Digital Commons Network^™

Analysis Of Cell-Associated Denv Rna By Oligo(Dt) Primed 5’ Capture Scrnaseq, Mark A. Sanborn, Tao Li, Kaitlin Victor, Hayden Siegfried, Christian Fung, Alan L. Rothman, Anon Srikiatkhachorn, Stefan Fernandez, Damon Ellison, Richard G. Jarman, Heather Friberg, Irina Maljkovic Berry, Jeffrey R. Currier, Adam T. Waickman

Cell and Molecular Biology Faculty Publications

Dengue is one of the most widespread vector-borne viral diseases in the world. However, the size, heterogeneity, and temporal dynamics of the cell-associated viral reservoir during acute dengue virus (DENV) infection remains unclear. In this study, we analyzed cells infected in vitro with DENV and PBMC from an individual experiencing a natural DENV infection utilizing 5’ capture single cell RNA sequencing (scRNAseq). Both positive- and negative-sense DENV RNA was detected in reactions containing either an oligo(dT) primer alone, or in reactions supplemented with a DENV-specific primer. The addition of a DENV-specific primer did not increase the total amount of DENV …

Transcriptome Analysis Provides A Blueprint Of Coral Egg And Sperm Functions, Julia Van Etten, Alexander Shumaker, Tali Mass, Hollie M. Putnam, Debashish Bhattacharya

Biological Sciences Faculty Publications

Background

Reproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data.

Methods

Here, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) …

Squeezed By A Habitat Split: Warm Ocean Conditions And Old‐Forest Loss Interact To Reduce Long‐Term Occupancy Of A Threatened Seabird, Matthew G. Betts, Joseph M. Northrup, Jennifer A. Bailey Guerrero, Lindsay J. Adrean, S. Kim Nelson, Jennifer L. Fisher, Brian D. Gerber, Marie‐Sophie Garcia‐Heras, Zhiqiang Yang, Daniel D. Roby, James W. Rivers

Natural Resources Science Faculty Publications

Theory predicts that species requiring multiple habitat types simultaneously should have heightened sensitivity to anthropogenic pressures, yet tests of this prediction are especially rare. We tested whether breeding site occupancy of the threatened marbled murrelet (Brachyramphus marmoratus) was driven by the synergistic effects of nesting habitat loss in forests, and changing ocean condi- tions. We paired 70,700 murrelet surveys at 19,837 sites across 20 years from the Oregon Coast Range with annual data on the extent of old forest and biophysical ocean conditions. Dynamic occupancy models indicated that local murrelet col- onization rates were strongly reduced during warm …

Science Communication Demands A Critical Approach That Centers Inclusion, Equity, And Intersectionality, Katherine N. Canfield, Sunshine Menezes, Shayle B. Matsuda, Amelia Moore, Alycia N. Mosley Austin, Bryan M. Dewsbury, Mónica I. Feliú-Mójer, Katharine W.B. Mcduffie, Kendall Moore, Christine A. Reich, Hollie M. Smith, Cynthia Taylor

Natural Resources Science Faculty Publications

We live in an era of abundant scientific information, yet access to information and to opportunities for substantive public engagement with the processes and outcomes of science are still inequitably distributed. Even with increasing interest in science communication and public engagement with science, historically marginalized and minoritized individuals and communities are largely overlooked and undervalued in these efforts. To address this gap, this paper aims to define inclusive science communication and clarify and amplify the field. We present inclusive science communication as one path forward to redress the systemic problems of inequitable access to and engagement with STEMM (science, technology, …

Greenhouse Gas Emissions From Advanced Nitrogen-Removal Onsite Wastewater Treatment Systems, Bianca Ross, Brittany V. Lancellotti, Elizabeth Q. Brannon, George W. Loomis, José A. Amador

