Digital Commons Network^™

Urinformed August 2013, Urinformed

URInformed: The URI Employees' Newsletter

No abstract provided.

T-Cell Dependent Immunogenicity Of Protein Therapeutics: Preclinical Assessment And Mitigation, Vibha Jawa, Leslie P. Cousens, Michel Awwad, Eric Wakshull, Harald Kropshofer, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Protein therapeutics hold a prominent and rapidly expanding place among medicinal products. Purified blood products, recombinant cytokines, growth factors, enzyme replacement factors, monoclonal antibodies, fusion proteins, and chimeric fusion proteins are all examples of therapeutic proteins that have been developed in the past few decades and approved for use in the treatment of human disease. Despite early belief that the fully human nature of these proteins would represent a significant advantage, adverse effects associated with immune responses to some biologic therapies have become a topic of some concern. As a result, drug developers are devising strategies to assess immune responses …

The I5k Initiative: Advancing Arthropod Genomics For Knowledge, Human Health, Agriculture, And The Environment, I5k Consortium, Marian Goldsmith

Biological Sciences Faculty Publications

Insects and their arthropod relatives including mites, spiders, and crustaceans play major roles in the world’s terrestrial, aquatic, and marine ecosystems. Arthropods compete with humans for food and transmit devastating diseases. They also comprise the most diverse and successful branch of metazoan evolution, with millions of extant species. Here, we describe an international effort to guide arthropod genomic efforts, from species prioritization to methodology and informatics. The 5000 arthropod genomes initiative (i5K) community met formally in 2012 to discuss a roadmap for sequencing and analyzing 5000 high-priority arthropods and is continuing this effort via pilot projects, the development of standard …

Blacker Than Death: Recollecting The “Black Turn” In Metal Aesthetics, Ian Reyes

Communication Studies Faculty Publications

This essay illuminates the construction of a newer, blacker, and heavier recollection of metal’s aesthetic potential. By analyzing recordings and popular press articles, and reading these through the historical and theoretical observations of academic metal studies, I argue that the precondition of 1990s black metal was the exhaustion of death metal aesthetics coinciding with the emergence of a more international metal scene. In the 90s, death metal—once undisputedly the heaviest of all metals—had become unspectacular, too familiar, and as a result less heavy. Innovating a sound heavier than death entailed a subcultural reorientation towards recordings forgotten under death metal’s hegemonic …

Using Hierarchical Bayes To Understand Movement, Health, And Survival In The Endangered North Atlantic Right Whale, Robert S. Schick, Scott D. Kraus, Rosalind M. Rolland, Amy R. Knowlton, Philip K. Hamilton, Heather M. Pettis, Robert D. Kenney, James S. Clark

Graduate School of Oceanography Faculty Publications

Body condition is an indicator of health, and it plays a key role in many vital processes for mammalian species. While evidence of individual body condition can be obtained, these observations provide just brief glimpses into the health state of the animal. An analytical framework is needed for understanding how health of animals changes over space and time.Through knowledge of individual health we can better understand the status of populations. This is particularly important in endangered species, where the consequences of disruption of critical biological functions can push groups of animals rapidly toward extinction. Here we built a state-space model …

Open Access Publishing And Intellectual Freedom: Remembering Aaron Swartz, Brendan Ryan, Andrée Rathemacher

Technical Services Faculty Presentations

Slides and other materials related to a presentation on open access at the 2013 Rhode Island Library Association Annual Conference, Navigating a Sea of Change. The presentation was part of a broader discussion on open access and Aaron Swartz. It took place on June 4, 2013 at Salve Regina University in Newport, RI.

The abstract for the presentation reads: "After an introduction to the concept of Creative Commons and the tragic case of Aaron Swartz, join the panelists in discussing open access, scholarly publishing and the flow of information as they relate to libraries."

