Digital Commons Network^™

Impacts Of Avian Predation On Juvenile Salmonids In Central California Watersheds, Danielle Frechette

Master's Theses

Central California coho salmon () are endangered and steelhead () are threatened under the U.S. Endangered Species Act. As part of local monitoring efforts, Passive Integrated Transponders (PIT tags) are used in population biology and marine survival studies of these stocks. Since 2006, PIT tags have been recovered on Año Nuevo Island (ANI), an important breeding site for several species of seabirds and marine mammals. The objective of this study was to assess magnitude and effects of avian predation on juvenile salmonids in central California. Objectives were accomplished by 1) identifying predators, timing of predation, and quantifying predation using PIT …

Ecology Of Foothill Yellow-Legged Frogs In Upper Coyote Creek, Santa Clara County, Ca, Thomas Earl Gonsolin

Master's Theses

Visual encounter surveys, mark-recapture technique, and telemetry were used investigate breeding, movement, growth, habitat preferences, and predators of foothill yellow-legged frogs on Coyote Creek in Santa Clara County, California, from March 2004 to March 2006. The main stem and tributaries were intermittent in summer in all three years. Thermal conditions for breeding initiation were alike during 2004, 2005, and 2006. Breeding occurred in the main stem on descending limbs of the hydrograph. No breeding occurred in the middle main stem reach, which is ephemeral. Breeding occurred at less than an order of magnitude greater than base flows. Typically, larger females …

Finding Duplication Events Using Genomevectorizer, Elena Kochetkova

Master's Theses

GenomeVectorizer is a software application designed to extend the functionality of GenomePixelizer, a genome-visualization tool that was developed for the Department of Plant Pathology at University of California, Davis, in 2002. GenomeVectorizer was written using XML, XSLT, and SVG technologies combined with JavaScript scripting to provide the level of flexibility, dynamism, and interactivity not supported by the TCL/TK written application (GenomePixelizer). This new visualization tool was tested with available data from the Arabidopsis NBS-LRR study, and its output was compared to the output of GenomePixelizer. The relationships drawn at the same identity value were identical.

GenomeVectorizer was successfully applied to …

In Search Of The Creative Scientific Personality, Maya Grosul

Master's Theses

This study investigates whether personality is a valid predictor of creativity in science above and beyond demographic characteristics, such as career age, gender, and scientific discipline. Creativity is an act of making something new, original, and useful. Creative achievement in science is the personal ability to generate original, useful, and adaptive scientific theories, research methods, or empirical findings. Personality characteristics can operate as valid predictors of creative achievement in science. This study surveyed 145 scientists throughout the United States. Total creativity index was computed by standardizing and summing the total number of publications, total number of citations, h-index, and Soler's …

Absence Of Keratin 8 Is Associated With Marked Colon Mast Cell Infiltration, Diana El Bezri Nasser

Master's Theses

Patients with inflammatory bowel disease (IBD) have increased numbers of numbers of intestinal mast cells (MCs). Chymases and tryptases are mast-cell-specific proteases (MCPs) that are reliable indicators of MC degranulation. The role of MCs in the pathophysiology of IBD is poorly understood, and it is unclear whether MCs play a role in patients or in experimental models of IBD. Furthermore, MCs have been characterized only in chemically induced models of colitis. In this study, we characterize MCs in inflamed colons of keratin 8 knock-out mice (K8-/-), a spontaneous model of colitis with primarily an epithelial cell defect. We used histologic, …

Reproductive Den Habitat Characterization Of American Badgers (Taxidea Taxus) In Central California, Katrina Louise Huck

Master's Theses

The American badger (Taxidea taxus) is a species of special concern in California, and, as such, conservation measures are necessary. The goal of this study was to identify potential reproductive den habitat characteristics in order to more accurately predict critical reproductive habitat in central California grasslands. A paired study design was used to examine differences between reproductive and non-reproductive sites, and logistical regression was used to analyze the variables and produce two predictive models, one with biotic factors and one with abiotic factors. Badgers in central Californian grasslands appear to rely on both biotic and abiotic factors when …

