Digital Commons Network^™

Rna-Protein Structure Classifiers Incorporated Into Second-Generation Statistical Potentials, Takayuki Kimura

Master's Theses

Computational modeling of RNA-protein interactions remains an important endeavor. However, exclusively all-atom approaches that model RNA-protein interactions via molecular dynamics are often problematic in their application. One possible alternative is the implementation of hierarchical approaches, first efficiently exploring configurational space with a coarse-grained representation of the RNA and protein. Subsequently, the lowest energy set of such coarse-grained models can be used as scaffolds for all-atom placements, a standard method in modeling protein 3D-structure. However, the coarse-grained modeling likely will require improved ribonucleotide-amino acid potentials as applied to coarse-grained structures. As a first step we downloaded 1,345 PDB files and clustered …

Variation In Organismic Rna And Dna Content: Analysis And Application To The Assessment Of Living Planktonic Biomass, Elizabeth Lam Gagneron

Master's Theses

Modern analysis of DNA and RNA nucleic acid sequences has yielded profound changes in our understanding of the genetic biodiversity of planktonic organisms within the microbial food web of aquatic ecosystems. However, the bulk environmental concentrations of DNA and RNA, and their relative ratios, also potentially provide important information on the biomass and metabolic activity of planktonic organisms. Currently, there is a need to quantify the relative living biomass levels of natural water contained in ships’ ballast tanks to regulate the spread of aquatic invasive species (AIS) resulting from ballast water discharge practices within the international shipping industry. Ultraviolet (UV) …

Elucidating The Role Of Mastermind-Like 1 In The Degradation Of Myocyte Enhancer Factor 2c, Azia S. Evans

Master's Theses

Mastermind-like 1 (MAML1) is well characterized for its involvement in the Notch signaling pathway where it functions as a transcriptional co-activator and facilitates the degradation of the Notch intracellular domain (NICD). MAML1 has recently been implicated as a multifunctional protein that interacts with a variety of other signaling pathways, including Wnt-β-catenin, NF-B, and MEF2C (myocyte enhancer factor 2C). MEF2C is a member of the family of transcription factors involved in muscle cell differentiation and proliferation. MAML1 has previously been shown to activate MEF2C transcription. Given that MAML1 is responsible for degradation of the NICD, we wanted to know if MAML1 …

“A (Blind) Woman's Place Is (Teaching) In The Home”: The Life Of Kate Foley, 1873-1940, Angela Gates

Master's Theses

This thesis examines the life and career of Kate Foley, home teacher of the blind with the California State Library from 1914-1940. The purpose of this investigation is to determine how Foley, who was disabled, built a successful career with the state library despite facing significant discrimination and prejudice. Using a wide variety of primary source material, including letters, library publications, conference proceedings, newspaper articles, and census data, this biography evaluates Foley’s pioneering role as well as the challenges she faced. Home teaching provided a new vocational opportunity for blind women, whose professional choices were extremely limited. Despite her unique …

Sex-Specific Diet And Rockfish Consumption In California Sea Lions (Zalophus Californianus): Insights From Molecular Scatology, Keith Michael Hernandez

Master's Theses

Molecular diet analysis has the potential to overcome the limitations of traditional methods. I used prey hard parts and molecular methods to examine sex-specific diet trends and rockfish consumption of California sea lions (Zalophus californianus, CSL). Fresh scat samples (n=219) were collected from Año Nuevo Island, CA (ANI), during the summers of 2013 and 2014. Prey taxa were identified from fish otoliths and cephalopod beaks recovered from cleaned scats. Sex of the CSL depositing the scat was assigned via multiplex PCR of a CSL microsatellite and a carnivore Y chromosome marker. Prey species also were identified using multiple loci in …

The Effects Of Repeated Global Self-Adapted Testing On Online Statistics Performance, Gita Sierra Hodell

Master's Theses

The purpose of this study was to evaluate the effectiveness of a computerized academic testing format. Centered on the motivating and stress-reducing aspects of personal control, a modified form of global self-adapted testing (GSAT) was explored to help students who are challenged by test anxiety or low academic motivation. Forty-two students completed multiple GSATs throughout one semester of college-level, online statistics. Of those students, 20 volunteered to complete an academic motivation questionnaire at the beginning of the semester. The relationships between scores on the motivation questionnaire, GSAT use characteristics, and statistics performance were analyzed. Students who used the GSATs correctly …

