Digital Commons Network^™

Annotation Of Non-Model Species’ Genomes, Taiya Jarva

Master's Theses

The innovations in high throughput sequencing technologies in recent decades has allowed unprecedented examination and characterization of the genetic make-up of both model and non-model species, which has led to a surge in the use of genomics in fields which were previously considered unfeasible. These advances have greatly expanded the realm of possibilities in the fields of ecology and conservation. It is now possible to the identification of large cohorts of genetic markers, including single nucleotide polymorphisms (SNPs) and larger structural variants, as well as signatures of selection and local adaptation. Markers can be used to identify species, define population …

Porotic Hyperostosis And Cribra Orbitalia In The Adult Population Of Tipu, Miranda Hahn

Master's Theses

Tipu is a contact period Maya site in western Belize where a mission church and cemetery was established around AD 1560. An archaeological excavation in the 1980s recovered the remains of more than 550 individuals. In its unique location on the fringes of Spanish control, Tipu was the site of both acceptance of introduced cultural traits as well as rebellion against them. The series has been intensively studied over the last decades, but an analysis of anemia using more recently developed and widely accepted standards has not yet been completed. Therefore, I scored adults using the new widely accepted standards …

Cultural Behaviors And Their Influence On The Proximal Femur: Comparisons Of Postural Behavior, Occupation, And Subsistence-Settlement Between A Pre-Contact And Historic Sample, Joanna Klein

Master's Theses

Little is known archaeologically about the Late Woodland Schroeder Mounds mortuary group from west-central Illinois. As such, bioarchaeological data is at the forefront of archaeological problem-solving for not only the site, but the geographical area as well. Skeletal data such as proximal femur angles and activity markers contribute to the understanding of subsistence-settlement trends and postural behavior of the mortuary complex. Femoral neck version is associated with postural behaviors such as squatting and kneeling. The neck-shaft angle is linked to mobility and settlement patterns. Bicondylar angle was explored to see if behaviors had any affect. Allen’s fossa and Poirier’s facet …

Characterization And Estimation Of Musculoskeletal Pain Using Machine Learning, Boluwatife Faremi

Master's Theses

Traditional scales utilized for recording pain are known to be highly subjective and biased due to inaccuracies in recollecting actual pain intensities. As a result, machine learning (ML) models that are trained using these scores as ground truth are reported to have low performance for objective pain classification because of the huge disparity between what was felt in moments of pain and the scores recorded afterward.

In the present study, two devices were designed for gathering real-time, continuous in-session subjective pain scores and the recording of the autonomic nervous system (ANS) altered endodermal (EDA) activity. 24 participants were recruited to …

Climate & Conflict: View Into A Warming World, Faelynn Carroll

Master's Theses

Unlike weather patterns, the El Niño Southern Oscillation (ENSO) is a large-scale, cyclical climate system that is now predictable for up to a year and a half in advance. ENSO cycles occur every two to seven years for approximately two years at a time, affecting large swaths of the globe with plausibly random variation in the exact location and strength of local effects. However, its systemic nature allows for aggregate effects to be accounted for by its outcomes. This research uses novel 0.5 x 0.5 degree ENSO teleconnection analysis for precipitation and temperature to uncover environmental mechanisms that underly the …

Identification Of Spring And Fall Spawned Eggs And The Genetic Distinction Of Gulf Sturgeon In The Choctawhatchee River, Alabama-Florida, Nicholas Lamey

Master's Theses

The Gulf Sturgeon (GS; Acipenser oxyrinchus desotoi) is a threatened subspecies of Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) which inhabits the Gulf Coast of the United States. Prior studies of Eurasian sturgeon species and Atlantic Sturgeon have revealed the existence of a dual spawning strategy (i.e. spring and fall). The presence of a fall spawn has also been proposed for GS, but only with the support of circumstantial evidence. This study used molecular techniques to investigate seasonality of GS spawning and the possibility that this has produced unique genetic groups in the Choctawhatchee River. Mitochondrial DNA from suspected …