Numerical Simulation Of Capsule Dissolution In The Usp Apparatus Ii, Jasmine Han

Master's Theses

The capsule is the second most common type of drug dosage form, yet detailed research of capsule dissolution in the USP Apparatus II (a paddle dissolution apparatus that mimics the drug dissolution process in an in vivo environment) is not well reported. In this work, a mathematical model was developed that incorporates both the dissolution of the capsule shell and the slug within the capsule shell. Capsule shell dissolution was modeled with the assumption that the shell undergoes an erosion process only. The capsule slug dissolution model incorporated mass transfer principles, Markov chain theory, and the influence of hydrodynamics on …

Functionalized Silica Nanostructures For Biosensing Applications, Hector Nuno

Master's Theses

This work covers both two dimensional (2D) and three dimensional (3D) silica-based nanostructures for use in biomedical sensing applications. The first section of this study discusses the formation of 2D nanostructured surface plasmon resonance (SPR)-based biosensor substrates. The surface of these biosensors was nanostructured by adding sacrificial star polymers or block copolymers to a silicate precursor solution. Subsequent vitrification resulted in two distinct morphological patterns: random and ordered porosity. Amino groups on the surface of the biosensors enabled the installation of analyte receptors and antifouling agents such as oligo (ethylene oxide).

The second section discusses the development of 3D core-shell …

Women With Facial Disfigurements: Impact Of Media-Constructed Images Of Beauty, Sophia M. Papadopoulos

Master's Theses

WOMEN WITH FACIAL DISFIGUREMENTS: IMPACT OF MEDIA-CONSTRUCTED IMAGES OF BEAUTY

by Sophia M. Papadopoulos

The purpose of this study was to analyze whether women with congenital or acquired facial disfigurements were negatively influenced by the images of beauty found in television, magazines, newspapers, and advertisements and to determine how these images affected their overall perceptions of self. A qualitative study was conducted through in-depth telephone interviews with 25 women with various facial disfigurements. The study showed that, although media-constructed images of beauty did have some influence on the participants' overall perceptions of self, other factors such as the manner in …

In Situ Detection Of Tbx5 Expression In Developing Chick Embryonic Heart, Vaishali Agarwal

Master's Theses

The Tbx 5 gene codes for a highly conserved transcription factor containing a DNA-binding motif called the T box (or T-domain). Tbx 5 is expressed in the posterior sinoatrial segment of the heart along with the developing forelimb buds. Mutations in Tbx 5 gene are associated with Holt Oram Syndrome (HOS), which is characterized by heart septal defects and forelimb abnormalities. Tbx 5 expression was examined during various stages of heart development in chick embryos using both a double stranded digoxygenin-labeled DNA probe and a single stranded digoxygenin-labeled anti-sense RNA probe (riboprobe). Due to the presence of homology in the …

Clustering And Validation Of Microarray Data Using Consensus Clustering, Sarbinder Kallar

Master's Projects

Clustering is a popular method to glean useful information from microarray data. Unfortunately the results obtained from the common clustering algorithms are not consistent and even with multiple runs of different algorithms a further validation step is required. Due to absence of well defined class labels, and unknown number of clusters, the unsupervised learning problem of finding optimal clustering is hard. Obtaining a consensus of judiciously obtained clusterings not only provides stable results but also lends a high level of confidence in the quality of results. Several base algorithm runs are used to generate clusterings and a co-association matrix of …

Parallel Programming Recipes, Thuy C. Nguyenphuc

Master's Projects

Parallel programming has become vital for the success of commercial applications since Moore’s Law will now be used to double the processors (or cores) per chip every technology generation. The performance of applications depends on how software executions can be mapped on the multi-core chip, and how efficiently they run the cores. Currently, the increase of parallelism in software development is necessary, not only for taking advantage of multi-core capability, but also for adapting and surviving in the new silicon implementation. This project will provide the performance characteristics of parallelism for some common algorithms or computations using different parallel languages. …

Reading Habits Of Senior Secondary Students At Allahabad City, U.P., India, Devendra Kumar, M. M.A. Ansari

Library Philosophy and Practice (e-journal)

This is a report on a readership survey carried out among the senior secondary students at Allahabad City, U.P. (India). The present study explores the reading habits of senior secondary students in Allahabad City. The present study demonstrates the various aspects of reading habits like the motives of study, reading materials borrowed from library, time spent for the serious reading, use reference materials, languages of newspaper that read daily, sections of newspapers read, place of reading, and to develop some suggestions for solution of the problem. Suggestions have been given to make the service more beneficial in the school libraries.

