Digital Commons Network^™

Simulating Epidemics And Interventions On High Resolution Social Networks, Christopher E. Siu

Master's Theses

Mathematical models of disease spreading are a key factor of ensuring that we are prepared to deal with the next epidemic. They allow us to predict how an infection will spread throughout a population, thereby allowing us to make intelligent choices when attempting to contain the disease. Whether due to a lack of empirical data, a lack of computational power, a lack of biological understanding, or some combination thereof, traditional models must make sweeping assumptions about the behavior of a population during an epidemic.

In this thesis, we implement granular epidemic simulations using a rich social network constructed from real-world …

Degradation Of Emerging Contaminants By Advanced Oxidation Using Multi-Walled Carbon Nanotubes And Continuous Ozone Injection, Emily N. Miller

Master's Theses

With a growing population and continuous accumulation of pollutants, water resources worldwide are quickly being depleted. Drastic improvements need to be made in both water conservation and treatment. Advanced oxidation processes (AOPs) have been developed to go above and beyond the capabilities of traditional wastewater treatment facilities to eliminate emerging contaminants from our water systems. AOPs increase the generation of hydroxyl radicals (•OH) in oxidation reactions, which are less selective and more reactive than other oxidants, such as ozone, so they are more effective at degrading persistent compounds. This study explored an AOP that utilizes ozonated multi-walled carbon nanotubes (MWCNTs) …

Robot Navigation In Cluttered Environments With Deep Reinforcement Learning, Ryan Weideman

Master's Theses

The application of robotics in cluttered and dynamic environments provides a wealth of challenges. This thesis proposes a deep reinforcement learning based system that determines collision free navigation robot velocities directly from a sequence of depth images and a desired direction of travel. The system is designed such that a real robot could be placed in an unmapped, cluttered environment and be able to navigate in a desired direction with no prior knowledge. Deep Q-learning, coupled with the innovations of double Q-learning and dueling Q-networks, is applied. Two modifications of this architecture are presented to incorporate direction heading information that …

Field Emissions Of Methane And Nitrous Oxide From California Landfills, Alexandra D. Limpert

Master's Theses

Comprehensive and systematic aerial and field investigations were conducted at representative California landfills to quantify emissions of methane and nitrous oxide. Landfills are highly engineered; however, they are one of the largest anthropogenic sources of greenhouse gases, causing human health and safety concerns. Methane (CH₄) and nitrous oxide (N₂O) are significant greenhouse gases with high global warming potentials that are generated in a landfill environment.

For site selection, sites were evaluated based on waste in place, climate zone, faults and oil and gas operations, population density, cover conditions and percentage of cover types, age of waste, …

The Effects Of Agricultural Waste-Based Compost Amendments In Organic Pest Management, Gregg T. Stephenson

Master's Theses

Soil-borne pests and pathogens, such as Verticillium dahliae, can devastate a wide range of annual and perennial crops. Current management options for organic production are limited and sustainable management of pathogens, weeds, and arthropods is important for staying profitable and reducing the use of harmful chemicals. Organic soil amendments play an important role in supplying some of the nutritional needs of vegetable crops and improving soil structure, while also contributing to pest control. The objective of this research was to determine the effects of grape and olive-based composts on soil pathogen load, arthropod communities, and weed biomass and diversity. …

A Homegrown Dsmc-Pic Model For Electric Propulsion, Dominic Charles Lunde

Master's Theses

Powering spacecraft with electric propulsion is becoming more common, especially in CubeSat-class satellites. On account of the risk of spacecraft interactions, it is important to have robust analysis and modeling tools of electric propulsion engines, particularly of the plasma plume. The Navier-Stokes equations used in classic continuum computational fluid dynamics do not apply to the rarefied plasma, and therefore another method must be used to model the flow. A good solution is to use the DSMC method, which uses a combination of particle modeling and statistical methods for modeling the simulated molecules. A DSMC simulation known as SINATRA has been …

