Digital Commons Network^™

Svm-Based Volitional Artificial Leg Control Via Ubiquitous Small And Low Power Architectures, Robert Hernandez

Open Access Dissertations

Presented within this dissertation is the evolution of the research leading to the selection of small, low power architectural solutions to the University of Rhode Island’s (URI) Neural Machine Interface (NMI) algorithm. The NMI is designed to provide volitional control of an artificial limb for transfemoral amputees. The NMI algorithm is based on neuromuscular–mechanical fusion, gait phase dependent, nonlinear support vector machine (SVM) classification. URI’s NMI algorithm utilizes electromyography to detect direct commands from the human brain to the residual thigh muscles in conjunction with mechanical signals derived from loadcell to determine the user’s intended locomotion mode.

Of utmost importance …

American Woodcock Ecology And Bird Conservation In Relation To Forest Management, Roger J. Masse

Open Access Dissertations

The extent of shrubland and young forest in the Northeast, USA, has declined rapidly since the mid-1900’s. Accordingly, the abundance of wildlife that depends on young forest has also declined. For example, American woodcock (Scolopax minor), an upland shorebird species, require an appropriate spectrum and spatial configuration of young forest to thrive and their populations have declined significantly since at least 1968. Active forest management is required to conserve populations of American woodcock and other young forest wildlife, but the importance of young forest management to some aspects of the ecology of key wildlife are not fully understood. I …

The Green Eating Project: Web-Based Intervention To Promote Environmentally Conscious Eating Behaviors, Jessica T. Nash

Open Access Dissertations

The food system has been cited as unsustainable due to the reliance on natural resources and contribution to global pollution. Technological advances will play a major role in mitigating these negative consequences but consumers will also play a role through food choices. Green Eating (GE) is the concept of practicing more environmentally conscious eating behaviors and is currently defined as: eating locally grown foods, limited amounts of processed/fast foods, eating meatless meals at least one day per week, choosing organic foods as much as possible, and only taking what you plan on eating. Little research exists investigating college student perspectives’ …

Carbon-Nitrogen Bond Formation Via Tandem Carbon-Hydrogen (C-H) And Nitrogen-Hydrogen (N-H) Bond Functionalization, Abhishek A. Kantak

Open Access Dissertations

The oxidative cross-coupling of carbon-hydrogen (C-H) and nitrogenhydrogen (N-H) bonds to form carbon-nitrogen (C-N) bonds is an important synthetic advance, as amine and amide functional groups are ubiquitous in biologically active molecules. This technique is orthogonal to conventional amination techniques, which rely on electrophilic nitration/reduction strategies or metal catalyzed coupling of prefunctionalized arenes.

This dissertation’s main focus is on the development of oxidative methods for constructing N-arylamines and amides via tandem C-H/N-H bond activation and increasing synthetic efficiency for total synthesis of an inhibitor of botulinum neurotoxin via direct C–H functionalization.

The first manuscript, “Metal-Free Intermolecular Oxidative C-N Bond …

Using Lagrangian Coherent Structures To Study Coastal Water Quality, Laura A. Fiorentino

Open Access Dissertations

The accumulation of pollutants near the shoreline can result in low quality coastal water with negative effects on human health. To understand the role of mixing by tidal flows in coastal water quality, we study the nearshore Lagrangian circulation of four recreational beaches in Miami, FL, who, despite close proximity, have varying microbial levels. Specifically, we reveal Lagrangian Coherent Structures (LCSs), i.e., distinguished material curves which shape global mixing patterns and thus act as skeletons of the Lagrangian circulation. We show how these material curves, which shape circulation and mixing patterns, can be used to explain the incongruous states of …

Design Of Endothelial Progenitor Cellular Constructs For Therapeutic Angiogenesis Applications, Ximena Vial

Open Access Dissertations

The goal of therapeutic angiogenesis is the development of functional and mature vasculature by combining biological and physical cues that mimic the native extracellular matrix. In this study we evaluated if immobilizing vascular endothelial growth factor (VEGF) gradients and SDF-1α on gelatin nanofibrous scaffolds with different fiber orientations (i.e. random or aligned) influence the angiogenic potential of endothelial progenitor cells (EPCs) and human umbilical vein endothelial cells (HUVECs). Both cell types successfully adhered onto gelatin B scaffolds. VEGF gradients alone or combined with SDF-1α as well as fiber orientation had a pronounced effect on cell behavior, morphology and orientation. Cells …