Relationship Between Postural Control And Restricted, Repetitive Behaviors In Autism Spectrum Disorders, K. J. Radonovich, K. A. Fournier, C. J. Hass

Kinesiology Faculty Publications

Restricted, repetitive behaviors (RRBs) are one of the core diagnostic criteria of autism spectrum disorders (ASD), and include simple repetitive motor behaviors and more complex cognitive behaviors, such as compulsions and restricted interests. In addition to the core symptoms, impaired movement is often observed in ASD. Research suggests that the postural system in individuals with ASD is immature and may never reach adult levels. RRBs have been related to postural sway in individuals with mental retardation. Our goals were to determine whether subjects with ASD had greater postural sway and whether RBS-R scores were related to the magnitude of postural …

The Effects Of Refuge On Escape Responses Of Two Caribbean Goby Species, Russell P. Dauksis

Senior Honors Projects

The Effects of Refuge Abundance on Escape Responses of the Bridled Goby (Coryphopterus glaucofraenum)

Russell P. Dauksis

Major

Marine Biology

Advisor

Dr. Graham Forrester

Advisor Department

Natural Resources Science

Date

5-2012

Keywords

Escapology, marine ecology, functional morphology, animal behavior, predator-prey interactions, Bridled Goby, Coryphopterus glaucofraenum

Abstract

Interactions between predators and prey species are arguably the most pervasive and important events in ecology. Predators have strong effects on the distribution and abundance of prey in virtually all environments. In the long-term, it is therefore hardly surprising that selective mortality imposed by predators has shaped a wide array of prey behaviors …

Subtlety Of Sound: A Study Of Foley Art, Jack Doyle

Senior Honors Projects

Each time a feature-length film or a television episode reaches its end, there appears on the screen a slowly rising roster of each individual involved with the production. Several of those names are credited with roles that are quite familiar to viewers: the cast, director, producers, stunt doubles, and makeup professionals, as well as their contributions, are readily apparent. These more glorified crew members, however, can only produce if supplemented by the nuanced efforts of the hundreds of other names that scroll across the screen. One of the more unsung heroes is the Foley Artist, whose tasks are hardly glamorous, …

European Tapestries: History, Conservation, And Creation, Chelsea Missaggia

Senior Honors Projects

Tapestry is an art that combines painting and weaving to reach a final product that is remarkable in detail and construction. Many cultures produced tapestries that have survived, specifically Coptic Egypt, Pre-Conquest Peru, and Northern Europe. European tapestries created between the fifteenth and eighteenth centuries are grand and elaborate decorative pieces commissioned by the nobility of the time period as status symbols and functional portable art. These massive textiles were very labor intensive and the most famous tapestry sets took a year or more to complete. The textile art of tapestry weaving is a concept not covered in detail during …

Guns Of Fortune: How Guns Move To Fulfill Demand, Michael J. Coates

Senior Honors Projects

Legislators face a compelling dilemma, how can they decrease the prevalence of gun violence? Cities and States around the United States have laws intended to prevent violent criminals from acquiring and using weapons, but it remains debatable whether these laws are effective.

This study posits that guns are subject to the laws of supply and demand and the variable gun laws in states across the country decreases the effectiveness of local and state gun legislation. In short, guns are trafficked across state lines to meet demand in states with stricter gun laws.

Data for the study was collected from the …

Bird Bone Taphonomy In The Tse-Whit-Zen Site, Marielle Lara Orff

Senior Honors Projects

Tse-whit-zen is a large well preserved archaeological site that was discovered in August 2003 in the Olympic Peninsula of Washington State. By 2004 an archaeological dig crew was working tirelessly on the site, which turned out to be one of the largest Native American villages ever found in the Pacific Northwest. This village was shown to have been inhabited by the Lower Elwha Klallam tribe, whose descendants still continue to live in the region. The site was occupied for thousands of years, with the oldest material dated at 2,700 years ago and the youngest at 100 years ago when the …

A Search For Light-Detecting Proteins In The Free-Living Protist, Tetrahymena Thermophila: Does Tetrahymena Have Opsin-Like Or Bacteriorhodopsin-Like Proteins?, Jillian Marie Rainville

Senior Honors Projects

Tetrahymena is a genus of ciliated protozoans, a diversified lineage of unicellular eukaryotes. They are freshwater organisms, and generally inhabit streams, lakes, and ponds. Tetrahymena thermophila is commonly studied as a model cell because of its unique variety of complex and specialized cell structures and processes, which are similar to those of higher animals.

