Digital Commons Network^™

Nyc Waterfronts, Pollution And Access, Guglielmo Mattioli

Capstones

This capstone is about the waterfronts of New York and their relation with access and pollution.

The city has come a long way since the 80s in terms of cleaning up open waters, rivers, and creeks. Many new promenades have been open and development spurred along the city shores. Yet too many miles of waterfront are still not accessible to the one most in need.

Jamaica Bay, Newtown Creek, and Flushing Bay are some of the most representative examples of where there is little access to the water and pollution levels are still too high. This capstone, organized in two …

The Last Gay Man On Earth -- Can The Mainstreaming Of A Culture Be Responsible For Its Demise?, Muri Assunção

Capstones

Social acceptance towards the Lesbian Gay Bisexual Transgender and Queer community (LGBTQ) has seen incredible progress in the last few decades. Less than 50 years ago, an act of rebellion against a homophobic police raid at Stonewall, a gay bar in Manhattan’s Greenwich Village, kicked off the gay liberation movement and the fight for LGBTQ rights. Today, the queer revolution has proved effective: same-sex unions in the U.S. are legally allowed, and gay parenting is socially accepted. But, at what cost? Are queer people conforming to a heteronormative way of life? Can such social advances be also responsible for the …

The Immigrants In The Central Coast Of California Need Motivation To Attend Classes And Learn English As Their Second Language, Martin Rodriguez-Juarez

Master's Projects and Capstones

This field project shows that the immigrant community that works in the fields from the Central Coast of California need the motivation to attend adult school to learn English as their second language. A six-week courses is included.

Fibroblast Growth Requires Ct10 Regulator Of Kinase (Crk) And Crk-Like (Crkl)., Taeju Park, Mateusz Koptyra, Tom Curran

Manuscripts, Articles, Book Chapters and Other Papers

CT10 regulator of kinase (Crk) and Crk-like (CrkL) are the cellular counterparts of the viral oncogene v-Crk Elevated levels of Crk and CrkL have been observed in many human cancers; inhibition of Crk and CrkL expression reduced the tumor-forming potential of cancer cell lines. Despite a close relationship between the Crk family proteins and tumorigenesis, how Crk and CrkL contribute to cell growth is unclear. We ablated endogenous Crk and CrkL from cultured fibroblasts carrying floxed alleles of Crk and CrkL by transfection with synthetic Cre mRNA (synCre). Loss of Crk and CrkL induced by synCre transfection blocked cell proliferation …

Black Minds Matter: The Academic Identity Of First Year African American Stem Students, Christa Dawn Platt

Theses and Dissertations

A national push exists to increase the number of African American students who pursue STEM majors (Baber, 2014). While African American students have high aspirations to pursue STEM disciplines, an incongruence remains between their aspirations and their attainment of STEM degrees (Archer, Dewitt, Osbourne, 2015). This work seeks to critically underscore the structural issues that impede African American students in their journey as STEM majors. These impediments have been explored as factors that influence the identity of African American students. In the spirit of Critical Race Theory, the goal of this study is to give voice to first year African …

Discharge Prospectus, Cynthia Y. Vasquez

Master's Projects and Capstones

Background and Purpose:

The goals of the project are to improve the efficiency of the discharge process, to increase bed availability, to decrease readmission rates, and to increase patient satisfaction through implementation of multidisciplinary huddles.

Methods:

The intervention of the huddle took place on a medical-surgical unit at UC Davis Medical Center in the local Sacramento area serving various Medical Services.

This was a prospective pre- and post-quality intervention by utilizing HCAPHS survey, electronic medical record, RN surveys, and discharge data collection.

Results:

Discharges were increased from 15% to 23%. Currently, data is up-to-date for nine months but the project …

Collections Management Systems At Natural History Museums: A Centralized Approach, Allison M. Pohl

Master's Projects and Capstones

Natural history museum collections are an invaluable learning tool for audiences of many ages. However, learning experiences can be hampered if collections are poorly managed. Inconsistent object numbering systems, scant information associated with a specimen, and differences in records management styles of individuals in the same organization all stem from the lack of collections management standards set forth by some institutions. Natural history museums historically manage their collections in a decentralized manner, with each collections department responsible for its own objects, managing records as the staff sees fit. This report advocates for the unification of collections in natural history museums …

A Cloud-Based Workflow To Quantify Transcript-Expression Levels In Public Cancer Compendia, P J. Tatlow, Stephen R. Piccolo