Assessing Dynamics And Trends Of Co2 Flux On The Louisiana Shelf, Claire Mcguire

Master's Theses

The Gulf of Mexico on an annual timescale acts as a sink for ­CO₂. Previous studies have investigated regional-scale trends in the Gulf based on model output. In our investigation of the northern Gulf of Mexico, and especially the area surrounding the Louisiana delta, we found different trends compared with previous studies of the open ocean Gulf and broader shelf region. Predictions of global patterns of the ocean CO₂ cycle require regional studies of unique areas like the Louisiana Shelf. The Louisiana Shelf is a shallow system, has input from river systems, experiences seasonal hypoxia, and is …

Evaluating The Field Efficacy Of Uv-C On Two California Strawberry Arthropod Pests, Jose Luis Alvarado Rojas

Master's Theses

The efficacy of two different autonomous Ultraviolet-C (UV-C) units on two spotted spidermite, Tetranychus urticae Koch (Acari: Tetranychidae), and greenhouse whitefly, Trialeurodes vaporariorum. (Hemiptera: Aleyrodidae). was tested in four commercial strawberry fields in California.

In 2020, California strawberry growers used 12 million pounds of active ingredients (AIs) to keep pests under economic thresholds. While pesticides are an important part of an integrated pest management program, their use poses threats to the environment and human health. To protect agricultural workers, the public and the environment, regulators in California have consistently limited or removed the use of certain pesticide AIs. For …

Analytical Pipeline To Facilitate Electroencephalography Pain State Identification In Patients With Chronic Low Back Pain, Emma Katharina Jacobs

Master's Theses

Chronic low back pain (cLBP) affects the quality of life of over 23% of American adults and places an immense burden on the economy.^1–3 To more effectively diagnose and treat cLBP, quantitative biomarkers are needed to objectively measure pain and better identify the underlying mechanisms of cLBP. The overarching goal of this work is to create an analytical pipeline to investigate brain activity patterns measured with electroencephalogram (EEG) data of cLBP patients treated with transcutaneous spinal cord stimulation (tSCS). The specific aims of this project are to 1) investigate whether there is a difference between baseline EEG measurements and …

Analysis Of Arterial Compliance Using A Surrogate Arm Bench Top Model For The Validation Of Oscillometric Blood Pressure Methods, Christopher J. Cunningham

Master's Theses

A study was performed on a recently developed prototype of the Yong-Geddes surrogate arm design to collect compliance data of the various system components and determine the accuracy of measurements made through the bench top model. The study was performed to perceive the effectiveness of the model as a tool for validating non-invasive blood pressure detection monitors. Three stages of testing were performed to gather pressure and volume data from an artificial artery component, a sphygmomanometer, and the surrogate arm system to produce compliance estimations. Mathematical equations from supported arterial hemodynamics studies and clinical trials were applied to the pressure …

Genetic Population Structure And Effective Number Of Breeders In Systems Across The Range Of The Gulf Sturgeon, Jacob Zona

Master's Theses

Gulf sturgeon (Acipenser oxyicnhus desotoi) are a large, anadromous fish belonging to an ancient lineage that diverged as early as 400 MYA. Overfishing for meat and caviar during the early 1900’s reduced their range and abundance and continued habitat destruction and mortality have limited their ability to recover, leading to their listing under the Endangered Species Act. This study uses genetic techniques to determine the effective number of breeders for multiple spawning groups of Gulf sturgeon in river systems across their range to set a baseline for tracking reproductive success of the species. Accompanying genetic information relevant to …

Reducing Scope 3 Emissions By Investing In Regenerative Agriculture In Supply Chains, Stephanie Cain

Master's Theses

The agricultural industry has an opportunity to shift to a more sustainable practice that helps restore vital topsoil, improve water quality, reduce environmental impact, and sequester atmospheric carbon into the vast soil carbon pool. However, to implement these practices at considerable scale, agricultural producers require access to resources and capital they rarely have and can be difficult to acquire. As a company, investing in regenerative agriculture in supply chains can lead to reduced Scope 3 emissions, more resilient supply chains, and better marketability as an investment fund, an employer, and a brand. Insetting regenerative agriculture can protect supply chains against …

Food For Thought: The Effects Of Feeding On Neurogenesis In The Ball Python, Python Regius, Hannah F. Bow

