Digital Commons Network^™

Nephromyces Encodes A Urate Metabolism Pathway And Predicted Peroxisomes, Demonstrating These Are Not Ancient Losses Of Apicomplexans, Christopher Paight, Claudio H. Slamovits, Mary Beth Saffo, Christopher E. Lane

Biological Sciences Faculty Publications

The Phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasitic sister taxon, Cardiosporidium, revealing an ancestral purine degradation pathway thought to have been lost early in apicomplexan evolution. The predicted localization of many of the purine degradation enzymes to peroxisomes, and the in silico identification of a full set of peroxisome proteins, indicates that loss of both features in other …

Tapestry Of Non-Equilibrium Phenomenon In Colloidal Domain: From Directed Assembly To Emergent Behavior, Bhuvnesh Bharti

Amgen Seminar Series in Chemical Engineering

The multiscale self-assembly of atoms, molecules, and particles is the origin of all physical mesoscopic matter. The spatial organization, symmetry, and physical properties of the assembled structures are determined by thermodynamic characteristics of their building blocks. Colloidal particles are emerging as models for understanding governing principles of directed-assembly and non-equilibrium response of advanced materials. Here, I will present the concept of using internal and external field driven interactions to direct the assembly and spatial migration of colloids. First, I will present the principle of using magnetostatic interactions to direct surface patterning using sessile drop drying. In droplets of magnetite nanoparticles, …

Development And Validation Of A Simple Convenience Store Shelf Audit, Tanya M. Horacek, Elif Dede Yildirim, Erin Kelly, Adrienne A. White, Karla P. Shelnutt, Kristin Riggsbee, Melissa D. Olfert, Jesse Stabile Morrell, Anne E. Mathews, Terezie T. Mosby, Tandalayo Kidd, Kendra Kattelmann, Geoffrey Greene, Lisa Franzen-Castle, Sarah Colby, Carol Byrd-Bredbenner, Onikia Brown

Nutrition Faculty Publications

Background This paper describes the development, reliability, and convergent validity of a practical tool—the Convenience Store Supportive Healthy Environment for Life-Promoting Food (SHELF) Audit. Methods Audit items included: a variety of fresh, processed, and frozen fruits and vegetables; low-fat dairy products; healthy staples and frozen meals; healthy food incentive programs; items sold in check-out areas; portion/cup sizes; and pricing. Each audit item was scored using a five-point semantic-differential scale (1 = provides little or no support for healthful foods to 5 = provides high support for healthful foods). Convergent validity was examined by comparing the SHELF audit to Ghirardelli et …

Fake Or Visual Trickery? Understanding The Quantitative Visual Rhetoric In The News, Rohit Mehta, Lynette Deaun Guzmán

Journal of Media Literacy Education

In online and video/television spaces, news media discourses incorporate multimodal design as a discursive move capable of steering meaning toward desirable implications. Around the 2016 U.S. presidential elections, while polarized news outlets made their positionality on the candidates obvious, more neutral or central news outlets revealed their preferences through subtle multimodal design choices. One of these design choices is using a quantitative visual rhetoric: persuasive multimodal moves that draw on quantification through visual, spatial, and textual manipulation—involving the choice of data representation, visual images, and illustrations, (im)balance between numeric and alphabetic texts, and general quantitative narrative. This quantitative visual rhetoric …

Media Literacy, Democracy, And The Challenge Of Fake News, Lance E. Mason, Dan Krutka, Jeremy Stoddard

Journal of Media Literacy Education

In this essay, the authors offer a context for discussions about fake news, democracy, and considerations for media literacy education. Drawing on media ecology and critical media studies, they highlight the longer history of fake news and how this concept cannot be separated from the media technologies in which cultures grow. They discuss current iterations of this phenomenon alongside the effects of social media and offer a preview of the special issue.