Exploring The Oncogenic Role Of P27 In Regulating Tumor Progression, Dekuang Zhao

Open Access Dissertations

p27 is a cell cycle regulator and an atypical tumor suppressor. However, p27 gene deletions or mutations are rarely observed in human cancers. Instead, p27 is frequently degraded or mislocalized to the cytoplasm in aggressive human cancers. Phosphorylation at T157 or T198 by different PI3K effector kinases leads to p27 cytoplasmic accumulation. However, the functional contribution of phosphorylated and cytoplasmic p27 to cancer progression remains unknown. By introducing a cell cycle defective (CK-) and double phosphomimetic p27 mutant (T157D/T198D or DD), we found that phosphorylation of p27 at T157 or T198 by PI3K/mTOR directly regulated tumor cell migration and invasion. …

Spatio-Temporal Visual Information Analysis For Moving Object Detection And Retrieval In Video Sequences, Dianting Liu

Open Access Dissertations

The development of the Internet makes the number of online videos increase dramatically, which brings new demands to the video search engines for automatic retrieval and classification. We propose an unsupervised moving object detection and retrieval framework by exploiting and analyzing spatio-temporal visual information in the video sequences. The motivation is to use visual content information to estimate the locations of the moving objects in the spatio-temporal domain. Compared with the existing approaches, our proposed detection algorithm is unsupervised. It does not need to train models for specific objects. Furthermore, it is suitable for the detection of unknown objects. Therefore, …

Haitian Parents' Experiences With The Iep Process And Their Involvement With The Special Education Program, Margarette Mahotiere

Open Access Dissertations

Current literature and recent legislation advocate parental involvement in education as ‘best subsequent reauthorizations practice.’ The Individuals with Disabilities Education Act (IDEA) Amendment of 1997 and its promote parental participation in the special education process by requiring schools to consider parents as equal partners in the development of the Individualized Education Plan (IEP) for students with disabilities. However, parents have reported the process as stressful and confusing. Prior research revealed barriers that marginalize culturally and linguistically diverse (CLD) parents to passive roles in the process. Using qualitative methods, this study focused on Haitian parents’ participation in both the IEP process …

Reflectance And Ultrastructure Of The Retinal Nerve Fiber Layer In Normal And Glaucomatous Retinas, Ye Spector

Open Access Dissertations

Glaucomatous damage to the RNFL usually precedes detectable visual field loss; clinical assessment of RNFL optical properties has been valuable in diagnosis of glaucoma and other neuropathic diseases. In this dissertation, we aimed to improve the understanding of the changes of RNFL reflectance and its underlying ultrastructure under the development of glaucoma. We used simultaneous immunohistochemical labeling and both en face and in-depth confocal imaging to study axonal cytoskeletal alteration of F-actin, MTs and NFs across the retina in the context of glaucoma. We have found that alteration of each cytoskeletal components is different from each other, and different degree …

An Inverse Relationship Between Resistance To 2-Deoxy-D-Glucose And Glucose Starvation In Tumor Cells Under Normoxia, Katherine Beth Philips

Open Access Dissertations

A distinguishing feature of tumor cells is their upregulation of glucose metabolism. This metabolic change from oxidative phosphorylation to aerobic glycolysis creates a selective window that can be exploited for anticancer therapy. Here we investigate mechanisms by which pancreatic cancer cells respond to therapeutic (2-deoxy-D-glucose, 2-DG) and physiologic (glucose starvation, GS) forms of glucose restriction. 2-Deoxy-d-Glucose (2-DG) is a sugar analog of both glucose and mannose and thus has established activities inhibiting glycolysis and interfering with glycosylation, respectively. Due to 2-DG’s dual functions, it has classically been thought of as a glucose deprivation mimetic. Additionally, these roles render 2-DG an …

Association Affinity Network Based Multi-Model Collaboration For Multimedia Big Data Management And Retrieval, Tao Meng

Open Access Dissertations

With the rapid development of smart devices and ever-increasing popularity of social media websites such as Flickr, YouTube, Twitter and Facebook, we have witnessed a huge increase of multimedia data. Recently, social media technology and big data have converged to provide rich content on what happens around the world via texts, images, videos, audios, etc. Given the enormous volumes of multimedia data, efficient and effective retrieval of relevant information according to users’ needs poses great challenges for traditional text-oriented storage and retrieval systems. Since manually annotating and managing the huge amount of information have become infeasible, data-driven approaches have received …

