Digital Commons Network^™

Cloud Shadows Drive Vertical Migrations Of Deep-Dwelling Marine Life, Melissa M. Omand, Deborah K. Steinberg, Karen Stamieszkin

Graduate School of Oceanography Faculty Publications

Many zooplankton and fishes vertically migrate on a diel cycle to avoid predation, moving from their daytime residence in darker, deep waters to prey-rich surface waters to feed at dusk and returning to depth before dawn. Verticalmigrations also occur in response to other processes that modify local light intensity, such as storms, eclipses, and full moons. We observed rapid, high-frequency migrations, spanning up to 60 m, of a diel vertically migrating acoustic scattering layer with a daytime depth of 300 m in the subpolar Northeastern Pacific Ocean. The depth of the layer was significantly correlated, with an ∼5-min lag, to …

Viral Suppression Of Ripk1-Mediated Signaling, Darshika J. Udawatte, Alan L. Rothman

Cell and Molecular Biology Faculty Publications

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) has emerged as a key upstream regulator of cell death and inflammation. RIPK1-mediated signaling governs the outcome of signaling pathways initiated by tumor necrosis factor receptor 1 (TNFR1), Toll-like receptor 3 (TLR3), TLR4, retinoic acid-inducible gene 1 (RIG-I)/melanoma differentiation-associated protein 5 (MDA-5), and Z-binding protein 1 (ZBP1) by signaling for NF-k B activation, mitogen-associated protein kinase (MAPK) and interferon regulatory factor 3/7 (IRF3/7) phosphorylation, and cell death via apoptosis and necroptosis. Both cell death and inflammatory responses play a major role in controlling virus infections. Therefore, viruses have evolved multifaceted mechanisms to exploit host immune …

Biodiversity Of Marine Microbes Is Safeguarded By Phenotypic Heterogeneity In Ecological Traits, Susanne Menden-Deuer, Julie Rowlett, Medet Nursultanov, Sinead Collins, Tatiana Rynearson

Graduate School of Oceanography Faculty Publications

Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both phenomena by investigating a non-cooperative game that interpolates between individual-level competitions and species-level outcomes. We identified all equilibrium strategies of the game. These strategies represent the probability distribution of competitive abilities (e.g. traits) and are characterized by maximal phenotypic heterogeneity. They are also neutral towards each other in the sense that an unlimited number of species can co-exist while competing according to the equilibrium strategies. Whereas prior …

"Going It Alone": Following The Male Cohort Of Survivors Of Sex Trafficking Of The Chab Dai Butterfly Longitudinal Research Project, Jarrett D. Davis, James Havey, Glenn M. Miles, Nhanh Channtha, Sreang Phally, Lim Vanntheary

Dignity: A Journal of Analysis of Exploitation and Violence

Over the past ten years, the Butterfly Longitudinal Research Project has followed 128 survivors of trafficking through their experiences in aftercare, reintegration, and beyond to better understand the recovery and reintegration of trafficking survivors within a Cambodian context. This paper focuses on the 19 males who were available to interview. Despite the project’s wealth of data and analysis, there are notable gaps regarding the male cohort. In response, this paper examines this cohort holistically, considering their statements and broader narratives, merging them with previous collective observations of the Butterfly Project. Throughout this paper, data indicates a pattern of violence among …

“Why Am I The Only One Responsible For The Whole Family?”: Expressions Of Economic Filial Piety And Financial Anxiety Among Female Survivors Of Sex Trafficking In Cambodia, Julia M. Smith-Brake, Lim Vanntheary, Nhanh Channtha

Dignity: A Journal of Analysis of Exploitation and Violence

Filial piety has evolved and spread in different ways throughout Asia, with the common thread of deep respect and gratitude towards one’s parents remaining a very strong cultural value. In Khmer culture, filial piety includes the expectation that daughters and daughters-in-law provide daily assistance to parents and parents-in-law. Financial anxiety includes the worry and negative mental health outcomes associated with financial stressors. This article presents findings from the Butterfly Longitudinal Research Study on themes on filial piety and financial anxiety, combining survey results from across multiple years as well as a thematic analysis of themes from focus group discussions and …

Alma Link Resolver Subject Report 2020-2021, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics for 2020-2021 on the number of OpenURL requests by Library of Congress classification code made to the Ex Libris Alma link resolver for items held by the University of Rhode Island Libraries.

Information provided includes Classification Code, Classifications, Number of Requests, Number of Clicked Requests, and % Clicks from Requests.

