Digital Commons Network^™

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 …

Development Of Dna Assembly And Error Correction Protocols For A Digital Microfluidic Device, Yuliya Khilko

Master's Theses

Customized production of synthetic DNA from oligonucleotides is in high demand. However, current technologies are costly and labor-intensive. A microfluidic technology can significantly decrease cost and labor. The purpose of this study was to develop a gene assembly protocol that was utilized on the Mondrian™ SP digital microfluidic device. The fragment of the human influenza virus hemagglutinin (HA) gene (339 bp) was assembled from 12 oligonucleotides by the Gibson assembly method and error corrected with CorrectASE™ enzyme twice. The samples were analyzed by Sanger sequencing to verify the final accuracy of the assembly. A complete automation of droplet generation and …

A Complete Study Of N,N’ Bis(1 Phenylpropyl) 2,6 Pyridinedicarboxamide, Victoria Y. Chang

Master's Theses

Biological systems are often chiral or involve chiral compounds, e.g. L amino acids, the neurotransmitter L epinephrine. In some cases, two enantiomers of a chiral drug will have different activities, and in extreme cases, one form is therapeutic while the other form is toxic. Therefore, the development of reliable molecular probes for biological applications and chiral sensing is an important area of study. The unique spectroscopic and coordination properties of some lanthanide ions (Ln3+) and their complexes make them suitable for use as molecular probes. Chiral ligand systems have been developed that can coordinate with lanthanide ions to form complexes …

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 …

Environmental And Climate Justice Along The Brahmaputra River In Northeast India, Costanza Rampini

Faculty Publications, Environmental Studies

The glaciers of the Himalayas are the source of all of Asia’s major rivers and are crucial to Asia’s water supply, economies, and livelihoods. The Himalayan region is uniquely vulnerable to the impacts of anthropogenic climate change, while also becoming one of the most dammed regions in the world. This case study explores the unequal distribution of the impacts of climate change and dam building along the Brahmaputra River in Northeast India. It examines how the combined impacts of these two processes negatively affect local communities and explores environmental and climate justice issues. In discussing climate change impacts and hydropower …

Exploring A School Culture And Climate Where Students Can Flourish: Using Focus Group Methodology To Capture Key Stakeholder Perceptions About School Culture And Climate In An Alternative Education High School., Michael Lee Paynter

Dissertations

This study was a qualitative action research project that involved focus groups of key stakeholders at an alternative education high school including: students, teaching staff, classified staff, supervisors, families, and collaborative partners. A semi-structured interview guide was used to discover their perceptions of a school culture and climate where students FLOURISH. The word FLOURISH is used in this research to describe the optimal experience of thriving and growing as well as an acronym that contains the elements that a literature review found to be important for such environments serving the most vulnerable student populations. This type of research is especially …

Comparing Ebooks Across Different Platforms, Providers, And Devices, Emily Chan, Susan Kendall

Faculty and Staff Publications

Health science Health science ebooks on eight different platforms eight different platforms eight different platforms were evaluated on their were evaluated on their were evaluated on their were evaluated on their ability ability ability to accommodate to accommodate to accommodate varying learning styles varying learning styles varying learning styles varying learning styles varying learning styles and needs in a responsive, a responsive, a responsive, device device -agnostic environment. These health environment. These health environment. These health environment. These health science ebooks from the San José José State University State University State University State University Library were evaluated on: Library were …

A Potential Tool For Clinicians; Evaluating A Computer-Led Dietary Assessment Method In Overweight And Obese Women During Weight Loss, Adrianne Widaman, Nancy Keim, Dustin Burnett, Beverly Miller, Megan Witbracht, Keith Widaman, Kevin Laugero

Faculty Publications

Many Americans are attempting to lose weight with the help of healthcare professionals. Clinicians can improve weight loss results by using technology. Accurate dietary assessment is crucial to effective weight loss. The aim of this study was to validate a computer-led dietary assessment method in overweight/obese women. Known dietary intake was compared to Automated Self-Administered 24-h recall (ASA24) reported intake in women (n = 45), 19–50 years, with body mass index of 27–39.9 kg/m2. Participants received nutrition education and reduced body weight by 4%–10%. Participants completed one unannounced dietary recall and their responses were compared to actual intake. Accuracy of …