Natural Resources Science Faculty Publications

Advanced onsite wastewater treatment systems (OWTS) designed to remove nitrogen from residential wastewater play an important role in protecting environmental and public health. Nevertheless, the microbial processes involved in treatment produce greenhouse gases (GHGs) that contribute to global climate change, including CO₂, CH₄, N₂O. We measured GHG emissions from 27 advanced N-removal OWTS in the towns of Jamestown and Charlestown, Rhode Island, USA, and assessed differences in flux based on OWTS technology, home occupancy (year-round vs. seasonal), and zone within the system (oxic vs. anoxic/hypoxic). We also investigated the relationship between flux and wastewater …

Neutron Radiography, Jesse Bibby, Sophia Fusco, Matthew Leger, Anthony Marshall

Mechanical Engineering Capstone Design Projects

Neutron radiography is a type of nondestructive imaging that utilizes slow moving thermal neutrons to penetrate an object and produce high resolution photographs. It is commonly used but not limited to the industries of aerospace, automotive, energy and medical applications. Images produced by neutron radiography appear similar to an X-ray image and can be used instead of or in conjunction with X-ray . The key difference between these imaging methods is while X-ray only allows neutrons to interact with a material’s electron shell, neutron radiography allows neutrons to interact with a material’s nucleus directly. This is an extremely beneficial tool …

“It Is Like Living In A Diminishing World”: Older Persons’ Experiences Of Living With Long-Term Health Problems – Prior To The Strength Intervention, Cecilia Åberg, Catharina Gillsjö, Jenny Hallgren, Mia Berglund

College of Nursing Faculty Publications

Introduction: Ageing is often associated with multiple long-term health problems influencing older persons’ well-being in daily living. It is not unusual that the point of interest in research is often on the management of the actual health problem instead of being holistic and person-centred.

Purpose: To describe the phenomenon of living with long-term health problems that influence daily living, from the older persons’ perspective.

Methods: Qualitative individual interviews were conducted with 34 older persons living with long-term health problems. The data were analysed using a Reflected Lifeworld Research (RLR) approach, grounded in phenomenology. Results: Life with long-term …

The Intertwining Of Reconciliation And Displacement: A Lifeworld Hermeneutic Study Of Older Adults’ Perceptions Of The Finality Of Life, Lina Palmér, Maria Nyström, Gunilla Carlsson, Catharina Gillsjö, Irene Eriksson, Ann-Charlotte Dalheim-Englund

College of Nursing Faculty Publications

Purpose: This study aimed to explain and understand the existential meaning of the finality of life from the perspective of healthy older adults.

Method: Participants were recruited from a major project on older adults’ life situations. They were interviewed about their thoughts on the end of life, and their responses were interpreted using a lifeworld hermeneutic approach.

Results: The findings showed that thinking about the inevitable finality of life involves feelings of liberation, frightening thoughts, a comforting promise of something beyond death, acceptance of the concept of death as a companion in life and a desire to …

Going Mobile With Primary Care: Smartphone-Telemedicine For Asthma Management In Young Urban Adults (Teams), Jennifer R. Mammen, Judith D. Schoonmaker, James Java, Jill Halterman, Marc N. Berliant, Amber Crowley, Marina Reznik, Jonathan M. Feldman, Robert J. Fortuna, Sean M. Frey, Kelsey Turgeon, Ashley Philibert, Kimberly Arcoleo

College of Nursing Faculty Publications

Background: The majority of adults with persistent asthma have chronically uncontrolled disease and interventions to improve outcomes are needed. We evaluated the efficacy, feasi- bility, and acceptability of a multi-component smartphone-telemedicine program (TEAMS) to deliver asthma care remotely, support provider adherence to asthma management guide- lines, and improve patient outcomes.