Alma Link Resolver Title & Issn Report (Top 500) 2020-2021, Andrée J. Rathemacher

Technical Services Reports and Statistics

Statistics for 2020-2021 on the total number of OpenURL requests by journal title and ISSN made to the Ex Libris Alma link resolver for items held by the University of Rhode Island Libraries. Includes only the top 500 journals.

Information provided includes journal Title, ISSN, EISSN, Number of Requests, Number of Clicked Requests, % Clicks from Requests.

Lake Superior Has Lost Over 90% Of Its Pesticide Hch Load Since 1986, Terry F. Bidleman, Sean Backus, Alice Dove, Rainer Lohmann, Derek Muir, Camilla Teixeira, Liisa Jantunen

Graduate School of Oceanography Faculty Publications

The time trend of α- and γ-hexachlorocyclohexane (HCH) isomers in Lake Superior water was followed from 1986 to 2016, the longest record for any persistent organic pollutant (POP) in Great Lakes water. Dissipation of α-HCH and γ-HCHs was first order, with halving times (t1/2) of 5.7 and 8.5 y, respectively. Loss rates were not significantly different starting a decade later (1996-2016). Concentrations of β-HCH were followed from 1996-2016 and dissipated more slowly (t1/2 = 16 y). In 1986, the lake contained an estimated 98.8 tonnes of α-HCH and 13.2 tonnes of γ-HCH; by 2016, only 2.7% and 7.9% of 1986 …

The Violence Of Postmodern “Gender Identity” Medicine, Heather Brunskell-Evans

Dignity: A Journal of Analysis of Exploitation and Violence

The medical “transition” of children with “gender dysphoria” is increasingly normalized in North America, Western Europe, Australia, New Zealand, and the United Kingdom. Although each country has specific national gender identity development services, the rationale for prescribing hormone treatment is broadly similar. A minority rights paradigm underpinned by postmodern theory has gained traction in the past 10 years and has been successful in influencing public policy, the education of pediatricians, endocrinologists, and mental health professionals. In this view, any response other than an affirmation of the child’s claim to be the opposite sex or “born in the wrong body” is …

Systematic Conservation Planning At An Ocean Basin Scale: Identifying A Viable Network Of Deep-Sea Protected Areas In The North Atlantic And The Mediterranean, Magali Combes, Sandrine Vaz, Anthony Grehan, Telmo Morato, Sophie Arnaud-Haond, Carlos Dominguez-Carrió, Alan Fox, José Manuel González-Irusta, David Johnson, Oisín Callery, Andrew Davies, Laurence Fauconnet, Ellen Kenchington, Covadonga Orejas, J. Murray Roberts, Gerald Taranto, Lénaick Menot

Biological Sciences Faculty Publications

Designing conservation networks requires a well-structured framework for achieving essential objectives such as connectivity, replication or viability, and for considering local management and socioeconomic stakes. Although systematic conservation planning (SCP) approaches are increasingly used to inform such networks, their application remains challenging in large and poorly researched areas. This is especially the case in the deep sea, where SCP has rarely been applied, although growing awareness of the vulnerability of deep-sea ecosystems urges the implementation of conservation measures from local to international levels. This study aims to structure and evaluate a framework for SCP applicable to the deep sea, focusing …

Pandemic, Human Precarity And Post-Pandemic Metaverses, Tracy Harwood

Markets, Globalization & Development Review

With the global COVID-19 pandemic and its continuing impacts, we have reached a nexus which places new emphasis on our understanding of ourselves and our relationship with others – other nations, other species, other worlds. A critical question is: Does this mean that our transition into the posthuman is complete? It is therefore with some interest that this Dialogue contribution approaches the review of Francesca Ferrando’s book (2019) titled Philosophical Posthumanism. Prior to and after the detailed review of the book, this Dialogue essay reflects on the precarity induced by the pandemic and possible socio-technological ways out of the current …

Biogenic Sinking Particle Fluxes And Sediment Trap Collection Efficiency At Ocean Station Papa, Margaret Estapa, Ken Buesseler, Colleen A. Durkin, Melissa Omand, Claudia R. Benitez-Nelson, Montserrat Roca-Martí, Elly Breves, R. P. Kelly, Steve Pike