Threshold Concepts And Core Competences In The Library And Information Science (Lis) Domain: Methodologies For Discovery, Virginia Tucker

Faculty Publications

Researchers have used a variety of methodologies for investigating threshold concepts, and this paper considers these approaches for library and information science (LIS) domains. The focus is on specific benefits of constructivist grounded theory for eliciting evidence of core knowledge, and elements of research design for this purpose are discussed, including the importance of collecting experiences from the learners themselves as well as effective protocols for data gathering and analysis through the use of active tasks and semi-structured interviews. The discussion extends to implications of the research design for how it may be applied to thematic analysis more broadly and …

Modeling Information Seeking Behavior Of Scholarly Community, Mudasir Khazer Rather, Shabir Ahmad Ganaie

Library Philosophy and Practice (e-journal)

Abstract

Purpose: A number of models have been designed from time to time globally by various authors and researchers relevant to information needs and seeking behavior of users in various academic institutions. The paper explores, introduces and discusses various information seeking models and explains various elements of each model with an aim to design a model showing the information seeking behavior of Research Scholars in Universities of Kashmir.

Design/methodology/approach: Various online resources like database, research articles and other web tools were accessed to retrieve relevant information related to the select models. To explore the information seeking behavior of Research …

Literature Growth And Development Of “Earthworm”: A Bibliometric Analysis, A. Vanitha, M. Mani, Dr. A. Thirumagal

Library Philosophy and Practice (e-journal)

An earthworm is a soil living organism and seems in soil. It helps to make the soil more nutritious and used as an organic fertilizer. So earthworms are called as best partner for the soil and the farmer. This research is concentrated on earthworm analysis. The records are collected from web of science database for the period of 2007 - 2016. Total number of publications collected for this study was 3939. Composting with worms is called as vermicomposting. It is a good way to dispose all organic wastes, such as vegetable and fruit peelings. By the vermicomposting, the wastes are …

Bibliometric Analysis Of Research Literature On Piper Betle, Dr. A. Thirumagal, A. Vanitha, M. Mani

Library Philosophy and Practice (e-journal)

Betel leaf plays an important role in ancient civilization. Chewing betel leaves with areca nut was pointed out in the pre-historic books. In 13^th century, Marco Polo mentioned about the betel chewing among kings and nobles in India. Betel and areca nut plays an important role in Indian Culture, especially among Hindus. On that basis of idea the keyword of “Piper betle” or betel was collected from the Web of Science. This study is limited for the period 1997- 2016 with Bibexcel and Pajek tool. Scientists are so much interested to publish the research immediately in the journal article. …

Predictors Of Information Retrieval Effectiveness Among Library And Information Science Undergraduates In Kwara State Universities, Adeyinka Tella

Library Philosophy and Practice (e-journal)

In this information age, it is observed that, as the quantity of information grows the ability of individuals to search and retrieve the needed information decreases in a dramatically manner, which implies that our information retrieval activity lacks effectiveness. It assumed that some factors should be responsible; however, there is no empirical evidence that predict or determine information retrieval effectiveness. This study examined predictors of information retrieval effectiveness among Library and Information Science (LIS) undergraduate students in universities in Kwara State, Nigeria; considered correlation among the predictors of information retrieval effectiveness, identify the best predictive factor of information retrieval effectiveness, …

Evolutionary Dynamics Of Tree Invasions: Complementing The Unified Framework For Biological Invasions, Rafael D. Zenni, Ian A. Dickie, Michael J. Wingfield, Heidi Hirsch, Casparus J. Crous, Laura A. Meyerson, Treena I. Burgess, Thalita G. Zimmermann, Metha M. Klock, Evan Siemann, Alexandra Erfmeier, Roxana Aragon, Lia Montti, Johannes J. Le Roux