Methods: TEAMS utilized: (1) remote symptom monitoring, (2) nurse-led smartphone-tele- medicine with self-management training for patients, and (3) Electronic medical record- based clinical decision support software. Adults aged 18-44 (N=33) and primary care providers (N=4) were recruited from a safety-net practice in Upstate New York. Asthma con- trol, quality of …

Effects Of The Intervention “Reflective Strength-Giving Dialogues” For Older Adults Living With Long-Term Pain: A Pilot Study, Lena Hedén, Mia Berglund, Catharina Gillsjö

College of Nursing Faculty Publications

Background. Long-term musculoskeletal pain is a major, often undertreated, disabling health problem among an increasing number of older adults. Reflective STRENGTH-giving dialogues (STRENGTH) may be a tool to support older adults living with long-term pain. The main aim of this pilot study was to investigate the immediate and longitudinal effect of the intervention STRENGTH on levels of pain, wellbeing, occurrence of depression symptoms, and sense of coherence (SOC) among community-dwelling older adults suffering from musculoskeletal pain compared to a control group. Methods. The study was semiexperimental with an intervention group and a control group. The effect of a …

Unmet Healthcare Needs Of Children In Vulnerable Families In South Korea: Finding From The Community Child Center Child Panel Survey, Suyon Baek, Eun-Hi Choi, Jung Eun Lee

College of Nursing Faculty Publications

Presented in this paper is a study that examined the status of unmet healthcare needs of children in vulnerable families and identified factors affecting such unmet needs. The Community Child Center (CCC) Child Panel Survey data in Korea were used. A multiple stepwise logistic regression analysis was performed to examine factors influencing unmet healthcare needs of children. Influencing factors comprised predisposing, enabling, and need factors based on the Andersen Behavioral Model of Health Services Utilization. A total of 340 sixth-graders from vulnerable families participated, and 96 (28.2%) children had unmet healthcare needs. Factors included absence of an after-school caregiver (OR …

A Mixed‐Methods Analysis Of Younger Adults' Perceptions Of Asthma, Self‐Management, And Preventive Care: "This Isn't Helping Me None", Jennifer R. Mammen, Kelsey Turgeon, Ashley Philibert, Judith D. Schoonmaker, James Java, Jill Halterman, Marc N. Berliant, Amber Crowley, Marina Reznik, Jonathan M. Feldman, Robert J. Fortuna, Kimberly Arcoleo

College of Nursing Faculty Publications

Background: Young adults (ages 18‐44) have increased emergency department use for asthma and poor adherence to medications. The objective of this mixed‐methods study was to understand experiences with and approaches to managing asthma, of which little is known in this age group.

Methods: Surveys (Asthma Control Questionnaire, Asthma Quality of Life Questionnaire) and 1:1 semi‐structured interviews were used to explore experiences with asthma, symptoms, self‐management behaviors, and relationship to asthma control and quality of life. Qualitative data were analyzed using content analysis techniques. Descriptive statistics and bivariate correlations were used to examine distributive characteristics and associations between variables.

Results: Forty …

Multivariate Ewma Models And Monitoring Health Surveillance During A Pandemic, Jeffrey E. Jarrett, Xia Pan

College of Business Faculty Publications

We examine a common problem is biological analytics and surveillance in health care. These methods can improve greatly the process of monitoring health data to assess changes in the likelihood of Pandemics and disease incidence in a world where medical knowledge is still largely in an embryonic period. Based on an illustration, we suggest that multivariate exponential moving-average (MEWMA) control charts are suitable in many cases where detection and inspection of several or more variables over a lengthy period of testing provide for the best analysis of data leading to pre-­diagnostic and diagnostic therapy. Though these methods came …

Isolation Of Isotrichophycin C And Trichophycins G–I From A Collection Of Trichodesmium Thiebautii, Kelly M. Mcmanus, Riley D. Kirk, Christopher W. Via, James S. Lotti, Alexandre F. Roduit, Roberta Teta, Silvia Scarpato, Alfonso Magoni, Matthew Bertin

Biomedical and Pharmaceutical Sciences Faculty Publications

The trichophycin family of compounds are chlorinated polyketides first discovered from environmental collections of a bloom-forming Trichodesmium sp. cyanobacterium. In an effort to fully capture the chemical space of this group of metabolites, the utilization of MS/MS-based molecular networking of a Trichodesmium thiebautii extract revealed a metabolome replete with halogenated compounds. Subsequent MS-guided isolation resulted in the characterization of isotrichophycin C and trichophycins G–I (1–4). These new metabolites had intriguing structural variations from those trichophycins previously characterized, which allowed for a comparative study to examine structural features that are associated with toxicity to murine neuroblastoma cells. Additionally, we propose the …

