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Nanotube Spectral Fingerprinting And Machine Learning For Optimized Bioimaging/Sensing Applications, Aceer Nadeem

Open Access Dissertations

This thesis presents a multifaceted exploration of the optimization and application of single-walled carbon nanotubes (SWCNTs) in biomedical contexts, with a specific focus on enhancing their stability, functionality, and use as optical biosensors. The research spans several key areas, including the development of innovative techniques that couple machine learning with spectral fingerprinting for advanced diagnostics, the investigation of SWCNT chirality and its implications for cellular interactions, and the optimization of lyophilization processes to improve long-term stability and reproducibility.

The first section of the thesis delves into the fundamental properties of SWCNTs, emphasizing their unique electronic and optical characteristics. These properties, …

Analysis Of Turkey Reovirus Using Machine Learning, Maryam Kafikang

Open Access Master's Theses

Avian reoviruses continue to cause disease in turkeys with varied pathogenicity and tissue tropism. Turkey enteric reovirus (TERV) has been identified as a causative agent of enteritis or inapparent infections in turkeys. The new emerging variants of turkey reovirus tentatively named as turkey arthritis reovirus (TARV) and turkey hepatitis reovirus (THRV) are linked to tenosynovitis/arthritis and hepatitis, respectively. Turkey arthritis and hepatitis reoviruses are causing significant economic losses to the turkey industry. These infections can lead to poor weight gain, uneven growth, poor feed conversion, increased morbidity and mortality, and reduced marketability of commercial turkeys. To combat these issues, it …

A Crew-Operated Data Recording System For Length-Based Stock Assessment Of Indonesia’S Deep Demersal Fisheries, Elle Wibisono, Peter Mous, Edwison Firmana, Austin T. Humphries

Fisheries, Animal and Veterinary Sciences Faculty Publications

Deep demersal fisheries in Indonesia yielded close to 90,000 metric tons of snapper and grouper in 2019, landed by a fleet of approximately 10,000 fishing boats. Prior to the present study, information on these multi-species, dispersed, small- to medium-scale fisheries was scarce, while reliable species-specific data on catch and effort were non-existent. This data-deficiency made stock assessments and design of harvest control rules impossible. We developed a new data collection method, the Crew Operated Data Recording System (CODRS), to collect verifiable species- and length-composition data from catches across all segments of the fleet. CODRS engaged crews of 579 fishing vessels …

Chemical Investigation Of Metabolites Produced By Marine Pseudoalteromonas Spp., Margaret Rosario

Open Access Dissertations

In natural environments, bacteria are surrounded by other organisms such as eukaryotic phytoplankton and other bacterial species. Specialized metabolites are encoded within bacterial genomes and are expected to play a large role in mediating interactions with other cells. Furthermore, chemical communication in bacterial communities is a key component to controlling group behaviors including virulence. Marine Pseudoalteromonas spp. Produce a plethora of specialized metabolites, suggesting a reliance on the biosynthesis, secretion, and response to chemical cues. This dissertation explores the prevalence and function of signaling molecules and specialized metabolites produced by two species of Pseudoalteromonas.

The first study, which is …

Synthesis And Biological Evaluations Of Oleanolic Acid Indole Derivatives As Hyaluronidase Inhibitors With Enhanced Skin Permeability, Hao He, Huifang Li, Toyosi Akanji, Shengli Niu, Zhujun Luo, Dongli Li, Navindra P. Seeram, Panpan Wu, Hang Ma

Biomedical and Pharmaceutical Sciences Faculty Publications

Oleanolic acid (OA) is a natural cosmeceutical compound with various skin beneficial activities including inhibitory effect on hyaluronidase but the anti-hyaluronidase activity and mechanisms of action of its synthetic analogues remain unclear. Herein, a series of OA derivatives were synthesised and evaluated for their inhibitory effects on hyaluronidase. Compared to OA, an induction of fluorinated (6c) and chlorinated (6g) indole moieties led to enhanced anti-hyaluronidase activity (IC50 = 80.3 vs. 9.97 and 9.57 µg/mL, respectively). Furthermore, spectroscopic and computational studies revealed that 6c and 6g can bind to hyaluronidase protein and alter its secondary structure leading …

