Digital Commons Network^™

Numerical Simulation And First-Order Hazard Analysis Of Large Co-Seismic Tsunamis Generated In The Puerto Rico Trench: Near-Field Impact On The North Shore Of Puerto Rico And Far-Field Impact On The Us East Coast, Stephan T. Grilli, S. Dubosq, N. Pophet, Y. Pérgnon, J. T. Kirby, F. Shi

Ocean Engineering Faculty Publications

We perform numerical simulations of the coastal impact of large co-seismic tsunamis, initiated in the Puerto Rican trench, both in far-field areas along the upper US East coast (and other Caribbean islands), and in more detail in the near-field, along the Puerto Rico North Shore (PRNS). We first model a magnitude 9.1 extreme co-seismic source and then a smaller 8.7 magnitude source, which approximately correspond to 600 and 200 year return periods, respectively. In both cases, tsunami generation and propagation (both near- and far-field) are first performed in a coarse 2′ basin scale grid, with ETOPO2 bathymetry, using a fully …

Red Algae Lose Key Mitochondrial Genes In Response To Becoming Parasitic, Lillian Hancock, Lynda Goff, Christopher E. Lane

Biological Sciences Faculty Publications

Red algal parasites are unusual because the vast majority of them parasitize species with which they share a recent common ancestor. This strategy has earned them the name “adelphoparasites,” from the Greek, adelpho, meaning “kin.” Intracellular adelphoparasites are very rare in nature, yet have independently evolved hundreds of times among the floridiophyte red algae. Much is known about the life history and infection cycle of these parasites but nearly nothing in known about their genomes. We sequenced the mitochondrial genomes of the free-living Gracilariopsis andersonii and its closely related parasite Gracilariophila oryzoides to determine what effect a parasitic lifestyle has …

Shark Scavenging Behavior In The Presence Of Competition, Shannon P. Gerry, Andrea J. Scott

Biological Sciences Faculty Publications

The distribution of organisms within a community can often be determined by the degree of plasticity or degree of specialization of resource acquisition. Resource acquisition is often based on the morphology of an organism, behavior, or a combination of both. Performance tests of feeding can identify the possible interactions that allow one species to better exploit a prey item. Scavenging behaviors in the presence or absence of a competitor were investigated by quantifying prey selection in a trophic generalist, spiny dogfish Squalus acanthias, and a trophic specialist, smooth-hounds Mustelus canis, in order to determine if each shark scavenged …

Critical Oxygen Levels And Metabolic Suppression In Oceanic Oxygen Minimum Zones, Brad A. Seibel

Biological Sciences Faculty Publications

The survival of oceanic organisms in oxygen minimum zones (OMZs) depends on their total oxygen demand and the capacities for oxygen extraction and transport, anaerobic ATP production and metabolic suppression. Anaerobic metabolism and metabolic suppression are required for daytime forays into the most extreme OMZs. Critical oxygen partial pressures are, within a range, evolved to match the minimum oxygen level to which a species is exposed. This fact demands that low oxygen habitats be defined by the biological response to low oxygen rather than by some arbitrary oxygen concentration. A broad comparative analysis of oxygen tolerance facilitates the identification of …

Tracking The Oxidative Kinetics Of Carbohydrates, Amino Acids And Fatty Acids In The House Sparrow Using Exhaled 13Co2, Marshall D. Mccue, O. Sivan, Scott R. Mcwilliams, B. Pinshow

Natural Resources Science Faculty Publications

Clinicians commonly measure the ¹³CO₂ in exhaled breath samples following administration of a metabolic tracer (breath testing) to diagnose certain infections and metabolic disorders. We believe that breath testing can become a powerful tool to investigate novel questions about the influence of ecological and physiological factors on the oxidative fates of exogenous nutrients. Here we examined several predictions regarding the oxidative kinetics of specific carbohydrates, amino acids and fatty acids in a dietary generalist, the house sparrow (Passer domesticus). After administering postprandial birds with 20 mg of one of seven ¹³C-labeled tracers, we measured rates …

Emerging Vaccine Informatics, Yongqun He, Rino Rappuoli, Anne S. De Groot, Robert T. Chen

Institute for Immunology and Informatics Faculty Publications

Vaccine informatics is an emerging research area that focuses on development and applications of bioinformatics methods that can be used to facilitate every aspect of the preclinical, clinical, and postlicensure vaccine enterprises. Many immunoinformatics algorithms and resources have been developed to predict T- and B-cell immune epitopes for epitope vaccine development and protective immunity analysis. Vaccine protein candidates are predictable in silico from genome sequences using reverse vaccinology. Systematic transcriptomics and proteomics gene expression analyses facilitate rational vaccine design and identification of gene responses that are correlates of protection in vivo. Mathematical simulations have been used to model host-pathogen interactions …

