-migrating salmonids, providing higher prey availability than streams, a physiological transition zone, and refugee from marine predators. Yet the diversity of estuaries makes it difficult to generalize the effect they have on salmonid recruitment. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low flow, closing access to the ocean and disrupting outmigration. In this thesis, I evaluated how residency in a bar-built estuary affects the growth, survival, and ultimately recruitment of Chinook salmon (Oncorhynchus tshawytscha) in Redwood Creek, California. I conducted a mark-recapture experiment on out-migrating …

Evaluation Of A Commercial Model For Predicting Growth Performance Of Pigs With Varying Diet Composition And Stocking Density, M. B. Menegat, F. Wu, J. C. Woodworth, M. D. Tokach, J. M. Derouchey, S. S. Dritz, R. D. Goodband

Kansas Agricultural Experiment Station Research Reports

The objective of this study was to validate the growth performance predictions of a commercial model (CAMERA®; INTL FCStone, New York, NY) by comparing the optimally-solved estimates with observed growth performance from published studies. Three studies were selected to create 3 feeding scenarios: 1) variation in dietary energy concentrations and fiber sources (Nitikanchana et al., 2015); 2) variation in dietary lysine level (Menegat et al., 2017); and 3) variation in space allowance (Carpenter et al., 2018). For each validation scenario, the growth performance of pigs from the best-performing treatment group was first estimated, calibrated using the observed performance, and used …

He Scenario Tree Epidemiological Model In Estimation Effects Of B. Melitensis Rev 1 Vaccination On Disease Prevalence, Sabina Seric Haracic, Nihad Fejzic, Ermin Saljic, Dzenita Hadzijunuzovic Alagic, Mo Salman

Turkish Journal of Veterinary & Animal Sciences

minant brucellosis. The stochastic scenario tree model was used to simulate vaccination and surveillance implementation during 8 years. Outputs were annual proportions of true positive, true negative, false positive, and false negative flocks. Vaccination coverage was described by the Pert distribution with average 70% and min and max 50% and 80%, respectively. Effects of risk factors (high prevalence-areas and transhumance) were considered. The model was separately simulated for three levels of initial average flock prevalence (2%, 5%, and 10%). In the following years, flock prevalence arising from the fitted distribution of the false negative flocks from the previous year increased …

Effects Of Standardized Ileal Digestible Histidine:Lysine Ratio On Growth Performance Of 15- To 25-Lb Pigs, H. S. Cemin, R. M. Karns, C. M. Vier, M. D. Tokach, S. S. Dritz, K. J. Touchette, J. C. Woodworth, J. M. Derouchey, R. D. Goodband

Kansas Agricultural Experiment Station Research Reports

Two experiments were conducted to determine the standardized ileal digestible (SID) His:Lys requirement of 15- to 25-lb nursery pigs. A total of 360 and 350 pigs (DNA 241 × 600), initially 15.6 and 14.5 lb body weight (BW), were used in Exp. 1 and 2, respectively. There were 5 pigs per pen and 12 and 10 replicates per treatment in Exp. 1 and 2, respectively. After weaning, pigs were fed a common pelleted diet for 10 d in Exp. 1 and 7 d in Exp. 2. Then, pens were assigned to treatments in a randomized complete block design with BW …

Ecosystem Metabolism Modeling Of Estuaries In Maine: Using Dissolved Oxygen As A Tool For Aquaculture Site Assessment, Katherine Miller

Honors College

The net primary productivity (NPP), also known as the net ecosystem metabolism, of an estuary is a value indicative of the growth and activity of an estuary’s primary producers, relative to the metabolic activity of its consumers. When NPP is high, estuaries exhibit autotrophic conditions that have the capacity to support fruitful bivalve aquaculture. For oyster farmers, the ability to monitor an estuary’s NPP would allow them to predict and prepare for seasonal changes to oyster growth that result from changes to their phytoplankton food source and access to dissolved oxygen (DO). Not only would this aid farmers on site …

Modeling With A Conceptual Representation: Is It Necessary? Does It Work?, Rebecca C. Jordan, Steven Gray, Amanda E. Sorensen, Samantha Pasewark, Suparna Sinha, Cindy E. Hmelo-Silver

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

In response to recent educational imperatives in the United States, modeling and systems thinking have been identified as being critical for science learning. In this paper, we investigate models in the classroom from two important perspectives: (1) from the teacher perspective to understand how teachers perceive models and use models in the classroom and (2) from the students perspective to understand how student use model-based reasoning to represent their understanding in a classroom setting. Qualitative data collected from 19 teachers who attended a professional development workshop in the northeastern United States indicate that while teachers see the value in teaching …

Multiscale Habitat Suitability Modeling For Canary Rockfish (Sebastes Pinniger) Along The Northern California Coast, Portia N. Saucedo