Probing Interactions Of Single-Walled Carbon Nanotubes At The Nano-Bio Interface, Mitchell Gravely

Open Access Dissertations

Non-covalent hybrids of single-stranded DNA and single-walled carbon nanotubes (DNA-SWCNTs) have demonstrated applications in biomedical imaging and sensing due to their enhanced biocompatibility and photostable, environmentally-responsive near-infrared (NIR) fluorescence. Significant progress has been made in developing robust biological probes based on the sensitive optical properties of SWCNTs, however biological environments introduce complex and dynamic conditions that interact with, and ultimately modulate, their intrinsic properties. These fundamental interactions within biological settings can determine whether a nanomaterial is biocompatible and robust, or cytotoxic and disruptive to biological processes. Thus, a mechanistic understanding of such interactions and their effect on cellular function is …

Icdp Workshop On The Lake Tanganyika Scientific Drilling Project: A Late Miocene-Present Record Of Climate, Rifting, And Ecosystem Evolution From The World's Oldest Tropical Lake, James M. Russell, Philip Barker, Andrew Cohen, Sarah Ivory, Ishmael Kimirei, Christine Lane, Melanie Leng, Neema Maganza, Michael Mcglue, Emma Msaky, Anders Noren, Lisa Park Boush, Walter Salzburger, Christopher Scholz, Ralph Tiedemann, Shaidu Nuru, Christian Albrecht, Rahma Ali, Ramon Arrowsmith, Danstan Asanga, Yemane Asmerom, Charles Bakundukize, Thorsten Bauersachs, Catherine Beck, Melissa Berke, Emily Beverley, Martin Blaauw, Lisa Boush, Erik Brown, Chris Campisano, Barbara Carrapa, Isla Castaûeda, Andy Cohen, Sylvia Dee, Alan Deino, Cindy Ebinger

Graduate School of Oceanography Faculty Publications

The Neogene and Quaternary are characterized by enormous changes in global climate and environments, including global cooling and the establishment of northern high-latitude glaciers. These changes reshaped global ecosystems, including the emergence of tropical dry forests and savannahs that are found in Africa today, which in turn may have influenced the evolution of humans and their ancestors. However, despite decades of research we lack long, continuous, well-resolved records of tropical climate, ecosystem changes, and surface processes necessary to understand their interactions and influences on evolutionary processes. Lake Tanganyika, Africa, contains the most continuous, long continental climate record from the mid-Miocene …

Moving Forward With Digital Disruption: What Big Data, Iot, Synthetic Biology, Ai, Blockchain, And Platform Businesses Mean To Libraries, Bohyun Kim

Technical Services Faculty Publications

Digital disruption, also known as “the fourth industrial revolution,” is blurring the lines between the physical, digital, and biological spheres. This issue of Library Technology Reports (vol. 56, no. 2) examines today’s leading-edge technologies and their disruptive impacts on our society through examples such as extended reality, Big Data, the Internet of Things (IoT), synthetic biology, 3-D bio-printing, artificial intelligence (AI), blockchain, and platform businesses in the sharing economy. This report explains

• how new digital technologies are merging the physical and the biological with the digital;
• what kind of transformations are taking place as a result in production, management, and …

Efficacy Of Seaweed (Sargassum Sp.) Extract To Prevent Vibriosis In White Shrimp (Litopenaeus Vannamei) Juvenile, Indriyani Nur Mulyadi, Wa Iba

Fisheries, Animal and Veterinary Sciences Faculty Publications

Background and Objectives: Marine algae, especially brown algae (Sargassum sp.), is a natural compound plant capable of being prophylactic and immunostimulant. This study was aimed to evaluate the efficacy of seaweed (Sargassum sp.) extract to improve resistance and immune response of juvenile white shrimps (Litopenaeus vannamei ) infected by Vibrio algynolyticus .