Master's Theses

Pythons are a well-studied model of postprandial physiological plasticity. Consuming a meal has been shown by past work to evoke a suite of physiological changes in pythons and elicit one of the largest documented increases in post-feeding metabolic rates relative to resting values. However, little is known about how this plasticity manifests in the brains of ball pythons, Python regius. Previous work using the cell-birth marker 5-bromo-12’-deoxyuridine (BrdU) has shown that cell proliferation in the python brain increases six days following meal consumption. This study aimed to confirm these findings and build on them in the long term by …

Predicting Location And Training Effectiveness (Plate), Erik Rolf Bruenner

Master's Theses

Abstract Predicting Location and Training Effectiveness (PLATE)
Erik Bruenner

Physical activity and exercise have been shown to have an enormous impact on many areas of human health and can reduce the risk of many chronic diseases. In order to better understand how exercise may affect the body, current kinesiology studies are designed to track human movements over large intervals of time. Procedures used in these studies provide a way for researchers to quantify an individual’s activity level over time, along with tracking various types of activities that individuals may engage in. Movement data of research subjects is often collected through …

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Neural Tabula Rasa: Foundations For Realistic Memories And Learning, Patrick R. Perrine

Master's Theses

Understanding how neural systems perform memorization and inductive learning tasks are of key interest in the field of computational neuroscience. Similarly, inductive learning tasks are the focus within the field of machine learning, which has seen rapid growth and innovation utilizing feedforward neural networks. However, there have also been concerns regarding the precipitous nature of such efforts, specifically in the area of deep learning. As a result, we revisit the foundation of the artificial neural network to better incorporate current knowledge of the brain from computational neuroscience. More specifically, a random graph was chosen to model a neural system. This …

Analyzing Tortuosity In Patterns Formed By Colonies Of Embryonic Stem Cells Using Topological Data Analysis, Jackie Driscoll

Master's Theses

Pluripotent stem cells have been observed to segregate into Turing-like patterns during the early stages of Dox-inducible hiPSC differentiation. In this thesis, we de- velop a tool to quantify the tortuosity in the patterns formed by colonies of pluripo- tent stem cells using methods from topological data analysis. We use clustering techniques and the mapper algorithm to create simplicial complexes representing samples of cells and detail a method of evaluating the tortuosity of these complexes. We use the resulting persistence landscapes and their associated norms to evaluate experimental data and simulated data from an agent based model. This thesis finds …

Effects Of Mature Recombinant Gdf9 And Bmp15 On In-Vitro Maturation Of Bovine Oocytes And Subsequent Embryo Development And Effects Of Antioxidants On Blastocyst Re-Expansion Rates, Jamie Thompson

Master's Theses

In-vitro produced embryos (IVP) differ greatly from in-vivo derived embryos (IVD) in gene expression, metabolism, development, and cryotolerance which limit the widespread use of this technology. In-vitro maturation (IVM) is one of the most important components for successful in-vitro embryo development. Growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) have been found to be essential during oocyte maturation and thus female fertility. These proteins are oocyte secreted factors (OSFs) and are produced with pro- and mature protein regions where the pro-regions are thought to aid in protein folding and dimerization where heterodimerization the two proteins has been …

California's Native Trees And Their Use In The Urban Environment, Camille Pawlak, Natalie Love, Jennifer Yost, Andrew Fricker, Jacqueline Doremus, Matthew Ritter

Master's Theses

California’s urban forest is composed of both native and non-native species. These trees improve the quality of life of urban residents and mitigate the effects of climate change by buffering local microclimates. A species’ native status is often defined at the scale of the state’s political boundaries, which doesn’t reflect its actual native range. Here we define the list of 95 tree species native to California, create digital range maps for each species, provide native species lists for every city in California, and analyze trends in native tree species in the state’s urban areas. We found that California’s urban areas …

Solving The Cable Equation, A Second-Order Time Dependent Pde For Non-Ideal Cables With Action Potentials In The Mammalian Brain Using Kss Methods, Nirmohi Charbe