Cal Poly Humboldt theses and projects

Detailed spatially-explicit data of the potential habitat of commercially important rockfish species are a critical component for the purposes of marine conservation, evaluation, and planning. Predictive habitat modeling techniques are widely used to identify suitable habitat in un-surveyed regions. This study elucidates the predicted distribution of canary rockfish (Sebastes pinniger) along the largely un-surveyed northern California coast using data from visual underwater surveys and predictive terrain complexity covariates. I used Maximum Entropy (MaxEnt) modelling software to identify regions of suitable habitat for S. pinniger greater than nine cm in total length at two spatial scales. The results of …

Effects Of Standardized Ileal Digestible Lysine On 15- To 25-Lb Nursery Pigs, G. E. Nichols, C. M. Vier, A. B. Clark, M. B. Menegat, H. S. Cemin, C. K. Jones, J. M. Derouchey, M. D. Tokach, R. D. Goodband, J. C. Woodworth, S. S. Dritz

Kansas Agricultural Experiment Station Research Reports

A total of 300 pigs (DNA 241 × 600; initial pen average BW of 15.4 lb) were used in a 22-d growth trial to determine the standardized ileal digestible (SID) lysine (Lys) requirement of nursery pigs from 15- to 25-lb. Pigs were weaned at approximately 21 d of age and allotted to pens based on BW and gender. There were 10 replicate pens per treatment and 6 pigs per pen. Pigs were fed a common pelleted diet for 10 d post-weaning. Subsequently, pens of pigs were randomly assigned to 1 of 6 experimental diets in a randomized complete block design, …

Understanding The Impact Of Commercial Harvest On White Suckers (Catostomus Commersonii) In Maine, Megan A. Begley

Electronic Theses and Dissertations

The State of Maine issues an unlimited number of commercial permits for the harvest of White Suckers Catostomus commersonii in Maine’s inland waters. The fishery provides a necessary source of fresh lobster Homarus americanus bait to coastal communities at a time when other bait sources are scarce. The impacts of the increasing number of permits and subsequent numbers of fishermen on the white sucker population is unknown. The Maine Department on Inland Fisheries and Wildlife (MDIFW) has closed a number of waters due to concerns that overfishing and incidental catch of other fish species may occur.

In Chapter 1, we …

Interdisciplinary Modeling For Water-Related Issues Graduate Course, Laurel Saito, Alexander Fernald, Timothy Link

All ECSTATIC Materials

The science and management of aquatic ecosystems is inherently interdisciplinary, with issues associated with hydrology, atmospheric science, water quality, geochemistry, sociology, economics, environmental science, and ecology. Addressing water resources issues in any one discipline invariably involves effects that concern other disciplines, and attempts to address one issue often have consequences that exacerbate existing issues or concerns, or create new ones (Jørgensen et al. 1992; Lackey et al. 1975; Straskraba 1994) due to the strongly interactive nature of key processes (Christensen et al. 1996). Thus, research and management of aquatic ecosystems must be interdisciplinary to be most effective, but such truly …

Using Capture-Mark-Recapture Techniques To Estimate Detection Probabilities & Fidelity Of Expression For The Critically Endangered James Spinymussel (Pleurobema Collina)., Alaina C. Esposito

Masters Theses, 2010-2019

The critically endangered James Spinymussel (Pleurobema collina) is a species of freshwater mussel endemic to Virginia’s James and Dan River basins. In the last 20 years, P. collina has experienced a substantial decline in numbers and currently occupies approximately 10% of its original habitat; however, little information is known about this species to assist in conservation. A 230-meter reach of transitional habitat in Swift Run was selected for repeat observations to estimate detection probabilities using a Capture-Mark-Recapture framework. In June 2014, visual scouting began to locate and tag P. collina (including other mussels in the community) with PIT …

Management Of Channel Catfish Ictalurus Punctatus In The Missouri River, Nebraska, Brandon L. Eder

School of Natural Resources: Dissertations, Theses, and Student Research

The popularity of catfish Ictaluridae nationally as a sport fish is well documented and angling for catfish on the Missouri River in Nebraska (NMR) is especially popular. Catfish monitoring program by the Nebraska Game and Parks Commission (NGPC) began in 1974 and several short-term evaluations of Channel Catfish population dynamics have been performed. However, no long term analyses of population characteristics have been conducted since the early 1990s. The focus of this research was to summarize the status of Channel Catfish populations in the NMR and give recommendations for future management. I summarized population characteristics, modeled length limit regulations, and …

Modeling Consumption Rates Of Atlantic Herring (Clupea Harengus), Mitchell Jones

Graduate College Dissertations and Theses

Pelagic forage fishes play critical roles in productive marine food webs by providing a link between zooplankton and piscivores and transferring energy from feeding grounds to other ecosystems. The amount of energy moved to higher trophic levels or new systems is directly linked to the consumption rate of pelagic forage fishes. In the Gulf of Maine, Atlantic herring (Clupea harengus) is the dominant forage fish; the purpose of this study is to determine their specific consumption rate (g prey/g fish/day). Using fish collected in autumn 2012 and spring 2013, we applied a mercury mass-balance model to estimate individual …