Building Resilience To Coastal Disasters: An Assessment Of Social Resilience During Recovery After The Indian Ocean Tsunami In Thailand, Dawn M. Kotowicz

Open Access Dissertations

The purpose of this dissertation is to evaluate changes in social resilience to coastal disasters in the coastal community of Suk Sumran in Thailand during recovery from the Indian Ocean tsunami. Specifically, the objective of this research is to determine if there was an increase in indicators of social resilience during the two years of recovery following the disaster. The assessment included an examination of the design of a sub-set of projects implemented during the recovery effort, description of the socio-economic changes related to social resilience over the course of recovery and an exploration of the perceptions related to social …

Rhetorics Of Place And Ecological Relationships: The Rhetorical Construction Of Narragansett Bay, Matthew Ortoleva

Open Access Dissertations

As an ethnographic study of how language and rhetorical acts are used to construct, challenge, and change ecological relationships to the Narragansett Bay watershed, this dissertation argues that there are three architectonic, master discourses that dominate the discursive domain of the Narragansett Bay watershed: the discourse of science, the discourse of economics, and the discourse of spirituality. These master discourses construct and authorize particular world-views, give human agents the vocabulary to speak about the world in particular ways, and produce multiple other sub-discourses, which in turn construct different ecological relationships to Narragansett Bay and lead to particular attitudes, beliefs, and …

Lipid Bilayer-Nanoparticle Interactions In Nanotoxicology And Nanomedicine, Yanjing Chen

Open Access Dissertations

Nanoparticle (NP) interactions that may destabilize cell membranes and cause toxicity can also be used to design and control therapeutic assemblies. Fundamentally examining interactions between NPs and cell membranes is crucial to understanding NP toxicity mechanisms and the development of safe and non-toxic NP-based commercial and therapeutic applications. In this dissertation it is demonstrated that self-assembled lipid bilayers can be employed as model membranes to determine NP interact ions. First, protocols were developed for examining hydrophobic and hydrophilic NP-bilayer interactions using lipid bilayer vesicles or liposomes. Second, interactions between liposomes and NPs were characterized by examining changes in liposome structure, …

Rewriting The Script: Using Rhetorical Theory To Mitigate The Effects Of Media Violence, Lee H. Marshall

Open Access Dissertations

Statement of problem. The approach that communications researchers have taken to try to combat media violence effects is inadequate. While some promising interventions have been discovered, the complexity of reactions to media and the differences in personal characteristics of viewers make empirical studies of limited use. Rhetorical theory is a more appropriate fit for analyzing media violence. The recent work by composition scholars dealing with the role emotion plays in moving people to action suggests a promising area for the development of theory. Educators can take the lead in responding to the media research findings appropriately, not through unnecessarily restrictive …

Around, Alongside, Inside, And In-Between: The Geometries Of Performance In Contemporary U.S. Play And Film, Piotr A. Skuza

Open Access Dissertations

Divided into four consecutive chapters, The Geometries of Performance is a study of how Don DeLillo's play Valparaiso and Barry Levinson's film production Wag the Dog both demonstrate and inform readers, spectators, and viewers, through the performative nature of both sources, about the intersections of Patricia Pisters's notion of "camera consciousness" and Roy Ascott's "network consciousness": how such intersections are formed, how they emerge and operate in the contexts of modern technologies of perception, and how they affect contemporary audience. In chapter 1, "Valparaiso: Möbius Strip I or, In the Regime of Monads (Tell us everything')," I study Don DeLillo's …

Lead Exposure, Aging And Biomarkers In Alzheimer's Disease, Aderemi Dosunmu

Open Access Dissertations

Alzheimer's disease (AD) is a progressive neurodegenerative disease. To investigate AD risk factors, we reviewed epidemiologic case control studies and recent research for AD's connection to the environment. Next, we examined the number one risk factor in AD, aging. We compared and contrasted lifespan profiles of AD-associated mRNA and protein levels in monkeys and mice. The AD-related biomarkers were APP mRNA and protein; Aβ levels; specificity protein 1 (SP1); and the β-amyloid precursor cleaving enzyme (BACE1). In mice, APP and Sp1 mRNA and their protein products were elevated late in life; Aβ levels declined. In monkeys, APP, Sp1, and BACE1 …

Regulation Of Muscle Growth In Teleost Fish By Members Of The Transforming Growth Factor β Superfamily, Michael Paul Phelps