Mémoires: The Revolutionary Map Of The Twentieth Century, Megan Merritt

Master's Theses

The artistic collaborations between Guy Debord and Asger Jorn blossomed in 1957, and have typically been explored in terms of their context within the canon of the Situationist International (SI), a notorious group of political thinkers and activists who formed in July, 1957, with a shared repulsion for capitalism and consumerism. Before co-founding the SI with Jorn and several other individuals, Debord was part of the Lettrist International, a splinter group of the Lettrists, which allowed Debord more authority and autonomy to create his first film, Hurlements en Faveur de Sade (Howls for Sade, 1954), and explore other media that …

Geochemical Modeling And Hydrothermal Experiments Used To Constrain The Conditions Of Illite Diagenesis In Sedimentary Basins, Michael Joseph Murphy

Master's Theses

Two hydrothermal experiments were performed using sandstone core material from

the Norwegian North Sea with synthetic brines reacted at approximately 150˚C and 450

bars, temperature and pressure calculated to simulate a depth of burial of approximately 4 km. The results of the experiments were analyzed with geochemical modeling and with

chemical and petrographic analyses. Geochemical modeling with several computer

programs indicated that the experimental fluid was undersaturated with respect to K-feldspar, kaolinite, and illite, but supersaturated with respect to muscovite. Chemical

analysis with inductively-coupled plasma mass spectrometry indicated that the fluid

reached saturation with respect to K-feldspar. Petrographic analysis with …

Estuarine Habitat Use By The California Sea Otter (Enhydra Lutris Nereis), Jacqueline Kimberly Lindsey

Master's Theses

As the southern sea otter (Enhydra lutris nereis) range expands into northern and southern California, it will encounter estuaries that have been historically occupied by sea otters. Understanding how otters use re-colonized estuarine environments will inform how estuaries might be managed to encourage future sea otter range expansion. This project addressed the question: how do southern sea otters use space in the unique estuarine habitats of Elkhorn Slough? I compared the locations and behaviors of 25 individual sea otters of different status (male, female, and female with pup) among eelgrass, saltmud, saltmarsh, tidal creek, and main channel habitats in Elkhorn …

Zircon Geochemical And Isotopic Constraints On The Evolution Of The Mount Givens Pluton, Central Sierra Nevada Batholith, Callie Sendek

Master's Theses

The Late Cretaceous Mount Givens pluton, located in the central Sierra Nevada batholith, is noteworthy for its large size (~1400 km2) and relative compositional and textural homogeneity. The pluton is characterized by a 30 km wide, ellipse-shaped northern lobe (ca. 98-91 Ma) that connects with a long mass (ca. 95-91 Ma) about 15 km wide and extends 50 km SE. Zircon trace elements and d18O and eHf from a sample suite representative of the observable petrologic diversity of the pluton document significant heterogeneities. All zircons have high Ti-in-zircon model temperatures (850-1000 °C), pronounced negative Eu anomalies, and concave down MREE …

Evaluating Contradicting And Confirming Evidence: A Study On Beliefs And Motivated Reasoning, Zachary Alan Caddick

Master's Theses

The purpose of this study is to examine ideological, psychological, and demographic predictors of motivated reasoning. Three-hundred and seventy-seven participants from Amazon’s Mechanical Turk system completed written responses critically evaluating strengths and weaknesses in a vignette on the topic of anthropogenic climate change. The vignette has two fictional scientists present prototypical arguments for and against anthropogenic climate change that are constructed with equally flawed and conflicting reasoning from both view points. Written responses were coded by a team of trained and reliability assessed qualitative raters. Motivated reasoning is operationalized by providing supporting evidence for the congruent belief and counter evidence …

Sers Intensity Correlations To Lspr On Aggregated Au@Ag Systems, Caesar Alexander Munera

Master's Theses

The optimal surface enhanced Raman scattering (SERS) intensity was correlated to the localized surface plasmon resonance (LSPR) of individual and aggregated gold core/silver shell (Au@Ag) nanoparticles (NPs) in titrations involving the addition of both SERS label (e.g., rhodamine 6G, R6G) and the non-SERS active aggregant (chemical species that triggers the aggregation of NPs) potassium chloride (KCl). Titrating NP solutions with pure SERS label has often resulted in highly non-linear calibrations. In some cases, addition of non-SERS active aggregating agents such as KCl has also resulted in a large increase in SERS signals. An order of initial addition was followed in …

