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Usage Statistics: Project Counter R5 Tr_J1 Report Fy2020 - Journal Requests (Excluding Oa_Gold) By Title, Andrée Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report TR_J1 for the University of Rhode Island for the period from July 1, 2019 - June 30, 2020. The TR_J1 report is defined as "Journal Requests (Excluding OA_Gold)." This report presents an annual total only of e-journal usage by title.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

• Total Item Requests - 846,964
• Unique Item Requests - 620,899

Usage Statistics: Project Counter R5 Tr_B1 Report Fy2020 - Book Requests (Excluding Oa_Gold) By Title, Andrée Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report TR_B1 for the University of Rhode Island for the period from July 1, 2019 - June 30, 2020. The TR_B1 report is defined as "Book Requests (Excluding OA_Gold)." This report presents an annual total only of e-book usage by title.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

• Total Item Requests - 70,859
• Unique Title Requests - 31,282

Usage Statistics: Project Counter R5 Dr_D1 Report Fy2020 - Database Search And Item Usage, Andrée Rathemacher

Technical Services Reports and Statistics

Project COUNTER R5 Report DR_D1 for the University of Rhode Island for the period from July 1, 2019 - June 30, 2020. The DR_D1 report is defined as "Database Search and Item Usage." This report presents an annual total only.

File for download is Excel spreadsheet generated by Alma Analytics.

Results:

• Searches Automated - 236,041
• Searches Federated - 12,211
• Searches Regular - 1,077,009
• Total Item Investigations - 637,104
• Total Item Requests - 291,719

Evolution Of Protein-Mediated Biomineralization In Scleractinian Corals, Tal Zaquin, Assaf Malik, Jeana L. Drake, Hollie M. Putnam, Tali Mass

Biological Sciences Faculty Publications

While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process …

Spatial Scaling Properties Of Coral Reef Benthic Communities, Helen V. Ford, Jamison M. Gove, Andrew J. Davies, Nicholas A.J. Graham, John R. Healey, Eric J. Conklin, Gareth J. Williams

Biological Sciences Faculty Publications

The spatial structure of ecological communities on tropical coral reefs across seascapes and geographies have historically been poorly understood. Here we addressed this for the first time using spatially expansive and thematically resolved benthic community data collected around five uninhabited central Pacific oceanic islands, spanning 6° latitude and 17° longitude. Using towed-diver digital image surveys over ~140 linear km of shallow (8–20 m depth) tropical reef, we highlight the autocorrelated nature of coral reef seascapes. Benthic functional groups and hard coral morphologies displayed significant spatial clustering (positive autocorrelation) up to kilometre-scales around all islands, in some instances dominating entire sections …

Polyamines Drive Myeloid Cell Survival By Buffering Intracellular Ph To Promote Immunosuppression In Glioblastoma, Jason Miska, Aida Rashidi, Catalina Lee-Chang, Peng Gao, Aurora Lopez-Rosas, Peng Zhang, Rachel Burga, Brandyn Castro, Ting Xiao, Yu Han, David Hou, Samay Sampat, Alex Cordero, Joshua S. Stoolman, Craig M. Horbinski, Mark Burns, Yana Reshetnyak, Navdeep S. Chandel, Maciej S. Lesniak

Physics Faculty Publications

Glioblastoma is characterized by the robust infiltration of immunosuppressive tumor-associated myeloid cells (TAMCs). It is not fully understood how TAMCs survive in the acidic tumor microenvironment to cause immunosuppression in glioblastoma. Metabolic and RNA-seq analysis of TAMCs revealed that the arginine-ornithine-polyamine axis is up-regulated in glioblastoma TAMCs but not in tumor-infiltrating CD8⁺ T cells. Active de novo synthesis of highly basic polyamines within TAMCs efficiently buffered low intracellular pH to support the survival of these immunosuppressive cells in the harsh acidic environment of solid tumors. Administration of difluoromethylornithine (DFMO), a clinically approved inhibitor of polyamine generation, enhanced animal survival …

Effect Of Ferrate And Monochloramine Disinfection On The Physiological And Transcriptomic Response Of Escherichia Coli At Late Stationary Phase, Sahar Daer, Joseph E. Goodwill, Kaoru Ikuma