Open Access Dissertations

Little is known of the mechanisms regulating the growth and development of muscle tissue in teleost fish. Mammalian muscle growth is negatively regulated by multiple signaling proteins of the transforming growth factor β superfamily (TGF-β), including myostatin. Teleost myostatin genes have high protein sequence conservation with the mammalian myostatin gene however, the levels of myostatin expression and tissue distribution as well as the overall muscle structure of fish and mammals, differ significantly. To determine whether TGF-β signaling is required for proper muscle growth and development in fish, two strains of transgenic rainbow trout (RBT; Oncorhynchus mykiss (Walbaum)) were produced overexpressing …

Physical And Chemical Interactions Between Marine Phytoplankton And Particle-Colonizing Bacteria, Jason Robert Graff

Open Access Dissertations

It is inherently difficult to study the direct interactions between marine microbes due to the size of the organisms and microscale environments in which they exist. Recent evidence suggests that the direct associations between marine phytoplankton and particle-colonizing bacteria can influence marine microbial community succession, microalgal primary production, toxin production by marine phytoplankton, and have potential implications for human health. The goal of this dissertation was to elucidate some of the physical and chemical mechanisms that regulate microbial interactions, particularly the colonization of phytoplankton and other marine particles by bacteria. To accomplish these goals, I used a creative and multi-disciplinary …

Taking Stock Of The Warehouse Cooperative School: A Personal Inventory Of The Formation Of Adolescent Subjectivity In The Context Of 1970s Alternative Education, Theo Greenblatt

Open Access Dissertations

Constructed according the conventions of a subgenre the author defines as "formation text," this creative non-fiction work is an experiment in form that addresses the experimental coming of age of a subject within an experimental era and within the more specific context of an experimental education. Playing off the name of a school the author attended in the 1970s, The Warehouse Cooperative School, its structure employs a series of lists, both organizationally--as a textual version of inventorying, and as metaphor for storage and retrieval of memory. As an overt challenge to the bildungsroman, and its unacknowledged influence on contemporary memoir, …

Experimental Study Of Organocatalyzed Homodimerization Reactions Of α,β-Unsaturated Enones, Vanina Valeria Guidi

Open Access Dissertations

This Thesis intends to elucidate the mechanism involved in a self condensation (Homodimerization) transformation of α, β-unsaturated ketones through the formation of a key enamine intermediate that arises as a consequence of the presence of an organocatalyst. The organocatyst utilized in this research is L-Proline, a natural occurring aminoacid. While the mechanism of the L-Proline organocatalyzed self-condensation reaction of α, β-unsaturated enals appears to proceed through an imine addition mechanism (Double Michael Addition), the analogous reaction pathway for Homodimerization of α, β-unsaturated enones has been postulated to proceed via a Diels-Alder reaction. This Thesis work is significant as the elucidation …

Seasonal Movement Of The American Horseshoe Crab Limulus Polyphemus In A Semi-Enclosed Bay On Cape Cod, Massachusetts (Usa) As Determined By Acoustic Telemetry, Mary-Jane James-Pirri

Graduate School of Oceanography Faculty Publications

American horseshoe crabs Limulus polyphemus were tracked using acoustic telemetry and traditional tagging in a semi-enclosed bay on Cape Cod (Pleasant Bay), Massachusetts, USA, to determine seasonal movement patterns. Fifty-five actively spawning females were fitted with transmitters in 2008 and 2009 and were tracked using acoustic telemetry from May 2008 through July 2010. Fifteen crabs with transmitters also had archive depth-temperature tags attached. In addition, over 2000 spawning crabs (males and females) were tagged with US Fish and Wildlife (USFWS) button tags over the same period. Ninety-one percent of the crabs with transmitters were detected during this study. In the …

Whose Identity Is It Anyway? A Study Of The Media's Representation Of Iraq Citizens And Their Culture, Joyce L'Heureux

Open Access Master's Theses

What happens to our perceptions when provided with an invitation by news media, specifically print media, to accept what is presented as reality? Does what we read in the news media constrict our thinking and create an acceptance of the words as they are written, a type of cultural blindness to the qualities, the humanness and individuality of other cultures? Or, do we read the words on the paper and open our lens to create a greater understanding of individuals who differ from us in values, attitudes and beliefs? The truth is the same stories which provide us with an …

In-Situ Feeding In The Northern Krill, Meganyctiphanes Norvegica: A Dna Analysis Of Gut Contents, Alison Cleary

Open Access Master's Theses

The northern krill, Meganyctiphanes norvegica, is an important member of North Atlantic shelf ecosystems, serving both as prey for whales, fish and seabirds, and as a predator on phytoplankton and other zooplankton. However, understanding in-situ krill feeding is technically challenging; incubations may not be representative of krill feeding in-situ, while biomarkers and microscopic examination of gut contents suffer from limited prey type resolution and have a limited range of detectible prey. Analyzing DNA in gut contents may offer insight into M norvegica feeding in-situ unobtainable using other methodologies. The major technical difficulty in using DNA as a marker …

Reference Database Usage Statistics 2008-2009

Technical Services Reports and Statistics

Statistics on the use of online reference databases at the University of Rhode Island during the period from July 2008 through June 2009. Includes COUNTER-compliant data on sessions, searches, turnaways, full text articles downloaded, cost per search, and other metrics.