G-protein-coupled receptors (GPCRs) are transmembrane proteins that transduce stimuli from outside of the cell into intracellular signals, through the interaction of their intracellular domains with heterotrimeric G proteins. GPCRs make up a vast protein family that includes a variety of subfamilies with distinct functions. They are …

La Barbe: Feminine Beards And Other Mysteries Of French Grammatical Gender, Robin F. Keller

Senior Honors Projects

Grammatical gender in French language is one of the biggest guessing games for a native English speaker. Why a table is feminine and a book is masculine is a question that plagues those learning French as a second language. In French, all nouns have gender, masculine and feminine. The complication: only a small percentage of the nouns are assigned gender semantically leaving the remaining which are assigned gender seemingly arbitrarily. For English native speakers, the distinction of these basic parts in a foreign language is not a natural skill. The simple fact that nouns are either feminine or masculine is …

Exploring Greenhouse Gas Emissions From Beaver Ponds In Southern Rhode Island, Molly K. Welsh

Senior Honors Projects

Climate change is one of the largest environmental issues facing humanity today, having the potential to alter fresh water availability, agricultural yields, forest productivity, and global sea levels. As climate change is likely to increase the intensity of extreme weather events, the potential for massive human and financial consequences is of further concern. The Intergovernmental Panel on Climate Change asserts that climate change is due to anthropogenic alterations of the atmosphere’s composition, with additional contributions from natural biochemical processes. In particular, the rapid increase in the concentrations of greenhouse gases (GHGs) in the atmosphere can trigger atmospheric warming as these …

Analysis Of The Chondroitinase Operon Of Flavobacterium Columnare, Erin L. Sorlien

Senior Honors Projects

Analysis of the chondroitinase operon of Flavobacterium columnare

Erin Sorlien

Major

Cell and Molecular Biology, Chemistry

Advisor

Dr. David R. Nelson

Date

May 2, 2013

Keywords

Flavobacterium columnare, columnaris disease, chondroitin AC lyase, complementation, csl operon

Abstract
Flavobacterium columnare, an opportunistic bacterial pathogen of fish, is the causative agent of columnaris disease (CD). The bacterium is a Gram-negative rod that exhibits gliding motility and avidly forms biofilms. CD affects both wild and cultured freshwater fish, and continues to cause large economic losses to the fish farming industry. According to an investigation conducted by the National Animal Health Monitoring System, CD …

The Good 5 Cent Cigar (4/16/2013), University Of Rhode Island

The Good 5 Cent Cigar (Student Newspaper Archives)

This is a digitized, downloadable version of the University of Rhode Island school newspaper.

Family Of Ph (Low) Insertion Peptides For Tumor Targeting, Dhammika Weerakkody, Anna Moshnikova, Mak S. Thakur, Valentina Moshnikova, Jennifer Daniels, Donald Engelman, Oleg A. Andreev, Yana K. Reshetnyak

Physics Faculty Publications

Cancer is a complex disease with a range of genetic and biochemical markers within and among tumors, but a general tumor characteristic is extracellular acidity, which is associated with tumor growth and development. Acidosis could be a universal marker for cancer imaging and the delivery of therapeutic molecules, but its promise as a cancer biomarker has not been fully realized in the clinic. We have discovered a unique approach for the targeting of acidic tissue using the pH-sensitive folding and transmembrane insertion of pH (low) insertion peptide (pHLIP). The essence of the molecular mechanism has been elucidated, but the principles …

Electronic Journals Overlap Analysis, Michael A. Cerbo Ii

Technical Services Reports and Statistics

Overlap analysis for the University of Rhode Island's electronic journals are complied alphabetically by database name. The report shows the number or titles that are exclusive to that database as compiled by Serials Solutions.

The table located under the report gives a brief explanation of the headings used in the analysis.

