Digital Commons Network^™

Drawing Place Field Diagrams Of Neural Codes Using Toric Ideals, Nida K. Obatake

Master's Theses

A neural code is a collection of codewords (0-1 vectors) of a given length n; it captures the co-firing patterns of a set of neurons. A neural code is convexly realizable in dimension two if there exist n convex sets in the plane so that each codeword in the code corresponds to a unique intersection carved out by the convex sets. There are some methods to determine whether a neural code is convexly realizable; however, these methods do not describe how to draw a realization, that is, a place field diagram of the code. In this work, we construct toric …

Effects Of Zoledronate During Simulated Weightlessness On Bone Structure And Mechanics, Ryan T. Scott

Master's Theses

Spaceflight causes astronauts to experience an unbalanced level of bone remodeling favoring resorption. The combination of an antiresorptive drug and weightlessness may have negative effects on the mechanical and structural properties of bone by increasing elastic stiffness but diminishing plasticity. At 16 weeks of age, skeletally postpubescent male mice (n = 32, C57BL/6) were evenly divided and subcutaneously given either zoledronate (45 µg/kg) or vehicle (saline, same volume). Three days postinjection, half of each group were divided to undergo 3 weeks of hindlimb unloading or act as a control undergoing normal ambulation (n = 8 for each of the 4 …

The Impact Of Climate Change On Coastal Fog Hours Of California's Central Coast, Chrissy Rogers

Master's Theses

This study used observations and downscaled model output from the Coupled Model Intercomparison Project 5 to investigate diurnal temperature differences and their relationship to the number of fog hours in the future along California’s central coast. The study area extended north-south from Bodega Bay to the Santa Lucia Range and east-west from the coast of California to the western flank of the Sierra Nevada Mountains. Analyses of Representative Concentration Pathway (RCP) scenarios 4.5 and 8.5 showed that most of California’s central coast will likely see minimal changes in the number of fog hours per day through the turn of the …

Exposure Assessment Of Asthma And Modeling Of Pm2.5 During The 2007 Southern California Wildfires, Areana Flores

Master's Theses

A three-year study (1 Jan 07 to 31 Dec 09) was conducted for Los Angeles and Riverside counties to validate current findings on impacts of wildfires on respiratory health. A dataset developed from multiple sources containing daily rates of air pollution (O3, NO2, CO, and PM2.5) and meteorological variables (temperature, dew point, wind speed, and inversion height) was correlated with asthma emergency department (ED) visits. A second correlation was calculated for a modified dataset that excludes all episodes of wildfire events within the study period. The difference in correlations between both datasets was computed. PM2.5 was positively associated with asthma …

Testing Camera Trap Density Estimates From The Spatial Capture Model And Calibrated Capture Rate Indices Against Kangaroo Rat (Dipodomys Spp.) Live Trapping Data, Timothy A. Walker

Master's Theses

Camera trapping studies often focus on estimating population density, which is critical for managing wild populations. Density estimators typically require unique markers such as stripe patterns to identify individuals but most animals do not have such markings. The spatial capture model (SC model; Chandler & Royle, 2013) estimates density without individual identification but lacks sufficient field testing. Here, both the SC model and calibrated capture rate indices were compared against ten sessions of live trapping data on kangaroo rats (Dipodomys spp). These camera and live trapping data were combined in a joint-likelihood model to further compare the two methods. From …

Deconstructing Exploitative Systems And Restoring A Balanced Biosphere: An Ecofeminist Posthumanist Reading Of Jane Smiley's A Thousand Acres And Barbara Kingsolver's Prodigal Summer, Aubrey A. Laughlin

Master's Theses

Although many scholarly articles have provided ecofeminist insights and

critiques of A Thousand Acres that connect the abuse of women to the abuse of the land, few have dealt specifically with the link between the treatment of women and the treatment of nonhuman animals. In the first chapter of this paper, I argue that associations between women and nonhuman animals in A Thousand Acres sustain the constructed reality of patriarchal communities. Similarly, Prodigal Summer’s narratives center around females and nonhuman animals, but also provide a broader focus that emphasizes the interconnectivity of the entire biotic pyramid and optimistically holds that …

