Digital Commons Network^™

West Indian Manatee (Trichechus Manatus) Habitat Characterization Using Side-Scan Sonar, Mindy J. Mclarty

Master's Theses

In this study, the reliability of low cost side-scan sonar to accurately identify soft substrates such as grass and mud was tested. Benthic substrates can be hard to classify from the surface, necessitating an alternative survey approach. A total area of 11.5 km² was surveyed with the sonar in a large, brackish mangrove lagoon system. Individual points were ground-truthed for comparison with the sonar recordings to provide a measure of accuracy. Five substrate types were identified: Dense seagrass, sparse seagrass, mangrove soil, mangrove soil with rock, and silt. A zoned benthic substrate map was created from the sonar recordings. …

The Water System Of Tall Jalul, Bruno Alves Barros

Master's Theses

The Problem

Components of the water system of Tall Jalul have been discovered since 2009 in Fields G and W. Although articles and reports have been written, no comprehensive study has been conducted. Therefore, this thesis will present and discuss the water system of Jalul from 2009 to 2016 and look for comparisons with similar Iron Age structures in the Ancient Near East.

The Method

For this project, the ruins from Fields G and W were analyzed. First, selected water systems in Palestine were introduced, followed by a review of preliminary reports and personal observations on the site of Tall …

Sin And Its Place In The Experience Of Suffering: Presenting The Basis For A Sound Theodicy, Roman Wiens

Master's Theses

Topic

One of the most significant issues in theism is the obvious existence of evil and suffering. Thus many philosophers (especially Atheists) propose this fact alone negates the existence of an all-loving, omnipotent, and caring God. This attacks both the integrity of God and the coherence of the scriptural accounts. In response, theologians around the world proposed theodicies to show that the existence of a God, as portrayed in the Bible, is coherent with suffering in this world.

Purpose

The different approaches to this problem are categorized in four categories, outlined, and evaluated in one chapter about the most noteworthy …

Theory Of Mind And Negation, Jasmine Buckins

Master's Theses

Problem

There is an extensive amount of research on theory of mind, which is the ability to attribute mental states (e.g., beliefs, intents, desires, knowledge, etc.) to oneself and others and to comprehend that others have beliefs, desires, intentions and perspectives that may be different from one’s own. Some researchers have investigated the potential prerequisites or developmental milestones that may be required in order for a theory of mind to be developed in young children. Some researchers have concluded that certain factors play a role in theory of mind development. These factors include environmental, cognitive and linguistic components. However, in …

Population Genetics And Distribution Of The Oriental Weatherfish, Misgurnus Anguillicaudatus, In Chicago Area Waterways, John Belcik

Master's Theses

Oriental Weatherfish (Misgurnus anguillicaudatus), native to Southeast Asia, are freshwater fish belonging to the family Cobitidae (loaches). They are benthic fish with the ability to breathe atmospheric air, and exhibit an unusual behavior of swimming vertically in the water column in response to changes in barometric pressure. Oriental Weatherfish appear to be successful invaders to North American waterways. Within the last century they have been sighted in freshwater systems throughout the United States, yet the distribution and source of this invasion are largely unknown. This study investigates the distribution patterns, surveying methods, and population genetics of the Oriental Weatherfish within …

Aquatic Insect Community Structure And Secondary Production In Coastal Wetland Ponds Of The Copper River Delta, Alaska: Influence Of Water Temperature And Macrophyte Community Structure, Chantel Caldwell

Master's Theses

The Copper River Delta (CRD), southcentral Alaska, is one of the world’s largest continuous coastal wetlands and is largely composed of sloughs, lakes, and ponds. Due to coastal topography the east side of the Copper River (East Delta) is disproportionately impacted by a cold continental air mass. Wetland communities of the CRD were also impacted by a 9.2 magnitude earthquake in 1964 that shifted the more coastal portion of the CRD from tidally influenced ponds to freshwater ponds.