Supplemental Feeding For Ecotourism Reverses Diel Activity And Alters Movement Patterns And Spatial Distribution Of The Southern Stingray, Dasyatis Americana, Mark J. Corcoran, Bradley M. Wetherbee, Mahmood S. Shivji, Matthew D. Potenski, Demian D. Chapman, Guy M. Harvey

Biological Sciences Faculty Publications

Southern stingrays, Dasyatis americana, have been provided supplemental food in ecotourism operations at Stingray City Sandbar (SCS), Grand Cayman since 1986, with this site becoming one of the world’s most famous and heavily visited marine wildlife interaction venues. Given expansion of marine wildlife interactive tourism worldwide, there are questions about the effects of such activities on the focal species and their ecosystems. We used a combination of acoustic telemetry and tag-recapture efforts to test the hypothesis that human-sourced supplemental feeding has altered stingray activity patterns and habitat use at SCS relative to wild animals at control sites. Secondarily, we …

Computational Vaccinology And The Icovax 2012 Workshop, Yongqun He, Zhiwei Cao, Anne S. De Groot, Vladimir Brusic, Christian Schönbach, Nikolai Petrovsky

Institute for Immunology and Informatics Faculty Publications

Computational vaccinology or vaccine informatics is an interdisciplinary field that addresses scientific and clinical questions in vaccinology using computational and informatics approaches. Computational vaccinology overlaps with many other fields such as immunoinformatics, reverse vaccinology, postlicensure vaccine research, vaccinomics, literature mining, and systems vaccinology. The second ISV Pre-conference Computational Vaccinology Workshop (ICoVax 2012) was held on October 13, 2013 in Shanghai, China. A number of topics were presented in the workshop, including allergen predictions, prediction of linear T cell epitopes and functional conformational epitopes, prediction of protein-ligand binding regions, vaccine design using reverse vaccinology, and case studies in computational vaccinology. Although …

Migrating Successful Student Engagement Strategies Online: Opportunities And Challenges Using Jigsaw Groups And Problem-Based Learning, José A. Amador, Helen Mederer

Natural Resources Science Faculty Publications

Online courses may be criticized for failing to engage students. Faculty members teaching in the classroom often employ a number of strategies that capture the interest of students, but may find the migration to the online environment a daunting prospect. This paper describes the transitioning of two common strategies to engage students in the classroom – jigsaw groups and problem-based learning – from face-to-face to online courses in sociology and soil science, respectively. The paper discusses the challenges and opportunities that were found to be common to the implementation of both these strategies online, and provides suggestions for faculty considering …

Sex-Specific Correlations Of Individual Heterozygosity, Parasite Load, And Scalation Asymmetry In A Sexually Dichromatic Lizard, Pei-Jen L. Shaner, Ying-Ru Chen, Jhan-Wei Lin, Jason J. Kolbe, Si-Min Lin

Biological Sciences Faculty Publications

Heterozygosity-fitness correlations (HFCs) provide insights into the genetic bases of individual fitness variation in natural populations. However, despite decades of study, the biological significance of HFCs is still under debate. In this study, we investigated HFCs in a large population of the sexually dimorphic lizard Takydromus viridipunctatus (Lacertidae). Because of the high prevalence of parasitism from trombiculid mites in this lizard, we expect individual fitness (i.e., survival) to decrease with increasing parasite load. Furthermore, because morphological asymmetry is likely to influence individuals' mobility (i.e., limb asymmetry) and male biting ability during copulation (i.e., head asymmetry) in this species, we also …

The Good 5 Cent Cigar (2/20/2013), University Of Rhode Island

The Good 5 Cent Cigar (Student Newspaper Archives)

This is a digitized, downloadable version of the University of Rhode Island school newspaper.

Competitor Avoidance Drives Within-Host Feeding Site Selection In A Passively-Dispersed Herbivore, Sara Gomez, Liahna Gonda-King, Colin M. Orians, Evan L. Preisser

Biological Sciences Faculty Publications

1. Evolutionary theory predicts that ovipositing females that can actively disperse should select hosts that increase offspring performance. However, for organisms that are exclusively passively dispersed, feeding site selection is possible only at the within-host level. This is particularly important for their offspring, which have strong temporal and spatial dispersal constraints within a host. Such constraints are probably magnified by tissue quality heterogeneity caused by competing herbivores.
2. We investigated within-host feeding site selection of passively dispersed neonates of a sessile herbivore, the hemlock woolly adelgid (Adelges tsugae Annand), when it shares its eastern hemlock (Tsuga canadensis Carrière) host with …

Nutritional Basis For Colonization Resistance By Human Commensal Escherichia Coli Strains Hs And Nissle 1917 Against E. Coli O157:H7 In The Mouse Intestine, Rosalie Maltby, Mary P. Leatham-Jensen, Terri Gibson, Paul S. Cohen, Tyrrell Conway