Comparative Evaluation Of Malnutrition Screening In Oncology Patients In An Acute Care Hospital: A Pilot Study, Chandni Sen Sinha

Master's Theses

Malnutrition is associated with negative health consequences in the vulnerable cancer population, making it imperative for an efficient interdisciplinary approach to conduct nutritional screening using an appropriate scale. For the present study, a comparison between an existing malnutrition risk-screening questionnaire (EMR-SQ) and a comprehensive screening questionnaire (CMR-SQ) was performed on 37 cancer patients. The first stage of data collection required the nurses to electronically complete the EMR-SQ. In the second stage, the same patients’ data were assessed using the CMR-SQ, developed by the authors based on the guidelines of the PG-SGA and A.S.P.E.N. The CMR-SQ identified 32.4% at low, 37.8% …

The Moderating Role Of Perceived Organizational Support And Perceived Supervisor Support On The Relationship Between Teamwork Behaviors And Affective Commitment, Carlie Ann Stephens

Master's Theses

Researchers have identified employee affective commitment as a key indicator of variables that are of great interest to organizations (Mowday, Porter, & Steers, 1982). Teamwork behaviors have been identified as predictors of affective commitment (Meyer, Stanley, Herscovitch, & Topolnytsky, 2002). However, very few studies have examined the moderating effect organizational and supervisor support may have on these relationships. The purpose of this study was to examine the moderating effects of perceived organizational support and perceived supervisor support on the relationship between teamwork behaviors and affective commitment. Results of a survey administered to 3,926 employees in a medical device company revealed …

Historical Trauma And Refugee Reception: Armenians And Syrian-Armenian Co-Ethnics, Nicole M. Campos

Master's Theses

This thesis considers the ways in which Armenian history has influenced integration of Syrian-Armenian refugees into Armenia due to the ongoing Syrian War. Ethnic Armenian outlooks were analyzed relative to the influx of Syrian refugees, particularly co-ethnic Syrian-Armenians. Field work in Armenia found a sustained cultural impression of Armenians’ Soviet membership and genocide. Findings suggest that recognizing the importance of history as it may or may not affect migration reception policies and attitudes is important to developing sustainable resettlement environments, at least until repatriation or third-country resettlement becomes an option to migrants. Ultimately, this thesis argues that more attention must …

The Eurasian Agenda: The International Relations Of Kyrgyzstan, Azamat Baiyzbekov

Master's Theses

The disintegration of the Soviet Union and the emergence of the newly independent states in Central Asia are among the most important historical events of the 20^th century. As one of these newly independent and sovereign state, Kyrgyzstan found itself in the sphere of the geopolitical rivalry among the Great Powers, such as the U.S., Russia, and China. Even though a relatively small and militarily weak state, Kyrgyzstan came to play an important role in their Eurasian agenda. In this thesis, I examine in detail the international relations of Kyrgyzstan with all its neighboring states, but focus extensively on …

Integrative Analysis Of Heterogeneous Genomics Data For Triple Negative Breast Cancer And High Grade Serous Ovarian Cancer, Abdelrahman Hosny Ibrahim

Master's Theses

The human body is made up of trillions of cells. Although all the human body cells contain the same DNA sequence inside their nuclei, each one carries out its own function. Normally, human cells grow and divide to form daughter cells as the body needs them. When cells grow old, or lose their ability to function properly, they die (in a very organized way called apoptosis or programmed cell death) and new cells take their role. Cancer is a disease that is caused by uncontrolled division of abnormal cells in some part of the body, breaking the natural process of …

Azeotrope Enabled Anionic Polymerization Of Ethylene Oxide Using Initiators With Different Functional Groups, Dronareddy Madugula

Master's Theses

Poly(ethylene oxide) (PEO) is a nonionic hydrophilic polymer having the same repeat unit as poly(ethylene glycol) (PEG). It is of interest in both biology and materials science. PEO surfaces demonstrate a unique lack of protein adhesion, and PEO block copolymers are widely used in applications such as drug delivery. Unfortunately, the synthesis of PEO homopolymers and block copolymers can be experimentally challenging, with a typical method involving air sensitive organometallics and the removal of compounds such as naphthalene from the final product. Here we report a synthetic route that avoids these difficulties by using azeotropic distillation to remove water from …