The West-East temperature gradient across the CRD coupled with landscape type (uplifted marsh (UM) and outwash plain (OP)) creates four regions (West-UM, …

Using Tcr Transgenic, Gp100 Reactive T Cells And Checkpoint Inhibition To Target Lymphangioleimyomatosis, Christian Ankney

Master's Theses

Lymphangioleiomyomatosis (LAM) is a low-grade neoplastic disease affecting primarily women. It is characterized by cystic lung disease as well as renal and retroperitoneal tumors called angiomyolipomas and lymphangiomas. Tumor cells have smooth muscle features as well as neuroendocrine cell surface markers, and the disease can be diagnosed by HMB45 staining of tumor cells. We questioned whether expression of melanocytic antigens, specifically gp100, creates an opportunity to treat LAM by adoptive T cell transfer. LAM lung lesions demonstrate poor immune surveillance, therefore adoptive T cell transfer could offer benefits in this disease.

A link was made between melanoma and depigmenting vitiligo …

Creating A Bret Assay To Monitor The Interaction Between Β-Arrestin-1 And Stam-1, James Buhrmaster

Master's Theses

CXCR4 is a chemokine receptor that is overexpressed in multiple disease states, including cancer. Understanding the mechanisms by which cells regulate CXCR4 expression is of high importance, as they can reveal downstream effectors that can potentially be targeted pharmacologically to more effectively treat diseases with fewer side effects.

CXCR4 is internalized in response to stimulation by its ligand CXCL12, and localizes to early endosomes as part of a homologous desensitization mechanism. From the endosome, CXCR4 can enter one of two pathways whereby it is either recycled back to the plasma membrane, where it can undergo another signaling event, or it …

Nutrient Removal And Vegetation Recovery Through Successive Harvesting Of The Invasive Hybrid Cattail (Typha X Glauca) In Great Lakes Coastal Wetlands, Kelsey Berke

Master's Theses

Excess nutrient levels have led to invasive hybrid cattail (Typha × glauca) dominance in many Laurentian Great Lakes coastal wetlands. Its ability to alter wetland structure and function has made T. × glauca a target invasive species with respect to Great Lakes coastal wetland

restoration. This study investigated the effect of harvesting invasive T. × glauca biomass on nutrient removal, specifically nitrogen and phosphorus, and plant diversity recovery in Great Lakes coastal wetland ecosystems. This study demonstrated that without considering external nutrient inputs and outputs, a single harvest at Cheboygan Marsh, MI could remove ~2% of the total N and …

The Effects Of Treating Multispecies Biofilms With Bacteriophage, Alexandria Francis Cooper

Master's Theses

Biofilms can be found in any environment within proximity to water and are problematic in an assortment of industries. Numerous efforts have been employed to dislodge biofilms including bacteriophages (viruses that infect bacteria). Phage remediation is a promising solution for combatting biofilms that form on catheters in long term use patients. These biofilms often result in catheter-associated urinary tract infections (CAUTIs) and are the most common type of healthcare related infection reported. Additionally, they result in longer hospital stays and increased morbidity. To date, most of the research on the topic focuses on single species biofilms, despite their rarity in …

Phenotyping Temperature-Sensitive Coronaviruses, Amani Eddins

Master's Theses

Coronaviruses (CoVs) can cause a range of symptoms; from a mild common cold to life threatening acute respiratory distress syndrome (ARDS) upon infection. These emerging viruses have the ability to be highly pathogenic and detrimental to the human population. Two prime examples of CoV emergence, SARS-CoV (Severe Acute Respiratory Syndrome) and MERS-CoV, (Middle Eastern Respiratory Syndrome), which exhibits the pandemic potential of emerging CoVs that gain human tropism. Given the increasing potential of an emerging CoV outbreak there is a state of urgency to develop vaccines that will help protect the human population against current and future circulating strains. The …

The Novel Characterization Of Extracellular Vesicles Containing Proteins Which Have Been Implicated In The Pathogenesis Of Hiv Associated Neurocognitive Disorders, Grace Ispas

Master's Theses

Although Anti-Retroviral Therapy (ART) is practiced, HIV-1 positive individuals still experience HIV-Associated Neurocognitive Disorders (HAND), collectively described as the presentation of neurocognitive, behavioral and motor dysfunctions that decrease the quality of life, while increasing the mortality in ART suppressed HIV-1 positive patients.

