Digital Commons Network^™

The Good 5 Cent Cigar (11/28/2012), 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.

Rare-Event Sampling: Occupation-Based Performance Measures For Parallel Tempering And Infinite Swapping Monte Carlo Methods, J. D. Doll, Nuria Plattner, David L. Freeman, Yufei Lu, Paul Dupuis

Chemistry Faculty Publications

In the present paper we identify a rigorous property of a number of tempering-based Monte Carlo sampling methods, including parallel tempering as well as partial and infinite swapping. Based on this property we develop a variety of performance measures for such rare-event sampling methods that are broadly applicable, informative, and straightforward to implement. We illustrate the use of these performance measures with a series of applications involving the equilibrium properties of simple Lennard-Jones clusters, applications for which the performance levels of partial and infinite swapping approaches are found to be higher than those of conventional parallel tempering.

Report Of The Ad Hoc Committee On Open Access, Andree Rathemacher, Laura Beauvais, Corey Lang, Julia Lovett, Louis Kirschenbaum

Technical Services Reports and Statistics

Report of the Ad Hoc Committee on Open Access, finalized November 27, 2012 and presented to the University of Rhode Island Faculty Senate on February 21, 2013.

The Ad Hoc Committee on Open Access was charged by the Faculty Senate Executive Committee to "look at some of the issues of Open Access in scholarly communication, look at some solutions, and present suggestions as to what approach would best fit URI's needs and how that might be realized."

The Ad Hoc Committee on Open Access recommended that the University of Rhode Island, through a vote of the Faculty Senate, adopt an …

Unusual Sequence Effects On Nucleotide Excision Repair Of Arylamine Lesions: Dna Bending/Distortion As A Primary Recognition Factor, Vipin Jain, Benjamin Hilton, Bin Lin, Satyakam Patnaik, Fengting Liang, Eva Darian, Yue Zou, Alexander D. Mackerell Jr., Bongsup P. Cho

Biomedical and Pharmaceutical Sciences Faculty Publications

The environmental arylamine mutagens are implicated in the etiology of various sporadic human cancers. Arylamine-modified dG lesions were studied in two fully paired 11-mer duplexes with a -G*C N- sequence context, in which G* is a C8-substituted dG adduct derived from fluorinated analogs of 4-aminobiphenyl (FABP), 2-aminofluorene (FAF) or 2-acetylaminofluorene (FAAF), and N is either dA or dT. The FABP and FAF lesions exist in a simple mixture of ‘stacked’ (S) and ‘B-type’ (B) conformers, whereas the N-acetylated FAAF also samples a ‘wedge’ (W) conformer. FAAF is repaired three to four times more efficiently than FABP and FAF. A …

Acculturation And Gestational Weight Gain In A Predominantly Puerto Rican Population, Alison Tovar, Lisa Chasan-Taber, Odilia I. Bermudez, Raymond R. Hyatt, Aviva Must

Nutrition Faculty Publications

Background:

Identifying risk factors that affect excess weight gain during pregnancy is critical, especially among women who are at a higher risk for obesity. The goal of this study was to determine if acculturation, a possible risk factor, was associated with gestational weight gain in a predominantly Puerto Rican population.

Methods:

We utilized data from Proyecto Buena Salud, a prospective cohort study of Hispanic women in Western Massachusetts, United States. Height, weight and gestational age were abstracted from medical records among participants with full-term pregnancies (n=952). Gestational weight gain was calculated as the difference between delivery and prepregnancy weight. Acculturation …

The Five Hundredth Report Of The Curricular Affairs Committee., University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

The Good 5 Cent Cigar (11/15/2012), 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.

Identifying Reference Genes With Stable Expression From High Throughput Sequence Data, Harriet Alexander, Bethany D. Jenkins, Tatiana A. Rynearson, Mak A. Saito, Melissa L. Mercier, Sonya T. Dyhrman

Graduate School of Oceanography Faculty Publications

Genes that are constitutively expressed across multiple environmental stimuli are crucial to quantifying differentially expressed genes, particularly when employing quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) assays. However, the identification of these potential reference genes in non-model organisms is challenging and is often guided by expression patterns in distantly related organisms. Here, transcriptome datasets from the diatom Thalassiosira pseudonana grown under replete, phosphorus-limited, iron-limited, and phosphorus and iron co-limited nutrient regimes were analyzed through literature-based searches for homologous reference genes, k-means clustering, and analysis of sequence counts (ASC) to identify putative reference genes. A total of 9759 genes were identified …

The Good 5 Cent Cigar (11/8/2012), 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.