Graduate School of Oceanography Faculty Publications

Comprehensive field observations characterizing the biological carbon pump (BCP) provide the foundation needed to constrain mechanistic models of downward particulate organic carbon (POC) flux in the ocean. Sediment traps were deployed three times during the EXport Processes in the Ocean from RemoTe Sensing campaign at Ocean Station Papa in August-September 2018. We propose a new method to correct sediment trap sample contamination by zooplankton “swimmers.” We consider the advantages of polyacrylamide gel collectors to constrain swimmer influence and estimate the magnitude of possible trap biases. Measured sediment trap fluxes of thorium-234 are compared to water column measurements to assess trap …

Coral Bleaching Response Is Unaltered Following Acclimatization To Reefs With Distinct Environmental Conditions, Katie L. Barott, Ariana S. Huffmyer, Jennifer M. Davidson, Elizabeth A. Lenzb, Shayle B. Matsuda, Joshua R. Hancock, Teegan Innis, Crawford Drury, Hollie M. Putnam, Ruth D. Gates

Biological Sciences Faculty Publications

Urgent action is needed to prevent the demise of coral reefs as the climate crisis leads to an increasingly warmer and more acidic ocean. Propagating climate change-resistant corals to restore degraded reefs is one promising strategy; however, empirical evidence is needed to determine whether stress resistance is affected by transplantation beyond a coral's native reef. Here, we assessed the performance of bleaching-resistant individuals of two coral species following reciprocal transplantation between reefs with distinct pH, salinity, dissolved oxygen, sedimentation, and flow dynamics to determine whether heat stress response is altered following coral exposure to novel physicochemical conditions in situ. Critically, …

Genome-Scale Metabolic Model Of Caldicellulosiruptor Bescii Reveals Optimal Metabolic Engineering Strategies For Bio-Based Chemical Production, Ke Zhang, Weishu Zhao, Dmitry A. Rodionov, Gabriel M. Rubinstein, Diep N. Nguyen, Tania N.N. Tanwee, James Crosby, Ryan G. Bing, Robert M. Kelly, Michael W.W. Adams, Ying Zhang

Cell and Molecular Biology Faculty Publications

Metabolic modeling was used to examine potential bottlenecks that could be encountered for metabolic engineering of the cellulolytic extreme thermophile Caldicellulosiruptor bescii to produce bio-based chemicals from plant biomass. The model utilizes subsystems-based genome annotation, targeted reconstruction of carbohydrate utilization pathways, and biochemical and physiological experimental validations. Specifically, carbohydrate transport and utilization pathways involving 160 genes and their corresponding functions were incorporated, representing the utilization of C5/C6 monosaccharides, disaccharides, and polysaccharides such as cellulose and xylan. To illustrate its utility, the model predicted that optimal production from biomass-based sugars of the model product, ethanol, was driven by ATP production, redox …

On Rates Of Isopycnal Dispersion At The Submesoscale, T. Rossby, M. Omand, J. Palter, D. Hebert

Graduate School of Oceanography Faculty Publications

Past studies of dispersion with float-pairs have indicated that they may remain close together for much longer when they equilibrate on the same isopycnal, presumably due to the reduced influence of vertical shear. To examine this question more closely, we use a set of 13 and 15 float pair combinations that equilibrated within 0.1 °C (∼σθ = 0.01 kg m−3) of each other on two density surfaces in the main thermocline in a Lagrangian dispersion study. Their average rate of separation after launch was 0.0021 ± 0.0014 ms−1 (∼5.5 km after 30 days). Relative dispersion is accurately expressed by = …

Children As Mischievous Spirits: Legitimizing Child Cruelty And Filicide In Contemporary Africa, Chima Agazue

Dignity: A Journal of Analysis of Exploitation and Violence

The belief that certain humans are spiritual entities and the belief that some people are spiritually possessed can be found across histories and cultures. While these individuals are not always viewed in the negative or treated inhumanely, cases abound whereby degrading and inhumane treatments are meted out to some of them. In the African continent, certain groups of people, particularly children are linked to certain mischievous spirits due to their unusual appearance, aberrant behavior, disability, chronic illness, psychopathology or exceptional ability. Some are also suspected and consequently mistreated due to events surrounding their birth. Such children are known by different …

Lithium Bis(Trimethylsilyl) Phosphate As A Novel Bifunctional Additive For High-Voltage Lini1.5mn0.5o4/Graphite Lithium-Ion Batteries, Jongjung Kim, Venkata A.K. Adiraju, Nuwanthi Rodrigo, Jennifer Hoffmann, Martin Payne, Brett L. Lucht