Faculty Publications

Public compendia of sequencing data are now measured in petabytes. Accordingly, it is infeasible for researchers to transfer these data to local computers. Recently, the National Cancer Institute began exploring opportunities to work with molecular data in cloud-computing environments. With this approach, it becomes possible for scientists to take their tools to the data and thereby avoid large data transfers. It also becomes feasible to scale computing resources to the needs of a given analysis. We quantified transcript-expression levels for 12,307 RNA-Sequencing samples from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas. We used two cloud-based configurations and …

Single Particle Tracking: Analysis Techniques For Live Cell Nanoscopy., Peter K. Relich

Physics & Astronomy ETDs

Single molecule experiments are a set of experiments designed specifically to study the properties of individual molecules. It has only been in the last three decades where single molecule experiments have been applied to the life sciences; where they have been successfully implemented in systems biology for probing the behaviors of sub-cellular mechanisms. The advent and growth of super-resolution techniques in single molecule experiments has made the fundamental behaviors of light and the associated nano-probes a necessary concern among life scientists wishing to advance the state of human knowledge in biology. This dissertation disseminates some of the practices learned in …

The Effect Of Agricultural Exposures And Genetics On Respiratory Phenotypes, Lisa W. Boyd

Theses & Dissertations

Agricultural workers are at risk for respiratory diseases, such as chronic obstructive pulmonary disease (COPD) and chronic bronchitis, due to exposures and inflammatory agents found in their work environment. While previous studies have been conducted to examine agricultural effects of chronic respiratory diseases more closely, there are still several significant gaps in the existing literature.

This dissertation explores the relationship between agricultural exposures and respiratory diseases. Utilizing two populations, the Keokuk Country Rural Health Study and the AgLung Study, this research: 1) used principal factor analysis (PFA) to distill exposure data into essential variables characterizing long-term agricultural exposures in order …

Defining The Role Of Phosphorylation And Dephosphorylation In The Regulation Of Gap Junction Proteins, Hanjun Li

Theses & Dissertations

Gap junctions are intercellular channels that permit the free passage of ions, small metabolites, and signaling molecules between neighboring cells. In the diseased human heart, altered ventricular gap junction organization and connexin expression (i.e., remodeling) are key contributors to rhythm disturbances and contractile dysfunction. Connexin43 (Cx43) is the dominant gap junction protein isoform in the ventricle which is under tight regulation by serine/tyrosine phosphorylation. Phosphorylation and dephosphorylation regulate many aspects of Cx43 function including trafficking, assembly and disassembly, electrical and metabolic coupling at the plaque, as well as to modulate the interaction with other proteins.

Serine phosphorylation has long been …

Chimerscope: A Novel Alignment-Free Algorithm For Fusion Gene Prediction Using Paired-End Short Reads, You Li

Theses & Dissertations

Fusion genes are those that result from the fusion of two or more genes, and they are typically generated due to the perturbations in the genome structure in cancer cells. In turn, fusion genes can contribute to tumor formation and progression by promoting the expression of an oncogene, deregulation of a tumor-suppressor, or producing much more active abnormal proteins. More importantly, oncogenic fusion genes are specifically expressed in the tumor cells, which provide enormous diagnostic and therapeutic advantages for cancer treatment. With the development of next-generation sequencing (NGS) technology, RNA-Seq becomes increasingly popular for transcriptomic study because of its high …

Dna Polymerase Zeta-Dependent Mutagenesis: Molecular Specificity, Extent Of Error-Prone Synthesis, And The Role Of Dntp Pools, Olga V. Kochenova

Theses & Dissertations

Despite multiple DNA repair pathways, DNA lesions can escape repair and compromise normal chromosomal replication, leading to genome instability. Cells utilize specialized low-fidelity Translesion Synthesis (TLS) DNA polymerases to bypass lesions and rescue arrested replication forks. TLS is a highly conserved two-step process that involves insertion of a nucleotide opposite a lesion and extension of the resulting aberrant primer terminus. The first step can be performed by both replicative and TLS DNA polymerases and, because of non-instructive DNA lesions, often results in a nucleotide misincorporation. The second step is almost exclusively catalyzed by DNA polymerase ζ …

Role Of Cbl-Family Ubiquitin Ligases As Critical Negative Regulators Of T Cell Activation And Functions, Benjamin Goetz

Theses & Dissertations

Adaptive T cell immunity is essential for defense against foreign antigens and immune surveillance against cancer. Tight regulation of T cell activation is required to avoid autoimmunity to self-antigens or protracted inflammation after foreign antigens are cleared. Incomplete or inappropriate stimulation leads to an active shutdown of T cell activation called anergy. The Casitas B-lineage Lymphoma (CBL)-family of ubiquitin ligases (E3s) are essential negative regulators of T cell activation that impinge on thymic selection as well as anergy induction programs. Single gene studies show that CBL is critical during T cell development while CBL-B plays an essential role in peripheral …