Molecular Subdivision Of The Marine Diatom Thalassiosira Rotula In Relation To Geographic Distribution, Genome Size, And Physiology, Kerry A. Whittaker, Dayna R. Rignanese, Robert J. Olson, Tatiana A. Rynearson

Graduate School of Oceanography Faculty Publications

Background:

Marine phytoplankton drift passively with currents, have high dispersal potentials and can be comprised of morphologically cryptic species. To examine molecular subdivision in the marine diatom Thalassiosira rotula, variations in rDNA sequence, genome size, and growth rate were examined among isolates collected from the Atlantic and Pacific Ocean basins. Analyses of rDNA included T. gravida because morphological studies have argued that T. rotula and T. gravida are conspecific.

Results:

Culture collection isolates of T. gravida and T. rotula diverged by 7.0 ± 0.3% at the ITS1 and by 0.8 ± 0.03% at the 28S. Within T. rotula, field …

The Good 5 Cent Cigar (10/25/2012), 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.

The Good 5 Cent Cigar (10/24/2012), 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.

Pollen Sterility—A Promising Approach To Gene Confinement And Breeding For Genetically Modified Bioenergy Crops, Joel P. Hague, Stephen L. Dellaporta, Maria A. Moreno, Chip Longo, Kimberly Nelson, Albert P. Kausch

Cell and Molecular Biology Faculty Publications

Advanced genetic and biotechnology tools will be required to realize the full potential of food and bioenergy crops. Given current regulatory concerns, many transgenic traits might never be deregulated for commercial release without a robust gene confinement strategy in place. The potential for transgene flow from genetically modified (GM) crops is widely known. Pollen-mediated transfer is a major component of gene flow in flowering plants and therefore a potential avenue for the escape of transgenes from GM crops. One approach for preventing and/or mitigating transgene flow is the production of trait linked pollen sterility. To evaluate the feasibility of generating …

Global Distribution Of Microbial Abundance And Biomass In Subseafloor Sediment, Jens Kallmeyer, Robert Pockalny, Rishi Ram Adhikari, David C. Smith, Steven D'Hondt

Graduate School of Oceanography Faculty Publications

The global geographic distribution of subseafloor sedimentary microbes and the cause(s) of that distribution are largely unexplored. Here, we show that total microbial cell abundance in subseafloor sediment varies between sites by ca. five orders of magnitude. This variation is strongly correlated with mean sedimentation rate and distance from land. Based on these correlations, we estimate global subseafloor sedimentary microbial abundance to be 2.9⋅10²⁹ cells [corresponding to 4.1 petagram (Pg) C and ∼0.6% of Earth’s total living biomass]. This estimate of subseafloor sedimentary microbial abundance is roughly equal to previous estimates of total microbial abundance in seawater and total …

Urinformed October 2012, Urinformed

URInformed: The URI Employees' Newsletter

No abstract provided.

Caring For Lesbian, Gay, Bisexual, And Transsexual Parents And Their Children, Gary J Burkholder, Pat Burbank

College of Nursing Faculty Publications

Estimates indicate that about 1% of all households are headed by gay and lesbian parents and that about 19.4% of these households report having children under the age of 18 years at home. There are a number of social, legal, and health care issues faced by lesbian, gay, bisexual and transgender (LGBT) families and their children. The purpose of this article is to provide information to health care professionals that can help them to better address the health care needs of LGBT families. Included are resources that nurses can use to understand the complex issues facing LGBT families.

Predator-Induced Fleeing Behaviors In Phytoplankton: A New Mechanism For Harmful Algal Bloom Formation?, Elizabeth L. Harvey, Susanne Menden-Deuer

Graduate School of Oceanography Faculty Publications

In the plankton, heterotrophic microbes encounter and ingest phytoplankton prey, which effectively removes >50% of daily phytoplankton production in the ocean and influences global primary production and biochemical cycling rates. Factors such as size, shape, nutritional value, and presence of chemical deterrents are known to affect predation pressure. Effects of movement behaviors of either predator or prey on predation pressure, and particularly fleeing behaviors in phytoplankton are thus far unknown. Here, we quantified individual 3D movements, population distributions, and survival rates of the toxic phytoplankton species, Heterosigma akashiwo in response to a ciliate predator and predator-derived cues. We observed predator-induced …

Prediction Of In Vivo Efficacy For Cell Cycle Inhibitors Using A Multiscale Tumor Growth Model, Feng Yang

Amgen Seminar Series in Chemical Engineering

Model-based drug development (MBDD) has been recognized as a new paradigm and mindset that will change the landscape of drug development. As a part of the wide Quantitative Pharmacology (QP) initiative within Lilly, we developed this cell-cycle based, multi-scale tumor growth model to predict In Vivo efficacy for Lilly cell cycle inhibitors. Cell cycle is a key area of focus in the Lilly oncology portfolio, reflecting essential mechanisms underlying tumor growth. We integrated diverse datasets such as pharmacokinetic data, tumor growth data, in vitro/invo flow cytometry data, and a variety of cell cycle biomarkers such as pTCTPs46, pHH3s10(mitotic marker), TUNEL(apoptotic …