Materials and Methods: The ethanolic extract of seaweed was used to evaluate its antibacterial effect by immerse the juvenile shrimp at a dose level of 0 (control), 150, 250 and 350 ppm for 3 h. Shrimp immune response was observed based on total haemocyte count (THC) and differential …

Chemical Investigations Of Pectic Oligosaccharides From Vaccinium Macrocarpon, Zhiyuan Peng

Open Access Master's Theses

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are a serious problem worldwide, especially for females. Previous research in our laboratory suggests that cranberry pectic oligosaccharides (cPOS) can reverse dormant phenotypes in UPEC and therefore could prove useful in the prevention of recurrent UTIs. This thesis focused on the purification and structure determination of purified pectic oligosaccharides from cranberry hull extract. The research helped established the structures of cPOS, provided high purity materials for biological testing, and enabled further studies on the effect of different degrees of polymerization (DP) in preventing dormant phenotypes in UPEC. More specifically, cPOS …

How Landscape Change Affects Commercial And Recreational Fishermen’S Perceptions And Place Meanings, Talya Syvann Ten Brink

Open Access Dissertations

It is critical to plan for environmental change in order to mitigate its adverse effects on human wellbeing. This series of manuscripts examines the impacts of landscape change on commercial and recreational fishermen. Each manuscript provides a unique perspective on place meaning and place change. Using a mixed methods approach, data were collected and analyzed on fishermen’s perceptions of familiar places and on the changes that these places undergo. The first manuscript investigates the impact of offshore wind farms on commercial and recreational fishermen, using the first offshore wind farm in North America – the Block Island Wind Farm (Rhode …

The Characterization Of Xanthene Dyes On A Glass Substrate From Different Coating Techniques, Elsa Ortega

Open Access Dissertations

Chapter 1 of this dissertation is an investigation of rhodamine 560 (Rh560), a cationic dye similar to the well-studied rhodamine 6G (Rh6G). The spectral properties of Rh560 and Rh6G have similar changes as a function of thickness. At low surface coverage the spectra indicate monomers, at 1-2 monolayers dimers dominate, and thicker films show larger aggregates. The difference between Rh6G and Rh560 is that the transition from monomer to dimer occurs at different thickness, ~1.2 nm for Rh6G and ~0.5 nm for Rh560. This difference is accounted for by the molecular size. Chapters 2 and 3 describe photophysical investigations of …

Chemical Synthesis, Characterization And Biological Evaluation Of Methylation And Glycation Dna Adducts, Qi Tang

Open Access Dissertations

The integrity of genomic DNA is constantly challenged by endogenous and environmental agents with the formation of DNA adducts. Some of these adducts are toxic and mutagenic to replication, thus potentially leading to cancer and other genetic diseases. To counteract the undesired DNA modifications from damaging agents, cells have evolved a number of repair pathways, such as base-excision repair, nucleotide-excision repair, mismatch repair, and direct reversal repair, to restore the intact DNA. However, DNA repair is not always efficient, there are many interfering factors, such as inherited deficiency in DNA repair pathways, or the abnormal uptake of substance with inhibitory …

Dietary Polyphenols And Their Gut Microbiota Metabolites As Potential Treatments For Alzheimer's Disease, Kenneth N. Rose

Open Access Dissertations

Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder that has no cure, no therapies to stop the disease progression, and limited palliative care options. As the 6th leading cause of death in the United States, it is necessary to discover therapeutics which can alter disease progression to alleviate the burden on patients, caregivers, and healthcare systems. In the search of therapeutics for AD, dietary polyphenols have become the topic of research as epidemiological evidence suggests that exposure to dietary polyphenols, such as a Mediterranean diet, over one’s life, reduces the risk of dying from AD. Additionally, evidence from rodent models …

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 …

Physical Characterization Of Warburg Effect In Cancer Cells, Da Wei

Open Access Dissertations

Cancer is the second leading cause of death in the United States after heart disease. Because the frequency of cancer diagnoses is correlated with life expectancy, we can expect the rate of cancer diagnosis to increase with the increase of life expectancy. Additionally, cancer treatments are notoriously costly and challenging due to the heterogeneity of the cancer cell population. For these reasons, devising methods to study the characteristics, efficiently diagnose and treat cancer is extremely important.

