Digital Commons Network^™

Development And Validation Of Immunoinformatics Tools For Swine Vaccine Development, Andres H. Guiérrez Núñez

Open Access Dissertations

Immunoinformatics tools have multiple applications in human immunology research. One of their most prominent applications is the prediction of T cell epitopes to accelerate vaccine development. T cell epitopes are short peptides derived from pathogens that are recognized by the cells of the immune system (T cells) when presented on the surface of cells bound to a major histocompatibility complex (MHC) molecule, which results in a specific immune response. For their role as key drivers of the immune response, numerous algorithms have been developed to predict binding of peptides to MHC molecules; however, comparable tools are limited for other species. …

The Business Case For Expanded Clozapine Utilization, Jessica L. Gören, J. Rose, Eric G. Smith, John P. Ney

Pharmacy Practice and Clinical Research Faculty Publications

Objective:

In most settings, less than 25% of patients with treatment-resistant schizophrenia receive clozapine, the only medication proven effective for treatment-resistant schizophrenia. Therefore, a business case analysis was conducted to assess whether increasing clozapine utilization for treatment-resistant schizophrenia in a health care system would result in direct health care cost savings.

Methods:

Veterans with treatment-resistant schizophrenia who were treated in the Veterans Health Administration (VHA) were studied. Treatment response, suicides, adverse drug reactions (and associated mortality), and effects on inpatient hospitalization related to clozapine were derived from a systematic review of published studies. A one-factor sensitivity analysis and …

Modeling Nitrogen Losses In Conventional And Advanced Soil-Based Onsite Wastewater Treatment Systems Under Current And Changing Climate Conditions, Ivan Morales, Jennifer Cooper, José A. Amador, Thomas B. Boving

Civil & Environmental Engineering Faculty Publications

Most of the non-point source nitrogen (N) load in rural areas is attributed to onsite wastewater treatment systems (OWTS). Nitrogen compounds cause eutrophication, depleting the oxygen in marine ecosystems. OWTS rely on physical, chemical and biological soil processes to treat wastewater and these processes may be affected by climate change. We simulated the fate and transport of N in different types of OWTS drainfields, or soil treatment areas (STA) under current and changing climate scenarios, using 2D/3D HYDRUS software. Experimental data from a mesocosm-scale study, including soil moisture content, and total N, ammonium (NH₄⁺) and nitrate (NO …

Agonistic Behavior And Costs Of Aggression In Decapod Crustaceans, Niels-Viggo Schou Hobbs

Open Access Dissertations

Animals that engage in aggressive behavior necessarily incur some costs (e.g., energy expenditure) and risk much greater costs (e.g., injury), both of which are presumably weighed against the potential benefits (e.g., refuge, food, or mates). Such costs and benefits directly impact their distribution, life history, and fitness, so an understanding of the role aggression plays is crucial to a complete understanding of a species’ ecological niche. The research presented here evaluates the degree to which aggression has ecological and life history consequences, using several species of co-occurring crabs as models in a combination of laboratory and field experiments. Specifically, we …

Effects Of Hiv Behavioral Interventions For Men Who Have Sex With Men - United States, 1988-2014, H. Elsa Larson

Open Access Dissertations

Men who have sex with men (MSM) in the United States continue to experience disproportionate HIV disease burden. Historically, most HIV prevention research has focused on reducing sexual risk behaviors through individual-level behavior change interventions. To date, behavioral interventions have not reduced HIV incidence among MSM and combination prevention approaches that package behavioral interventions with additive biomedical or structural interventions are now recommended. The last meta-analysis of HIV behavioral interventions for MSM was conducted in 2008. Since then sixteen new rigorous trials have been identified. New evidence and new recommendations justify an updated meta-analysis to identify the most promising and …

Research Into Computer Hardware Acceleration Of Data Reduction And Svms, Jason Kane

Open Access Dissertations

Yearly increases in computer performance have diminished as of late, mostly due to the inability of transistors, the building blocks of computers, to deliver the same rate of performance seen in the 1980’s and 90’s. Shifting away from traditional CPU design, accelerator architectures have been shown to offer a potentially untapped solution. These architectures implement unique, custom hardware to increase the speed of certain tasking, such as graphics processing. The studies undertaken for this dissertation examine the ability of unique accelerator hardware to provide improved power and speed performance over traditional means, with an emphasis on classification tasking.