Perceptions Of Commercial And Recreational Fishers On The Potential Ecological Impacts Of The Block Island Wind Farm (Us), Talya S. Ten Brink, Tracey Dalton

Marine Affairs Faculty Publications

Offshore wind is gaining momentum in the United States as a viable source for meeting domestic energy needs. Although offshore wind farms have been developed in Europe and Asia, the Block Island Wind Farm (BIWF) is the first offshore wind farm built in North America. To improve marine resource management, it is critical to understand the impacts of the wind farm on marine resource users in context. Little is known about the impacts of offshore wind farms on marine resource users in the United States. This study investigates recreational and commercial fishers' perceptions of the impacts of the BIWF on …

Ms In Cytopathology, Joanna Burkhardt

Library Impact Statements

No abstract provided.

Microbiomes, Biofilms And Bacterial Communities Cmb 420x, Michael Cerbo

Library Impact Statements

No abstract provided.

Bs In Biotechnology, Joanna Burkhardt

Library Impact Statements

No abstract provided.

The Past, Present, And Future Of The Hemlock Woolly Adelgid (Adelges Tsugae) And Its Ecological Interactions With Eastern Hemlock (Tsuga Canadensis) Forests, Aaron M. Ellison, David A. Orwig, Matthew C. Fitzpatrick, Evan L. Preisser

Biological Sciences Faculty Publications

The nonnative hemlock woolly adelgid is steadily killing eastern hemlock trees in many parts of eastern North America. We summarize impacts of the adelgid on these forest foundation species; review previous models and analyses of adelgid spread dynamics; and examine how previous forecasts of adelgid spread and ecosystem dynamics compare with current conditions. The adelgid has reset successional sequences, homogenized biological diversity at landscape scales, altered hydrological dynamics, and changed forest stands from carbon sinks into carbon sources. A new model better predicts spread of the adelgid in the south and west of the range of hemlock, but still under-predicts …

Diffusion And Stability Of Magnetic Nanoparticles In Complex And Biological Fluids, Carlos Rinaldi

Amgen Seminar Series in Chemical Engineering

Magnetic nanoparticles are of interest in a variety of applications that take advantage of their manipulation using externally applied magnetic fields. In this talk I will summarize our recent work on characterizing the diffusion and stability of magnetic nanoparticles in complex and biological fluids through their response to time-varying magnetic fields. I will discuss the physical principles of this measurement technique and then demonstrate how quantitative measurements can be made accurately in simple fluids. Then I will show results for nanoparticles suspended in complex fluids, such as gelling solutions, polymer solutions, and polymer melts. Finally, I will present results for …

Communicating Science Through Data Visualization Bio 230g, Michael Cerbo

Library Impact Statements

No abstract provided.

Curricular Report No. 2018-19-3 From The Graduate Council To The Faculty Senate, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

Biodiversity Assessments: Origin Matters, Aníbal Pauchard, Laura A. Meyerson, Sven Bacher, Tim M. Blackburn, Giuseppe Brundu, Marc W. Cadotte, Franck Courchamp, Franz Essl, Piero Genovesi, Sylvia Haider, Nick D. Holmes, Philip E. Hulme, Jonathan M. Jeschke, Julie L. Lockwood, Ana Novoa, Martin A. Nuñez, Duane A. Peltzer, Petr Pyšek, David M. Richardson, Daniel Simberloff, Kevin Smith, Brian W. Van Wilgen, Montserrat Vilà, John R. U. Wilson, Marten Winter, Rafael D. Zenni

Natural Resources Science Faculty Publications

No abstract provided.

Techniques In Medicinal Chemistry And Molecular Biology Bps 451, Joanna Burkhardt

Library Impact Statements

No abstract provided.

Environmental Health And Saafety For Scientists Bps 357x, Joanna Burkhardt

Library Impact Statements

No abstract provided.

All That Is Gold Does Not Glitter' - Environmental Applications Of Gold Enabled Plasmonics, Peter J. Vikesland

Amgen Seminar Series in Chemical Engineering

Clean air and clean water are the cornerstones of environmental engineering and environmental science. To assure the quality of these matrices, we currently rely upon a broad range of monitoring techniques - many of which are outdated, unreliable, or excessively expensive. Recent advances in both nanotechnology and biotechnology, however, are poised to provide novel and previously unattainable alternatives that have the potential to be more sensitive as well as more cost-effective than many existing methods. In this presentation, we will present work conducted to develop gold enabled plasmonic platforms that facilitate detection of inorganic, organic, biologic, and nanoparticulate contaminants. As …

