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 …

What's Happened To France? Sundays, Socialism, And Neoliberal Modernity, Michael Vincent Metz

Master's Theses

The "Macron Law," liberalizing French Sunday shopping hours, created great controversy in the French media in the winter of 2014-15, with particular opposition coming from the political left and the religious right. The controversy seemed to symbolize deeper issues for French society, appearing to some as a watershed, to others a threat. Some citizens expressed concern that the “European way of life" was disappearing, being replaced by a more materialist, consumerist, extreme capitalist economic model that posed an overt threat to the traditional social protection system. Were these fears real or only imagined? To an observer, shops open on Sundays …

Trail Vision: Utilizing Leopold As Environmental Equipment For Living, Kendall Elizabeth Barrett

Master's Theses

Hiking trails are one of the major ways citizens make observations about the natural world. An analysis of trail maintenance texts demonstrates a focus on concealment and camouflage of human construction and upkeep in National Scenic Trails. These practices are detrimental to environmentalism, since the resulting ideology frames nature as overly self-sufficient and not in need of human stewardship. Trail maintenance practices are analyzed in reference to the nature/culture dichotomy. Perceptions of nature’s self-healing ability are analyzed through a comparison of the oil spills in Santa Barbara during 1969 and 2015. An alternative approach is found through Aldo Leopold. Leopold …

Silicon Revolution: Sustainability Disclosures And Performance In The Semiconductor Manufacturing Industry (2010-2014), Swarali Bhat

Master's Theses

This exploratory work investigates the sustainability performance and reporting practices in 20 semiconductor companies from 2010-2014 using content analysis, survey, and interview methods. The sample consists of companies that are either integrated chip manufacturers (ICMs) or semiconductor foundries with annual net revenue of $0.2 billion to $55.9 billion. A sustainability matrix based on the Global Reporting Initiative guidelines assesses the reporting completeness. Sustainability performance is measured based on two factors, identification of trends in social and environmental data and adoption of 28 sustainability best practices specific to this manufacturing sector. The majority of the resource use and emissions data followed …

Mindfulness Modulated Attention With Neurofeedback In Multiple Object Tracking, Jennifer M. Brennan

Master's Theses

Attention determines what we selectively perceive out of all available stimuli. The multiple-object tracking paradigm is a way of examining divided attention for object tracking in a complex visual scene. Mindfulness is a broad term for a set of diverse and specific methods for distinct attentional engagement and is one technique for increasing visual attentional ability and decreasing distractibility. Neurofeedback can be a way of enhancing mindfulness training for novice participants. This study examined the relationship between attention and mindfulness with neurofeedback through performance on a multiple-object tracking task and the Five Facet Mindfulness Questionnaire. We examined the effectiveness of …

Dynamics And Control Of A Suspended Atn Vehicle, Wade Patterson Brown

Master's Theses

In order to enhance the research into Automation Transit Network (ATN) systems

performed by the Spartan Superway team, a simulation environment and controller is

developed for a suspended ATN vehicle. The equations of motion are derived for a

suspended ATN vehicle constrained to move on a circular guideway (referred to as the

Planar System) and for an ATN vehicle constrained to move on a guideway of arbitrary

geometry (referred to as the General System). Additionally, a controller using feedback

linearization is designed that tracks the position of the ATN for a conditioned displacement

profile and minimizes the lateral acceleration experienced …

Achieving Higher Academic Performance: Access At The Intersections Of Culturally Diverse Populations In Higher Education On-Campus Communities, Koryn Calee Dillard

Master's Theses

San José State University students living in the residence halls were sent a questionnaire via Google Docs. Students were requested to complete the questions about their experiences and knowledge of the campus community. This study focuses on feelings of acceptance, expression, resources, living circumstances, and behaviors of the racially/ethnically diverse students living on campus that urges them to success in the field of higher education. A total of 66 students living on campus completed the survey. The findings indicated that the on-campus Latina/Latino/Hispanic American students struggled more with their academics and had a significantly lower grade point averages than their …

Debris Flow Fans In Yosemite Valley National Park, California, Evan Scott Enriquez

Master's Theses

Formation of debris flow fans poses a potential hazard to the infrastructure and inhabitants of Yosemite Valley. Research was conducted on debris flow fans at three field sites in Yosemite Valley: Indian Creek, Eagle Creek, and Sentinel Creek. The study utilized a Trimble Pro XR Differential Global Positioning System (DGPS), Cosmogenic Berellium-10 (10Be) dating, and debris flow volume measurements to better understand the spatial distribution, age, and magnitude of prehistoric debris flow deposits at each field site. It is hypothesized that all three fans were constructed quickly after the last glacial maximum (LGM), which is dated at 19.8 ka. It …

The Role Of Psychological States In Predicting Work Engagement: A Test Of Kahn's Model, Taylor Gatti

Master's Theses

Researchers have consistently found engagement to be linked to positive individual and organizational outcomes such as job satisfaction, job performance, customer satisfaction, and productivity. Although task characteristics, transformational leadership, and core self-evaluations have been found to be important determinants of engagement, the mechanisms of why they are related to engagement are not well understood. Kahn (1990) argues that individuals become engaged through three psychological states: meaningfulness, safety, and availability. Using Kahn’s theory, the present study was conducted to test whether task characteristics, transformational leadership, and core self-evaluations were related to engagement through its respective psychological state. Data were collected from …

