Digital Commons Network^™

Urinformed December 2015, Urinformed

URInformed: The URI Employees' Newsletter

No abstract provided.

Diurnal Variation Of Testosterone In Beluga Whale Blow, Renee Bakker

Senior Honors Projects

Studies on the concentrations of certain hormones in cetaceans and their effects on cetacean biology are useful to determining physical conditions such as age, sex, and reproductive status of individuals. Hormone concentrations can be determined through blood samples, but collection of blow (exhaled respiratory vapor) has proven to be a noninvasive method of obtaining samples that can be analyzed for hormone concentrations. The existence of diurnal variation in hormone concentrations greatly affects the value of what time of day samples are collected. Previous studies have found that other mammalian species exhibit diurnal variation of testosterone and that for many species …

2015-11 Afs 101/103 Food From The Oceans: New England, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for AFS 101/103 Food from the Oceans: New England. This course was supported with no need for additional resources. Responding library faculty member: Michael Cerbo. Requesting faculty member: Austin Humphries.

Persistent Intra-Specific Variation In Genetic And Behavioral Traits In The Raphidophyte, Heterosigma Akashiwo, Elizabeth L. Harvey, Susanne Menden-Deuer, Tatiana A. Rynearson

Graduate School of Oceanography Faculty Publications

Motility is a key trait that phytoplankton utilize to navigate the heterogeneous marine environment. Quantifying both intra- and inter-specific variability in trait distributions is key to utilizing traits to distinguish groups of organisms and assess their ecological function. Because examinations of intra-specific variability are rare, here we measured three-dimensional movement behaviors and distribution patterns of seven genetically distinct strains of the ichthyotoxic raphidophyte, Heterosigma akashiwo. Strains were collected from different ocean basins but geographic distance between isolates was a poor predictor of genetic relatedness among strains. Observed behaviors were significantly different among all strains examined, with swimming speed and …

2015-11 Bes 551x: Ecosystem Science And Sustainability, Michael Cerbo

Library Impact Statements

Library Impact Statement submitted in response to new course proposal for BES 551X: Ecosystem Science and Sustainability. This course was supported with no need for additional resources. Responding library faculty member: Michael Cerbo. Requesting faculty member: Austin Humphries.

Faculty Senate Meeting Minutes November 19, 2015, University Of Rhode Island Faculty Senate

Faculty Senate Meeting Minutes

No abstract provided.

Construction, Complete Sequence, And Annotation Of A Bac Contig Covering The Silkworm Chorion Locus, Zhiwei Chen, Junko Nohata, Huizhen Guo, Shenglong Li, Jianqiu Liu, Youbing Guo, Kimiko Yamamoto, Keiko Kadono-Okuda, Chun Liu, Kallare P. Arunkumar, Javaregowda Nagaraju, Yan Zhang, Shiping Liu, Vassiliki Labropoulou, Luc Swevers, Panagiota Tsitoura, Kostas Iatrou, Karumathil P. Gopinathan, Marian R. Goldsmith, Qingyou Xia, Kazuei Mita

Biological Sciences Faculty Publications

The silkmoth chorion was studied extensively by F.C. Kafatos’ group for almost 40 years. However, the complete structure of the chorion locus was not obtained in the genome sequence of Bombyx mori published in 2008 due to repetitive sequences, resulting in gaps and an incomplete view of the locus. To obtain the complete sequence of the chorion locus, expressed sequence tags (ESTs) derived from follicular epithelium cells were used as probes to screen a bacterial artificial chromosome (BAC) library. Seven BACs were selected to construct a contig which covered the whole chorion locus. By Sanger sequencing, we successfully obtained complete …

A Comprehensive Analysis Of The Chorion Locus In Silkmoth, Zhiwei Chen, Junko Nohata, Huizhen Guo, Shenglong Li, Jianqiu Liu, Youbing Guo, Kimiko Yamamoto, Keiko Kadono-Okuda, Chun Li, Kallare P. Arunkumar, Javaregowda Nagaraju, Yan Zhang, Shiping Liu, Vassiliki Labropoulou, Luc Swevers, Panagiota Tsitoura, Kostas Iatrou, Karumathil P. Gopinathan, Marian R. Goldsmith, Qingyou Xia, Kazuei Mita

Biological Sciences Faculty Publications

Despite more than 40 years of intense study, essential features of the silkmoth chorion (eggshell) are still not fully understood. To determine the precise structure of the chorion locus, we performed extensive EST analysis, constructed a bacterial artificial chromosome (BAC) contig, and obtained a continuous genomic sequence of 871,711 base pairs. We annotated 127 chorion genes in two segments interrupted by a 164 kb region with 5 non-chorion genes, orthologs of which were on chorion bearing scaffolds in 4 ditrysian families. Detailed transcriptome analysis revealed expression throughout choriogenesis of most chorion genes originally categorized as “middle”, and evidence for diverse …

Reference Databases Usage Statistics 2014-2015, Michael A. Cerbo Ii, Sarah Bannister

Technical Services Reports and Statistics

Statistics on the use of online reference databases at the University of Rhode Island during the period from July 2014 through June 2015. Includes COUNTER-compliant data on sessions, searches, turnaways, full text articles downloaded, and other metrics.