In the …

A Vulnerability Assessment Of Fish And Invertebrates To Climate Change On The Northeast U.S. Continental Shelf, Jonathan A. Hare, Wendy E. Morrison, Mark W. Nelson, Megan M. Stachura, Eric J. Teeters, Roger B. Griffs, Michael A. Alexander, James D. Scott, Larry Alade, Richard J. Bell, Antonie S. Chute, Kiersten L. Curti, Tobey H. Curtis, Daniel Kircheis, John F. Kocik, Sean M. Lucey, Camilla T. Mccandless, Lisa M. Milke, David E. Richardson, Eric Robillard, Harvey J. Walsh, M. Connor Mcmanus, Katrin E. Marancik, Carolyn A. Grisworld

Graduate School of Oceanography Faculty Publications

Climate change and decadal variability are impacting marine fish and invertebrate species worldwide and these impacts will continue for the foreseeable future. Quantitative approaches have been developed to examine climate impacts on productivity, abundance, and distribution of various marine fish and invertebrate species. However, it is difficult to apply these approaches to large numbers of species owing to the lack of mechanistic understanding sufficient for quantitative analyses, as well as the lack of scientific infrastructure to support these more detailed studies. Vulnerability assessments provide a framework for evaluating climate impacts over a broad range of species with existing information. These …

Phytoplankton Size Impact On Export Flux In The Global Ocean, Colleen B. Mouw, Audrey Barnett, Galen A. Mckinley, Lucas Gloege, Darren Pilcher

Graduate School of Oceanography Faculty Publications

Efficiency of the biological pump of carbon to the deep ocean depends largely on biologically mediated export of carbon from the surface ocean and its remineralization with depth. Global satellite studies have primarily focused on chlorophyll concentration and net primary production (NPP) to understand the role of phytoplankton in these processes. Recent satellite retrievals of phytoplankton composition now allow for the size of phytoplankton cells to be considered. Here we improve understanding of phytoplankton size structure impacts on particle export, remineralization, and transfer. A global compilation of particulate organic carbon (POC) flux estimated from sediment traps and ²³⁴Th are …

Environmental Change Explains Cichlid Adaptive Radiation At Lake Malawi Over The Past 1.2 Million Years, Sarah J. Ivory, Margaret W. Blome, John W. King, Michael M. Mcglue, Julia E. Cole, Andrew S. Cohen

Graduate School of Oceanography Faculty Publications

Long paleoecological records are critical for understanding evolutionary responses to environmental forcing and unparalleled tools for elucidating the mechanisms that lead to the development of regions of high biodiversity. We use a 1.2-My record from Lake Malawi, a textbook example of biological diversification, to document how climate and tectonics have driven ecosystem and evolutionary dynamics. Before ∼800 ka, Lake Malawi was much shallower than today, with higher frequency but much lower amplitude water-level and oxygenation changes. Since ∼800 ka, the lake has experienced much larger environmental fluctuations, best explained by a punctuated, tectonically driven rise in its outlet location and …

Atmosphere‐Ocean Linkages In The Eastern Equatorial Pacific Over The Early Pleistocene, Patricia Povea, Isabel Cacho, Ana Moreno, Leopoldo D. Pena, Melisa Menéndez, Eva Calvo, Miquel Canals, Rebecca S. Robinson, Fernando J. Méndez, Jose-Abel Flores

Graduate School of Oceanography Faculty Publications

Here we present a new set of high‐resolution early Pleistocene records from the eastern equatorial Pacific (EEP). Sediment composition from Ocean Drilling Program Sites 1240 and 1238 is used to reconstruct past changes in the atmosphere‐ocean system. Particularly remarkable is the presence of laminated diatom oozes (LDOs) during glacial periods between 1.85 and 2.25 Ma coinciding with high fluxes of opal and total organic carbon. Relatively low lithic particles (coarse and poorly sorted) and iron fluxes during these glacial periods indicate that the increased diatom productivity did not result from dust‐stimulated fertilization events. We argue that glacial fertilization occurred through …

Co2 And Fire Influence Tropical Ecosystem Stability In Response To Climate Change, Timothy M. Shanahan, Konrad A. Hughen, Nicholas P. Mckay, Jonathan T. Overpeck, Christopher A. Scholz, William D. Gosling, Charlotte S. Miller, John S. Peck, John W. King, Clifford W. Heil

Graduate School of Oceanography Faculty Publications

Interactions between climate, fire and CO₂ are believed to play a crucial role in controlling the distributions of tropical woodlands and savannas, but our understanding of these processes is limited by the paucity of data from undisturbed tropical ecosystems. Here we use a 28,000-year integrated record of vegetation, climate and fire from West Africa to examine the role of these interactions on tropical ecosystem stability. We find that increased aridity between 28–15 kyr B.P. led to the widespread expansion of tropical grasslands, but that frequent fires and low CO₂ played a crucial role in stabilizing these ecosystems, even …