Egg Turning Behavior And Egg Temperature In Relation To Mercury Contamination Of Forster's Terns (Sterna Forsteri), Gregory T. Taylor

Master's Theses

Several avian species exhibit reduced hatching success as a result of mercury contamination, but the mechanism by which this occurs is unknown. We examined egg turning rates and egg temperatures, two important determinants of egg hatchability, in relation to egg mercury contamination of Forster’s terns (Sterna forsteri) in San Francisco Bay. Here, we used artificial eggs containing a data logger with a 3-D accelerometer, a magnetometer, and a temperature thermistor to monitor parental incubation behavior (sampled at 1 Hz) of 186 tern nests. Overall, adults turned their eggs an average of 3.8 ± 0.8 SD turns h^(-1), which is nearly …

Learning Delays In A Mouse Model Of Autism Spectrum Disorder, Amanda R. Rendall

Master's Theses

Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental disorder with core symptoms of atypical social interactions and repetitive behaviors. It has also been reported that individuals with ASD have difficulty with multisensory integration, and this may disrupt higher-order cognitive abilities such as learning and social communication. Impairments in the integration of sensory information could in turn reflect diminished cross-modal white matter connectivity. Moreover, the genetic contribution in ASD appears to be strong, with heritability estimates as high as 90%. However, no single gene has been identified, and over 100 risk genes have been reported. One of these genes -- contactin-associated-like-protein …

Spatial And Temporal Use Of Early Successional Habitat Patches By A Community Of Mammals In The Northeastern United States, Kelly M. O'Connor

Master's Theses

No abstract provided.

Revisiting Community Water Fluoridation, Jessica Marie Seyfried

Master's Theses

There is a bourgeoning controversy unknown to many surrounding one of the CDC’s top ten public health achievements of the 20^th century. After more than 50 years of implementation, community water fluoridation may not have achieved the declines in caries rates we once thought or hoped for, especially in light of alternative approaches to preventing caries including but not limited to other sources of fluoride supplementation, changes in diet, and tooth brushing behavior.

In fact, a survey of past research highlights the fact that this policy decision may be based on out of date and/or a lack of research …

The Role Of The State, Multinational Oil Companies, International Law & The International Community: Intersection Of Human Rights & Environmental Degradation Climate Change In The 21st Century Caused By Traditional Extractive Practices, The Amazon Rainforest, Indigenous People And Universal Jurisdiction To Resolve The Accountability Issue, Marcela Cabrera Luna

Master's Theses

Local, national and international conventions that protect indigenous sovereignty and their territories, where many of the resources are extracted from by multinational corporations (MNCs) particularly oil, the number one commodity of the world and cause of climate change, continue to be jeopardized because of the lack of a clear international legal framework that can protect them and potentially hold multinationals accountable for their actions. These practices are causing not only environmental issues to the indigenous and surrounding communities, but climate change is in fact, the real human rights issue of the 21^st century and it affects everyone. By using …

Photooxidation Reactions Of Small-Chain Methyl Esters, Aerosol Photoelectron Spectroscopy, And The Photodissociation Of Ethylenediamine, Giel Muller

Master's Theses

Research conducted at the University of San Francisco is presented within this masters thesis, including the Cl-initiated photooxidation reactions of methyl propanoate, methyl butanoate, and methyl valerate (pentanoate), the aerosol photoelectron spectroscopy of isoprene and gamma-valerolactone, and the TPEPICO investigation of ethylenediamine. Experiments were conducted at the Lawrence Berkeley National Lab Advanced Light Source (ALS), the National Synchrotron Radiation Research Center in Hsinchu City (NSRRC), and the University of Stockton in California, respectively.