Current literature suggests that extracellular vesicles are involved in the pathogenesis of HAND as they are believed to be transferring HIV-1 proteins to nearby neuronal cells. Although most studies assume homogeneity among populations, characterizing cellular proteins or RNA levels in bulk, we hypothesize that distinct populations of extracellular vesicles are released and that environmental conditions, including viral infections, …

Optimizing Clean Catch Urine Collection And Its Applications In Urinary Microbiome Studies, Danielle Johansen

Master's Theses

Clean catch was developed before the advancement of more sensitive assays for culturing urinary bacteria. I reassessed clean catch, endeavoring to optimize this method. Periurethral swabs and voided urines were routinely collected, while analyzing different aspects of the method. I determined that midstream urine contained the least amount of vulvo-vaginal contamination and that the time of collection did not impact the results. I also determined that the use of antiseptic wipes prior to void increased the level of vulvo-vaginal contamination. A small cohort of females collected daily urines over a 17-day period and kept a strict alcohol diary. Females who …

Functional Studies Of Novel Mosquito Stage-Specific Genes In The Malaria Parasite, Plasmodium Berghei., Kaitlyn Kiernan

Master's Theses

The development and survival of the malaria parasite Plasmodium within its mosquito vector is not very well understood. When the parasite is taken up by an Anopheles mosquito, it is exposed to digestive enzymes, reactive oxygen species, increasing pH, decreasing temperature, and a diverse microbial flora. Our lab is studying the adaptive mechanisms underlying parasite survival in this hostile environment, one of which is movement out of the midgut. In order to escape the midgut, the parasite develops into an elongated, motile form called the ookinete. I am investigating two genes, thioredoxin-like protein 1 (trxl-1) and subpellicular microtubule protein 1 …

Comparative Studies On Biochemical And Pharmacological Profiles Of Bovine, Ovine And Porcine Heparins, Ahmed Kouta

Master's Theses

Heparin, a highly sulfated glycosaminoglycan (GAG), is used extensively as an anticoagulant. It consists of repeating disaccharide units, containing iduronic acid (or glucuronic acid) and glucosamine, exhibiting variable degrees of sulfation. Heparin, and its analogues, are used during surgery and dialysis, and are often used to coat indwelling catheters and other devices where the vascular system is exposed. Administered parenterally, often continuously due to its short half-life, over 0.5 billion doses are required per year. Heparin is currently obtained from mucosal tissue of meat animals, mainly porcine intestine, and to a lesser extent bovine and ovine sources. The early stages …

Dexamethasone Treatment Effects On H3k27me3 Chromatin Organization Is Related To Nk Cell Immune Dysregulation, Michael Sarafeno Misale

Master's Theses

It is well-established that psychological stress reduces natural killer (NK) cell immune function. This reduction is mediated by stress-induced release of glucocorticoids (GC), which can suppress immune function. Associated with suppression of a particular immune function are GC induced histone-epigenetic marks. Histone-epigenetic marks are responsible for the organization and compartmentalization of genomes into transcriptionally active euchromatin domains that are localized to the interior of the nucleus. Transcriptionally silent heterochromatic domains are enriched with methylated epigenetic marks and are localized to the nuclear periphery. The purpose of this investigation was to assess the influence of GC on H3K27me3 chromatin organization by …

Multifunctional Regulatory T Cells From Human Umbilical Cord Blood And The Role Of Tumor Necrosis Factor In Immune Homeostasis, Alexander Nelson

Master's Theses

Regulatory T cells (Tregs) are required to suppress inflammation and prevent autoimmunity. During fetal development Tregs are crucial to maintain tolerance between mother and child. After birth, neonates require tolerance to avoid harmful immune responses to foreign antigens in food and allow colonization with commensal microbes. We demonstrate a propensity for T cells in human umbilical cord blood to differentiate into Tregs in response to antigen receptor stimulation ex vivo. Cord blood-derived Tregs potently suppress T cell proliferation, but also produce pro-inflammatory cytokines known to activate innate immune responses. These results suggest that antigen exposure during early life results in …

Characterization Of Inhibitory Molecules Produced By Lactobacillus Crispatus, Giuseppe Anthony Pistone

Master's Theses

Lactobacillus species are widely accepted as beneficial bacteria of the human microbiota1-8. Lactobacilli spp. are well documented to inhibit pathogens by production and secretion of hydrogen peroxide (H2O2), organic acids, and/or proteinaceous bacteriocins into their environment. Most research attributes bactericidal activity of cell free supernatant (CFS) to H2O2 and/or lactic acid. Here, I demonstrate that CFS from a clinical isolate of Lactobacillus crispatus contains a molecule(s) that inhibits uropathogenic Escherichia coli (UPEC) colony formation independently of H2O2 and organic acids. Physiologic concentrations of H2O2 and organic acids produced by L. crispatus do not inhibit UPEC colony formation. Incubation of UPEC …