Biophysical Studies Of Transmembrane Helix Dimerization, Edwin Li

Amgen Seminar Series in Chemical Engineering

My research lab works towards the understanding of the physical and chemical principles governing the interaction of membrane proteins. Of particular interest is the role of the transmembrane domains in these interactions. The focus, thus far, has been on fibroblast growth factor receptors and mucin proteins and the formation of dimers. These membrane proteins are important because they regulate many vital cellular processes. Furthermore, diseases may arise when homo- and heterodimerization are not controlled properly due to mutations or overexpression of the membrane protein. Thus, these studies may provide useful information towards the development of better therapeutics. I will present …

Continuous 1.3-Million-Year Record Of East African Hydroclimate, And Implications For Patterns Of Evolution And Biodiversity, Robert P. Lyons, Christopher A. Scholz, Andrew S. Cohen, John W. King, Erik T. Brown, Sarah J. Ivory, Thomas C. Johnson, Alan L. Deino, Peter N. Reinthal, Michael M. Mcglue, Margaret W. Blome

Graduate School of Oceanography Faculty Publications

The transport of moisture in the tropics is a critical process for the global energy budget and on geologic timescales, has markedly influenced continental landscapes, migratory pathways, and biological evolution. Here we present a continuous, first-of-its-kind 1.3-My record of continental hydroclimate and lake-level variability derived from drill core data from Lake Malawi, East Africa (9–15° S). Over the Quaternary, we observe dramatic shifts in effective moisture, resulting in large-scale changes in one of the world’s largest lakes and most diverse freshwater ecosystems. Results show evidence for 24 lake level drops of more than 200 m during the Late Quaternary, including …

Energy Dissipation And Constitutive Modeling For A Mechanistic Description Of Pad Scratching In Chemical-Mechanical Planarization, David Ponte, D.M.L. Meyer

Mechanical, Industrial & Systems Engineering Faculty Publications

A thermomechanical model to describe the mechanisms of polishing pad scratching in chemical–mechanical planarization (CMP) has been formulated and investigated. CMP is a necessary process in integrated circuit (IC) fabrication to planarize wafers with nanoscale features after patterned layer deposition. Polishing pad asperities can produce microscale scratches on the wafer surface during CMP, reducing IC manufacturing yields. The constructed thermomechanical model accounts for stresses of the pad and wafer contact and also provides the means to track input energy dissipation during CMP. Tracking energy dissipation offers information about processes that may influence scratch production. This knowledge ultimately produces a greater …

Decadal Patterns Of Westerly Winds, Temperatures, Ocean Gyre Circulations And Fish Abundance: A Review, Candace A. Oviatt, Leslie Smith, M. Conor Mcmanus, Kimberly Hyde

Graduate School of Oceanography Faculty Publications

The purpose of this review is to describe the global scope of the multidecadal climate oscillations that go back at least, through several hundred years. Literature, historic data, satellite data and global circulation model output have been used to provide evidence for the zonal and meridional jet stream patterns. These patterns were predominantly zonal from the 1970s to 1990s and switched since the 1990s to a meridional wind phase, with weakening jet streams forming Rossby waves in the northern and southern hemispheres. A weakened northern jet stream has allowed northerly winds to flow down over the continents in the northern …

Curricular Affairs Committee Minutes October 19, 2015, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

Reverse Engineering Tumor Invasion And Resistance Using Micro/Nano Technologies, Ian Y. Wong

Amgen Seminar Series in Chemical Engineering

Tumor invasion and metastasis, as well as the emergence of drug resistance, confound existing anti-cancer therapies and result in over 9 out of 10 cancer-related fatalities. However, this complex and emergent phenomenon remains poorly understood, particularly from a physical and mechanical perspective. Engineering approaches based on micro/nano technologies may enable new insights into cancer biology and their translation for preclinical drug testing. Here, I describe the use of engineered microenvironments to profile single cell invasion and drug resistance. These behaviors can be comprehensively analyzed in space and time using computer vision, revealing an unexpected analogy with phase transitions during binary …

Effects Of Co2 On Growth Rate, C:N:P, And Fatty Acid Composition Of Seven Marine Phytoplankton Species, Andrew L. King, Bethany D. Jenkins, Joselynn R. Wallace, Yuan Liu, Gary H. Wikfors, Lisa M. Milke, Shannon L. Meseck