Faculty Publications, Environmental Studies

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary …

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 …

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 …

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 …

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 …

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 …

Expansion Of The Molecular And Morphological Diversity Of Acanthamoebidae (Centramoebida, Amoebozoa) And Identification Of A Novel Life Cycle Type Within The Group, Alexander Tice, Lora Shadwick, Anna Maria Fiore-Donno, Stefen Geisen, Seungho Kang, Gabriel Schuler, Frederick Spiegel, Katherine Wilkinson, Michael Bonkowski, Kenneth Dumack, Daniel Lahr, Eckhard Voelcker, Steffen Claub, Junling Zhang, Matthew Brown

Faculty Publications, Biological Sciences

Background Acanthamoebidae is a “family” level amoebozoan group composed of the genera Acanthamoeba, Protacanthamoeba, and very recently Luapeleamoeba. This clade of amoebozoans has received considerable attention from the broader scientific community as Acanthamoeba spp. represent both model organisms and human pathogens. While the classical composition of the group (Acanthamoeba + Protacanthamoeba) has been well accepted due to the morphological and ultrastructural similarities of its members, the Acanthamoebidae has never been highly statistically supported in single gene phylogenetic reconstructions of Amoebozoa either by maximum likelihood (ML) or Bayesian analyses. Results Here we show using a phylogenomic approach that the Acanthamoebidae is …

Real-Time Online Chinese Character Recognition, Wenlong Zhang

Master's Projects

In this project, I built a web application for handwritten Chinese characters recognition in real time. This system determines a Chinese character while a user is drawing/writing it. The techniques and steps I use to build the recognition system include data preparation, preprocessing, features extraction, and classification. To increase the accuracy, two different types of neural networks ared used in the system: a multi-layer neural network and a convolutional neural network.

Deep Data Analysis On The Web, Xuanyu Liu

Master's Projects

Search engines are well known to people all over the world. People prefer to use keywords searching to open websites or retrieve information rather than type typical URLs. Therefore, collecting finite sequences of keywords that represent important concepts within a set of authors is important, in other words, we need knowledge mining. We use a simplicial concept method to speed up concept mining. Previous CS 298 project has studied this approach under Dr. Lin. This method is very fast, for example, to mine the concept, FP-growth takes 876 seconds from a database with 1257 columns 65k rows, simplicial complex only …

Stress Physiology And Weapon Integrity Of Intertidal Mantis Shrimp Under Future Ocean Conditions, Maya Devries, Summer Webb, Jenny Tu, Esther Cory, Victoria Morgan, Robert Sah, Dimitri Deheyn, Jennifer Taylor

Faculty Publications, Biological Sciences

Calcified marine organisms typically experience increased oxidative stress and changes in mineralization in response to ocean acidification and warming conditions. These effects could hinder the potency of animal weapons, such as the mantis shrimp’s raptorial appendage. The mechanical properties of this calcified weapon enable extremely powerful punches to be delivered to prey and aggressors. We examined oxidative stress and exoskeleton structure, mineral content, and mechanical properties of the raptorial appendage and the carapace under long-term ocean acidification and warming conditions. The predatory appendage had significantly higher % Mg under ocean acidification conditions, while oxidative stress levels as well as the …

Scientometric Portrait Of Mike Thelwall, Vellaichamy A, Amsan E

Library Philosophy and Practice (e-journal)

Mike Thelwall was honoured with the Derek John de Solla Price Award (2015) at his 50 years age and at 20 years of research publishing career. The first contribution of the author was in 2000 at the age of 35. His publications were analysed by year, growth of publication pattern, collaboration pattern, authorship pattern, channels of communications used and keywords etc. He had 297 publications during 2000-2015 in domains: Computer Science (237), Social Sciences (183), Decision Sciences (50), Mathematics (45), Engineering (11), Medicine(7), Agricultural and Biological Sciences (6), Biochemistry, Genetics and Molecular Biology (6), Economics, Econometrics and Finance (3), Physics …

Spartan Daily, December 6, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 147, Issue 39