The Influence Of Increased Co2 On Early Developmental Stages Of Cobia, Rachycentron Canadum, Dwight A. Ebanks

Open Access Dissertations

Projected increases in atmospheric CO2 and the resulting decrease in oceanic pH over the course of the 21st century warrant studies on the effects of these changes on marine teleosts. The goal of this dissertation was to assess the impact of projected changes in CO2 on the early physiological dynamics and development of cobia, Rachycentron canadum. Spermatozoa respiration rates displayed a non significant decrease from 1.0 + 0.2 nmol O2/mL semen•sec + S.E. at 380 ppm CO2 to 0.7 + 0.1 nmol O2/mL semen•sec + S.E. at 800 ppm CO2. Spermatozoa velocity decreased from 22.1 + 0.5 to 14.9 + …

Lightweight Moral Realism: Objectivity And Reasoning Without Heavyweight Facts, Mark Douglas Warren

Open Access Dissertations

In this dissertation, I develop a non-representational approach to metaethics that avoids the ontological and epistemic problems that traditional realist views face: accounting for the nature of moral facts and our knowledge of these facts in a way that comports with naturalism. According to expressivism—the most popular non-representational account in contemporary metaethics—moral claims don’t aim to represent moral facts or properties, but instead function to express our non-cognitive attitudes like approval or disapproval. This is a promising approach, but the view has substantial difficulties accounting for important features of moral discourse, like objectivity and complicated moral reasoning. I develop an …

A Study Of Internal Solitary Waves In Satellite Images Of The Mid-Atlantic Bight, Jingshuang Xue

Open Access Dissertations

Satellite imagery has been widely used to study internal solitary wave (ISW) generation mechanisms, evolution, and properties. The Nonlinear Internal Wave Initiative/Shallow Water 2006 (SW06) experiment in the Mid-Atlantic Bight (MAB) provided a unique dataset to study the vertical structure from their surface manifestation in the images, which can improve our understanding of ISW evolution, energy dissipation, and mixing processes. This thesis has two parts. First, the applicability of various weakly nonlinear theories including the Korteweg-de Vries (KdV), Intermediate Long Wave (ILW), Benjamin-Ono (BO), and higher-order KdV models is tested to describe large amplitude ISWs in the MAB. Based on …

The Mechanisms Of Synaptic Maintenance, Shaoyun Zang

Open Access Dissertations

Synapses are specialized cell-cell contacts where signals are reliably transduced from a neuron to its target cell in a regulated manner. Structurally, synapses are comprised of the pre- and post-synaptic terminals, and the synaptic cleft. Within each of these compartments is a complex network of molecular machinery, the components of which require constant turnover and “maintenance” to ensure a consistent relay of information. In neurodegenerative diseases, such as Alzheimer’s (AD), Parkinson’s (PD), and prion-related diseases, synaptic degeneration is often an early event associated with disease severity, which is evinced by the degree of cognitive decline. A dysfunction of synaptic maintenance …

Evaluation Of Insulin-Like Growth Factor Receptor 1 Inhibition As A Treatment For Prostate Cancer: Preclinical Efficacy And Resistance, Cale Fahrenholtz

Open Access Dissertations

Prostate cancer is the most commonly diagnosed non-cutaneous malignancy in U.S. men. While tumors initially respond to androgen-deprivation therapy, the standard care for advanced or metastatic disease, tumors eventually recur as castration-resistant prostate cancer. Upregulation of the insulin-like growth factor signaling axis drives growth and progression of prostate cancer by promoting proliferation, survival, and angiogenesis. Ganitumab (formerly AMG 479) is a fully human antibody that inhibits binding of IGF-1 and IGF-2 to IGF-1R. Ganitumab decreased IGF-1 induced phosphorylation of the downstream effector AKT and reduced proliferation of multiple androgen-dependent and castration-resistant human prostate cancer cell lines in vitro albeit to …

The Role Of Algal Symbiont Community Dynamics In Reef Coral Responses To Global Climate Change, Ross Cunning

Open Access Dissertations

The continued growth and survival of reef-building corals is essential to sustain the goods and services provided by coral reefs, worth billions of dollars annually. However, warming oceans are causing more frequent and severe episodes of coral bleaching, the breakdown of symbiosis between corals and their algal symbionts (Symbiodinium spp.), which threatens corals’ survival unless they can adapt or acclimatize. One way that corals may increase their thermal tolerance is by associating with different Symbiodinium types. Changes in partner abundance may also have functional consequences, but these symbiont dynamics are poorly understood. This dissertation aims to provide a clearer understanding …