Structure And Composition Of Leachfield Bacterial Communities: Role Of Soil Texture, Depth And Septic Tank Effluent Inputs, José A. Amador, Janet A. Atoyan

Natural Resources Science Faculty Publications

Although groundwater quality depends on microbial processes in the soil treatment area (STA) of onsite wastewater treatment systems (OWTS), our understanding of the development of these microbial communities is limited. We examined the bacterial communities of sand, sandy loam, and clay STAs at different depths in response to septic tank effluent (STE) addition using mesocosms. Terminal restriction fragment length polymorphism (TRFLP) analysis was used to compare the bacterial community structure and composition of STE, native soil prior to STE addition (UNX) and soil exposed to STE (EXP). Principal component analysis separated communities with depth in sand but not in sandy …

Journal Usage Report For Fiscal Year 2012, Michael A. Cerbo Ii

Technical Services Reports and Statistics

Journal usage for the University Libraries are listed alphabetically by authority title. The report includes the usage statistics taken from each vendor and incorporated in Serials Solutions 360 Counter.

The report is broken down monthly for fiscal year 2012 and shows each journal's usage per month and the cost per use for the year, if available.

Nanoparticles For Cancer Treatment, Wei Lu

Biomedical and Pharmaceutical Sciences Faculty Publications

No abstract provided.

Pharmacy Research At Uri: Bile Acids And Bile Salt Export Pump: Physiology And Pathology, Ruitang Deng

Biomedical and Pharmaceutical Sciences Faculty Publications

No abstract provided.

A Ten-Year Experience Of A Pharmacist Consulting Team For Statewide Bioterrorism And Emergency Preparedness, Brett Feret, P. Bratberg

Pharmacy Practice and Clinical Research Faculty Publications

No abstract provided.

Going Deep For Drug Discovery: An Ocean To Bedside Approach To Explore Sub-Seafloor Microbes For The Next Generation Of Antibiotics, Stephanie Forschner-Dancause, L. Laplante, David C. Smith, David C. Rowley

Pharmacy Practice and Clinical Research Faculty Publications

No abstract provided.

Serials Solutions Click-Through Statistics By Provider And Database 2011-2012, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics on the total number of database and journal-level clicks, by provider and database, of Serials Solutions tools at the University of Rhode Island Libraries by month for 2011-2012. Clicks may have originated from the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/), from OpenURL links ("360 Link"), or the 856 fields of Serials Solutions-generated MARC records ("360 MARC Updates").

Serials Solutions Subject Search Report 2011-2012, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics on the total number of Serials Solutions subject searches at the University of Rhode Island Libraries by month for 2011-2012. Shows how many times the A-Z full text electronic journal list (at http://zu4tq4pb5v.search.serialssolutions.com/) was browsed by specific subjects.

Ebsco Historical Price Analysis Report 2012, Andrée J. Rathemacher

Technical Services Reports and Statistics

This report lists all periodicals subscribed to in 2012 through EBSCO Subscription Services by the University Libraries, University of Rhode Island. This report analyzes prices over a five-year period. Information provided includes title, frequency, price in each of the last five years, and percent changes in price over five years. The list is sorted by LC Classification to better show the price changes in each discipline/subject area. The associated spreadsheet includes additional information such as ISSN, Library of Congress Classification number, country of origin, publisher name, and title format (print or online). The spreadsheet may be downloaded and sorted by …

Ebsco Library Of Congress Classification Report 2012, Andrée Rathemacher

Technical Services Reports and Statistics

This report lists all periodicals subscribed to in 2012 through EBSCO Subscription Services by the University Libraries, University of Rhode Island. Information provided includes title, ISSN, Library of Congress Classification number and name, and account number (for URI, Pell, or CCE). The list is sorted by LC Classification to better show the journals that support each discipline/subject area. Not included here are titles available through online journal packages and reference databases, which now comprise the majority of the Libraries' subscriptions. The journals listed here are those to which the Libraries subscribe to individually, title-by-title, through EBSCO.

Acquisitions Unit Annual Report 2011-2012, Andrée J. Rathemacher

Technical Services Reports and Statistics

Annual Report of the Acquisitions Unit, University Libraries, University of Rhode Island for FY12. Covers personnel, work flow, special projects, serial and monograph acquisitions, and goals for the coming year. Supplemental files include data on library materials expenditures by a number of variables as well as important working documents from the year.

Reference Databases Usage Statistics 2011-2012, 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 2011 through June 2012. Includes COUNTER-compliant data on sessions, searches, turnaways, full text articles downloaded, cost per search, and other metrics.