Digital Commons Network^™

Acquisitions Unit Annual Report 2012-2013, Andrée J. Rathemacher

Technical Services Reports and Statistics

Annual Report of the Acquisitions Unit, University Libraries, University of Rhode Island for FY13. Covers personnel, work flow, special projects, and serial, monograph, and e-resource acquisitions. Supplemental files include data on library materials expenditures by a number of variables as well as important working documents from the year.

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 …

Oa Policy Development At Uri, Andrée Rathemacher

Technical Services Faculty Presentations

Slides and other materials related to a presentation on the development of an open access policy at the University of Rhode Island.

The presentation was part of a discussion on recent OA policy development in New England at the ACRL New England Chapter Scholarly Communication Interest Group Summer Program, New Roles for Supporting Digital Scholarship in Academic Libraries. The program took place on June 19, 2013 at Northeastern University in Boston, MA.

Copper(Ii) Triflate-Mediated Synthesis Of 1,3,5-Triarylpyrazoles In [Bmim][Pf6] Ionic Liquid And Evaluation Of Their Anticancer Activities, V. Kameshwara Rao, Rakesh Tiwari, Bhupender S. Chhikara, Amir Nasrolahi Shirazi, Keykavous Parang, Anil Kumar

Biomedical and Pharmaceutical Sciences Faculty Publications

A simple, efficient, and environmentally friendly protocol for the synthesis of 1,3,5-triarylpyrazole in [bimm][PF₆] ionic liquid mediated by Cu(OTf)₂ is described. The reaction protocol gave 1,3,5-triarylpyrazoles in good to high yields (71-82%) via a one-pot addition–cyclocondensation between hydrazines and chalcones, and oxidative aromatization without requirement for an additional oxidizing reagent. The catalyst can be reused up to four cycles without much loss in the catalytic activity. The pyrazoles (4a-o) and pyrazolines (3a-n) were evaluated for antiproliferative activity in SK-OV-3, HT-29, and HeLa human cancer cells lines. Among all compounds, 3b inhibited cell proliferation …

Disease Prevention Without Relapse: Processes Of Change For Hpv Vaccination, Anne C. Fernandez, Andrea L. Paiva, Jessica M. Lipschitz, H. Elsa Larson, Nicole R. Amoyal, Cerissa L. Blaney, Marie A. Sillice, Colleen A. Redding, James O. Prochaska

Cancer Prevention Research Center Faculty Publications

Background: Human papillomavirus is the most prevalent sexually transmitted infection in the United States and is associated with 70% of cervical cancers as well as over 90% of genital warts. Although the HPV vaccine appears in the US immunization schedule during adolescence, a large percentage of women reach adulthood without being vaccinated. The Transtheoretical Model’s (TTM) Processes of Change (POC) construct provides an assessment of participants’ experiences with HPV vaccination and is a central component of computer-tailored interventions designed to increase compliance with medical recommendations, such as vaccination. This study describes development and validation of a POC measure for increasing …

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 …

Response Of Nitrous Oxide Flux To Addition Of Anecic Earthworms To An Agricultural Field, José A. Amador, Edward J. Avizinis

Natural Resources Science Faculty Publications

The burrowing and feeding activities of earthworms may have a strong effect on the flux of N₂O from agricultural soils. As such, shifts to agricultural management practices that increase the number of earthworms require an understanding of the role of earthworms in N₂O dynamics. We conducted a field experiment to examine the effects of addition of anecic earthworms (Lumbricus terrestris) on N₂O flux in a field previously planted with corn (Zea mays) in southern Rhode Island, USA. Plots were amended with (¹⁵NH₄)₂SO₄ and …

Antipsychotic Prescribing Pathways, Polypharmacy, And Clozapine Use In Treatment Of Schizophrenia, Jessica L. Gören, Meterko, Sandra Williams, Gary J. Young, Errol Baker, Chia-Hung Chou, Amy M. Kilbourne, Mark S. Bauer

Pharmacy Practice and Clinical Research Faculty Publications

Objective

To ensure optimal care for patients with schizophrenia, antipsychotic medications must be appropriately prescribed and used. Therefore, the primary objectives of this study were to identify and describe pathways for antipsychotic prescribing, assess the consistency of observed pathways with treatment guidelines, and describe variability across facilities.