Clozapine And Hematologic Adverse Reactions: Impact Of The Risk Evaluation And Mitigation Strategy Program, Eric P. Borrelli, Y. Lee, Aisling R. Caffrey

Pharmacy Practice and Clinical Research Faculty Publications

Introduction: In October 2015, the Food and Drug Administration (FDA) instituted an update to the mandatory Risk Evaluation and Mitigation Strategy (REMS) program for clozapine to improve safety monitoring of hematologic events. However, the impact of the clozapine REMS program on reporting of hematologic adverse events has not been quantified.

Methods: We assessed adverse event reports for agranulocytosis, granulocytopenia, leukopenia, and neutropenia from the FDA Adverse Event Reporting System (FAERS) for a 1-year time period before (October 2014 to September 2015, pre-REMS) and after (October 2015 to September 2016, post-REMS) the implementation of the clozapine REMS program. The AERSMine platform …

Hands-Free Tree Climbing Machine, Michael Kowalski, Sam Anderson, Matt Chambers, Matt Nelson

Mechanical Engineering Capstone Design Projects

Team 18 was assembled and approached by Professor Nassersharif to develop a new product. This product was to carry an average individual up a tree at least 20 feet high, hands free. During discussion of the future of the product, the Tree Climbing team was told this device needed to have many different abilities. These abilities include adjustability to climb different size trees ranging from 12 inches in diameter, to 24 inches in diameter. The development of such a device needed to be researched, designed, and constructed within a budget of $300. To begin the process, a previous design was …

Effects Of Nanoparticle Size And Radiation Energy On Copper-Cysteamine Nanoparticles For X-Ray Induced Photodynamic Therapy, Bindeshwar Sah, Jing Wu, Adam Vanasse, Nil Kanatha Pandey, Lalit Chudal, Zhenzhen Huang, Wenzhi Song, Hongmei Yu, Lun Ma, Wei Chen, Michael Antosh

Physics Faculty Publications

The Copper-cysteamine (Cu-Cy) nanoparticle is a novel sensitizer with a potential to increase the effectiveness of radiation therapy for cancer treatment. In this work, the effect of nanoparticle size and the energy of X-rays on the effectiveness of radiation therapy are investigated. The effect of the particle size on their performance is very complicated. The nanoparticles with an average size of 300 nm have the most intense photoluminescence, the nanoparticles with the average size of 100 nm have the most reactive oxygen species production upon X-ray irradiation, while the nanoparticles with the average size of 40 nm have the best …

Autonomous Pool Skimmer, Kyle Banna, Ben Crichton, Tony Pina, Huy Truong

Mechanical Engineering Capstone Design Projects

The work discussed in this paper is based around the designing, manufacturing and testing of an autonomous pool skimmer composed almost exclusively of 3D printed parts. Most pool owners would agree that cleaning their pool is among the most time-consuming activities associated with owning one. Whether it be bugs, leaves, grass, or any other number of debris, there seems to always be particulates floating along the surface, and eventually sinking to the bottom. However, with advancing technology, innovative solutions are being created to make cleaning the debris off the surface of the pool hassle-free. Team 19 was tasked to investigate …

Visionary Politics And Methods In Feminist Disability Studies, Jess Waggoner, Ashley Mog

Journal of Feminist Scholarship

In this introduction we explore the genealogies and methodologies of feminist disability studies (FDS). A feminist methodology is politically situated with a focus on the material conditions and social and cultural structures that marginalized people bear, experience, and resist. Methods, and the theories that underpin and create those methodological tools, can open or foreclose possibilities for praxis. Considering theory and method as mutually informative intellectual projects, we ask, how can our methods influence political investments that open up visionary possibilities and plans? How can we take a coalitional approach to disability politics as a method that is informed by collaboration, …