Psychopathology And Creativity Among Creative And Non-Creative Professions, Victor Kwan

Master's Theses

The mad genius debate has been a topic that has been discussed in both popular culture and academic discourse. The current study sought to replicate previous findings that linked psychopathology to creativity. A total of 165 biographies of eminent professionals (artists, scientists, athletes) were rated on 19 mental disorders using a three point scale of not present (0), probable (1), and present (2) for potential symptoms. Athletes served as an eminent but not creative comparison group in order to discern whether fame, independent of creativity, was associated with psychopathology. Comparison of proportion analyses were conducted to identify differences of proportion …

Trapped In Endoderm-1 Reveals A Novel Role For Fruitless In Drosophila Melanogaster Courtship, Peter Luu

Master's Theses

Understanding how genes can direct behaviors has been a prevailing goal of neuroscience. Courtship in D. melanogaster is a complex yet stereotyped array of behaviors established by sex-specific genetic pathways mediated by sensory inputs by the nervous system. However, much remains to be discovered about the neurobiological and molecular mechanisms that regulate this complex set of behaviors. We have identified a group of cells expressing Trapped in endoderm 1 (Tre1) in which male Fruitless proteins are required to reduce the speed of courtship initiation. Tre1 encodes a G-protein-coupled receptor required for establishment of cell polarity and cell migration and has …

The Mediating Role Of Psychological Empowerment On The Relationship Between Job And Personal Resources And Employee Engagement, Ian Mcallister

Master's Theses

Employee engagement is one of the most researched topics in the field of industrial and organizational psychology, mainly because it has been shown to be linked to many positive individual and organizational outcomes. Although past research has consistently shown that job and personal resources are related to employee engagement, little attention has been paid to understand the underlying mechanisms of such relationships. The present study hypothesized that psychological empowerment would be a mediator between job and personal resources (i.e. supervisor support, opportunities for growth, and core self-evaluations) and employee engagement. Using survey response data from 165 employees throughout several industries, …

Living Between Borders: Transnational Marriage And Us Resettlement Patterns In Sudanese Refugee Populations, Deirdre Patterson

Master's Theses

Many South Sudanese refugees who have resettled in the USA have actively sought to maintain their unique cultural identity while simultaneously working to integrate into American society through the pursuit of formal higher education and successful careers. One of the most interesting developments within this population is the establishment and maintenance of transna- tional families. The process for marriage is economically tiresome and, due to strict immigration policies, often compels family members to live transnational lives. Systems of transnational mar- riage—often arranged by families—and married life allow Sudanese refugees living in the USA to continue important cultural practices, speak their …

Wilderness State Park Volunteers: A Qualitative Case Study Of Meaning And Sustainability, Christina A. Peterson

Master's Theses

In an increasingly urbanized world, parks, open space and wilderness areas are vitally important to human well-being. California State Parks provide people with the ability to connect with nature and engage in outdoor recreation. Moreover, these parks protect natural and cultural resources and preserve biodiversity. California State Parks are underfunded and rely on volunteers to support essential park services. The Wilderness State Park Uniformed Volunteer Program provides essential recreation, resource protection, and biodiversity services. In order to determine the elements of the volunteering experience that contribute to a strong sense of volunteer identity and meaning, a qualitative case study was …

Uncovering “New Man” Feminism: Arthur F. Mathews At The San Francisco School Of Design, 1890-1896, Mary Okin

Master's Theses

This thesis presents the first feminist reading of Arthur F. Mathews (1860-1945), a once celebrated academic painter, life-drawing instructor, and arts administrator in San Francisco. Using a case study approach, it contributes original research to existing scholarship on Mathews, as well as the history of art education, the rise of women artists, and male feminism in the United States. By synthesizing primary sources from the 1890s related to Arthur and Lucia Mathews, the Académie Julian, the San Francisco School of Design, the San Francisco Sketch Club, and the San Francisco Commission for the Suppression of Vice, it presents new insights …

Experiments With And Implementation Of A Context Sensitive Text Summarizer, Charles Joseph Bocage

Master's Theses

Automatic text summarization is the ability to obtain key ideas from a text passage using as few words as possible. With the increase in data on the web, manual summarization of web pages has become unfeasible, and the need for automatic text summarization has become ever greater. This project explored and implemented various parts of the automatic text summarization process for an open source search engine, Yioop. These parts included stemming, text segmentation, term frequency weighting, automatic sentence compression, and content management system detection.

In addition, experiments were conducted on different pre-existing Yioop summarizers. These results served as a baseline …

Stakeholder Engagement In Marine Protected Area Network Planning In Southern California: Understanding Fishing, Government, And Environmental Perspectives, Nicole Catalano

Master's Theses

This study focuses on the MPA network planning process associated with California’s Marine Life Protection Act (MLPA) in southern California, occurring between 2008-2009. This case study demonstrates the ongoing complexity of MPA planning efforts in balancing social and science goals and reinforces the view that public participation alone may not be sufficient in achieving the type of stakeholder support needed for successful MPA implementation. Using a qualitative approach, this research draws upon the field of public participation to examine the efficacy of the planning process from the perspectives of fishing, government, and environmental stakeholders. Findings reveal significant differences in perceptions …