Warburg effect has been considered as the most unique mechanism that differ cancer cells from normal cells. Normally, most of the healthy cells predominantly …

Knowledge, Attitudes, Practices And Willingness To Vaccinate In Preparation For The Introduction Of Hpv Vaccines In Bamako, Mali, Anne S. De Groot, Karamoko Tounkara, Mali Rochas, Sarah Beseme, Shahla Yekta, Fanta Siby Diallo, J. Kathleen Tracy, Ibrahima Teguete, Ousmane A. Koita

Institute for Immunology and Informatics Faculty Publications

Although screening for pre-cancerous cervical lesions and human papilloma virus (HPV) vaccination are accepted and effective means to prevent cervical cancer, women in Mali have limited access to these interventions. In addition, cervical cancer prevention by HPV vaccination has been controversial in some settings. To reduce cervical cancer prevalence and increase HPV vaccine uptake, it is important to understand the level of knowledge about cervical cancer screening and practices related to vaccination in at-risk populations. In this study, the level of knowledge about HPV and cervical cancer and attitudes towards vaccination were assessed among 301 participants (male and female, adults …

Prevalence Of Hpv 16 And 18 And Attitudes Toward Hpv Vaccination Trials In Patients With Cervical Cancer In Mali, Ibrahima Téguété, Amadou Dolo, Kotou Sangare, Abdoulaye Sissoko, Mali Rochas, Sarah Beseme, Karamoko Tounkara, Shahla Yekta, Anne S. De Groot, Ousmane A. Koita

Institute for Immunology and Informatics Faculty Publications

Background: Cervical cancer is one of the most common and lethal cancers in West Africa. Even though vaccines that protect against the most common Human papillomavirus (HPV) strains, 16 and 18, are currently in use in developed countries, the implementation of these vaccines in developing countries has been painfully slow, considering the pre-eminence of HPV-associated cervical cancer among women in those countries.

Aim: We performed serological and PCR-based assessment of blood and tissue specimens obtained from women undergoing cervical cancer-related surgery at a major urban hospital in Bamako. Since several therapeutic HPV vaccines are currently in clinical trials, we …

Effect Of Cranberry (Vaccinium Macrocarpon) Oligosaccharides On The Formation Of Advanced Glycation End-Products, Jiadong Sun, Weixi Liu, Hang Ma, Jannie P.J. Marais, Christina Khoo, Joel A. Dain, David C. Rowley, Navindra P. Seeram

Biomedical and Pharmaceutical Sciences Faculty Publications

Background: The formation and accumulation of advanced glycation end-products (AGEs) are implicated in several chronic human illnesses including type-2 diabetes, renal failure, and neurodegenerative diseases. The cranberry (Vaccinium macrocarpon) fruit has been previously reported to show anti-AGEs effects, attributed primarily to its phenolic constituents. However, there is lack of similar data on the non-phenolic constituents found in the cranberry fruit, in particular, its carbohydrate constituents. Herein, a chemically characterized oligosaccharide-enriched fraction purified from the cranberry fruit was evaluated for its potential anti-AGEs and free radical scavenging effects.

Objective: The aim of this study was to evaluate …

Investigations On Biologically Active Carbohydrates From Natural Sources, Jiadong Sun

Open Access Dissertations

Complex carbohydrates exist in almost all species of plants, animals and microorganisms. Because of their physiochemical properties, they have been traditionally applied as emulsifiers and stabilizers in food, cosmetics, textiles and as pharmaceutical ingredients. Complex carbohydrates generally exist as a layer of thick, sequential, hydrous polymers consisting of monosaccharides and non-carbohydrate substituents such as acetate, pyruvate, and phosphate. While complex carbohydrates are generally believed to serve as structural support or energy sources for the producing organisms, their potential biomedical properties have been less investigated. Our understanding of the biological activities of complex carbohydrates is further complicated since most have been …