A Mobile App Illustrating Sensory Neural Coding Through An Efficient Coding Of Collected Images And Sounds, Xiaolu Zhao

Master's Theses

Sensory neuroscience in the early auditory and visual systems appears distinct not

only to outside observers, but to many trained neuroscientists as well. However, to a computational neuroscientist, both sensory systems represent an efficient neural coding of information. In fact, on a computational level it appears the brain is using the same processing strategy for both senses - the same algorithm with just a change in inputs. Insights like this can greatly simplify our understanding of the brain, but require a significant computational background to fully appreciate. How can such illuminating results of computational neuroscience be made more accessible to …

Spatial Distribution Of Artesian Conditions Within The Niles Cone Basin, Alameda County, California, Anthony Wade Fisher

Master's Theses

The Niles Cone Basin (NCB) within Alameda County, California, contains portions of the basin under perennial and ephemeral artesian groundwater conditions. This study used 349 wells installed throughout the basin’s four-aquifer system to delineate the spatial distribution of the 86 wells that have gone artesian between 1995 and 2015. Artesian wells within all four aquifers occur at elevations below 5.2 meters above sea level (MASL) but predominantly below 3.0 MASL. Even at lower elevations, artesian conditions do not occur in regions of major pumping owing to significant drawdown. Within topographically-low regions, wells may not be artesian where well-heads are located …

Green Vs. White: An Examination Of Of Media Portrayals Of Radical Environmentalists And White Supremacists, Laurence Pedroni

Master's Theses

The rise of the Trump presidency has highlighted not only the white supremacist history of the U.S., but also reflects danger to the survival of the species in the form of wholesale climate change denial. These ideologies are not unique to Trump or his cabinet, instead reflecting long standing U.S. policy. This research seeks to examine how the U.S. media supports and propagates propaganda to support these hegemonic goals. Relevant literature and research seem to suggest that because radical environmental movements often challenge the hegemony of capital accumulation, they might be portrayed as more violent and a greater terrorist threat …

Evaluation Of Oyster Shell Enhancement On Western Snowy Plover Breeding Success, Karine Tokatlian

Master's Theses

The Pacific Coast population of the western snowy plover (Charadrius nivosus nivosus; plover) is listed as a federally threatened species under the U.S. Endangered Species Act due to poor reproductive success from anthropogenic habitat loss, and high predation pressure. Plovers in the South San Francisco Bay use dry salt evaporation ponds, and wildlife-managed ponds, to breed and winter. However, the South Bay Salt Pond Restoration Project aims to restore up to 6,110 hectares of this habitat back to native tidal marsh, which will force plovers to breed in smaller areas and in higher densities. In order to recover plovers in …

Quantifying The Functional Consequences Of Spanish [S] Lenition: Plural Marking And Derived Homophony In Western Andalusian And Castilian, Mary Catherine Moran Ryan

Master's Theses

In this thesis, a new methodology is proposed for investigating Spanish [s] lenition (sound weakening or loss) via morphological analysis instead of phonetics. Word-final [s] is a morphological plural marker in Castilian Spanish, but is rarely produced in Western Andalusian Spanish (WAS). It is often asserted in the literature that the loss of [s] in WAS requires plurality to be expressed via alternative means. The results of this study rule out lexical and morpho-syntactic compensation for [s] lenition in WAS in several previously untested domains, and imply that there is no functional motivation in Modern Spanish driving a need for …

Life History Aspects And Taxonomy Of Deep-Sea Chondrichthyans In The Southwestern Indian Ocean, Paul Joseph Clerkin

Master's Theses

During the last quarter of a century, the conservation and management of chondrichthyans (collectively, sharks, rays, and chimaeras) has received considerable focus. This is especially true for deep-sea chondrichthyans. As technologically advanced fisheries expand into deeper waters of the high seas, new chondrichthyan species are being discovered and described at an increasing rate. The objectives of this study were to investigate the deep-sea chondricthyan fauna in a remote region of the Southwestern Indian Ocean Offshore and provide descriptions of three species of Chimaeridae previously unknown to science, and collect and analyze biological parameters relating to the life histories of all …