Cell and Molecular Biology Faculty Publications

Escherichia coli is a single species consisting of many biotypes, some of which are commensal colonizers of mammals and others that cause disease. Humans are colonized on average with five commensal biotypes, and it is widely thought that the commensals serve as a barrier to infection by pathogens. Previous studies showed that a combination of three pre-colonized commensal E. coli strains prevents colonization of E. coli O157:H7 in a mouse model (Leatham, et al., 2010, Infect Immun 77: 2876–7886). The commensal biotypes included E. coli HS, which is known to successfully colonize humans at high doses with no adverse effects, …

Swim Speed, Behavior, And Movement Of North Atlantic Right Whales (Eubalaena Glacialis) In Coastal Waters Of Northeastern Florida, Usa, James H.W. Hain, Joy D. Hampp, Shelia A. Mckenney, Julie A. Albert, Robert D. Kenney

Graduate School of Oceanography Faculty Publications

In a portion of the coastal waters of northeastern Florida, North Atlantic right whales (Eubalaena glacialis) occur close to shore from December through March. These waters are included within the designated critical habitat for right whales. Data on swim speed, behavior, and direction of movement – with photo-identification of individual whales – were gathered by a volunteer sighting network working alongside experienced scientists and supplemented by aerial observations. In seven years (2001–2007), 109 tracking periods or “follows” were conducted on right whales during 600 hours of observation from shore-based observers. The whales were categorized as mother-calf pairs, singles …

Ph (Low) Insertion Peptide (Phlip) Targets Ischemic Myocardium, Eugene A. Sosunov, Evgeny P. Anyukhovsky, Alexander A. Sosunov, Anna Moshnikova, Dayanjali Wijesinghe, Donald M. Engelman, Yana K. Reshetnyak, Oleg A. Andreev

Physics Faculty Publications

The pH (low) insertion peptide (pHLIP) family enables targeting of cells in tissues with low extracellular pH. Here, we show that ischemic myocardium is targeted, potentially opening a new route to diagnosis and therapy. The experiments were performed using two murine ischemia models: regional ischemia induced by coronary artery occlusion and global low-flow ischemia in isolated hearts. In both models, pH-sensitive pHLIPs [wild type (WT) and Var7] or WT-pHLIP–coated liposomes bind ischemic but not normal regions of myocardium, whereas pH-insensitive, kVar7, and liposomes coated with PEG showed no preference. pHLIP did not influence either the mechanical or the electrical activity …

Multiple Forms Of Vector Manipulation By A Plant-Infecting Virus: Bemisia Tabaci And Tomato Yellow Leaf Curl Virus , Baiming Liu, Evan L. Preisser, Dong Chu, Huipend Pan, Wen Xie, Shaoli Wang, Qingjun Wu, Xuguo Zhou, Youjun Zhang

Biological Sciences Faculty Publications

For many insect-vectored plant viruses, the relationship between feeding behavior and vector competence may prove integral to an understanding of the epidemiology of the resulting plant disease. While plant-infecting viruses are well known to change host plant physiology in a way that makes them more attractive to vectors, viral manipulation of the vectors themselves has only recently been reported. Previous research suggested that the rapid spread of Tomato yellow leaf curl virus (TYLCV) throughout China has been facilitated by its primary vector, the whitefly Bemisia tabaci. We conducted two experiments testing the impact of TYLCV infection of the host …

The Real Limits To Marine Life: A Further Critique Of The Respiration Index, Brad A. Seibel, J. J. Childress

Biological Sciences Faculty Publications

The recently proposed "Respiration Index" (RI = log PO₂/PCO₂) suggests that aerobic metabolism is limited by the ratio of reactants (oxygen) to products (carbon dioxide) according to the thermodynamics of cellular respiration. Here, we demonstrate further that, because of the large standard free energy change for organic carbon oxidation (ΔG° = −686 kcal mol⁻¹), carbon dioxide can never reach concentrations that would limit the thermodynamics of this reaction. A PCO₂ to PO₂ ratio of 10⁵⁰³ would be required to reach equilibrium (equilibrium constant, K …