Mechanical Regulation Of Cancer Cell Angiogenic Activity, Gargi Ghosh

Amgen Seminar Series in Chemical Engineering

Angiogenesis is a requisite not only for tumors to grow beyond 1-2 mm³ and meet their insatiable metabolic demands but also to act as conduits for cancer cells to reach distant organs and form metastatic lesions. Limited clinical efficacy of angiogenesis inhibitors highlights the need to identify new therapies that can either act alone or synergistically to suppress tumor vascularization. Even though the extracellular matrices (ECM) of solid tumors are stiffer than the native tissue and mechanotransduction events are known to impact tumor progression by altering cell-matrix interactions, whether matrix stiffening impacts the angiogenic activity of cancer cells is …

Curriculum And Standards Committee Report #2018-19-2: Curricular Changes, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

Curricular Report No. 2018-19-2 From The Graduate Council To The Faculty Senate: Curricular Changes, University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

The Open Science Framework & Reproducible Research: A New Space For Scholars & Librarians, Amanda Izenstark, Andrée Rathemacher

Technical Services Faculty Presentations

Slides from a presentation, "The Open Science Framework & Reproducible Research: A New Space for Scholars & Librarians," presented at the NELA & RILA Joint 2018 Annual Conference, Welcome: The Library is Your Space, on October 22, 2018 in Warwick, Rhode Island.

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Room: Greenwich

The Open Science Framework is a tool created to help address two crises in research: transparency and reproducibility. In this session, learn more about the reproducibility crisis and how librarians’ knowledge of the Open Science Framework can help researchers at all levels improve and share their work.

ALS Academic Librarians Section

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Additional files include …

Discovering In Vivo Cytokine-Eqtl Interactions From A Lupus Clinical Trial, Emma E. Davenport, Tiffany Amariuta, Maria Gutierrez-Arcelus, Kamil Slowikowski, Harm Jan Westra, Yang Luo, Ciyue Shen, Deepak A. Rao, Ying Zhang, Stephen Pearson, David Von Schack, Jean S. Beebe, Nan Bing, Sally John, Michael S. Vincent, Baohong Zhang, Soumya Raychaudhuri

Cell and Molecular Biology Faculty Publications

Background: Cytokines are critical to human disease and are attractive therapeutic targets given their widespread influence on gene regulation and transcription. Defining the downstream regulatory mechanisms influenced by cytokines is central to defining drug and disease mechanisms. One promising strategy is to use interactions between expression quantitative trait loci (eQTLs) and cytokine levels to define target genes and mechanisms. Results: In a clinical trial for anti-IL-6 in patients with systemic lupus erythematosus, we measure interferon (IFN) status, anti-IL-6 drug exposure, and whole blood genome-wide gene expression at three time points. We show that repeat transcriptomic measurements increases the number of …

Recent Simulation Methods For Resolving Molecular Details In Thermodynamics And Kinetics, Cameron F. Abrams

Amgen Seminar Series in Chemical Engineering

Molecular dynamics (MD) simulations are increasingly powerful tools for augmented thinking about molecular-level phenomena and their links to macroscopic properties. Fundamentally, MD propagates atomic positions and velocities by numerical integration of equations of motion subject to forces representing interatomic interactions. Unfortunately, even with present day computational power, it is nearly impossible to directly observe phenomena that have natural timescales of greater than about a microsecond or length scales greater than a few tens of nanometers using MD. This is because the ceaseless thermal agitation resolved by MD only very rarely and unpredictably rectifies itself along productive directions in some more …

Curriculum And Standards Committee Report #2018-19-2 (Courses), University Of Rhode Island Faculty Senate

Faculty Senate Bills

No abstract provided.

Seminar In Biological Sciences Bio 266x, Michael Cerbo

Library Impact Statements

No abstract provided.