Change In Urban Fabric Through Space And Time At Differing Levels Of Automobility, Kristin A. Floberg

Master's Theses

For thousands of years cities have been centers for commerce, creativity, and livelihood, consisting of relatively unchanged characteristics such as walkable streets, diverse land-uses, and human-scaled buildings and streets. With the introduction of the automobile, this past century the desire for free-flowing traffic and convenient parking has drastically transformed the fabric of many cities. Transforming cities into places that accommodate automobiles has transformed downtowns into office parks rather than vibrant mixed-use environments and destroyed communities.

Investigation into reducing automobiles in cities has increasingly piqued the interest of stakeholders in the environmental, safety and economic development communities. This body of research …

The Acidic Sulfonimidation Of Aryl–Oxazolines And The Electrophilic Fluorination Of Aryl–Oxazolines, David Gutierrez

Master's Theses

Aryl oxazolines have been employed as directing groups for several different coupling reactions. In the exploration of using phenyl oxazoline as a directing group for electrophilic fluorination, it was discovered that acidic sulfonimide nucleophiles including dibenzenesulfonimide, o–benzenesulfonimide, dimethanesulfonimide, and N–(methylsulfonyl)–benzenesulfonamide are discovered to open a variety of alkyl, aryl and heteroaryl–2–oxazoline rings to provide the sulfonimidation products in refluxing 1,4–dioxane. The electron rich 2–oxazoline substrates worked well for the nucleophilic ring opening reactions while no reaction took place for the electron poor 2–oxazoline substrates. 4,4–dimethyl–2–phenyl–2–oxazoline was thus rationally designed inhibit sulfonimidation and to act as a removable ortho directing group …

The Inter- And Intra-Rater Reliability Of Athletic Trainers At Identifying Acl Injury Risk Factors Using The Cutting Screening Tool, Kelly Buckholz Smallbeck

Master's Theses

Background: ACL injuries are a frequently talked about injury in sports and have a multitude of negative side effects. A majority of injuries occur during single-leg cutting motions. Clinical screening tools are an effective way to identify those demonstrating more ACL injury risk factors. Recent research has created a variety of clinical screening tools to identify ACL injury risk factors, however none screen athletes during a single-leg cutting motion.

Hypothesis: A clinical screening tool using a single-leg cutting motion (the Cutting Screening Tool, or CST) will reliably identify ACL injury risk factors when used by athletic trainers.

Methods: Six currently …

The Symbiotic Green Algae, Oophila (Chlamydomonadales, Chlorophyceae): A Heterotrophic Growth Study And Taxonomic History, Nikolaus Schultz

Master's Theses

The green alga Oophila ambystomatus (Chlamydomonadales, Chlorophyceae) is

well known as the symbiotic partner of Ambystoma maculatum, the yellow-spotted

salamander. Recent molecular work has revealed phylogenetic diversity within isolates of

Oophila from New England. Here I investigate physiological properties and genetic

diversity of the algal symbionts representing different evolutionary lineages. In other

well-studied symbiotic systems involving algae, e.g., Chlorella and Hydra, algae and

lichen, or Symbiodinium and Scleractinian corals, the algal symbiont is capable of

multiple trophic modes, thus influencing its capacity as a partner. In this study I

investigated whether genetically differentiated strains of Oophila are capable of

absorbing …

Phylogenetics, Biogeography, And Climate Niche Variation Of South Pacific And Hawaiian Psychotria, Elaine Zhang

Master's Theses

Why do some species have broad geographic distributions, while other species are confined to a narrow distribution? Species age, ecological niche, or dispersal traits may help explain why some insular species are abundant and found on many islands, while others are rare and restricted to one island. In this study, I inferred a robust, time-calibrated phylogeny of the Hawaiian Psychotria, using two nuclear and eight chloroplast loci, sampling 67 individuals. I coupled my phylogenetic hypothesis with climatic data, ecological niche modeling, and morphological dispersal characteristics to explain the variation in number of islands occupied by each species. My inferred phylogeny …