Systematic Ichthyofaunal Surveys In Urban And Non-Urban Watersheds, Eugene G. Maurakis, David V. Grimes, Amanda Schutt, Suzy Short

Virginia Journal of Science

Objectives were to model fish species richness relative to natural and anthropogenic variables in Quantico Creek, a forested undisturbed stream environment, and Cameron Run, a highly disturbed urban stream environment in the lower Piedmont-Fall Line region of the Potomac River watershed. Species richness in all stream orders (e.g. avg. range=2.5-9.65 in 1st-3rd orders) of Quantico Creek were significantly higher than those (e.g. avg. range=2.1- 7.6 in 1st -4th orders) of Cameron Run. Fish species richness in Quantico Creek watershed can be modeled by eight factors: season, stream order, elevation, river km, stream width and depth, watershed size, and percent of …

An Assessment Of Moose (Alces Alces Americana) And Moose Management In Connecticut, Andrew M. Labonte

Master's Theses

Eastern moose (Alces alces americana) populations have been increasing in New England over the past decade. Moose populations have the potential to generate human conflict due to their size, speed, nocturnal behavior, and seasonal mobility. As problems associated with increasing moose populations become more common, the need to develop management strategies that are both effective and acceptable to stakeholders becomes increasingly important. The potential for moose to continue to expand in southern New England and the long-term impacts they may have on Connecticut residents, is unclear. The overall purpose of this study was to assess how suitable Connecticut …

Single-Screw Extrusion Modeling Effects On Extrusion Processing Parameters And Physical Properties Of Ddgs-Based Nile Tilapia ( Oreochromis Niloticus ) Feeds, Ferouz Y. Ayadi, Parisa Fallahi, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan

Kurt A. Rosentrater

A single-screw laboratory extruder was used to conduct an L 18 (2 2 X 3 6 ) Taguchi fractional factorial study of aquafeed processing. The ingredients were based on a formulation for nutritionally-balanced Nile tilapia diets containing distillers dried grains with solubles (DDGS) and soybean meal as the main protein sources, in addition to constant amounts of corn flour, whey, and fish meal. The effects of three levels of DDGS (20, 30 and 40%), soybean meal (30, 40 and 50%), ingredient moisture content (20, 30 and 40% db), screw speed (100, 150 and 200 rpm), barrel temperatures (80-100-100°C, 80-120-120°C and …

Fish Acoustics: Physics-Based Modeling And Measurement, Davis Benjamin Reeder

Journal of Marine Science and Technology

The U.S. Office of Naval Research has sponsored research in the area of marine organism acoustics for many years. The research program has included development of theoretical physics-based acoustic scattering models of single animals, high-resolution laboratory measurements of scattering by individual animals, and at-sea field experiments. The program has been focused on the backscattered signal, but has also included investigation of the forward-scattered signal. Downward-looking acoustic surveys using ship borne echosounders rely on the backscattered signal and provide non-invasive, non-destructive, rapid, high-resolution, large area survey capability compared to traditional net tows. Horizontally-oriented acoustic surveys provide the opportunity to investigate both …

Multidisciplinary Assessment And Documentation Of Past And Present Human Impacts On The Neotropical Forests Of Petén, Guatemala, Christopher Stephen Balzotti

Theses and Dissertations

Tropical forests provide important habitat for a tremendous diversity of plant and animal species. However, limitations in measuring and monitoring the structure and function of tropical forests has caused these systems to remain poorly understood. Remote-sensing technology has provided a powerful tool for quantification of structural patterns and associating these with resource use. Satellite and aerial platforms can be used to collect remotely sensed images of tropical forests that can be applied to ecological research and management. Chapter 1 of this article highlights the resources available for tropical forest remote sensing and presents a case-study that demonstrates its application to …

Slides: Groundwater Declines, Climate Change And Approaches To Adaptation, Katharine Jacobs

Western Water Law, Policy and Management: Ripples, Currents, and New Channels for Inquiry (Martz Summer Conference, June 3-5)

Presenter: Katharine Jacobs, Director of the Arizona Water Institute, University of Arizona

37 slides

Shellfish Aquaculture Suitability Within Baylor Grounds Of The Lower Rappahannock River, Center For Coastal Resources Management, Virginia Institute Of Marine Science

Reports

Should the Commonwealth of Virginia ever consider a regulated expansion of the aquaculture industry to public Baylor ground, timely information regarding the productivity of these grounds and the ability to support aquaculture would be highly desirable information. In this scenario, public bottom will be opened to private shellfish growers in the Commonwealth under what will likely be a tightly monitored regulation. The demise in productivity of natural oyster beds within Baylor Grounds is well known. However, there is no comprehensive resource that addresses whether Baylor Grounds would be suitable for aquaculture. This study uses Geographic Information Systems (GIS) to model …

Slides: Water Needs And Strategies For A Sustainable Future, Shaun Mcgrath

Shifting Baselines and New Meridians: Water, Resources, Landscapes, and the Transformation of the American West (Summer Conference, June 4-6)

Presenter: Shaun McGrath, Program Director, Western Governors’ Association

25 slides