Civil & Environmental Engineering Faculty Publications

Biological mechanisms of disinfection not only vary by disinfectant but also remain not well understood. We investigated the physiological and transcriptomic response of Escherichia coli at late stationary phase to ferrate and monochloramine in amended lake water. Although ferrate and monochloramine treatments similarly reduced culturable cell concentrations by 3-log10, 64% and 11% of treated cells were viable following monochloramine and ferrate treatment, respectively. This observed induction of viable but non-culturable (VBNC) state following monochloramine treatment but not ferrate is attributed to slower monochloramine disinfection kinetics (by 2.8 times) compared to ferrate. Transcriptomic analysis of E. coli at 15 min of …

Impact Of Increased Nutrients And Lowered Ph On Photosynthesis And Growth Of Three Marine Phytoplankton Communities From The Coastal South West Atlantic (Patagonia, Argentina), Takako Masuda, Ondřej Prášil, Virginia E. Villafañe, Macarena S. Valiñas, Keisuke Inomura, E. Walter Helbling

Graduate School of Oceanography Faculty Publications

Effect of global change variables on the structure and photosynthesis of phytoplankton communities was evaluated in three different sites of the Patagonian coast of Argentina: enclosed bay (Puerto Madryn, PM), estuarine (Playa Unión, PU), and open waters (Isla Escondida, IE). We exposed samples to two contrasting scenarios: Present (nutrients at in situ levels) vs. Future (with lowered pH and higher nutrients inputs), and determined growth and photosynthetic responses after 2 days of acclimation. Under the Future condition phytoplankton growth was higher in the estuarine site compared to those in PM and IE. This effect was the most pronounced on large …

Validation Of Oil Trajectory And Fate Modeling Of The Deepwater Horizon Oil Spill, Deborah P. French-Mccay, Malcolm Spaulding, Deborah Crowley, Daniel Mendelsohn, Jeremy Fontenault, Matthew Horn

Ocean Engineering Faculty Publications

Trajectory and fate modeling of the oil released during the Deepwater Horizon blowout was performed for April to September of 2010 using a variety of input data sets, including combinations of seven hydrodynamic and four wind models, to determine the inputs leading to the best agreement with observations and to evaluate their reliability for quantifying exposure of marine resources to floating and subsurface oil. Remote sensing (satellite imagery) data were used to estimate the amount and distribution of floating oil over time for comparison with the model’s predictions. The model-predicted locations and amounts of shoreline oiling were compared to documentation …

The Contribution Of Water Radiolysis To Marine Sedimentary Life, Justine F. Sauvage, Ashton Flinders, Arthur J. Spivack, Robert Pockalny, Ann G. Dunlea, Chloe H. Anderson, David C. Smith, Richard W. Murray, Steven D'Hondt

Graduate School of Oceanography Faculty Publications

Water radiolysis continuously produces H₂ and oxidized chemicals in wet sediment and rock. Radiolytic H₂ has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth’s surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H₂ production, amplifying yields by up to 27X …

Evolution Of A Subducted Carbon-Rich Filament On The Edge Of The North Atlantic Gyre, Alexis R. Johnson, Melissa M. Omand

Graduate School of Oceanography Faculty Publications

The oceanic biological carbon pump encompasses a variety of mechanisms by which CO2, fixed into organic form by phytoplankton, is transported from the sunlit surface layers to the interior ocean. Here, we investigate submesoscale and mixed layer subduction, estimated to represent ∼20% of global particulate organic carbon (POC) export. Seven Biogeochemical (BGC) Argo profiling floats were analyzed for evidence of subduction of POC in the North Atlantic Ocean, revealing a pattern in the seasonality. Although vertical processes that give rise to subduction are enhanced during late winter and spring, the bio-optical evidence for intrusions—namely a deep local maxima in POC, …

Ghosts Of Landuse Past: Legacy Effects Of Milldams For Riparian Nitrogen (N) Processing And Water Quality Functions, Shreeram Inamdar, Marc Peipoc, Arthur Gold, Evan Lewis, Johanna Hripto, Melissa Sherman, Kelly Addy, Dorothy Merritts, Jinjun Kan, Peter M. Groffman, Robert Walter, Tara L E Trammel