Structure Activity Related, Mechanistic, And Modeling Studies Of Gallotannins Containing A Glucitol-Core And Α-Glucosidase, Hang Ma, Ling Wang, Daniel B. Niesen, Ang Cai, Bongsup P. Cho, Wen Tan, Qiong Gu, Jun Xu, Navindra P. Seeram

Biomedical and Pharmaceutical Sciences Faculty Publications

Gallotannins containing a glucitol core, which are only produced by members of the maple (Acer) genus, are more potent α-glucosidase inhibitors than the clinical drug, acarbose. While this activity is influenced by the number of substituents on the glucitol core (e.g. more galloyl groups leads to increased activity), the mechanisms of inhibitory action are not known. Herein, we investigated ligand–enzyme interactions and binding mechanisms of a series of ‘glucitol-core containing gallotannins (GCGs)’ against the α-glucosidase enzyme. The GCGs included ginnalins A, B and C (containing two, one, and one galloyl/s, respectively), maplexin F (containing 3 galloyls) and …

Going Global: The Introduction Of The Asian Isopod Ianiropsis Serricaudis Gurjanova (Crustacea: Peracarida) To North America And Europe, Niels-Viggo Hobbs, Eric Lazo-Wasem, Marco Faasse, Jeffrey R. Cordell, John W. Chapman, Carter S. Smith, Robert Prezant, Rebecca Shell, James T. Carlton

Biological Sciences Faculty Publications

The Asian isopod Ianiropsis serricaudis is now well established in fouling communities, often associated with introduced ascidians, throughout the Northern Hemisphere but has gone largely unnoticed because of its diminutive size (typically less than 3 mm in length) and the difficulties of identifying small peracarid crustaceans. Known locations include the northeastern Pacific (Puget Sound, San Francisco Bay, and Monterey Bay), the northwestern Atlantic (from the Gulf of Maine to Barnegat Bay, NJ), and the northeastern Atlantic (England and the Netherlands). We predict that this species is widespread along North America and European coasts, and may already be introduced to cold …

Garcinia Kola: Phytochemical, Biological And Formulation Studies, Yasah Vezele

Open Access Master's Theses

The objective of this research was to search for an antiviral compound, garcinol (or guttiferone F) from the Garcinia kola nuts using two different extraction techniques and formulate a suitable liposome for control release using an antiviral compound. The two extraction techniques used were: liquid-liquid extraction (for simplicity purposes, the term solvent-solvent, S-S, will be used interchangeable) and Supercritical Fluid Extraction (SFE). Both techniques were used to profile compounds found in Garcinia kola and for statistical comparison purposes. Extracts from both techniques were collected and analyzed for separation using Reversed-Phase High Performance Liquid Chromatography (RP-HPLC) using Ultraviolet Photodiode Array (UV-PDA) …

Evaluation Of In Vitro Anti-Inflammatory, Anti-Diabetic And Anti-Lipogenic Activity Of Natural Polyphenolic Extracts And Their Pure Constituents, Pragati P. Nahar

Open Access Dissertations

The long-term goals and objectives of our group are to identify bioactive natural products relevant to human disease prevention and health promotion. To attain this goal, the objective of this thesis was to demonstrate that bioactive polyphenol-rich extracts or preparations exert positive health benefits beyond basic nutrition, thus impacting overall health and wellness. We believe that this project has immense scientific merit from a human health perspective and will be of great public impact given that consumers are seeking natural and organic choices for improving health. In this investigation, we have focused our attention on investigating the biological activities of …

Phytochemical Investigation Of The Traditional Botanical Medicine Iresine Celosia, Caroline Grace Killian