Master's Theses

In this thesis we shall perform the comparisons of a Krylov Subspace Spectral method with Forward Euler, Backward Euler and Crank-Nicolson to solve the Cable Equation. The Cable Equation measures action potentials in axons in a mammalian brain treated as an ideal cable in the first part of the study. We shall subject this problem to the further assumption of a non-ideal cable. Assume a non-uniform cross section area along the longitudinal axis. At the present time, the effects of torsion, curvature and material capacitance are ignored. There is particular interest to generalize the application of the PDEs including and …

The Effect Of Adding Mango To A Breakfast Meal On Glycemic And Satiety Responses And Next Meal Energy Consumption, Natalie R. Ramos

Master's Theses

Spikes in blood glucose (BG) result in adverse health consequences in people with and without diabetes. This study aimed to compare the BG and satiety responses of adding mango or sugar to a high glycemic load (HGL) breakfast. A randomized, controlled trial (cross-over design) was conducted with 18 participants. Participants consumed cornflakes and almond milk (Control), control plus 34gm added sugar (ASug), or added mango (AMango) with 34gm carbohydrate. BG was determined at fasting, 15, 30, 60, 90, 120min postprandial; satiety was rated with a visual analog scale at each time point. At 120min, subjects consumed a snack of hummus …

Investigation Of Placement Of Polyethylenimine Within Thin Film Composite Reverse Osmosis Membranes For Enhanced Anti-Fouling Properties, Taylor F. Austin

Master's Theses

Fresh water scarcity is an alarming issue for communities across the globe. The development of water recycling and reuse technologies has become crucial in expanding the limited water resources. Reverse osmosis (RO) is among the key processes that can treat wastewater to meet potable water reuse standards. Despite the advancements in RO membrane technologies, many challenges persist regarding the operation and maintenance of RO membranes, such as membrane fouling. Extensive research investigations have focused on developing RO membrane modifications to combat the decreased performance due to fouling. Polyethylenimine (PEI) is a promising polymer used for enhancing the anti-fouling properties of …

Integrative Analyses Of Genomic And Metabolomic Data Reveal Molecular Mechanisms Associated With Uterine Disease Traits In Transitioning Dairy Cattle, Leanna C. Sanchez, Mohammed Abo-Ismail, Daniel Peterson, Fernando Campos-Chillon

Master's Theses

The metritis complex (MC), characterizing post-partum uterine diseases in dairy cattle has negative implications on animal welfare, production efficiency, and the economic stability of the dairy industry. The studies in this thesis aimed to investigate the genetic architecture of the metritis complex and identify genomic regions and metabolites associated with the development of MC. Thereby enhancing our understanding of the biological pathways and molecular mechanisms involved in the pathophysiology of MC during the transition period in Jersey and Holstein dairy cattle.

Chapter 2 sheds light on the previous work done on MC. The goals of this review were to (1) …

Southern Sea Otter (Enhydra Lutris Nereis) Fur Morphology, Thermal Function, And Buoyancy Across Ontogeny, Kate Riordan

Master's Theses

Sea otters (Enhydra lutris) have the densest fur of any animal, and the hairs function to trap a layer of air that is used for insulation. When a sea otter is born, it has a natal pelage (baby fur), and sea otters eventually molt that fur and replace it with a pelt resembling the adult fur. Sea otter fur is composed of 3 types of hairs: underhairs, intermediate hairs, and guard hairs. Sea otters are more susceptible to the negative effects of oiling from oil spills compared to other marine mammal species because they solely rely on fur …

Marine Protected Areas And Oceanographic Variability: Impacts On Blue Rockfish (Sebastes Mystinus) And The Human Dimensions Of Collaborative Fisheries Research, Erin M. Johnston

Master's Theses

Fishing pressure and environmental variability are two of the most impactful drivers of fish populations worldwide. It is critical to effective management to understand the intersection between the two and how each may affect fish population dynamics, especially for exploited nearshore species like rockfishes (Sebastes spp.). This is especially true as models indicate that global climate change will dramatically increase the frequency and severity of large-scale oceanographic perturbations. We were interested in whether we could detect changes in relative abundance of nearshore rockfishes relative to large-scale oceanographic events using a broad-scale index like the Multivariate Ocean Climate Indicator …