Natural Resources Science Faculty Publications

Milldams and their legacies have significantly influenced fluvial processes and geomorphology. However, less is known about their effects on riparian zone hydrology, biogeochemistry, and water quality. Here, we discuss the potential effects of existing and breached milldams on riparian nitrogen (N) processing through multiple competing hypotheses and observations from complementary studies. Competing hypotheses characterize riparian zone processes that remove (sink) or release (source) N. Elevated groundwater levels and reducing soil conditions upstream of milldams suggest that riparian zones above dams could be hotspots for N removal via denitrification and plant N uptake. On the other hand, dam removals and subsequent …

Genome-Scale Profiling Reveals Noncoding Loci Carry Higher Proportions Of Concordant Data, Robert Literman, Rachel Schwartz

Biological Sciences Faculty Publications

Many evolutionary relationships remain controversial despite whole-genome sequencing data. These controversies arise in part due to challenges associated with accurately modeling the complex phylogenetic signal coming from genomic regions experiencing distinct evolutionary forces. Here we examine how different regions of the genome support or contradict well-established hypotheses among three mammal groups using millions of orthologous parsimony-informative biallelic sites [PIBS] distributed across primate, rodent, and Pecora genomes. We compared PIBS concordance percentages among locus types (e.g. coding sequences, introns, intergenic regions), and contrasted PIBS utility over evolutionary timescales. Sites derived from noncoding sequences provided more data and proportionally more concordant sites …

Parisitology Bio 331, Michael Cerbo

Library Impact Statements

No abstract provided.

Computational Study Of Helical And Helix-Hinge-Helix Conformations Of An Anti-Microbial Peptide In Solution By Molecular Dynamics And Vibrational Analysis, Faramarz Joodaki, Lenore M. Martin, Michael L. Greenfield

Chemical, Biomolecular, and Materials Engineering Faculty Publications

Many classical antimicrobial peptides adopt an amphipathic helical structure at a water-membrane interface. Prior studies led to the hypothesis that a hinge near the middle of a helical peptide plays an important role in facilitating peptide-membrane interactions.Here, dynamics and vibrations of a designed hybrid antimicrobial peptide LM7-2 in solution were simulated to investigate its hinge formation.Molecular dynamics simulation results on the basis of the CHARMM36 force field showed that the $\alpha$-helix LM7-2 bent around two or three residues near the middle of the peptide, stayed in a helix-hinge-helix conformation for a short period of time, and then returned to a …

Structure Of Erm-Modified 70s Ribosome Reveals The Mechanism Of Macrolide Resistance, Maxim S. Svetlov, Egor A. Syroegin, Elena V. Aleksandrova, Gemma C. Atkinson, Steven Gregory, Alexander S. Mankin, Yury S. Polikanov

Cell and Molecular Biology Faculty Publications

Many antibiotics inhibit bacterial growth by binding to the ribosome and interfering with protein biosynthesis. Macrolides represent one of the most successful classes of ribosome-targeting antibiotics. The main clinically relevant mechanism of resistance to macrolides is dimethylation of the 23S rRNA nucleotide A2058, located in the drug-binding site, a reaction catalyzed by Erm-type rRNA methyltransferases. Here, we present the crystal structure of the Erm-dimethylated 70S ribosome at 2.4 Å resolution, together with the structures of unmethylated 70S ribosome functional complexes alone or in combination with macrolides. Altogether, our structural data do not support previous models and, instead, suggest a principally …

Behavioral And Demographic Responses Of Mule Deer To Energy Development On Winter Range, Joseph M. Northrup, Charles R. Anderson Jr, Brian D. Gerber, George Wittemyer

Natural Resources Science Faculty Publications

Anthropogenic habitat modification is a major driver of global biodiversity loss. In North America, one of the primary sources of habitat modification over the last 2 decades has been exploration for and production of oil and natural gas (hydrocarbon development), which has led to demographic and behavioral impacts to numerous wildlife species. Developing effective measures to mitigate these impacts has become a critical task for wildlife managers and conservation practitioners. However, this task has been hindered by the difficulties involved in identifying and isolating factors driving population responses. Current research on responses of wildlife to development predominantly quantifies behavior, but …

Biological Oceanography Laboratory Ocg 562, Joanna Burkhardt

Library Impact Statements

No abstract provided.