The Ecological Importance Of Brachiopods Versus Bivalves In The Paleozoic: Taphonomy, Biomass, And Energy Use, Shannon (Shin-Nan) Hsieh

Master's Theses

Brachiopods have commonly been considered more important than bivalves in Paleozoic ecosystems due to their greater global diversity and greater abundance in many fossil assemblages. New sampling-standardized diversity curves verify that brachiopods were more diverse than bivalves at the global level in the Paleozoic; they declined in the Permian-Triassic extinction, largely recovered, then faded away later in the Mesozoic. However, the subordinate ecological status of bivalves within local Paleozoic ecosystems has been challenged on two fronts. First, bivalve abundance may be underestimated due to preferential dissolution of aragonitic shells. Second, bivalve contribution to ecosystem function may be underestimated by abundance …

Density-Based Clustering Of High-Dimensional Dna Fingerprints For Library-Dependent Microbial Source Tracking, Eric Johnson

Master's Theses

As part of an ongoing multidisciplinary effort at California Polytechnic State University, biologists and computer scientists have developed a new Library-Dependent Microbial Source Tracking method for identifying the host animals causing fecal contamination in local water sources. The Cal Poly Library of Pyroprints (CPLOP) is a database which stores E. coli representations of fecal samples from known hosts acquired from a novel method developed by the biologists called Pyroprinting. The research group considers E. coli samples whose Pyroprints match above a certain threshold to be part of the same bacterial strain. If an environmental sample from an unknown host animal …

Una Legua Cuadrada: Exploring The History Of Swanton Pacific Ranch And Environs, Jeanine Marie Scaramozzino

Master's Theses

Swanton Pacific Ranch is an educational and research facility owned by the Cal Poly Corporation and managed by the Cal Poly State University (Cal Poly) College of Agriculture, Food and Environmental Sciences. Located about 180 miles north of campus and just 14 miles north of Santa Cruz, California on Highway 1, the property was first leased to and then donated to Cal Poly by the late Albert E. Smith in 1993. The rancho’s original inhabitants included Native Americans, Spaniards, Mexicans, as well as various European immigrants and their descendants; currently, the staff, faculty, and students of Cal Poly occupy the …

An Evaluation Of The Disposition Of R941000, A Tetrazolone-Telmisartan Analog: A Case Study Of The Suitability Of Tetrazolone As A Carboxylic Acid Bioisostere, Ryan Brant Murray

Master's Theses

Carboxylic acids are ubiquitous in medicinal compounds, such as nonsteroidal anti-inflammatories, statins, hypertensives, and anticoagulants. Despite their prolific use, unfavorable characteristics such as metabolic instability, poor membrane permeability, and toxicity have been associated with this moiety in some instances. Bioisosteres have been employed to attenuate these issues. However, bioisostere use can alter drug potency and disposition. Recently, our company demonstrated the feasibility of the tetrazolone moiety as a carboxylic acid bioisostere for the angiotensin II antagonist telmisartan. R941000 (telmisartan-tetrazolone analog) was a potent in vitro inhibitor of angiotensin II and possessed a similar disposition to telmisartan. To the best of …

Preschool Creative Drama: A Curriculum And Its Effects On Learning, Erin Kelli Lindberg

Master's Theses

No abstract provided.

The Vascular Flora Of Wayne County, Mississippi, Daniel M. Mcnair

Master's Theses

The vascular flora of Wayne County, Mississippi, was surveyed from 2013–2015, and the species of native and naturalized plants are listed. In total, 1,135 species were identified from field collections, previously collected herbarium specimens, and field observations. These belong to 556 genera and 165 families. Four of these species represent first recorded occurrences in the state of Mississippi: Blyxa aubertii Rich., Gomphrena serrata Pav. ex Moq., Isoetes valida (Engelm.) Clute, and Polypogon interruptus Kunth. GPS coordinates are given for important collection sites representing the diversity of plant communities in the county. All voucher specimens from the survey are deposited in …

Are Large Dogs Smarter Than Small Dogs? Investigating Within Species Differences In Large And Small Dogs: Spatial Memory, Megan S. Broadway