Electric Field Assisted Hydrodynamic Studies On Emulsion Droplets; From Fundamental To Application, Jinkee Lee

Amgen Seminar Series in Chemical Engineering

We studied experimentally, theoretically, and numerically how electrohydrodynamic deformation and breakup of emulsion droplets occurs under a direct current electric field. Numerical simulation was performed by coupling Navier Stokes equation with governing equations of leaky dielectrics and interface tracking by level set method. Experiments were conducted using high speed camera and high precision voltage supplier. A single emulsion droplet breaks either before showing the slow deformation stage or rapidly. For the droplet breakup, sufficiently large Maxwell stresses are essential in comparison with the capillary pressure. For a double emulsion droplet, it shows that there are four distinct modes of breakup …

Trichophycins B–F, Chlorovinylidene-Containing Polyketides Isolated From A Cyanobacterial Bloom, Matthew Bertin, Josep Sauri, Yizhou Liu, Christopher W. Via, Alexandre F. Roduit, R. Thomas Williamson

Biomedical and Pharmaceutical Sciences Faculty Publications

NMR-guided isolation (based on 1D ¹H and ¹³C NMR resonances consistent with a chlorovinylidene moiety) resulted in the characterization of five new highly functionalized polyketides, trichophycins B-F (1-5) and one non-chlorinated metabolite tricholactone (6) from a collection of Trichodesmium bloom material from the Gulf of Mexico. The planar structures of 1-6 were determined using 1D and 2D NMR spectroscopy, mass spectrometry and complementary spectroscopic procedures. Absolute configuration analysis of 1 and 2 were carried out by ¹H NMR analysis of diastereomeric Mosher esters in addition to ECD spectroscopy, J-based configuration analysis and …

A Dexterous, Glove-Based Teleoperable Low-Power Soft Robotic Arm For Delicate Deep-Sea Biological Exploration, Brennan Phillips, Kaitlyn P. Becker, Shunichi Kurumaya, Kevin C. Galloway, Griffin Whittredge, Daniel M. Vogt, Clark B. Teeple, Michelle H. Rosen, Vincent A. Pieribone, David F. Gruber, Robert J. Wood

Ocean Engineering Faculty Publications

Modern marine biologists seeking to study or interact with deep-sea organisms are confronted with few options beyond industrial robotic arms, claws, and suction samplers. This limits biological interactions to a subset of “rugged” and mostly immotile fauna. As the deep sea is one of the most biologically diverse and least studied ecosystems on the planet, there is much room for innovation in facilitating delicate interactions with a multitude of organisms. The biodiversity and physiology of shallow marine systems, such as coral reefs, are common study targets due to the easier nature of access; SCUBA diving allows for in situ delicate …

An Essential Staphylococcus Aureus Cell Division Protein Directly Regulates Ftsz Dynamics, Prahathees J. Eswara, Robert S. Brzozowski, Marissa G. Viola, Gianni Graham, Catherine Spanoudis, Catherine Trebino, Jyoti Jha, Joseph I. Aubee, Karl M. Thompson, Jodi L. Camberg, Kumaran S. Ramamurthi

Cell and Molecular Biology Faculty Publications

Binary fission has been well studied in rod-shaped bacteria, but the mechanisms underlying cell division in spherical bacteria are poorly understood. Rod-shaped bacteria harbor regulatory proteins that place and remodel the division machinery during cytokinesis. In the spherical human pathogen Staphylococcus aureus, we found that the essential protein GpsB localizes to mid-cell during cell division and co-constricts with the division machinery. Depletion of GpsB arrested cell division and led to cell lysis, whereas overproduction of GpsB inhibited cell division and led to the formation of enlarged cells. We report that S. aureus GpsB, unlike other Firmicutes GpsB orthologs, directly …

Bayesian Modeling And Inference For Nonignorably Missing Longitudinal Binary Response Data With Applications To Hiv Prevention Trials, Jing Wu, Joseph G. Ibrahim, Minghui Chen, Elizabeth D. Schifano, Jeffrey David Fisher

Computer Science and Statistics Faculty Publications

Missing data are frequently encountered in longitudinal clinical trials. To better monitor and understand the progress over time, one must handle the missing data appropriately and examine whether the missing data mechanism is ignorable or nonignorable. In this article, we develop a new probit model for longitudinal binary response data. It resolves a challenging issue for estimating the variance of the random effects, and substantially improves the convergence and mixing of the Gibbs sampling algorithm. We show that when improper uniform priors are specified for the regression coefficients of the joint multinomial model via a sequence of one-dimensional conditional distributions …