A Comparison Of Term Clusters For Tokenized Words Collected From Controlled Vocabularies, User Keyword Searches, And Online Documents, Elaine Maytag Nowick, Daryl Travnicek, Kent M. Eskridge, Stephen Stein

Library Philosophy and Practice (e-journal)

Tokenized word terms were collected from three sources: controlled vocabulary headings, user keyword searches, and html documents all dealing with issues in water quality. Distances were calculated between word pairs using the Jacquard formula. Distances from the three sources were compared using Spearman rank correlations and clusters were calculated on distances transformed for non-normality using the SAS pseudo-centroid method. Word pair distances from controlled vocabularies were more closely correlated to keyword searches than document distances were to users’ keywords. The mean distance of controlled vocabularies was also closer to that of users. Clusters produced from the three sources were most …

Open Source Analysis Of Biomedical Figures, David Shao

Master's Projects

With a selection of biomedical literature available for open access, a natural pairing seems to be the use of open source software to automatically analyze content, in particular, the content of gures. Considering the large number of possible tools and approaches, we choose to focus on the recognition of printed characters. As the problem of optical character recognition (OCR) under rea- sonable conditions is considered to be solved, and as open source software is fully capable of isolating the location of characters and identifying most of them accurately, we instead use OCR as an application area for the relatively recent …

Habitat Conditions And Steelhead Abundance And Growth In A California Lagoon, Kristine Ann Atkinson

Master's Theses

To better understand the temporal and spatial relationships of water quality parameters, as well as steelhead (Oncorhynchus mykiss) habitat use and growth in San Gregorio Creek estuary / lagoon, water quality and steelhead at San Gregorio Creek estuary / lagoon were studied over a period of two years. During both years, there was above-average rainfall, and during the dry seasons of both years the lagoon was repeatedly artificially breached. In spite of the breaching, variations in growth and population size relative to variable sandbar dynamics were measured both within and between years. Data showed that repeated artificial breaching …

Introducing Stem Majors To The Teaching Profession Through Authentic Experiences As Tutors, Grinell Smith

Faculty Publications

Recruiting people with rich backgrounds in science, technology, engineering, and mathematics (STEM) into the teaching profession has historically been difficult and remains so today. In this bounded instrumental case study, undergraduate STEM majors were trained and placed as science and math tutors in grades 9-12, with an overarching goal of encouraging them to consider teaching as a possible career path. Several themes emerged from the tutors’ experiences as significant in their willingness to consider a career in teaching, including altruism from helping others, satisfaction from tutees’ improved academic performance, and a more nuanced understanding of the complex nature of teaching.

Undergraduate Music Student Stress And Burnout, Helen Jane Orzel

Master's Theses

Burnout is fatigue and diminished interest caused by long-term stress. It is characterized by emotional exhaustion, depersonalization, and lack of personal accomplishment. In the university music atmosphere, stress and burnout are prevalent and accepted as part of the culture. Symptoms and causes of general stress and burnout have been well researched, but much less has been presented on college musicians' burnout, let alone how to deal with it. This study examines the sources of stress, burnout, and ways of coping for undergraduate music students.