Methods

Data from Veterans Affairs administrative data sets from fiscal year (FY) 2003 to FY 2007 were gathered for analysis in this retrospective cohort study of antipsychotic prescribing pathways among 13 facilities across two regional networks. Patients with a new episode of care for schizophrenia or schizoaffective disorder in FY 2005 were identified, …

Phlip-Mediated Delivery Of Pegylated Liposomes To Cancer Cells, Lan Yao, Jennifer Daniels, Dayanjali Wijesinghe, Oleg A. Andreev, Yana K. Reshetnyak

Physics Faculty Publications

We develop a method for pH-dependent fusion between liposomes and cellular membranes using pHLIP (pH Low Insertion Peptide), which inserts into lipid bilayer of membrane only at low pH. Previously we establish the molecular mechanism of peptide action and show that pHLIP can target acidic diseased tissue. Here we investigate how coating of PEGylated liposomes with pHLIP might affect liposomal uptake by cells. The presence of pHLIP on the surface of PEGylated-liposomes enhanced membrane fusion and lipid exchange in a pH dependent fashion, leading to increase of cellular uptake and payload release, and inhibition of cell proliferation by liposomes containing …

"Happy Teeth, Happy Me" - Teaching Oral Health In Campur, Guatemala, Staci Smith

Senior Honors Projects

As a part of the Frontlines Mission’s team, I joined their mission to teach, build, and restore the poor and indigenous areas of Guatemala. With the goal of combining my passion and pursuit of a dental career with public health, I joined the medical team and assisted in treatment of over 1000 Q’eqchi’ locals for a variety of conditions such as scabies, stomach ailments, asthma, arthritis, and parasites. I assisted professionals in the oral surgery procedures including multiple extractions and cleft palate cases. Perhaps most importantly for the future oral health of the Q’eqchi’ people, I was able to introduce …

Examining The Confluence Of Literature And Mathematics Through Art, Sofia Alavosius

Senior Honors Projects

Twentieth century novelist and scientist C. P. Snow noted the division of “two cultures,” namely the divide between the sciences and the humanities. Snow argued these were distinctive and separated cultures in the mid 1950s. The “two cultures” are also present during the Renaissance. This appears in the artwork and literary and mathematical texts of the period. The divide between the humanities and sciences is something that we can easily distinguish in the twenty-first century as well.

I use the discourse of C. P. Snow’s “two cultures” to work through this relationship and to explore the cultural perspectives of these …

Exploring The Role Of Cesa5 In The Synthesis Of Cellulose Using Physcomitrella Patens, Oumie Ceesay

Senior Honors Projects

Cellulose is very essential to plants because it determines the shape of cells, protects them from pathogens, and helps retain water that is needed for plant functions. It is also the major component of wood, cotton, and paper, which are items we use on a daily basis. Also, it can be used for the synthesis of biofuels. However, cellulose exists as strong fibers, which make it hard to breakdown for biofuel synthesis. If we can understand how cellulose is synthesized we can manipulate its fibers to make them stronger, more flexible, more absorbent, or easier to break down for use …

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 …

Brown Algal Diversity In Bermuda Revealed Using Molecular Tools, Alyssa L. Rogers

Senior Honors Projects

For nearly 60 years there has been very little investigation of the marine algal flora in Bermuda, which is an ideal location for a biodiversity assessment due to its size and location. Residing approximately 1000km off the coast of North Carolina, Bermuda is influenced by the cool water from the north during winter and by the warm water eddies that spin off the Gulf Stream for the much of the other seasons. The Bermuda Seaweed Project aims to extensively survey the marine algal flora in Bermuda and generate morphological and molecular data for all three major groups of macroalgae present. …