Finding Tender Roots: Affiliation, Disability, And Racial Melancholia In Monique Truong’S Bitter In The Mouth, Amanda Ong

Journal of Feminist Scholarship

Early on in Bitter in the Mouth, we learn that the protagonist, Linda Linh-Dao Nguyen Hammerick, has auditory-gustatory synesthesia—that is, nearly every word she hears evokes a specific taste. Hammerick, for example, tastes like Dr. Pepper and Linda tastes like mint. There are many articles that analyze Linda’s synesthesia but few articles approach the text through the lens of disability studies. In this article, I employ feminist disability studies and diaspora studies to argue that Linda's identity as a disabled transracial adoptee allow her to seek out additional forms of affiliation and kinship. By constructing an alternative family tree …

Salt Marsh Management: Monitoring Threats And Implementing Climate Adaptation Initiatives, Danielle C. Perry

Open Access Dissertations

Salt marshes serve as important coastal resources both economically and environmentally and are particularly susceptible to the negative implications of climate change. As climate change impacts become more prevalent, it is important to understand how salt marshes will respond. Two climate change impacts on salt marshes are macroalgae inundation and accelerated relative sea-level rise (hereafter referred to as SLR). Due to warming temperatures and sea level rise, salt marshes can be inundated by macroalgae through tidal movement, and the impacts of this excess macroalgal accumulation are poorly understood. Sea level rise also has negative implications on salt marsh by leading …

Nitrogen-Removing Wastewater Treatment Systems: Microbial Communities And Greenhouse Gas Emissions, Sara Katherine Wigginton

Open Access Dissertations

Wastewater is a major source of anthropogenic nitrogen (N) pollution that causes groundwater contamination and eutrophication in coastal ecosystems. The negative effects of excess N from wastewater on human and environmental health have led the United States Environmental Protection Agency (USEPA) and many state and local agencies to set maximum N concentrations for treated wastewater before it can be discharged to ground and surface water bodies. Wastewater treatment systems that include biological nitrogen removal (BNR) can help meet these standards by promoting microbial N removal in centralized wastewater treatment plants (WTP) as well as decentralized, onsite wastewater treatment systems (OWTS; …

Determining Impacts Of Iron Limitation On Diatom Chloroplast Metabolism And Physiology, Kristofer Gomes

Open Access Dissertations

Within the marine ecosystem, phytoplankton such as diatoms experience regions of nutrient limitation including macronutrients such as nitrogen, silica, and phosphate. In regions with high concentration of these nutrients but low chlorophyll a concentrations (HNLCs), phytoplankton are limited for micronutrients such as iron (Fe) an element that serves as a co-factor in proteins involved in cellular redox reactions. Of particular interest for diatoms is the Fe requirement of cellular processes localized to the chloroplast. These Fe requirements are in multiple metabolic pathways such as light reactions of photosynthesis that generate the necessary energy and reducing power necessary for anabolic processes …

Modulation Of Receptor Interacting Protein Kinase 1 (Ripk1) Signaling During Dengue Virus Infection, Darshika Jeewanthi Udawatte

Open Access Dissertations

Dengue virus (DENV) infection is the most prevalent arthropod-borne virus disease. There are estimated 100 million symptomatic cases of dengue disease per year worldwide. A lack of effective antiviral therapies or vaccines makes DENV infections a major global health concern. Therefore, understanding the viral and host factors contributing to the disease pathogenesis is critical. DENV has been shown to effectively counteract host innate immune mechanisms. In particular, DENV protease, NS3 has emerged as an inhibitor of host cellular signaling by targeting crucial host proteins. Here we identified RIPK1 as a novel target of DENV NS3. RIPK1 is a central mediator …

The Frequent Flyer’S Guide To Migration: How Songbird Metabolism And Oxidative Status Respond To Endurance Flight And Diet Quality, Kristen J. Demoranville