Composite Solid Rocket Motor Case Optimization With Matlab Genetic Algorithm, Aleksandr Breit

Master's Theses

This study utilizes MATLAB genetic algorithm (GA) to perform optimization on a solid rocket motor (SRM) chamber structure. The (SRM) structure is modelled as a cylindrical composite laminate where unidirectional fiber orientations are the primary design variable in the optimization problem formulation. Additional design variables such as chamber length, diameter, and internal pressure are altered along with the ply angles to minimize the safety margin towards a near-zero value and encourage efficient layup design. Classical lamination theory with Tsai-Wu failure criterion are used to calculate ply-level safety margins. A thickness minimization scheme is employed to reduce the ply count from …

Hydric Physiology Of Lizards, Savannah Weaver

Master's Theses

Chapter 1: Animals can respond to extreme climate by behaviorally avoiding it, or by physiologically coping with it. We understand behavioral thermoregulation and physiological thermal tolerances, but water balance has largely been neglected. Climate change includes both global warming and changes in precipitation regimes, so improving our understanding of organismal water balance is increasingly urgent. We assessed the hydric physiology of endangered Blunt-nosed Leopard Lizards (Gambelia sila) by measuring cutaneous evaporative water loss (CEWL), plasma osmolality, body mass, and body condition throughout their active season. On average, G. sila had low CEWL that is likely desert-adaptive, and high …

Analyzing Robustness Of An Agent Based Model On Action Potentials In Cardiac Tissue, Marion Jon Zollinger Lara

Master's Theses

An agent based model (ABM) is a computational model with ``agents'' that interact with each other in an ``environment.'' This paper analyzes a particular ABM simulating individual ions in cardiac tissue, with the goal of modelling the strength and consistency of the electrical signals needed for a healthy heartbeat. We build several frameworks based on work by M. A. Yereniuk and S. D. Olson to demonstrate robustness of the original model. We conclude a moderate level of robustness using those frameworks, through a combination of proofs and empirical evidence.

Mmf-Drl: Multimodal Fusion-Deep Reinforcement Learning Approach With Domain-Specific Features For Classifying Time Series Data, Asmita Sharma

Master's Theses

This research focuses on addressing two pertinent problems in machine learning (ML) which are (a) the supervised classification of time series and (b) the need for large amounts of labeled images for training supervised classifiers. The novel contributions are two-fold. The first problem of time series classification is addressed by proposing to transform time series into domain-specific 2D features such as scalograms and recurrence plot (RP) images. The second problem which is the need for large amounts of labeled image data, is tackled by proposing a new way of using a reinforcement learning (RL) technique as a supervised classifier by …

Effects Of Intertidal Position On The Response To Oxygen And Desiccation Stress In The Common Acorn Barnacle, Balanus Glandula, Megan M. Dotterweich

Master's Theses

Sessile invertebrates in the rocky intertidal experience intermittent periods of air exposure due to tidal flux, presenting risks of temperature extremes, hypoxia, nutrient limitation, and most dangerously, desiccation. Microscale variation in severity and frequency of these risks is widely dependent on vertical position within the intertidal zone. Common acorn barnacles (Balanus glandula) have a wide vertical distribution in the intertidal, creating large differences in microhabitat between the highest and lowest individuals in the population. This study set out to explore whether tidal position dependent differences exist in the response to oxygen and desiccation stress in B. glandula. …

Development Of Wiskott-Aldrich Syndrome Knock Out Protocol For Drug Substance Assay Development, Julia C. Hanna

Master's Theses

Wiskott-Aldrich Syndrome (WAS) is a rare X-linked primary immunodeficiency affecting approximately 1 in 100,000 live XY births in North America and is caused by a mutation to the WAS gene which is expressed across hematopoietic lineages. The WAS protein (WASp) plays a role in regulating actin polymerization. On a cellular level, there are a variety of effects of a lack of WASp or expression of a dysfunctional WASp protein for patients including issues with migration, adhesion, chemotactic response, phagocytosis, activation, and proliferation across different cell types in addition to reduced platelet size and output. This can lead to several systematic …