Estimates Of Eddy Heat Flux Crossing The Antarctic Circumpolar Current From Observations In Drake Passage, D. Randolph Watts, Karen L. Tracey, Kathleen A. Donohue, Teresa K. Chereskin

Graduate School of Oceanography Faculty Publications

The 4-yr measurements by current- and pressure-recording inverted echo sounders in Drake Passage produced statistically stable eddy heat flux estimates. Horizontal currents in the Antarctic Circumpolar Current (ACC) turn with depth when a depth-independent geostrophic current crosses the upper baroclinic zone. The dynamically important divergent component of eddy heat flux is calculated. Whereas full eddy heat fluxes differ greatly in magnitude and direction at neighboring locations within the local dynamics array (LDA), the divergent eddy heat fluxes are poleward almost everywhere. Case studies illustrate baroclinic instability events that cause meanders to grow rapidly. In the southern passage, where eddy variability …

Estimating The Recharge Properties Of The Deep Ocean Using Noble Gases And Helium Isotopes, Brice Loose, William J. Jenkins, Roisin Moriarty, Peter Brown, Loic Jullion, Alberto C. Naveiro Garabato, Sinhue Torres Valdes, Mario Hoppema, Chris Ballentine, Michael P. Meredith

Graduate School of Oceanography Faculty Publications

The distribution of noble gases and helium isotopes in the dense shelf waters of Antarctica reflects the boundary conditions near the ocean surface: air‐sea exchange, sea ice formation, and subsurface ice melt. We use a nonlinear least squares solution to determine the value of the recharge temperature and salinity, as well as the excess air injection and glacial meltwater content throughout the water column and in the precursor to Antarctic Bottom Water. The noble gas‐derived recharge temperature and salinity in the Weddell Gyre are −1.95°C and 34.95 psu near 5500 m; these cold, salty recharge values are a result of …

Winter Distribution And Size Structure Of Antarctic Krill Euphausia Superba Populations In-Shore Along The West Antarctic Peninsula, Alison C. Cleary, Edward G. Durbin, Maria C. Casas, Meng Zhou

Graduate School of Oceanography Faculty Publications

Antarctic krill Euphausia superba are a key component of food webs in the maritime West Antarctic Peninsula, and their life history is tied to the seasonal cycles of sea ice and primary production in the region. Previous work has shown a general in-shore migration of krill in winter in this region; however, the very near-shore has not often been sampled as part of these surveys. We investigated distribution, abundance, and size structure of krill in 3 fjordic bays along the peninsula, and in the adjacent Gerlache Strait area using vertically stratified MOCNESS net tows and ADCP acoustic biomass estimates. Krill …

Traits Controlling Body Size In Copepods: Separating General Constraints From Species-Specific Strategies, Neil S. Banas, Robert G. Campbell

Graduate School of Oceanography Faculty Publications

A new synthesis of laboratory measurements of food-saturated development and growth across diverse copepod taxa was conducted in a theoretical framework that distinguishes general allometric constraints on copepod physiology from contingent strategies that correlate with size for other reasons. After temperature correction, the allometry of growth rate is inconsistent between the ontogeny of Calanus spp., where it follows the classic -0.3 power-law scaling, and a broader spectrum of adult size W_a (0.3 to 2000 µg C, Oithona spp. to Neocalanus spp.), across which the classic scaling appears to represent only an upper limit. Over the full size spectrum, after …

Temporal Variation Of Skeletonema Community Composition From A Long-Term Time Series In Narragansett Bay Identified Using High-Throughput Dna Sequencing, Kelly L. Canesi, Tatiana A. Rynearson

Graduate School of Oceanography Faculty Publications

Phytoplankton species cannot always be identified by their morphology using light microscopy, which makes inferring the ecological and biogeochemical importance of individual species a difficult task. Here, a combination of microscopy and high-throughput DNA sequencing was used to examine morphologically cryptic and pseudo-cryptic species in the diatom genus Skeletonema from the Long-Term Plankton Time Series in Narragansett Bay (NBay), where Skeletonema is ecologically important, comprising up to 99% of microplankton cells in surface waters. The 28S rDNA from mock phytoplankton communities comprising known species was amplified and sequenced using newly developed Skeletonema-specific primers. The relative abundances of species in …

Metagenomic Signatures Of Bacterial Adaptation To Life In The Phyllosphere Of A Salt-Secreting Desert Tree, Omri M. Finkel, Tom O. Delmont, Anton F. Post, Shimshon Belkin

Graduate School of Oceanography Faculty Publications

The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla …

Uri Undergraduate And Graduate Course Catalog 2016-2017, University Of Rhode Island

URI Course Catalogs Archive

This is a downloadable PDF version of the University of Rhode Island course catalog.