Strawberries And Gut Health In Postmenopausal Women, Morgan T. Macneill

Master's Theses

The gut microbiota has been implicated in both health and disease. As such, diet is a significant determinant of gut health, whereby diet induced dysbiosis is associated with cardiometabolic risk. Interestingly, a higher proportion of Firmicutes and a lower proportion of Bacteroidetes are implicated in obesity. Strawberry polyphenols have been shown to reduce cardiovascular disease risk in addition to exhibiting prebiotic activity by increasing probiotic bacteria in the gut. Polyphenols have also been shown to reduce the ratio of Firmicutes to Bacteroidetes. Therefore, dietary modifications such as strawberry consumption may help improve health outcomes through the gut. The objective of …

Evaluation Of Human Umbilical Vein Endothelial Cells In Blood Vessel Mimics Through Changes In Gene Expression And Caspase Activity, Conor Charles Hedigan

Master's Theses

Blood vessel mimics (BVMs) are simple tissue engineered blood vessel constructs intended for preclinical testing of vascular devices. This thesis developed and implemented methods to characterize two of these components. The first aim of this thesis investigated the effect of cell culture duration and flow conditions on endothelial cell gene expression, especially regarding endothelial-to-mesenchymal transition (EndMT). A trend of decreased endothelial marker gene expression and increased mesenchymal marker gene expression would indicate EndMT. qPCR analysis revealed that increased cell culture duration did not result in EndMT, and in fact increased endothelial marker expression as cell culture duration increased. Disturbed flow …

Dna And Protein Sequence Analysis Of Neuronal Markers Neuronal Nuclei (Neun) And Doublecortin (Dcx) In The Northern Pacific Rattlesnake (Crotalus Oreganus) And Western Fence Lizard (Sceloporus Occidentalis)., Brett M. Vassar

Master's Theses

Neuronal Nuclei (NeuN) and Doublecortin (DCX) are neuron specific proteins that are used in histological studies of brain structure in a variety of vertebrate taxa.Antibodies against NeuN (anti-NeuN) bind to the Fox-3 protein, an RNA binding protein common in mature neurons. Anti-DCX labels a microtubule-associated protein expressed in actively dividing neural progenitor cells and migrating neurons. The DCX gene encodes a protein that is well conserved across mammalian, avian, and a few reptilian species, therefore anti-DCX staining has been used successfully across a range of vertebrate taxa. Successful neuronal staining using anti-NeuN has been demonstrated in mammals, birds, and the …

The Effects Of Providing Social And Nutritional Enrichment To Dairy Calves On Development, Behavior And Learning, Kendra Leigh Kutina

Master's Theses

The objective of this study was to measure the effects of both a nutritional (water nipple) and social (partner calf) enrichment on calf body weight, grain intake, water intake, behavior and learning. The enrichments included 1) water provided from a nipple vs. a bucket (nutritional) and 2) visual and tactile access to a partner vs. isolated rearing with no visual or tactile access to a partner calf (social). A total of 72 Holstein and Jersey dairy calves were pseudo-randomly distributed into 4 treatments at birth [Individual/Bucket (IB), Paired/Bucket (PB), Individual/Nipple (IN), Paired/Nipple (PN)]. Socially and nutritionally enriched calves drank more …

Transmission Probability Of Embolic Debris Through The Aortic Arch And Daughter Vessels During A Transcatheter Aortic Valve Replacement Procedure, Jessica Lena Wirth

Master's Theses

Cerebral ischemia leading to an ischemic stroke is a possible complication of a transcatheter aortic valve replacement (TAVR) procedure. This is because embolic debris can become dislodged and travel through the aortic arch, where they either continue to the descending aorta and join the systemic circulation or travel into the cerebral vasculature through the three daughter vessels that branch off the top of the aortic arch. These three vessels are the brachiocephalic artery, the left subclavian artery, and the left common carotid artery. These three vessels lead either directly or indirectly to the cerebral vasculature, where the diameter of vessels …

Sidewalks To Nowhere: A Tool To Prioritize Pedestrian Improvements, Ho Yan Lai

Master's Theses

Walkability as a concept that captures the ability to walk from one place to another has multiple dimensions. Between traversability to being a proxy for better urban places, there are also numerous measurements of walkability that attempts to quantify certain or all aspects of walkability. It is, however, unclear, through a review of available literature, how these measurements of walkability relate to each other statistically. This methodology focuses on generating a framework for analysts to evaluate and prioritize pedestrian infrastructure. WalkScore™ (WS), HCM Pedestrian Level of Service (PLOS), Average Nodal Degree (AND), and Intersection Density are the four metrics selected …