Regulation Of Alteration/Deficiency In Activation 3 (Ada3) By Acetylation And Its Role In Cell Cycle Regulation And Oncogenesis, Shashank Srivastava

Theses & Dissertations

The ADA3 (Alteration/Deficiency in Activation 3) protein is a transcriptional adaptor protein that was initially discovered as a component of several HAT (Histone Acetyltransferase) complexes, the enzyme complex responsible for histone acetylation, which is a prerequisite for transcription. Earlier the studies from Dr. Band’s laboratory and that of others’ have deciphered a crucial role of ADA3 in cell cycle regulation (both through G₁/S and G₂/M phase transitions) and in maintaining the genomic stability.

While our laboratory investigated the mechanism behind the role of ADA3 in G₁/S transition, the same remained unknown for G_{2 …}

Amino Acid Catabolism In Staphylococcus Aureus, Cortney Halsey

Theses & Dissertations

Staphylococcus aureus must rapidly adapt to a variety of carbon and nitrogen sources during invasion of a host. Within a staphylococcal abscess, preferred carbon sources such as glucose are limiting, suggesting S. aureus survives through the catabolism of secondary carbon sources. S. aureus encodes pathways to catabolize multiple amino acids including those that generate pyruvate, 2-oxoglutarate, and oxaloacetate. To assess amino acid catabolism, S. aureus JE2 and mutants were grown in complete defined medium containing 18 amino acids but lacking glucose (CDM). A mutation in glutamate dehydrogenase (gudB), which generates 2-oxoglutarate from glutamate, abrogated growth in CDM suggesting …

Flight Of The Freshwater Fish, Michael H. Wilson

Capstones

Michael H. Wilson

Capstone Abstract

December 27, 2016

Flight of the Freshwater Fish

The Hudson River provides for millions of people as a path for commercial and private transportation, a source of food and energy, and perhaps most importantly for many living in the tri-state area as a destination for recreation and relaxation. The most overlooked feature of the river is how the wildlife shows clear signs of a changing climate and rapid environmental response to the impacts of global warming on the river.

Entire populations of fish species in the lower Hudson have been forced to leave the river …

Staphylococcus Aureus Biofilms Interfere With Macrophage Antimicrobial Responses Through Differential Gene Regulation, Toxin Production, And Purine Metabolism, Tyler D. Scherr

Theses & Dissertations

Staphylococcus aureus (S. aureus) is an opportunistic pathogen that is a leading cause of both nosocomial and community-associated infections. Armed with a myriad of virulence factors and the propensity to form a biofilm on native tissues and implanted medical devices alike, S. aureus infections represent a very real public health threat, the treatment of which results in an excessive economic burden. S. aureus biofilm infections are notoriously recalcitrant to antibiotic therapy and adept at evading and neutralizing the host immune antimicrobial response. Previous studies from our laboratory have shown that S. aureus biofilms are able to cause persistent …

Pancreatic Cancer Invasion Of The Lymphatic Vasculature And Contributions Of The Tumor Microenvironment: Roles For E-Selectin And Cxcr4, Maria M. Steele

Theses & Dissertations

As the fourth leading cause of cancer-related deaths, pancreatic cancer is one of the most lethal forms of cancers in the United States. Lymphatic vessel invasion and subsequent metastasis to the lymph nodes are early and significant events observed during pancreatic cancer progression and are used to determine patient prognosis and therapy selection. Although clinicians and researchers recognize the importance of lymph node involvement for patient prognosis and therapy selection, the biological mechanisms that govern lymphatic invasion and metastasis and the contributions of the pancreatic tumor microenvironment to these processes remain poorly understood. In this dissertation, we characterize the interactions …

Mitogen And Morphogen Signaling Dysregulation: Pathophysiological Influence In Pancreatic Cancer And Alzheimer’S Disease, Eric Cruz

Theses & Dissertations

Although the etiology of a particular disease will vary, there are genetic and epigenetic bottlenecks that frequently converge resulting in dysregulation of mitogenic and morphogenetic signaling. This propensity is acutely experienced in malignancy and neurodegenerative disease.