Emotional Reactivity Monitoring Using Electrodermal Activity Analysis In Individuals With Suicidal Behaviors, Amir Mohammad Amiri, Mohammadreza Abtahi, Anna Rabasco, Michael Armey, Kunal Mankodiya

Electrical, Computer, and Biomedical Engineering Faculty Publications

Suicide, considered as one of the leading causes of death, has not been given enough attention in order to reduce it's rate. The problem addressed in this paper is the analysis of the relation between an extra stimulus and physiological data's responses. In order to record the physiological data set from multiple subjects over many weeks, we used an acoustic startle during a Paced Auditory Serial Addition Task (PASAT) test that spontaneously leads subjects to real emotional reactivity, without any deliberate laboratory setting. Crucially, we show that, by inducing anxiety during the test, changes appear in Electrodermal activity, Electrocardiogram, Heart …

Social Media, Public Discourse And Civic Engagement In Modern China, Yinjiao Ye, Ping Xu, Mingxin Zhang

Political Science Faculty Publications

Drawing on the theoretical view of cyberspace’s role in engagement in public discourse and civic activities, the current study investigates how social media use is related to public discourse and civic engagement in mainland China. Moreover, we examine how political interest, general trust in people, and life satisfaction modify the interdependence of social media use and public discourse and civic engagement. Data analyses based on a survey of 1, 202 online Chinese show that social media use is significantly related to both public discourse and civic engagement. In addition, political interest has a consistent, strong modification on the role of …

Anthropocene Anthropology: Reconceptualizing Contemporary Global Change, Amelia Moore

Marine Affairs Faculty Publications

The Anthropocene is the scientific label given by earth scientists to the current epoch of unprecedented anthropogenic planetary change. The Anthropocene is also a political label designed to call attention to this change and evolving notions of agency and responsibility in contemporary life. This article critically explores what I call ‘the Anthropocene idea’ and the condition of ‘Anthropocene spaces’ through selected anthropological writing about recent planetary change and through analysis of current events in a specific ‘vulnerable’ location. By considering recent events in The Bahamas, I arrive at an orientation that I call simply Anthropocene anthropology. Rather than advocating for …

Relationship Of Bacterial Richness To Organic Degradation Rate And Sediment Age In Subseafloor Sediment, Emily A. Walsh, John B. Kirkpatrick, Robert Pockalny, Justine Sauvage, Arthur J. Spivack, Richard W. Murray, Mitchell L. Sogin, Steven D'Hondt

Graduate School of Oceanography Faculty Publications

Subseafloor sediment hosts a large, taxonomically rich, and metabolically diverse microbial ecosystem. However, the factors that control microbial diversity in subseafloor sediment have rarely been explored. Here, we show that bacterial richness varies with organic degradation rate and sediment age. At three open-ocean sites (in the Bering Sea and equatorial Pacific) and one continental margin site (Indian Ocean), richness decreases exponentially with increasing sediment depth. The rate of decrease in richness with increasing depth varies from site to site. The vertical succession of predominant terminal electron acceptors correlates with abundance-weighted community composition but does not drive the vertical decrease in …

Studying School Improvement Teams To Analyze Multiple Stakeholder Engagement In Decision-Making In Public Education, Julie A. Dibari

Open Access Dissertations

Since the Industrial Revolution, when schools became larger and the missions broader, there has been an attempt by a wide range of stakeholders to have a voice in public education. More recently, through No Child Left Behind and Race to the Top, the federal government began to increase requirements for multiple stakeholder engagement in decision-making for schools requesting Title I funds. As the need for a more educated workforce has grown, businesses have also sought to have a voice in improving education. Additionally, experts in the field of parent, school and community engagement, have called for the inclusion of parents, …

Does One Size Fit All? A Case For Context-Driven Null Hypothesis Statistical Testing, Grayson L. Baird, Lisa L. Harlow

Psychology Faculty Publications

Rodgers (2010a) asserted that the practice of null hypothesis statistical testing (NHST) follows a mechanistic and rule-based epistemology. This concern is addressed using historical and modern sources as evidence for NHST as a dynamic, context-driven framework for empowering researchers in scientific inquiry.