A questionnaire with both quantitative and open-ended questions was administered during the 2009 spring semester. Participants …

Computational Fluctuating Fluid Dynamics, Alejandro Garcia, J. B. Bell, S. Williams

Faculty Publications

This paper describes the extension of a recently developed numerical solver for the Landau-Lifshitz Navier-Stokes (LLNS) equations to binary mixtures in three dimensions. The LLNS equations incorporate thermal fluctuations into macroscopic hydrodynamics by using white-noise fluxes. These stochastic PDEs are more complicated in three dimensions due to the tensorial form of the correlations for the stochastic fluxes and in mixtures due to couplings of energy and concentration fluxes (e.g., Soret effect). We present various numerical tests of systems in and out of equilibrium, including time-dependent systems, and demonstrate good agreement with theoretical results and molecular simulation

Interannual Differences In The Estuarine Ghost Shrimp, Neotrypaea Californiensis, Michael Buncic

Master's Theses

The dispersal of invertebrate marine larvae can be expected to be wide ranging and show little population structure. Neotrypaea californiensis, the burrowing ghost shrimp, is found throughout the waters and coastal estuaries of the northwestern United States. Three hundred and four larval samples were used to study population diversity and structural difference occurring over the course of spawning periods from June to September in successive years (2005 and 2006). Data and genetic analysis from nucleotide sequencing of a section of the mitochondrial Cytochrome C oxidase subunit I (COI) gene suggest that ocean-borne larvae off the coast of Oregon and Washington …

Distribution, Abundance, Growth, And Habitat Use Of Steelhead In Uvas Creek, Ca, Joel Malone Casagrande

Master's Theses

Distribution, abundance, growth, and habitat use of juvenile steelhead (Onorhynchus mykiss) were studied in a central California stream under two increased summer flow reservoir release strategies. The effect of habitat quality (including longitudinal changes in flow, water temperature, canopy closure, substrate quality, and turbidity) on abundance and growth of steelhead among sites was determined. Increased stream flow extended rearing habitat and steelhead distribution downstream to reaches that previously would have been dry. Yearling or older steelhead were relatively scarce at all Uvas Creek sites. Steelhead were most abundant, but small, in the upstream half of the study reach, …

The Response Of Zigadenus Fremontii To Variation In Fire Regime, Shannon Elizabeth Dinis

Master's Theses

California's chaparral shrub communities are naturally exposed to dry-season fire. It could be reasoned that prescription burns set during the wet season by land managers would have more detrimental effects on plant regeneration than dry season fires because wet season burns are more likely to kill newly emergent seedlings and damage newly emerged leaves of mature plants. Six field sites with flowering Zigadenus fremontii, an herbaceous perennial geophyte common to chapparal and part of the post-fire bloom, were established at Henry W. Coe State Park in Nothern California. Three sites were part of the September 2007 Lick Wildfire and …

Western Pond Turtle Summer Habitat Use In A Coastal Watershed, Jae Abel

Master's Theses

Western pond turtle (Actinemys marmorata) habitat use was studied in a coastal pond, lagoon, and stream system during the summer of 1995 and 1996 at Waddell Creek, Santa Cruz County, California. Location and habitat association data were recorded for locations and sightings of radio-tagged and un-tagged turtles during the normal active season. Summary comparison of habitat associations and habitat availability provided inference of habitat preference at several habitat scales. For most of the active season the turtles were in relatively sunny aquatic habitat, in deeper, slower velocity water. In addition, the turtles were most commonly associated with exposed …

Synthesis Of A Potentially Insulin-Mimetic, Lipid-Linked Inositol Glycan, Meenakshi Goel

Master's Theses

Inositol glycans (IGs) are naturally occurring oligosaccharides that can stimulate insulin sensitive cells. Several synthetic IG analogues have been shown to activate the insulin-signaling pathway, including the stimulation of the enzyme pyruvate dehydrogenase (PDH) phosphatase that can further stimulate aerobic metabolism in cells. Cancer cells shift to anaerobic metabolism in order to escape intrinsic apoptosis (Warburg Effect). IG's ability to stimulate aerobic metabolism might provide a method to reverse the Warburg Effect and thereby induce apoptosis in the cancer cells. One specific palmitoylated IG analogue has been shown to selectively kill cancer cells while having no adverse effect on normal …

If I Could Choose: Internalized Homophobia Of The Queer Cinema Movement, James Joseph Flaherty