Chemistry Faculty Publications

The beneficial role of lithium bis(trimethylsilyl) phosphate (LiTMSP), which may act as a novel bifunctional additive for high-voltage LiNi1.5Mn0.5O4 (LNMO)/graphite cells, has been investigated. LiTMSP is synthesized by heating tris(trimethylsilyl) phosphate with lithium tert-butoxide. The cycle performance of LNMO/graphite cells at 45 °C significantly improved upon incorporation of LiTMSP (0.5 wt %). Nuclear magnetic resonance analysis suggests that the trimethylsilyl (TMS) group in LiTMSP can react with hydrogen fluoride (HF), which is generated through the hydrolysis of lithium hexafluorophosphate (LiPF6) by residual water in an electrolyte solution or water generated via oxidative electrolyte decomposition reactions to form TMS fluoride. Inhibition …

Musical Chairs On Temperate Reefs: Species Turnover And Replacement Within Functional Groups Explain Regional Diversity Variation In Assemblages Associated With Honeycomb Worms, Alexandre Muller, Camille Poitrimol, Flávia L.D. Nunes, Aurélien Boyé, Amelia Curd, Nicolas Desroy, Louise B. Firth, Laura Bush, Andrew J. Davies, Fernando P. Lima, Martin P. Marzloff, Claudia Meneghesso, Rui Seabra, Stanislas F. Dubois

Biological Sciences Faculty Publications

Reef-building species are recognized as having an important ecological role and as generally enhancing the diversity of benthic organisms in marine habitats. However, although these ecosystem engineers have a facilitating role for some species, they may exclude or compete with others. The honeycomb worm Sabellaria alveolata (Linnaeus, 1767) is an important foundation species, commonly found from northwest Ireland to northern Mauritania, whose reef structures increase the physical complexity of the marine benthos, supporting high levels of biodiversity. Local patterns and regional differences in taxonomic and functional diversity were examined in honeycomb worm reefs from 10 sites along the northeastern Atlantic …

Platformization Of Covid And The Rise Of Biosocial Surveillance, Handan Vicdan

Markets, Globalization & Development Review

The emergence of participatory medicine and patient-generated medical research and knowledge is gaining more traction, especially with the current global health crisis. Digital platform organizations bring together diverse market actors for partnership for the creation and distribution of aggregate medical data and find cures for diseases, hence challenging the conventional medical knowledge production and disease control. In this paper, I articulate how such platformization of patient/citizen-led medical research and disease control is organized and sustained through Foucauldian notion of biopower and Rabinow’s concept of biosociality to then draw attention to what I call biosocial surveillance, which is becoming increasingly relevant …

Multiple Integrated Metabolic Strategies Allow Foraminiferan Protists To Thrive In Anoxic Marine Sediments, Fatma Gomaa, Daniel R. Utter, Christopher Powers, David J. Beaudoin, Virginia P. Edgcomb, Helena L. Filipsson, Colleen M. Hansel, Scott D. Wankel, Ying Zhang, Joan M. Bernhard

Cell and Molecular Biology Faculty Publications

Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a …

Microbiome Analysis Reveals Diversity And Function Of Mollicutes Associated With The Eastern Oyster, Crassostrea Virginica, Zachary T. Pimentel, Keith Dufault-Thompson, Kayla T. Russo, Abigail K. Scro, Roxanne M. Smolowitz, Marta Gomez-Chiarri, Ying Zhang

Cell and Molecular Biology Faculty Publications

Abstract Marine invertebrate microbiomes play important roles in diverse host and ecological processes. However, a mechanistic understanding of host-microbe interactions is currently available for a small number of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene-based amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. Relatively high variability of the microbiome was observed across individual oysters and among different tissue types. Specifically, a significantly higher alpha diversity was observed in the inner shell than in the gut, gill, mantle, and pallial fluid samples, and a …

Peptidomimetic Inhibitors: Molecular Modeling And 3d Visualization, Sonika Tahiliani

Senior Honors Projects

Zoonotic viruses, including coronaviruses, Ebola virus, HIV, influenza, and more, are ubiquitous and can emerge as significant human pathogens capable of global epidemics and pandemics. Most often, researchers spend their time and resources targeting only the human pathogens and developing therapeutic compounds to treat the associated diseases. However, a missed opportunity is targeting the zoonotic host instead and aiming to acquire the chemical and structural knowledge to inform us of the evolutionary path of the virus. The bat coronavirus HKU4 belongs to the same lineage as the Middle East Respiratory Syndrome coronavirus (MERS-CoV) and shows high sequence similarity. This is …

Seeking Asylum In A Modern Society: Global Responses To Latin American Migration, Rebecca Dickinson

Senior Honors Projects

The United States is no stranger to asylum seekers and refugees. The most famous seaport in the country houses a 305-foot-tall statue of a woman bearing a torch with words from the poem The New Colossus by Emma Lazarus etched at her feet: “‘Give me your tired, your poor, /Your huddled masses yearning to breathe free.’”^[1] The Statue of Liberty is a symbolic representation of open arms to immigrants from all walks of life. But if everyone is welcome, why do so few actually gain entrance?