Cell and Molecular Biology Faculty Publications

Carbon dioxide (CO₂) is the primary substrate for photosynthesis by the phytoplankton that form the base of the marine food web and mediate biogeochemical cycling of C and nutrient elements. Specific growth rate and elemental composition (C:N:P) were characterized for 7 cosmopolitan coastal and oceanic phytoplankton species (5 diatoms and 2 chlorophytes) using low density, nutrient-replete, semi-continuous culture experiments in which CO₂ was manipulated to 4 levels ranging from post-bloom/glacial maxima (ppm) to geological maxima levels (>2900 ppm). Specific growth rates at high CO₂ were from 19 to 60% higher than in low CO_{2 …}

Analysis Of Cell-Mediated Immune Responses In Support Of Dengue Vaccine Development Efforts, Alan L. Rothman, Jeffrey R. Currier, Heather L. Friberg, Anuja Mathew

Institute for Immunology and Informatics Faculty Publications

Dengue vaccine development has made significant strides, but a better understanding of how vaccine-induced immune responses correlate with vaccine efficacy can greatly accelerate development, testing, and deployment as well as ameliorate potential risks and safety concerns. Advances in basic immunology knowledge and techniques have already improved our understanding of cell-mediated immunity of natural dengue virus infection and vaccination. We conclude that the evidence base is adequate to argue for inclusion of assessments of cell-mediated immunity as part of clinical trials of dengue vaccines, although further research to identify useful correlates of protective immunity is needed.

Assessing Shoreline Exposure And Oyster Habitat Suitability Maximizes Potential Success For Sustainable Shoreline Protection Using Restored Oyster Reefs, Megan K. La Peyre, Kayla Serra, T. Andrew Joyner, Austin T. Humphries

Fisheries, Animal and Veterinary Sciences Faculty Publications

Oyster reefs provide valuable ecosystem services that contribute to coastal resilience. Unfortunately, many reefs have been degraded or removed completely, and there are increased efforts to restore oysters in many coastal areas. In particular, much attention has recently been given to the restoration of shellfish reefs along eroding shorelines to reduce erosion. Such fringing reef approaches, however, often lack empirical data to identify locations where reefs are most effective in reducing marsh erosion, or fully take into account habitat suitability. Using monitoring data from 5 separate fringing reef projects across coastal Louisiana, we quantify shoreline exposure (fetch + wind direction …

Concentrations, Trends, And Air-Water Exchange Of Pahs And Pbdes Derived From Passive Samplers In Lake Superior In 2011, Zoe Ruge, Derek Muir, Paul Helm, Rainer Lohmann

Graduate School of Oceanography Faculty Publications

Polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenylethers (PBDEs) are both currently released into the environment from anthropogenic activity. Both are hence primarily associated with populated or industrial areas, although wildfires can be an important source of PAHs, too. Polyethylene passive samplers (PEs) were simultaneously deployed in surface water and near surface atmosphere to determine spatial trends and air-water gaseous exchange of 22 PAHs and 11 PBDEs at 19 sites across Lake Superior in 2011. Surface water and atmospheric PAH concentrations were greatest at urban sites (up to 65 ng L-1 and 140 ng m-3, respectively, averaged from June to October). …

Bacterial Diversity And Community Composition From Seasurface To Subseafloor, Emily A. Walsh, John B. Kirkpatrick, Scott D. Rutherford, David C. Smith, Mitchell Sogin, Steven D'Hondt

Graduate School of Oceanography Faculty Publications

We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (1.5 meters below seafloor). Abundance-weighted community compositions …

Multi-Attribute Networks And The Impact Of Partial Information On Inference And Characterization, Natalia Katenka

Amgen Seminar Series in Chemical Engineering

Our work is motivated by application of association networks in computa- tional biology, specifically in the context of gene/protein regulatory networks in human cancer cells. Association networks represent systems of interacting elements, where a link between two different elements indicates a sufficient level of similarity between element attributes. While in reality relational ties between elements can be expected to be based on similarity across multiple attributes, the vast majority of work to date on association networks involves ties defined with respect to only a single attribute. We propose an approach for the inference of multi-attribute association networks from measurements …

Acquisitions Unit Annual Report 2014-2015, Andrée J. Rathemacher

Technical Services Reports and Statistics

Annual Report of the Acquisitions Unit, University Libraries, University of Rhode Island for FY15. 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.