Open Access Dissertations

Migratory songbirds are among the best high-performance endurance athletes on the planet and during their annual peregrinations they are particularly vulnerable to oxidative damage because they maintain relatively high metabolic rates at rest, they are able to fly for long durations while operating at 9 times their resting metabolic rate, and they rely on fats to fuel this exercise which increases reactive oxygen species (ROS) formation. The concept of evolutionary economic design of physiological systems considers such phenotypic flexibility in metabolic and antioxidant responses adaptive in that it allows birds to match the capacity of key physiological systems to prevailing …

Design And Validation Of Smart Fabric Sensors Based On Semiconductive Polymer Composites, Arar Alkhader

Open Access Dissertations

Smart Fabric Sensors (SFSs) have recently gained much interest as they are convenient as a long-term wearable as well as for their simplicity, lightweight, low manufacturing cost, high sensitivity, and flexibility. Semiconductive polymer composites SCPCs can be used as smart fabrics to create force or pressure sensors based on the piezoresistive effect, however, their wider application is limited due to their narrow sensing range, hysteresis and output drift issues as well as due to the lack of literature studying their voltage response related errors especially under high impact forces. In this Doctoral research, eight proposed designs of a smart fabric …

Regulating Quiescence And Division In Escherichia Coli, Eric Charles Dibiasio

Open Access Dissertations

The decision for a bacterium to grow and divide may seem like a simple process, but in reality, there are many factors that influence and regulate this choice. Bacteria have been known to respond to many environmental signals or cues that represent either favorable or non-favorable growth conditions, as well as cues, secreted from other bacteria or, in the case of a pathogen, the host. It is not uncommon for bacteria that find their environment unfavorable, to alter their growth, and in some cases, even enter into a type of non-proliferative state, which we term, dormancy. Bacterial dormancy has many …

Function And Variability Of Metabolic Networks, Keith Dufault-Thompson

Open Access Dissertations

The study of bacterial growth has highlighted the importance of metabolism in how microorganisms have evolved and how they survive in different conditions. The introduction of next-generation sequencing methods has allowed for the study of metabolism in new ways by predicting metabolic phenotypes based on gene annotations. The development of GEnome-scale models (GEMs) of metabolism from these annotations has provided another method to investigate microbial metabolism. An overview of GEM development and simulation methods is provided in Appendix I.

In Manuscript I, a GEM was developed for the psychrotolerant, piezotolerant, deep-sea bacteria Shewanella piezotolerans WP3. Despite the broad differences in …

The Biogeography Of Antarctic Marine Diatoms And Their Response To Varied Iron Concentrations, Laura Z. Holland

Open Access Dissertations

Diatoms are a group of highly diverse photosynthetic eukaryotes that account for about 40% of oceanic primary production. In large areas of the ocean deemed high nitrate, low chlorophyll (HNLC) regions, dissolved macronutrient (nitrogen, phosphorus, silica) concentrations are high in the surface but diatom biomass is consistently low. The Southern Ocean (SO) is the largest of these environments, and when exogenous Fe is supplied to this region, large diatoms blooms and subsequent carbon export are promoted. As such, SO diatoms are major players in the global carbon cycle and were the focus of this dissertation. This work sought to determine …

Self-Injurious Thoughts And Behaviors Among College Students: A Latent Class Analysis, Marisa E. Marraccini, A. Brick, Conor O'Neill, Lisa L. Weyandt, Ashley L. Buchanan

Pharmacy Practice and Clinical Research Faculty Publications

This study explored emerging typologies of self-injurious thoughts and behaviors and how they relate to known psychological and cognitive correlates. Latent class analysis was employed to identify subgroups of college students (n = 626, mean age = 20, 73% female, and 83% White) based on history of self-injurious thoughts and behaviors. Differences among classes were tested to examine their associations with suicidal ideation, fearlessness of death, depression/hopelessness, thwarted belongingness, problems with alcohol or drugs, behavioral inhibition, and emotional control. Results of the latent class analysis supported a 3-class solution, with students classified as being likely to have (1) no history …