Here, we have first investigated the role of dysregulated signaling in the context of pancreatic cancer (PC). Morphogenetic signaling has been regarded as a pleiotropic pathway with the potential to promote and inhibit metastatic features. Our investigation of bone morphogenetic protein 2 (BMP-2), an archetypical member of the BMP superfamily, has revealed the presence of extracellular, intracellular, and long non-coding RNA products. Our findings …

The History Of Sociology Teaching In United Kingdom (Uk) Undergraduate Medical Education: An Introduction And Rallying Call!, T Collett, L Brooks, S Forrest

Peninsula Medical School

Based on a review of the literature, this article provides an introduction to the history of sociology teaching in UK undergraduate medical education. Aimed at an international community and at individuals either new to the field or with a general interest, our objectives are to situate sociology teaching in UK medical education within its broader historical and political setting, to highlight the work of past social science teachers, to draw attention to the modern day context and to ask: ‘what now’? We are particularly interested in the changing role of the sociologist in teaching medical sociology. The behavioral and social …

It’S Just Common Sense! Why Do Negative Perceptions Of Sociology Teaching In Medical Education Persist And Is There Any Change In Sight?, L Brooks, T Collett, S Forrest

Peninsula Medical School

Based on a review of the literature pertaining to sociology teaching in medical education, this paper asks why does the problem of relevance with regards to sociology teaching in medical education still persist? And is there any change in sight? The literature suggests that epistemological understandings of medicine as represented by the biomedical model are deeply entrenched with far reaching consequences for sociology teaching. Notions of the social components of medicine as ‘irrelevant’ or ‘common sense’ have over time been reinforced by students’ expectations of medicine on entering medical education; by the attitudes of clinical and biomedical staff members who …

Alternative Protein Sources In The Diet Modulate Microbiota And Functionality In The Distal Intestine Of Atlantic Salmon ( Salmo Salar ), Karina Gajardo, Alexander Jaramillo-Torres, Trond M. Kortner, Daniel L. Merrifield, John Tinsley, Anne Marie Bakke, Åshild Krogdahl

School of Biological and Marine Sciences

No abstract provided.

Gros, Jean-Germain. Healthcare Policy In Africa: Institutions And Politics From Colonialism To The Present. Lanham: Rowman & Littlefield, 2016, 283 Pp., Richard Ehui

Journal of Retracing Africa

No abstract provided.

Rights For The Ladies Of The Night: Race, Gender, And Prostitution In Sarkozy’S Domestic Security Bill, Danielle Vermazen

Historical Perspectives: Santa Clara University Undergraduate Journal of History, Series II

No abstract provided.

Contaminating Civil Rights: Revitalizing The Pathologization Of African Americans In Post World War Ii America, Christina Forst

Historical Perspectives: Santa Clara University Undergraduate Journal of History, Series II

No abstract provided.

Use Of Microplate Respirometry To Measure Respiration Of Individual Adult Coral Polyps Exposed To Deepwater Horizon Oil, Brittany A. Jensen

Open Access Theses

The Deepwater Horizon (DWH) blowout of 2010 exposed many coastal and marine ecosystems in the Gulf of Mexico (GoM) to the acute and chronic effects of crude oil. To date, no studies have investigated the toxicity of DWH oil on shallow reef-building corals despite the relative proximity of some reef sites to the DWH (Flower Garden Banks, TX) and the potential for downstream oil transport to other more distant sites (Pulley Ridge and Florida Keys, FL). In this study, we investigated the effect of acute DWH oil exposure on reef corals, both alone and in combination with elevated temperature, to …

Comprehensive Applications Of Rice Husk Biomass, Zichao Wei

Master's Theses

Rice husks (RHs) have recently attracted high attention due to their potential for many applications, including construction materials, composite materials, adsorption materials, chemical production, and power generation. RHs are an appealing alternative because of their low cost and high silica content. So far, most researchers mainly focus on the utilization of one component (such as silica) while ignoring others. Comprehensive utilization of RH biomass and diversified products are the key goals for this research field.

In this thesis, the two main components of RHs, silica and lignocellulose, were extracted from RH biomass. The high tempered calcination served as the extraction …

Developing An Educational Toolkit For Caregivers Of Six-To-Eighteen-Month-Olds Mixing Developmental Milestones And Outdoor Education, Jessica K. Hillstrom

School of Education and Leadership Student Capstone Theses and Dissertations

This capstone addressed the research question, Would the creation of an environmental, outdoor education toolkit help significantly benefit very young children reach their childhood milestone goals? It documents the creation of an educational toolkit for children aged 6 – 18 months old, which integrated age appropriate developmental milestone games and activities with outdoor themed activities. The goal was to prove that proving parents and caregivers with a toolkit for this age group of 6–18-month-old children would help make parents interested in spending more time outdoors, provide a cost-affective method for early outdoor exposure, and help parents save time by using …

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 …