A Sense Of Belonging Among College Students With Disabilities: An Emergent Theoretical Model, Annemarie Vaccaro, Meada Daly-Cano, Barbara M. Newman

Human Development and Family Science Faculty Publications

Higher education research suggests that the development of a sense of belonging is key to academic success and persistence, yet we know little about how first-year students with disabilities develop a sense of belonging as they transition into and through their first year in postsecondary environments. Themes from a grounded theory study of 8 college students, most of whom had invisible disabilities, provided the foundation for an emerging model of belonging. Student narratives suggest there are interconnections between the development of a sense of belonging, self-advocacy, social relationships, and mastery of the student role for first-year students with disabilities.

Rapid And Efficient Pesticide Detection Via Cyclodextrin-Promoted Energy Transfer, Nicole Serio, John Roque, Andrew Badwal, Mindy Levine

Chemistry Faculty Publications

Cyclodextrins facilitate non-covalent fluorescence energy transfer from a variety of pesticides to high quantum-yield fluorophores, resulting in a rapid, sensitive detection scheme for these compounds with detection limits as low as two micromolar. Such a facile detection tool has significant potential applications in agriculture and public health research.

Satellite Based Assessment Of Hydroclimatic Conditions Related To Cholera In Zimbabwe, Antarpreet Jutla, Haidar Aldaach, Hannah Billian, Ali S. Akanda, Anwar Huq, Rita Colwell

Civil & Environmental Engineering Faculty Publications

Introduction:

Cholera, an infectious diarrheal disease, has been shown to be associated with large scale hydroclimatic processes. The sudden and sporadic occurrence of epidemic cholera is linked with high mortality rates, in part, due to uncertainty in timing and location of outbreaks. Improved understanding of the relationship between pathogenic abundance and climatic processes allows prediction of disease outbreak to be an achievable goal. In this study, we show association of large scale hydroclimatic processes with the cholera epidemic in Zimbabwe reported to have begun in Chitungwiza, a city in Mashonaland East province, in August, 2008.

Principal Findings:

Climatic factors in …

3d Printed Microtransporters: Compound Micromachines For Spatiotemporally Controlled Delivery Of Therapeutic Agents, Tian-Yun Huang, Mahmut Selman Sakar, Angelo Mao, Andrew Petruska, Xue-Bo Chen, Stephen Kennedy, David Mooney, Bradley J. Nelson

Electrical, Computer, and Biomedical Engineering Faculty Publications

A design methodology is reported to fabricate functional compound micromachines using 3D direct laser writing and selective physical vapor deposition of magnetic materials. Microtransporters with a wirelessly controlled Archimedes screw pumping mechanism are engineered. Spatiotemporally controlled collection, transport, and delivery of microparticles as well as magnetic nanohelices inside microfluidic channels are demonstrated.

Theory And Simulations Of Macromolecular Soft Materials: Linking Molecular Design To Macroscale Morphology And Function, Arthi Jayaraman

Amgen Seminar Series in Chemical Engineering

We use theory and simulation techniques to connect molecular features of macromolecular materials, specifically polymers, to their morphology and macroscopic properties, thereby guiding synthesis of materials for various applications in the energy and biomedical fields.

In the first part of my talk I will present our recent theory and simulation studies of polymer functionalized nanoparticles in polymer nanocomposites. The goal of this work is to control spatial arrangement of nanoparticles in a polymer nanocomposite so as to engineer materials with target mechanical or optical properties. One can tailor the inter-particle interactions and precisely control the assembly of the particles in …

Genome Reconstructions Indicate The Partitioning Of Ecological Functions Inside A Phytoplankton Bloom In The Amundsen Sea, Antarctica, Tom O. Delmont, A. M. Eren, Joseph H. Vineis, Anton F. Post

Graduate School of Oceanography Faculty Publications

Antarctica polynyas support intense phytoplankton blooms, impacting their environment by a substantial depletion of inorganic carbon and nutrients. These blooms are dominated by the colony-forming haptophyte Phaeocystis antarctica and they are accompanied by a distinct bacterial population. Yet, the ecological role these bacteria may play in P. antarctica blooms awaits elucidation of their functional gene pool and of the geochemical activities they support. Here, we report on a metagenome (῀160 million reads) analysis of the microbial community associated with a P. antarctica bloom event in the Amundsen Sea polynya (West Antarctica). Genomes of the most abundant Bacteroidetes and Proteobacteria populations …

Curricular Affairs Committee Minutes September 21, 2015, University Of Rhode Island Faculty Senate

Faculty Senate Committee Reports and Appendices

No abstract provided.

2015-09 Library Impact Statement For Bio 401x Survey Of Tropical Ecotourism, Michael Cerbo

Collection Development Reports and Documents

Library Impact Statement submitted in response to new course proposal for BIO 401X Survey of Tropical Ecotourism. This class was supported with no need for additional resources. Responding library faculty: Michael Cerbo. Requesting faculty: Brad Wetherbee.