Feasibility Study For Detection Of Retinal Amyloid In Clinical Trials: The Anti-Amyloid Treatment In Asymptomatic Alzheimer's Disease (A4) Trial, Jennifer Ngolab, Michael Donohue, Alison Belsha, Jennifer Salazar, Paula Cohen, Sandhya Jaiswal, Veasna Tan, Devon Gessert, Shaina Korouri, Neelum T. Aggarwal, Jessica Alber, Ken Johnson, Gregory Jicha, Christopher Van Dyck, James Lah, Stephen Salloway, Reisa A. Sperling, Paul S. Aisen, Michael S. Rafii, Robert A. Rissman

Biomedical and Pharmaceutical Sciences Faculty Publications

Introduction: The retina and brain exhibit similar pathologies in patients diagnosed with neurodegenerative diseases. The ability to access the retina through imaging techniques opens the possibility for non-invasive evaluation of Alzheimer's disease (AD) pathology. While retinal amyloid deposits are detected in individuals clinically diagnosed with AD, studies including preclinical individuals are lacking, limiting assessment of the feasibility of retinal imaging as a biomarker for early-stage AD risk detection.

Methods:

In this small cross-sectional study we compare retinal and cerebral amyloid in clinically normal individuals who screened positive for high amyloid levels through positron emission tomography (PET) from the Anti-Amyloid Treatment …

Designing Multifunctional Urban Agroforestry With People In Mind, John Taylor, Sarah Taylor Lovell

Plant Sciences and Entomology Faculty Publications

Urban landscapes combining trees and crops—urban agroforestry (UAF) systems—may offer greater ecological and cultural benefits than annual cropping systems. Interest in UAF is growing, as evidenced by an increasing number of built projects and articles in the popular press and the academic literature on the subject. However, the practice of UAF appears to far outpace research on its scientific underpinnings or its design. Developing sustainable, resilient UAF sites can be challenging because of biophysical and sociocultural conditions unique to the city; however, cities offer opportunities not found in rural environments including the potential to close open nutrient loops between consumers …

Environmental Optima For An Ecosystem Engineer: A Multidisciplinary Trait-Based Approach, Amelia Curd, Aurélien Boyé, Céline Cordier, Fabrice Pernet, Louise B. Firth, Laura E. Bush, Andrew J. Davies, Fernando P. Lima, Claudia Meneghesso, Claudie Quéré, Rui Seabra, Mickaël Vasquez, Stanislas F. Dubois

Biological Sciences Faculty Publications

A complex interplay of biotic and abiotic factors underpins the distribution of species and operates across different levels of biological organization and life history stages. Understanding ecosystem engineer reproductive traits is critical for comprehending and managing the biodiversity-rich habitats they create. Little is known about how the reproduction of the reef-forming worm, Sabellaria alveolata, varies across environmental gradients. By integrating broad-scale environmental data with in-situ physiological data in the form of biochemical traits, we identified and ranked the drivers of intraspecific reproductive trait variability (ITV). ITV was highest in locations with variable environmental conditions, subjected to fluctuating temperature and …

Long-Term Observations Reveal Environmental Conditions And Food Supply Mechanisms At An Arctic Deep-Sea Sponge Ground, Ulrike Hanz, Emyr Martyn Roberts, Gerard Duineveld, Andrew J. Davies, Hans Van Haren, Hans Torre Rapp, Gert-Jan Reichart, Furu Mienis

Biological Sciences Faculty Publications

Deep-sea sponge grounds are hotspots of benthic biomass and diversity. To date, very limited data exist on the range of environmental conditions in areas containing deep-sea sponge grounds and which factors are driving their distribution and sustenance. We investigated oceanographic conditions at a deep-sea sponge ground located on an Arctic Mid-Ocean Ridge seamount. Hydrodynamic measurements were performed along Conductivity-Temperature-Depth transects, and a lander was deployed within the sponge ground that recorded near-bottom physical properties as well as vertical fluxes of organic matter over an annual cycle. The data demonstrate that the sponge ground is found at water temperatures of −0.5°C …

Metabolomic Shifts Associated With Heat Stress In Coral Holobionts, Amanda Williams, Eric N. Chiles, Dennis A. Conetta, Jananan S. Pathmanathan, Phillip A. Cleves, Hollie M. Putnam, Xiaoyang Su, Debashish Bhattacharya

Biological Sciences Faculty Publications

Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is “coral bleaching,” usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and …

Editorial: Marine Environmental Epigenetics, Jose M. Eirin-Lopez, Hollie M. Putnam

Biological Sciences Faculty Publications

No abstract provided.