Master's Theses

The study of canine cognition can be useful in understanding the ontology and selective pressures that affect the development of cognitive abilities. Dogs have undergone intensive artificial selection yielding distinctive breeds which differ both phenotypically and behaviorally. Breed based cognitive differences have not been found but some studies suggest there may be differences in broader categories such as working disposition and sex. The influence of size on canine cognition has not been thoroughly addressed despite the fact that large dogs are often perceived to be ‘smarter’ than small dogs. This preconception has only recently been addressed and supported in one …

A Platform For Fast Detection Of Let-7 Micro Rna Using Polyaniline Fluorescence And Image Analysis Techniques, Partha P. Sengupta

Master's Theses

The project describes a new strategy for transducing hybridization events through modulating intrinsic properties of the electroconductive polymer polyaniline (PANI). When DNA based probes electrostatically interact with PANI, its fluorescence properties are increased, a phenomenon that can be enhanced by UV irradiation. Hybridization of target nucleic acids results in dissociation of probes causing PANI fluorescence to return to basal levels. By monitoring restoration of base PANI fluorescence as little as 10^-11 M (10 pM) of target oligonucleotides could be detected within 15 minutes of hybridization. Detection of complementary oligos was specific, with introduction of a single mismatch failing to …

High Resolution Melt Analysis Of Samples With Differential Dna Methylation To Identify Tissue Source Of Origin, Stephanie M. Ledgerwood

Master's Theses

In Forensic Science casework, identifying the source of a tissue can assist in crime scene reconstruction. Currently, presumptive testing methods to identify tissue type are utilized in crime scene laboratories, but there is a need for a more reliable confirmatory test for tissue type identification. High Resolution Melt (HRM) analysis is an innovative technology that has the potential to determine tissue types through variations in DNA methylation patterns. Recently, DNA methylation patterns have been found to correspond with specific tissue types in particular regions of DNA. Two markers, B_SPTB_03 and DDX4 have been effective in differentiating sperm from other tissue …

Gut Microbiota Of Migratory Passerines At Stopover, William Bagley Lewis

Master's Theses

Although the gut microbiota provides many beneficial functions to animal hosts, relatively little is known about the gut microbiota of passerines. It is likely that gut microbes are especially important during the migratory phase; however gut atrophy experienced during prolonged migratory flight may cause disruptions of the stable microbiota. Fecal samples were collected from several species of passerine after crossing the Gulf of Mexico during spring migration and before crossing during fall, and microbiota communities were analyzed using next-generation sequencing. Despite showing large inter-individual variation, a core microbiota composed largely of Firmicutes and Proteobacteria was identified in all birds. Microbiota …

Effects Of Failure On Subsequent Performance In The Bottlenose Dolphin (Tursiops Truncatus), Lisa Kay Lauderdale

Master's Theses

The current study examined the immediate effects of two types of failure during operant-conditioning based training sessions in 11 bottlenose dolphins (Tursiops truncatus) at the U.S. Navy Marine Mammal Program in San Diego, CA. While learning a multi-faceted behavior not commonly found in nature, such as beaching, animals are likely to perform approximations of the behavior that are not successful and do not result in reinforcement. The effects of failure on beaching trials were systematically investigated over a three-month period by determining the mean failure rate and the probability of success after initial success, initial attempts, and initial …

An Integrated Drought Index (Idi) Incorporating Physical And Social Aspects, Rebecca L. Lanier

Master's Theses

The purpose of this research was to determine significant bio-physical (physical and environmental) and social variables that can be integrated into a drought index to predict areas susceptible to drought. Severe drought events are capable of causing millions of dollars in damage. The 1988 drought caused the United States approximately $40 billion in damage. Drought forecasting, modeling, and detection have, therefore, become imperative to understand the social, economic and environmental impacts of droughts, and also to explore how these impacts play a role in the occurrence of a drought. A number of drought indices widely used in the U.S. rely …