How Do Prey Refuges Affect Predator-Prey Interactions?, Justin Vendettuoli

Senior Honors Projects

While it is well known that predators eat their prey, prey that avoid predation risk can also incur substantial fitness costs through risk-induced changes in survival and reproduction, growth, and morphology. Changes in prey that occur without the predator physically consuming the prey are referred to as ‘non-consumptive effects’. One way to reduce the risk of predation is to use a refuge. While refuge use may reduce predation risk, however, it may also be costly to the prey. These costs may include within-refuge competition for resources, which can alter prey population dynamics, coexistence, and metapopulation dynamics. While these costs may …

Shape Changes In Hyoid Arch Elements In Four Shark Species, Isabel S. Nowinowski

Senior Honors Projects

The hyoid arch is critical in expanding the oral cavity during feeding and ventilation in fishes. The elements of the hyoid arch vary widely in morphology among fish taxa. The hyoid arch is medial to the jaws and is made up of paired hyomandibular cartilages (HY) dorsally, paired ceratohyal cartilages (CH) ventral to the HY, and a single, medial basihyal cartilage (BH) that interconnects the two sides. As the jaws open, the CH-BH complex is depressed expanding the floor of the oral cavity. The coracohyoideus muscle pulls the BH ventroposteriorly, which in turn swings the CH ventroposteriorly. As the coracohyoideus …

Reimagining The Silver Screen: Contemporary Film Stills, Kyle Demartino

Senior Honors Projects

During the late 19^th century longer rolls of celluloid photographic film, and motion picture cameras were first introduced, which allowed for the capture of rapid sequences of still images at a relatively high speeds. The first films shown to audiences on a larger screen, although rudimentary, caused people to gasp or run from the cinema, as they believed the images on screen were real. As technology increased feature films progressed from only showing a simple static event to creating full stories spanning over various sets and containing multiple characters. With the advent of sound, filmmakers were given another tool …

The Utility Of Planning And Other Spatial Concepts In Marine Spatial Management, Samuel Martin, Brandyn Lucca

Senior Honors Projects

No abstract provided.

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 …

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

The Utility Of Planning And Other Spatial Concepts In The Marine Spatial Management Of Marine Protected Areas (Mpas), Marine Reserves, Marine Zoning, Marine Sanctuaries And Parks, Marine Spatial Planning (Msp), Large Marine Ecosystems (Lmes) And Seascape / Marine Design., Samuel Martin, Brandyn Lucca, Dr. William R. Gordon Jr.

Senior Honors Projects

In the last fifty years, man has demonstrated an increased interest in gaining access to and apportioning the near and offshore marine environment. Governments, coastal and marine managers, economic-based users, stakeholders, and academics have gained an interest and involvement in the demarcation of marine boundaries. Many land-based spatial applications, utilized from disciplines such as planning, geography, landscape architecture and regional science have been applied to the spatial acquisition and management of ocean resources. In the last four decades new marine applications have emerged, they include: 1) Marine Protected Areas (MPAs), 2) Marine Reserves, 3) Marine Zoning, 4) Marine Sanctuaries, and …

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 …

Water As A New Matrix For Global Assessment Of Hydrophilic Pops, Derek Muir, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

With the addition of perfluorooctanesulfonate (PFOS), chlordecone, hexachlorocyclohexane (HCH) isomers and endosulfan to the Stockholm Convention, the list of chemicals addressed by the Convention no longer consists solely of hydrophobic organics. Water has become a widely used environmental matrix for monitoring POPs, particularly for the chlorinated pesticides, despite challenges related to collecting samples and determining trace levels. Here we review the sampling and analytical considerations for water sampling of POPs in general, and the hydrophilic POPs in particular, with the goal of identifying and recommending best approaches particularly for assessment of spatial and temporal trends on a global scale. Methods …

Microbial Community Structure Of A Leachfield Soil: Response To Intermittent Aeration And Tetracycline Addition, Janet A. Atoyan, Andrew M. Staroscik, David R. Nelson, Erika L. Patenaude, David A. Potts, José A. Amador