The Proteomic Response Of Northern Elephant Seal (Mirounga Angustirostris) Pups To Physiological Stress During Development, Melissa P. Voisinet

Master's Theses

Background: Northern elephant seals transition from terrestrial nursing pups to pelagic foraging juveniles in a short period of just 8-12 weeks. During the post-weaning period, pups rely solely on the energy reserves gained during nursing for their caloric demands and water supply. The prolonged absence of food after weaning is the first of many fasts for which the seals have evolved adaptations such as decreased urine production and increased blubber reserves. The stressors experienced from learning to dive for the first time are also stressors that they will experience frequently as an adult and for which they have evolved adaptations. …

A Paper-Based Elisa Device For The Rapid Detection Of Ischemic Stroke, Andrea Elisabeth Larsen

Master's Theses

Diagnosing an ischemic stroke quickly and accurately is essential for appropriate treatment and results in more effective management of the stroke, leading to better patient outcomes. Specifically, the determination of ischemic versus hemorrhagic stroke leads to critically different treatment paths, which would be potentially fatal if administered incorrectly. Currently, ischemic strokes are diagnosed through a series of tests, including a physical examination, CT scans, and a panel of blood tests to exclude hemorrhagic stroke or other similarly presenting conditions, in order to administer tPA (the main treatment) within the three hour window.

The discovery of biomarkers, molecules which are upregulated …

The Investigation Of Methylidyne Radical (Ch) Reactions With Furan, 2-Methylfuran, And 2,5-Dimethlyfuran And The Photoionization And Photodissociation Of Valeric Acid, Erica Carrasco

Master's Theses

This thesis presents the combustion study of three furanic compounds using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at 298 K. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The reactions of the three furanic compounds with methylidyne (CH) radicals were analyzed based on their photoionization spectra and kinetic profiles.

Additionally, the unimolecular dissociation of valeric acid was also studied and presented in this work using the double imaging photoelectron photoion spectrometry (i2PEPICO) coupled with synchrotron radiation from the VUV beamline. The experiments were carried out …

Competition And Cooperation In Polygynous & Monogamous Households: Experimental Evidence From Sierra Leone, Bethany Gerdemann

Master's Theses

Competition and cooperation in polygynous households have both been widely documented across various disciplines. There is contradictory evidence as to whether these interpersonal dynamics produce better or worse outcomes for the household. This study uses a competitiveness game and a series of dictator games to measure competition and cooperation within households and between marriage types. Results show that there are key differences between monogamy and polygyny. Monogamous women compete less with their husbands than stranger and less in comparison to polygynous women. Monogamous spouses are more likely to forgo economic opportunities than polygynous spouses and have a greater preference for …

Effects Of Leaf Litter On Amphibian Site Selection, Rebekah Magee

Master's Theses

Leaf litter plays an important role in the forest ecosystem, impacting various processes and hindering erosion. While there is variability in the chemical and nutritional properties of leaf litter, the effects these variables have on organisms within the environment are not well known. In this study, we examined the effects of leaf litter chemistry on amphibian oviposition site selection. Artificial ponds were created using small, plastic pools, and leaf litter of 15 different tree species (including two invasive species) was added. During the 60 day experiment, water quality measurements (including temperature, pH, dissolved oxygen, conductivity, and water depth) were taken …

Seizure Detection Using Teager-Kaiser Energy And A Channel Signal Quality Assessment Algorithm, Samuel Clary

Master's Theses

This study investigated the possibility of reducing the time required for accurate epileptic seizure detection through a retroactive analysis. Epilepsy is a neurological disorder affecting over 50 million individuals globally and is defined as a disorder which results in two seizures unprovoked by fever or medication. Diagnosis of epilepsy typically involves a monitored stay at an Epilepsy Monitoring Unit (EMU). The monitoring and diagnosis process ranges on average from $35,000 to $40,000 for a single stay, and the patient results from EMU are not instantly available to the patient. The collected electroencephalogram (EEG) must be analyzed by a trained EMU …