Achieving Relationships, Frederick C. Melancon

Master's Theses

These stories attempt to follow John Gardner’s instruction to create a dream that will engage the reader. Mirroring the goal that an author has to create a relationship with his audience, each story in turn focuses on emotional details that convey the characters’ feelings of isolation or, alternatively, inclusion in their communities. In the first story, a young man tries to recreate his father’s king cake. In the next, a middle school girl fixates on her relationship with her sister. Trying to recapture the memory of a lost daughter, a man searches for the perfect nectar snowball. A mom, then, …

Same-Sex Socio-Sexual Interactions Among A Group Of Captive Bottlenose Dolphins (Tursiops Truncatus), Natalia Botero Acosta

Master's Theses

Bottlenose dolphins (Tursiops truncatus) frequently engage in non-reproductive sexual behavior, including homosexual encounters. In order to better understand the nature and function of these interactions, a longitudinal study of the patterns of association and the dynamics of initiator/recipient role exchange was conducted. Underwater video footage of a colony of bottlenose dolphins housed at the Roatan Institute for Marine Sciences (RIMS), collected between March of 2010 and May of 2013, was analyzed. Associations occurring during homosexual interactions were transitory for most individuals. Nonetheless, subsequent analyses allowed the rejection of the null hypothesis of random association, suggesting the existence of …

Paleopathology At The Shady Grove Site (22qu525): A Study Of Health In The Upper Yazoo Basin During The Middle Mississippian Period, Christopher Brady Davis

Master's Theses

The Mississippian Period (AD 1000-1539) is characterized by increasingly sedentary populations, mound building, ranked societies, and intensified agriculture. As agriculture spread throughout the Eastern Woodlands, it led to widespread health consequences, including poor nutrition and increased levels of infection. Also, environmental shifts during the Mississippian Period (AD 1000-1539) caused drier conditions, potentially leading to crop failures further exacerbating nutritional problems.

This thesis focuses on the health of the Shady Grove site in the Upper Yazoo Basin, a Middle to Late Mississippian medium sized mound center where an ossuary containing up to 100 individuals was excavated in 2010. Focusing only on …

Maternal Effects And Offspring Behavior: Potential Contributors To The Lack Of Recruitment In Mississippi Gopher Tortoises (Gopherus Polyphemus), Aaron L. Holbrook

Master's Theses

Federally threatened in Mississippi, gopher tortoise (Gopherus polyphemus) populations within the state have strongly variable recruitment and are generally in decline. Hatching success is significantly lower in Mississippi than in any other part of the species’ range , and most hatchlings die within the first year. There are few refuges where survival and hatching success is high. Here I compare two populations that differ in recruitment and offspring survival for differences in corticosterone. Corticosterone is a hormone that influences both energy availability and is released in elevated levels during stressful events, like living in poor quality habitat. Prolonged corticosterone elevation …

Feeding The South: An Assessment Of Food Availability In Rural Mississippi, Nicole Baiza Lawrence

Master's Theses

The overall goal of this project is to investigate Mississippi’s rural food environment by assessing the food resources available to rural Mississippians. The primary objectives were to identify sample locations in each of the four cultural regions of Mississippi and determine the food resources available to residents of those counties. The intellectual merit of this research lies in its in-depth exploration of food accessibility in rural areas. Though there is a wealth of literature on the topics of urban food access and food deserts, very little research has been done in rural areas. Most studies focus on urban environments which …

Territorial Defense Strategies In The Northern Cardinal (Cardinalis Cardinalis): Who Is The Bigger Threat?, Kaylee M. Gentry

Master's Theses

This thesis examines the use of defensive strategies in relation to territories year round in the northern cardinal (Cardinalis cardinalis). Responses to recorded neighbor song and stranger song playback from the middle of a focal male’s territory were measured. This allowed for an estimation of aggression in both the winter and spring seasons. Each focal male was subjected to both treatments (stranger song and neighbor song). Males were more responsive over-all to neighbor song playback, however in the winter months, persistence of response to neighbor song playback increased. It was also shown that southeastern United States cardinals show …