Neurocognitive Enhancement Or Impairment? A Systematic Meta-Analysis Of Prescription Stimulant Effects On Processing Speed, Decision-Making, Planning, And Cognitive Perseveration, Marissa E. Marraccini, Lisa L. Weyandt, Joseph S. Rossi, Bergljot Gyda Gudmundsdottir

Psychology Faculty Publications

Increasing numbers of adults, particularly college students, are misusing prescription stimulants primarily for cognitive/academic enhancement, so it is critical to explore whether empirical findings support neurocognitive benefits of prescription stimulants. Previous meta-analytic studies have supported small benefits from prescription stimulants for the cognitive domains of inhibitory control and memory; however, no meta-analytic studies have examined the effects on processing speed or the potential impairment on other domains of cognition, including planning, decision-making, and cognitive perseveration. Therefore, the present study conducted a meta-analysis of the available literature examining the effects of prescription stimulants on specific measures of processing speed, planning, decision-making, …

Using Smartphone Video “Selfies” To Monitor Change In Toothbrushing Behavior After A Brief Intervention: A Pilot Study, Parangimalai Diwakar Madan Kumar, Anusa Arunachalam Mohandoss, Theodore A. Walls, Thavarajah Rooban, Lance T. Vernon

Psychology Faculty Publications

Background: Attempts to refine toothbrushing (TB) technique, an ingrained habit in adults, can meet with some challenges. Recently, the role of proactive interference as a barrier to improving the learning of proper brushing has been proposed. This pilot feasibility study was designed to investigate TB behavior and to see how it changes after training. Smartphone video “selfies” (SPVSs) are increasingly being used in the medical field to assess, monitor, and determine the progression of diseases.

Materials and Methods: We used SPVS to study TB skills in a small sample of volunteers. Over a period of 14 days, after …

Nitrogen And Warming Effects On Nitrous Oxide Production Associated With Coastal Macroinvertibrates, Melanie H. Gárate

Open Access Master's Theses

Bivalve shellfish potentially reduce excess nitrogen in the water column, however they can also be involved in the emission of nitrous oxide (N₂O), a potent greenhouse gas. Environmental controls on N₂O production from bivalves have not been well quantified. We tested responses of N2O production by three bivalves (Mytilus edulis, Mercenaria mercenaria and Crassostrea virginica) to nitrogen (N) loading and/or warming after immediate (1 day) and short-term (14-28 days) exposure. This two-factor laboratory study had four treatments: (1) ammonium nitrate (N) addition (targeting 100μM-N), (2) warming (22^oC), (3) N addition + …

The Synthesis Of Rotaxane Probes For Magnetic Resonance Imaging (Mri), Scott Macgill Karas

Open Access Master's Theses

Rotaxanes are simple molecules made by an interaction between a host and a guest.¹ Research has shown that rotaxanes have the capability of exchanging a hyperpolarized inert gas atom for use in Magnetic Resonance Imaging (MRI).² Currently, MRI contrast is enhanced by the injecting a magnetic gadolinium (III) [Gd(III)] ions into the human body prior to the imaging experiment.³ Unfortunately, these contrast agents are expensive and toxic; as a result, there is need for a cheaper and less toxic imaging agent. Additionally, it would be beneficial to develop targeted contrast agents, i.e. macromolecules that bind specific analytes, …

Temperature Effects On The Proteome Of Ciona Intestinalis, Chelsea Lopez

Open Access Master's Theses

Ciona intestinalis is a solitary ascidian that lives in temperate waters around the globe. C. intestinalis in Rhode Island exhibit normal embryonic development at water temperatures between 10° C and 18° C. This thesis is interested in what changes occur in the ovary tissue at temperatures above 18° C and below 10° C. A preliminary study to assess the reproductive fitness of C. intestinalis, found that C. intestinalis raised at 22 °C had lower embryo viability when compared to the normal temperature range. 22 °C was chosen to mimic the high temperature predicted in some climate change models (IPCC, …

Evaluation Of The Efficacy Of Candidate Probiotics For Disease Prevention In Shellfish Hatcheries, Saebom Sohn

Open Access Dissertations

In the United States of America, oyster production is an important component of the seafood economy in many communities in coastal states. The severe impact of disease outbreaks and mass mortality of oyster larvae in hatcheries impacts production, since the oyster industry is largely dependent on hatchery and nursery production. The use of probiotics has been proposed as a potential preventative measure to limit the impact of bacterial diseases in shellfish hatcheries. In previous laboratory studies, the probiotic bacteria Phaeobacter inhibens S4 and Bacillus pumillus RI06-95 improved the survival of eastern oyster (Crassostrea virginica) larvae against the pathogens …