US interventionism policies in the 20th century have defined the lives of millions …

Sharing Raw Data From Bacterial Genomes For Collaborative Research On The Amped Server At Uri, Deborah Adenekan

Senior Honors Projects

No abstract provided.

Contaminant Transport And Fate, Thomas B. Boving, William J. Blanford

Civil & Environmental Engineering Faculty Publications

No abstract provided.

Twilight Zone Observation Network: A Distributed Observation Network For Sustained, Real-Time Interrogation Of The Ocean’S Twilight Zone, Simon R. Thorrold, Allan Adams, Ann Bucklin, Ken Buesseler, Godi Fischer, Annette Govindarajan, Porter Hoagland, Di Jin, Andone Lavery, Joel Llopez, Larry Madin, Melissa Omand, Philip G. Renaud, Heidi M. Sosik, Peter Wiebe, Dana R. Yoerger, Weifeng Zhang

Electrical, Computer, and Biomedical Engineering Faculty Publications

The ocean’s twilight zone (TZ) is a vast, globe-spanning region of the ocean. Home to myriad fishes and invertebrates, mid-water fishes alone may constitute 10 times more biomass than all current ocean wild-caught fisheries combined. Life in the TZ supports ocean food webs and plays a critical role in carbon capture and sequestration. Yet the ecological roles that mesopelagic animals play in the ocean remain enigmatic. This knowledge gap has stymied efforts to determine the effects that extraction of mesopelagic biomass by industrial fisheries, or alterations due to climate shifts, may have on ecosystem services provided by the open ocean. …

Comparative Gait Analysis Of Transtibial Amputees Versus, Charlotte Vitale

Senior Honors Projects

While individuals with lower limb prosthetics make up a very small percentage of the population, their musculoskeletal deformities impair their abilities to produce “normal” biomechanical actions. The deviations in their walking patterns can further inhibit their efficacy in other activities of basic living. Understanding the distinct kinematic comparisons during gait between lower limb amputees and able-bodied individuals is critical for those planning to enter such a field of study working with this specific population. As an aspiring specialized Physical Therapist, it is very likely that I will be assisting clients to regain a healthy walking pattern after a traumatic accident, …

On The Front Line: Uri's Response To Covid-19 And The Role Of The Student-Run Emergency Medical Services, Michael C. Brennan

Senior Honors Projects

The COVID-19 pandemic has affected all aspects of society, including universities, and we are just beginning to understand its impacts. This project looks at how universities have responded to the pandemic by focusing on the University of Rhode Island, the largest university in the state of Rhode Island. A key aspect of this project is a timeline that documents the policies implemented by URI leadership and relevant policies adopted by the State of Rhode Island. The timeline also includes data about the number of cases at URI and state-wide, as well as figures for the number of students in isolation …

The Public Health Crisis Of Alcoholism: What Could Be Done Better In Rhode Island?, Carlos Borges

Senior Honors Projects

Alcoholism is a chronic issue that affects over 3 million people per year in the United States. It is characterized by an individual who is physiologically dependent on alcohol to the point where they cannot carry out common social activities such as having friends or holding down a job. Approximately 88,000 people die per year due to alcohol related events. The economic impact due to hospital bills, criminal justice costs, and lost productivity of the abuser is estimated at $400 billion annually. Alcohol abuse can be used as a coping mechanism in adolescents who are struggling with behavioral health issues …

Particle Tracking Reveals Pelagic Red Crabs As Indicators Of Climate-Driven Range Expansion In The California Current, Elizabeth Saraf

Senior Honors Projects

Since their first recorded occurrence in 1859, Pelagic Red Crabs (PRC; Pleuroncodes planipes) have experienced increased frequency of episodic mass stranding events in the Eastern Pacific Ocean. PRC’s are transported over 1,000 km northward of their central domain from the coast of central Baja California, Mexico. They have been reported by the thousands on the beaches of central and southern California. Their presence influences the surrounding ecosystem and commercial fisheries because they are nutritional prey items and large predators change their diet to incorporate PRC’s when they are available. Seasonal coastal currents and the California Undercurrent transport warmer waters …