Cell and Molecular Biology Faculty Publications

Soil-based wastewater treatment systems, or leachfields, rely on microbial processes for improving the quality of wastewater before it reaches the groundwater. These processes are affected by physicochemical system properties, such as O2 availability, and disturbances, such as the presence of antimicrobial compounds in wastewater. We examined the microbial community structure of leachfield mesocosms containing native soil and receiving domestic wastewater under intermittently-aerated (AIR) and unaerated (LEACH) conditions before and after dosing with tetracycline (TET). Community structure was assessed using phospholipid fatty acid analysis (PLFA), analysis of dominant phylotypes using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE), and cloning and sequencing …

Invasion Of The Red Seaweed Heterosiphonia Japonica Spans Biogeographic Provinces In The Western North Atlantic Ocean, Christine Newton, Matthew E.S. Bracken, Megan Mcconville, Katherine Rodrigue, Carol S. Thornber

Biological Sciences Faculty Publications

The recent invasion of the red alga Heterosiphonia japonica in the western North Atlantic Ocean has provided a unique opportunity to study invasion dynamics across a biogeographical barrier. Native to the western North Pacific Ocean, initial collections in 2007 and 2009 restricted the western North Atlantic range of this invader to Rhode Island, USA. However, through subtidal community surveys, we document the presence of Heterosiphonia in coastal waters from Maine to New York, USA, a distance of more than 700 km. This geographical distribution spans a well-known biogeographical barrier at Cape Cod, Massachusetts. Despite significant differences in subtidal community structure …

Designer Materials By Self- And Directed Assembly: Photorheological Fluids, Magnetic Microchains And Hemostatic Dressings, Srinivasa Raghavan

Amgen Seminar Series in Chemical Engineering

Our laboratory seeks to engineer the assembly of “building blocks” such as polymers, surfactants, or colloids into higher-order materials. Such assembly can be induced spontaneously, guided by thermodynamic forces – this is called self-assembly. Alternately, assembly can be directed in specific ways, e.g., by bringing materials into contact at interfaces or around predefined templates – this can be termed directed assembly. Both processes have their analogs in biology and nature, and both are of great technological interest.

This talk will provide illustrative examples of our work with self- and directed assembly. We have created assemblies that respond to …

Organochlorine Pollutants In Western Antarctic Peninsula Sediments And Benthic Deposit Feeders, Lin Zhang, Rebecca Dickhut, Dave Demaster, Kari Pohl, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

Sediments and benthic deposit feeding holothurians were collected near the Palmer Long Term Ecological Research grid during the austral winter of 2008. Polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) were measured in Western Antarctic Peninsula continental shelf sediments, porewater, and benthic biota. Concentrations and fluxes in sediments decreased sharply away from the tip of the peninsula toward its interior. Sedimentary PCB fluxes were an order of magnitude lower than reported elsewhere, supporting the notion of a pristiner Antarctic environment. Hexa-chlorinated biphenyls dominated (40–100%) the PCB profiles in the sediments, while trichlorinated biphenyl 28 was the most abundant PCB congener in …

A Simple And Efficient Synthesis Of 2,3-Diarylnaphthofurans Using Sequential Hydroarylation/Heck Oxyarylation, V. Kameshwara Rao, Gamesh M. Shelke, Rakesh Tiwari, Keykavous Parang, Anil Kumar

Biomedical and Pharmaceutical Sciences Faculty Publications

An efficient and simnple strategy has been developed for the synthesis of 2,3-diarylnaphthofurans using sequential hydroarylation of naphthols and alkynes in the presence of In(OTf)₃ under microwave irradiation followed by one-pot Heck-oxyarylation of generated 1-substituted-a-hydroxy styrenes.

Writing With(Out) Pain: Computing Injuries And The Role Of The Body In Writing Activity, Kim Hensley Owens, Derek Van Ittersum

Professional and Public Writing Faculty Publications

This article uses the lens of computer writing injuries to explore writing as an embodied activity. We use philosopher Mark Johnson's five-part definition of embodiment to develop an analysis that examines the physical, flesh-and-blood aspects of writing in addition to the social and cultural aspects of embodied activity. With this framework, we show the limits of purely technological solutions to writing injuries (like ergonomic keyboards) and explore the difficulties of including somatic training in the writing classroom. Rather than prescribing a single solution, we propose that these injuries require multifaceted infrastructural changes, and point to the benefits of approaching writing …