Master's Theses

This thesis offers a critical examination of essentialist and constructionist theories of queer identities, with emphasis on portrayals of internalized homophobia in film. The thesis examines three films released at the latter part of the first New Queer Cinema movement (1991 - 2000) - American Beauty (1999), Urbania (2000) and Velvet Goldmine (1998). Using criticisms of Queer as performativity, as theorized by Judith Butler, in addition to the works of Gregory M. Herek, Harry M. Benshoff, Jeffrey Weeks, and other theorists and academics, the thesis analyzes the use of characterization, mise-en-scene, and spatial and temporal relationships in these films as …

Flow Cytometry Of Alexandrium Catenella From Elkhorn Slough, California., Phillip Roland Hawkins

Master's Theses

This study describes the use of flow cytometry for the enumeration of the toxic marine dinoflagellate Alexandrium catenella in both estuarine samples from Elkhorn Slough, California and from sea water samples from inner Monterey Bay. Samples were subjected to a density-barrier sample enrichment technique employing percoll to separate debris from phytoplankton prior to sample fixation, labeling and analysis. Clarified, enriched preparations of phytoplankton were subjected to whole cell Fluorescent In Situ Hybridization (FISH) using a ribosomal DNA (rDNA) probe specific for the North American ribotype (NA1) of the dinoflagellate genus Alexandrium and analysis by flow cytometry. Flow cytometry was validated …

Where's My Daddy? Effects Of Fatherlessness On Women's Relational Communication, Latoya Marie Jackson

Master's Theses

The purpose of this thesis research was to understand the relationship between father absence and women's communication styles in romantic heterosexual relationships under social cognitive theory. Two studies were conducted using a multi-method research approach in order to triangulate the results. Seven fatherless women were interviewed to arrive at a better understanding of how father absence informed their romantic relational experiences. Specifically, the topics of relationship roles, self-disclosure, expression, and self-silencing in romantic relationships were examined in the interviews. Participants reflected on what growing up fatherless meant to them and whether or not this had any influence on the role …

Synthesis And Evaluation Of Silica Hydride-Based Fluorinated Stationary Phases, Kavita Vipool Prajapati

Master's Theses

Silica-based fluorinated bonded stationary phases have shown enhanced selectivity with altered elution orders for molecules differing in hydrophobicity and hydrophilicity in comparison with C8 and C18 reversed phase columns. Hence, two novel silica hydride-based fluorinated bonded phases have been synthesized using a hydrosilation

procedure to exploit fluorine-based unique selectivity for polar basic metabolites. Bonded moieties have been characterized by elemental and spectral analyses. Silica hydride-based aqueous normal phase (ANP) chromatography has retention behavior similar to normal phase chromatography, except for the use of water as a part of the binary solvent (>60 % acetonitrile : water). In ANP, a …

Trophic Interactions Among Chlorostoma Brunnea, Macrocystis Pyrifera, And Fungi, Selena Mcmillan

Master's Theses

The purpose of this study was to evaluate how one of the most abundant kelp forest herbivores in central California, the trochid snail Chlorostoma brunnea, affects the productivity and survivorship of the giant kelp Macrocystis pyrifera within central California. The effects of this turban snail species were investigated using experimental field manipulations of snail abundance on Macrocystis sporophytes and supplementary laboratory experiments. Experimental field manipulation of C. brunnea densities (0-450 snails per sporophyte) revealed an overcompensation of growth by Macrocystis in response to moderate snail densities. This finding is consistent with a terrestrial growth premise, the Grazing Optimization Hypothesis. …

Difference And Accommodation In Visigothic Gaul And Spain, Craig H. Schamp

Master's Theses

This thesis examines primary sources in fifth- and sixth-century Gaul and Spain and finds a surprising lack of concern for ethnicity. Authors in the fifth century expressed concern for the sanctity and safety of the church, their patria, and themselves, but seldom mention any issues that could be related to ethnicity. Even the Arian Christianity of the Goths seems to be of little or no concern. This changes in the middle of the sixth century, when Arian Christianity becomes an overarching issue in Visigothic history. The sources portray nearly every political concern in the second half of the sixth century …