Fenamates As Potential Therapeutics For Neurodegenerative Disorders, Jaunetta Hill, Nasser H. Zawia

Biomedical and Pharmaceutical Sciences Faculty Publications

Neurodegenerative disorders are desperately lacking treatment options. It is imperative that drug repurposing be considered in the fight against neurodegenerative diseases. Fenamates have been studied for efficacy in treating several neurodegenerative diseases. The purpose of this review is to comprehensively present the past and current research on fenamates in the context of neurodegenerative diseases with a special emphasis on tolfenamic acid and Alzheimer’s disease. Furthermore, this review discusses the major molecular pathways modulated by fenamates.

Potentiation Of Recombinant Np And M1-Induced Cellular Immune Responses And Protection By Physical Radiofrequency Adjuvant, Yibo Li, Zhoufan Li, Yiwen Zhao, Xinyuan Chen

Biomedical and Pharmaceutical Sciences Faculty Publications

Nucleoprotein (NP) and matrix protein 1 (M1) are highly conserved among influenza A viruses and have been attractive targets to develop vaccines to elicit cross-reactive cytotoxic T lymphocytes (CTLs). Yet, external antigens are often presented on major histocompatibility complex class II molecules and elicit humoral immune responses. In this study, we present a physical radiofrequency adjuvant (RFA) to assist recombinant NP and M1 to elicit potent CTL responses. We found recombinant NP/M1 immunization in the presence of RFA could elicit potent anti-NP CTLs and confer significant protection against homologous viral challenges, while NP/M1 immunization alone failed to elicit significant CTL …

Ch. 27: There Is No Evolutionary "Obstetrical Dilemma", Holly M. Dunsworth

Sociology and Anthropology Faculty Publications

No abstract provided.

Is Violence, Violence No Matter Where It Strikes? Adjudicated Boys, Thwarted Belongingness, Perceived Burdensomeness, And Acquired Capability For Suicide, Judy Van Wyk

Sociology and Anthropology Faculty Publications

This study explores treating violence against others as a precursor to self-directed violence. It tests the utility of including violence against others in the measure of acquired capability to test assumptions from the interpersonal theory of violence. Four theoretical hypotheses are assessed that are consistent with the theory: (1) thwarted belongingness (parental abandonment and rejection) and perceived burdensomeness (exposure to parental interpersonal violence and child abuse) independently increase the likelihood of suicidal ideation; (2) the interaction of thwarted belongingness and perceived burdensomeness increases the likelihood of suicidal ideation controlling for other pertinent variables; (3) the three-way interaction of thwarted belongingness, …

Autonomy Of Nations And Indigenous Peoples And The Environmental Release Of Genetically Engineered Animals With Gene Drives, Zahra Meghani

Philosophy Faculty Publications

This article contends that the environmental release of genetically engineered (GE) animals with heritable traits that are patented will present a challenge to the efforts of nations and indigenous peoples to engage in self-determination. The environmental release of such animals has been proposed on the grounds that they could function as public health tools or as solutions to the problem of agricultural insect pests. This article brings into focus two political-economic-legal problems that would arise with the environmental release of such organisms. To address those challenges, it is proposed that nations considering the environmental release of GE animals must take …

An Inexpensive, 3d-Printable Breast Muscle Meter For Field Ornithologists, Luke L. Powell, Adam Metallo, Crinan Jarrett, Nathan W. Cooper, Peter P. Marra, Scott R. Mcwilliams, Ulf Bauchinger, Bryant C. Dossman

Natural Resources Science Faculty Publications

The size of the pectoral muscle is an important component of body condition in birds and has been linked to indices of fitness and migratory performance. Bauchinger et al. (2011. Journal of Ornithology 152: 507–514) developed, calibrated, and validated an aluminum “muscle meter” device that estimates the size of pectoral muscles noninvasively. To make this tool more widely available, we created a CAD model from 3D-scan data of the aluminum muscle meter that can be 3D-printed in durable plastic for ~ $30 USD. We tested this device on seven species of songbirds in Jamaica, The Bahamas, Cameroon, Equatorial Guinea, and …