Construction Of Bacterial Strains Containing A Plasmid Producing An Opossum-Based Anti-Venom Peptide For Low Cost Production Of The Peptide, Angela Cifelli

Master's Theses

A cost-effective therapy for snake bites and other biological toxins could save thousands of lives each year. A low-cost therapy can be achieved using a bacterial host that expresses a peptide that prevents death when administered after exposure to these toxins. A protein expressed in opossums, lethal toxin neutralizing factor (LTNF), provides the animal’s resistance to venom and a variety of other toxins. A small peptide fragment of this protein provides the same lifesaving properties as the full protein sequence. A synthetic copy of this peptide was tested in mice exposed to rattlesnake venom and showed lifesaving potential. The peptide …

Isolated Incidents: A Short Story Collection, Justin Bryant

Master's Theses

In my collection titled Isolated Incidents: A Short Story Collection, I explore the themes of isolation and loneliness while using dark humor and a satirical voice as an undercurrent to move the narratives. Isolation and loneliness intrigue me, because they are triggered and motivated by contradictory emotions inside of us. Fear, love, hate, and even nonchalant attitude and happiness can all mix to make us feel isolated even when we are not alone. People can be isolated when surrounded by others at a dinner table, or in a crowed bar, or even a small office filled with co-workers. Loneliness is …

Crafting Autonomy: A Reevaluation Of The Pedestal In The Sculpture Of Arlene Shechet, Nicole Cherubini, And Francesca Dimattio, Sara Morris Morris

Master's Theses

New York-based contemporary artists Arlene Shechet, Nicole Cherubini, and Francesca DiMattio have each developed a sculptural style that integrates the pedestal within their sculptures. Primarily made from clay, unconventional craft materials, and commonplace objects, these sculptures formally and conceptually blur the lines between craft and fine art, décor and sculpture, as well as private and institutional space. With a renewed interest in craft and feminism, these artists test the material hierarchies that have historically determined the categorization of art inside institutional spaces. This study investigates how these sculptures gain autonomy when exhibited inside museums in light of contemporary theories on …

Taxonomic Revision Of The Short Nose Chimaeras (Genus Hydrolagus) From The Southern African Region, Kristin Walovich

Master's Theses

Short-nose chimaeras are an enigmatic and understudied group of deep-sea Chondrichthyan fishes. To resolve decades of confusion and misidentification in the southern African region, morphometric and genetic data were utilized to resolve taxonomic confusion for the genus Hydrolagus. Nearly 100 chimaeroid specimens were examined from numerous national and international museum ichthyology collections. A series of 96 measurements per specimen were recorded and analyzed with multivariate statistics to determine differences among species. Tissue was collected from various southern African species for analysis of the mitochondrial gene NADH2. The resulting genetic information was compared to morphologically similar species and those within the …

Illegal Dumping As An Indicator For Community Social Disorganization And Crime, Amory Anne Brandt

Master's Theses

Illegal dumping of household waste in and around city streets results in many negative health, economic, and environmental effects. This goal of this study was to understand the systemic causes of illegal dumping within San José, California. Illegal dump sites were identified, quantified, characterized, and mapped within urban census block groups at a range of median family income levels. Results showed that commonly dumped debris types were furniture, and garbage. The most illegal dumping occurred within census block groups with low median family incomes, high percentages of non-English speaking individuals, and high percentages of renters. Factors such as social disorganization, …

An Analysis Of The Attitudes Of Undergraduate Theology Majors Towards Members Of The Lesbian, Gay, Bisexual, And Transgender Community, Jephet Williams

Master's Theses

Problem and Purpose

Research has identified students’ attitudes towards the lesbian, gay, bisexual, and transgender community as being determined partly by the students’ understanding of gender identity, and partly by a further mixture of variables that include religiosity, gender, and ethnicity. Most of this previous research has been undertaken in either secular or non-Adventist settings. This present study examines attitudes of undergraduate theology majors at two Adventist universities in North America and the Caribbean.

Method

A Likert Scale was constructed consisting of eight questions geared to elicit attitudes across a number of areas. Sixty-three students completed the questionnaire. Participating students …