The Real-Time Application Of Control Theory To Pharmacokinetics, George W. Carpenter Iii

Master's Theses

An optically-based injection control system has been developed as a proof-of- concept that such is of use for an intravenous drug delivery application. Current clinical drug delivery for oncology typically provides for intravenous administration without providing awareness of achieved plasma concentration, yet interpatient variability produces consequences ranging from toxicity to ineffectual treatments. We report a closed loop injection system integrating a pulse-photoplethysmograph to measure the concentration of indocyanine green (ICG) in the circulating blood of a one-compartment murine model. A proportional-derivative (PD) controller manages the injection rate in real-time. The target function for the controller is the population estimate of …

The Effects Of A Low-Glycemic Index Diabetes Management Program On Weight, Body Mass Index, Triglycerides, Cholesterol And Hemoglobin A1c Values, Morgan Williston

Master's Theses

The purpose of this study was to evaluate effects of a low-glycemic index diet on weight, body mass index (BMI), triglycerides, cholesterol levels, and hemoglobin A1c

(HbA1c) following participation in a 12-hour outpatient diabetes self- management education (DSME) program. This DSME program is unique as it

focuses on a low-glycemic index diet rather than the traditional carbohydrate consistent diet to control blood glucose levels. Health outcomes obtained post participation were compared to baseline data. Participants were 283 individuals with type 2 diabetes including 94 (33%) men and 189 (67%) women, with a mean baseline HbA1c of 8.7 ±2.2%. Statistically significant …

Effects On Strength And Corrosive Characteristics Of Hardened Cement Paste Using Rice Husk And Sugarcane Bagasse, Travis D. Garrett

Master's Theses

Cement is one of the most used building materials in the world. The production of ordinary Portland cement contributes to the release of harmful greenhouse gasses. In an effort to reduce these emissions, different materials are being evaluated for their use as partial replacements for ordinary Portland cement. Rice husk and sugarcane bagasse are agricultural waste products and large amounts of these are currently landfilled, making them inexpensive and available. When combusted at high temperatures they form rice husk ash and sugarcane bagasse ash that have pozzolanic characteristics. The high silicon dioxide in these products makes them good options to …

Food Systems Adverse Health Impacts On Latinx Immigrant Communities By Lisa Marquez, Lisa Marquez

Master's Theses

This thesis focuses on the adverse health impacts food systems have on Latinx immigrant communities. Marquez looks closely at emergency services programs using the food bank run by the Our Lady of the Pillar in Half Moon Bay, California, and interviewed five Latina immigrants from Mexico and Central America. While the food banks provided these families with fresh produce, the women expressed that it is substandard to the produce in their home countries. The interviews are supplemented with the analysis of three spoken word poems by youth who are second generation or whom have spent the majority of their lives …

Measuring Cocoa Agricultural Productivity: A Spatio-Temporal Econometric Approach, Yurlady Chaverra-Palacios

Master's Theses

A significant increase of 50.5 percent in the national production of cocoa was registered between 2011 and 2015 in Colombia. Nevertheless, 5,890 tons were imported in 2015 to supply domestic demand. Unlike other crops, the production of cocoa has made a significant contribution to the income of approximately 38,000 families of which 90 percent are small farm-producers with very little capital. Facilitating credit for investment is one of the main strategies of the national government to increase cocoa productivity. Correspondingly, the impact of the credit for investment on the cocoa agricultural productivity and if those investments have a spillover effect …

Indigenous Women's Bodies: Primer Territorio De Defensa, Ana Gabriela Avalos Tizol

Master's Theses

The teen pregnancy “epidemic” in Guatemala is a focal point when international and national NGOs demand that the government protect the civil and political rights of girls. In accordance, the state created laws (legal age for marriage - Ordinance 13-2017), implemented penal codes (statutory rape - Article 173) and created Programa Vida (conditional cash transfer of Q. 1,500 - $200 every two months) to address this ‘epidemic.’ Yet, only sixty-one teen mothers were involved in the program by the first year in 2018, indicating its inaccessibility. This thesis proposes to challenge the dominant narrative on teenage pregnancies, which blames “Mayan …