Beyond The Cloth: Exploring How Women Are Represented In Human Rights Organizations Through Bangladesh's Garment Industry, Briawna Gillespie

Master's Theses

Understanding Beyond the Cloth

This thesis conducts a textual analysis of several human rights organizations. It looks at how human rights organizations represent women in the garment industry. I investigate a variety of organizations and look at how they utilize women’s voices to demonstrate how human rights organizations frame women’s narratives in a way that supports their own claims. When organizations representing women in this way, it only limits women’s voices from being heard and hinders them from being empowered and a leading force in the industry. On the one hand, we see organizations create spaces where women’s narratives are …

State Failure In Venezuela, Marcus Littman

Master's Theses

The role of the state is to provide political goods such as security and an environment conducive to economic growth. The Venezuelan state is failing to provide both security and conditions capable of producing economic growth. The government has exacerbated both by enacting failed policies. I measure the economic crisis in Venezuela based on the rates of inflation, falling foreign currency reserves, the food and medical supply shortage, falling government spending, and negative GDP growth. I measure the security crisis based on the escalating rate of kidnapping, human trafficking, drug sales, smuggling, theft, gun distribution, and homicide. In this thesis, …

"Who Am I?": The Development Of A Male Palestinian Political Identity, Tala J. Dayyat

Master's Theses

The Palestinian people have lived under numerous imperial rulers; first, the Ottoman Empire, then later the British. Today they live under the military occupation of the state of Israel as second class citizen millions more living abroad as refugees. Young Palestinian men have become the leaders and the physical manifestation of the struggle against Israel, a political Goliath that has used tactics to repress the Palestinians such as, detentions, beatings, and land confiscation, which many outside of the Israeli state deem as illegal. Scholar Rashid Khalidi states that “the quintessential Palestinian experience, which illustrates some of the most basic issues …

Long Working Hours, Happiness, And Quality Of Democracy With The Case Studies Of Japan And Denmark, Yu Namie

Master's Theses

This thesis aims to reveal the hypothesis that long working hour reduce people’s happiness and undermine democracy. For achieving this goal, this study clarifies the relationship between long working hours, happiness, and political engagement. Moreover, in order to seek the way to increase social happiness, it tries to figure out how global free market economy relates the working hours. The research method mainly relies on the fieldwork in Japan and Denmark.

First, this study succeeded to reinforce the argument that long working hour negatively influenced people’s happiness. Also, if we define the quality of democracy as the society constituted with …

Plastic Oceans: A New Way In Solving Our Plastic Pollution, Dakota S. Floyd

Master's Theses

By 2050, the world’s oceans will have more plastic than fish with potentially catastrophic consequences on sea life and the health of the ocean. Economically, countries with coastal boundaries will be heavily impacted as plastic pollution has already generated a 13 billion dollars in monetary losses. Considering that this is an extreme problem that we are currently facing the current solution is not enough in curbing our plastic pollution. While, recycling programs have been beneficial in reclaiming some plastic our mass consumption of plastic has outpaced the capabilities of recycling efforts. If we are to find a solution in our …

Islamophobia In The United States How American News Coverage And Social Media Perpetuate Fear & Hate Against Islam, Rida Kazmi

Master's Theses

In recent years, Islamophobia in the United States has risen to levels never seen before. While 2016 marks the 15-year anniversary of the 9/11 attacks, hatred and fear of Muslims and Islam has reached an all-time high instead of steadily decreasing. The rise in Islamophobia is due in large part to the news coverage that people are exposed to, with media stories on terrorist attacks often conflating Islam and violence in both subtle and other ways. Furthermore, we see that similar coverage of acts of violence committed by non-Muslims is often markedly different, both in tone and language. Through American …

Challenging Filipino Colonial Mentality With Philippine Art, Francesca V. Mateo

Master's Theses

For 350 years, the Philippines was colonized by Spain and the United States. The Philippines became a sovereign nation in 1946 yet, fifty years later, colonial teachings continue to oppress Filipinos due to their colonial mentality (CM.) CM is an internalized oppression among Filipinos in which they experience an automatic preference for anything Western—European or U.S. American—and rejection of anything Filipino. Although Filipinos show signs of a CM, there are Filipinos who are challenging CM by engaging in Philippine art. Philippine art is defined as Filipino-made visual art, literature, music, and dance intended to promote Philippine culture. This …