Curricular Affairs Committee Minutes November 23, 2009, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Extensive Conserved Synteny Of Genes Between The Karyotypes Of Manduca Sexta And Bombyx Mori Revealed By Bac-Fish Mapping, Yuji Yasukochi, Makiko Tanaka-Okuyama, Fukashi Shibata, Atsuo Yoshido, Frantisek Marec, Chengcang Wu, Hongbin Zhang, Marian R. Goldsmith, Ken Sahara

Biological Sciences Faculty Publications

Background: Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes.

Methodology/Principal Findings: We isolated 214 clones …

Serials Unit Annual Report 2008-2009, Andree J. Rathemacher

Technical Services Reports and Statistics

Annual report of the Serials Unit, University Library, University of Rhode Island. Covers personnel, work flow, subscriptions, and statistics on expenditures by a number of variables.

Library Impact Statement For Afs 132 Aminal Agriculture, Food Policy And Society

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for AFS 132 Animal Agrriculture, Food Policy and Society. New course was supported with no need for additional resources. Responding library faculty member: Andrée J. Rathemacher. Requesting faculty member: Professor Michael A. Rice.

Serials Solutions Click-Through Statistics By Provider And Database 2008-2009

Technical Services Reports and Statistics

Statistics on the total number of database and journal-level clicks, by provider and database, of Serials Solutions tools at the University of Rhode Island Libraries by month for 2008-2009. Clicks may have originated from the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/), from OpenURL links ("360 Link"), or the 856 fields of Serials Solutions-generated MARC records ("360 MARC Updates").

Digitalcommons@University Of Rhode Island Statistics 2008-2009

Technical Services Reports and Statistics

Statistics on the total number of full text downloads from the DigitalCommons@University of Rhode Island institutional repository for 2008-2009. Data are provided monthly on the number of full text downloads by collection and document, and on the number of referrals by domain and country. Dissertations are included in the statistics. Digital Commons statistics are COUNTER-compliant, with downloads from robots and automated processes filtered out.

Serials Solutions Subject Search Report 2008-2009

Technical Services Reports and Statistics

Statistics on the total number of Serials Solutions subject searches at the University of Rhode Island Libraries by month for 2008-2009. Shows how many times the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/) was browsed by specific subjects.

Secret Identities: Graphic Literature And The Jewish-American Experience, Brian Klotz

Senior Honors Projects

During the 1930’s and 40’s, rampant anti-Semitism prevented many Jewish-Americans from getting hired to a respectable job in publishing. Around this same time, an industry sprang up around the idea that comic strips (which had previously been confined solely to the pages of newspapers) could be printed in pamphlet form and sold on newsstands for profit. These “comic books,” while commercially successful, were considered the lowest rung on the ladder of artistic respectability, a trashy medium for children and borderline illiterates. This attitude, however, allowed it to become a field into which young Jewish-American artists and writers were not barred …

War And Video Games, Nicholas A. Perry

Senior Honors Projects

War has been a subject of many different mediums. Through the portrayal of war, great movies have given insights on human conditions in wartime. War has also been the subject of several video games that are incredibly popular in mass culture. The difference between war movies and war games are that war games are interactive, requiring the players to act out violence in a digital form whereas movies are passive and reiterative in outcome.

There have been many criticisms of war video games ranging from their ability to condition players to violence to their role as propaganda for recruitment, but …

Starring Mark Twain And Hank Morgan: Performance In A Connecticut Yankee, Lisa Mcgunigal

Senior Honors Projects

Samuel Clemens, in his persona of Mark Twain, is recognized as one of the preeminent performers of the nineteenth century both on stage and in print. Twain clearly reveals his views on performance in his book, A Connecticut Yankee in King Arthur’s Court. In reviewing the text of the novel, I have examined the aspects and forms of performance Twain disclosed in relation to his characters. I have focused on: importance of dialect, power of costume changes, and the significance of settings.

A Connecticut Yankee (1889) describes the journeys of Hank Morgan, a time traveler from nineteenth-century Connecticut, into sixth-century …