Open Access Dissertations

Iresine celosia L. is a traditional medicine used by the indigenous Mayan people for a variety of ailments. It is also the sole active ingredient in the Odyliresin™ formulation currently marketed to humans worldwide as an antioxidant and for the promotion of prostate health. However, Odyliresin™ has not been characterized phytochemically, or evaluated biologically for its intended use. This work represents the first comprehensive phytochemical investigation of the Odyliresin™ formulation botanical extract. To better understand its constitutive phytochemistry, a tailored isolation scheme was developed, using various chromatography resins (silica gel, LH-20), separation and purification techniques. In all, eleven compounds were …

A Cross-Sectional Study To Assess Hpv Knowledge And Hpv Vaccine Acceptability In Mali, Danielle N. Poole, J. Kathleen Tracy, Lauren Levitz, Mali Rochas, Kotou Sangare, Shahla Yekta, Karamoko Tounkara, Ben Aboubacar, Ousmane Koita, Mark Lurie, Anne S. De Groot

Institute for Immunology and Informatics Faculty Publications

Despite a high prevalence of oncogenic human papilloma virus (HPV) infection and cervical cancer mortality, HPV vaccination is not currently available in Mali. Knowledge of HPV and cervical cancer in Mali, and thereby vaccine readiness, may be limited. Research staff visited homes in a radial pattern from a central location to recruit adolescent females and males aged 12–17 years and men and women aged ≥18 years (N = 51) in a peri-urban village of Bamako, Mali. Participants took part in structured interviews assessing knowledge, attitudes, and practices related to HPV, cervical cancer, and HPV vaccination. We found low levels of …

Immunopathogenesis Versus Protection In Dengue Virus Infections, Alan L. Rothman, Carey L. Medin, Heather Friberg, Jeffery R. Currier

Institute for Immunology and Informatics Faculty Publications

Dengue viruses (DENV) are mosquito-borne viruses that cause significant morbidity. The existence of four serotypes of DENV with partial immunologic cross-reactivity creates the opportunity for individuals to experience multiple acute DENV infections over the course of their lifetimes. Research over the past several years has revealed complex interactions between DENV and the human innate and adaptive immune systems that can have either beneficial or detrimental influences on the outcome of infection. Further studies that seek to distinguish protective from pathological immune responses in the context of natural DENV infection as well as clinical trials of candidate DENV vaccines have an …

Phytochemicals From The Roots Of Northern Highbush Blueberry (Vaccinium Corymbosum), Amanda Cirello

Open Access Master's Theses

Growing evidence from many in vitro studies suggest that plants produce secondary metabolites which may have potential physiological properties. The northern highbush blueberry (Vaccinium corymbosum L.) plant is commercially cultivated for its valuable dark-blue fruit, which has been extensively researched and has been shown to contain phenolic compounds recognized to have positive health benefits. Thus, an evaluation of other parts of the plant, that as of yet have not been investigated, could be worthwhile. There may be undiscovered bioactive compounds within the roots of this plant that may contribute to the improvement of human health. This rationale supports further …

The Good 5 Cent Cigar (10/25/2012), University Of Rhode Island

The Good 5 Cent Cigar (Student Newspaper Archives)

This is a digitized, downloadable version of the University of Rhode Island school newspaper.

Coupling Sensitive In Vitro And In Silico Techniques To Assess Cross-Reactive Cd4+ T Cells Against The Swine-Origin H1n1 Influenza Virus, Brian C. Schanen, Anne S. De Groot, Leonard Moise, Matt Ardito, Elizabeth Mcclaine, William Martin, Vaughan Wittman, William L. Warren, Donald R. Drake Iii

Institute for Immunology and Informatics Faculty Publications

The outbreak of the novel swine-origin H1N1 influenza in the spring of 2009 took epidemiologists, immunologists, and vaccinologists by surprise and galvanized a massive worldwide effort to produce millions of vaccine doses to protect against this single virus strain. Of particular concern was the apparent lack of pre-existing antibody capable of eliciting cross-protective immunity against this novel virus, which fueled fears this strain would trigger a particularly far-reaching and lethal pandemic. Given that disease caused by the swine-origin virus was far less severe than expected, we hypothesized cellular immunity to cross-conserved T cell epitopes might have played a significant role …