Shifting Views: How Experiential Learning Shapes University Students’ Sense Of Civic Engagement And Solidarity On Migration, Karen Larke

Master's Theses

Higher education institutions have put more weight on the use of experiential learning to provide students with opportunities to grow intellectually and develop as engaged citizens. Many recent studies have looked at the quality and educational impacts of a variety of experiential and service learning experiences, yet few have explored what other ideological impacts may result from specific non-curricular experiential learning experiences. This study measured the impact of experiential learning, in the form of week-long migration-themed trips, on undergraduate student’s self-reported levels of solidarity, and related measures of civic engagement and political engagement and activism around migration issues. This study …

Frogs Hiding In Plain Sight: Phylogenetic Systematics Of Myanmar’S Occidozyga Species Complex, And The Identification Of A Novel Species, Allison Bogisich

Master's Theses

Different species can be difficult to distinguish from one another when they are morphologically similar. Such cryptic species are the reason many anuran species go undetected. For this study, the taxonomic identity of the Occidozyga complex across Myanmar was investigated. An integrated approach was used combining molecular, morphological and phylogeographic data to better assess its taxonomy. Results indicate the presence of three new candidate species within Occidozyga, and three evolutionarily significant unit (ESU) lineages. Two mitochondrial gene fragments (16S, COI) and one nuclear gene fragment (Rhodopsin) were examined from DNA isolated from forty-seven preserved specimens from the California Academy …

Wildfire Exposure To Critical Habitat Of Endangered And Threatened Species In California, Kristin Butcher

Master's Theses

Researchers, fire ecologists and wildlife managers are concerned about impact to endangered and threatened species and their critical habitat due to the projected increase in future wildfires. Wildfires have been studied in California for the last six decades and have been increasing at an alarming rate since the 1980’s. In this study, I use the 2018 spatial dataset for critical habitat of federally endangered and threatened species located in the state boundaries of California and compare it to a spatial dataset for wildfires that have occurred over the span of 32 years (1984 to 2016). Trends are derived from spatial …

Examining Genetic And Ecological Differentiation Of An Endemic Plant Species Found Across The Hawaiian Archipelago, Psychotria Mariniana, Tiffany L. Kho

Master's Theses

Speciation is a fundamental evolutionary process that remains poorly understood. Speciation ultimately begins with population divergence, so we can elucidate the complexities of speciation by first understanding the process and drivers of population divergence. To conduct population-level analyses, ecologists and evolutionary biologists have turned to island systems, primarily for their geographic orientation and high endemism. The Hawaiian archipelago is home to over 8,700 endemic species making it a great natural laboratory to study species diversification at the population level. The Hawaiian Psychotria (kōpiko, or wild coffee) make up 11 of these species and have been used to understand colonization and …

Play Behavior And The Development Of Boldness And Caution In Juvenile Belding’S Ground Squirrels (Urocitellus Beldingi), Madelene Shehan

Master's Theses

The ubiquity of play among juvenile mammals suggests it provides adaptive benefits, potentially through influences on the development of temperament in young animals. Juvenile Belding’s ground squirrels (Urocitellus beldingi) must balance competing demands for boldness and caution imposed by the fundamental trade-off between their short active season and their vulnerability to predation. In this study, I evaluated whether play helps to facilitate the development of an appropriate balance between boldness and caution in juvenile U. beldingi.I observed the play behavior of juvenile U. beldingiand conducted flight-initiation distance tests to measure boldness-caution at the beginning and toward …

Are Menstrual Cycles A Biological Determinant Of Well-Being Amongst Sierra Leonean Schoolchildren?, Ashwini Shridhar

Master's Theses

The influence of hormones and biology on behavior is a topic that is rife with controversy, especially when it comes to sexual hormones. There is even more murkiness when it comes to the topic of menstruation and knowledge about women’s menstrual cycles. Recent research on this topic have seen a link between the hormonal fluctuations during menstrual cycles and various behavioral implications on competition, cooperation, and risk behavior. This study tries to expand existing knowledge by examining whether there is a link between hormonal fluctuations during menstrual cycles and risk preferential behavior using economic experiments in the largely understudied context …