Towards On-Site Detection Of Nucleic Acids For Pathogen Monitoring, Daohong Zhang

Open Access Dissertations

As a leading cause of death in developing countries and a persistent problem elsewhere, pathogenic organisms are as ubiquitous as they are dangerous. Significant worldwide resources are directed toward their detection and eradication, leading to a broad coalition of government agencies, healthcare providers, academic researchers, and food manufacturers dedicated to providing the best-available prevention strategies for mitigating exposure risk. At the forefront of this effort is the field of pathogen detection. Our work directly addresses the current lack of simple, rapid, sensitive, and selective pathogen detection methods needed for frontline intervention in the most at-risk populations. To begin, we focused …

Integrated Theoretical And Computational Approaches To Study Hydrolysis And Aggregation Of Biomolecules, Mehmet Ozbil

Open Access Dissertations

In this thesis, we have focused on the following two projects: (1) mechanisms of peptide hydrolysis, and (2) aggregation of biomolecules. A plethora of theoretical and computational techniques; quantum mechanics, molecular dynamics, and molecular docking have been employed to accomplish the goals of these projects. The selective hydrolytic cleavage of the extremely stable peptide bond (-(O=)C-NH-) of peptides and proteins by enzymes and their analogues is required in a wide range of biological, biotechnological and industrial applications. In the first project, we have elucidated the mechanisms of peptide hydrolysis by non-metallic (beta secretase (BACE)) and metallic (insulin degrading enzyme (IDE) …

Human Recombineering, Melvys Valledor

Open Access Dissertations

Genome editing by homologous recombination (HR) is centrally important for functional genomics, making disease models, bioengineering and for gene therapy. Viral HR relies on a SynExo complex comprised of an exonuclease and a synaptase. Genome editing by the phage lambda synaptase Beta approaches HR rates of 10% in E. coli using ssDNA-mediated Recombineering but is much less efficient in mammalian cells. SynExos are common to dsDNA viruses that infect a variety of hosts and their mechanisms are conserved, suggesting that direct genome Recombineering can be extended beyond bacteria. Our hypothesis is that co-evolution of viral SynExo recombinases with host proteins …

Elucidating The Complex Interplay Between Host And Virus, Linlin Gao

Open Access Dissertations

Upon virus infection, the innate immune response provides the first line of protection and rapidly induces type I interferons (IFN alpha/beta), which mediate potent antiviral effects. To maintain homeostasis and prevent autoimmunity, IFN production is tightly regulated; however, the mechanisms of negative regulation are poorly understood. Herein, we demonstrate that the A20 binding inhibitor of NF-kappaB 1 (ABIN1) is a novel negative regulator of antiviral signaling. Overexpression of ABIN1 inhibited IFN-beta promoter activation in response to virus infection or poly(I:C) transfection, whereas siRNA-mediated knockdown of ABIN1 enhanced IFN-beta production upon virus infection. ABIN1 interacted with the A20 regulatory molecule TAX1BP1 …

Horizontal Vs. Vertical Connectivity In Caribbean Reef Corals: Identifying Potential Sources Of Recruitment Following Disturbance, Xaymara M. Serrano

Open Access Dissertations

The extent to which reefs are effectively connected to one another, and their potential to serve as sources of larval replenishment following disturbance, are topics of considerable interest in contemporary reef science. To date, most assessments of reef connectivity have emphasized long-distance horizontal dispersal of propagules from one shallow reef to another. The extent of short-distance vertical connectivity, however, has been largely unquantified. To fill this gap in knowledge, I developed DNA microsatellite loci for two Caribbean depth-generalist coral species with different life-history reproductive strategies (Montastraea cavernosa and Porites astreoides), and assessed connectivity in >1,200 coral samples collected from 3 …

Fine-Scale Distributions Of Plankton And Larval Fishes: Implications For Predator-Prey Interactions Near Coastal Oceanographic Features, Adam Tyler Greer

Open Access Dissertations

Describing the distributions of organisms on scales relevant to individuals (1-100 m) is critical to understanding predator-prey interactions within the plankton. This has driven the development of plankton imaging technology with synoptic physical parameters (temperature, salinity, depth), which facilitates high-resolution taxonomic and spatial descriptions. We utilized a novel In Situ Ichthyoplankton Imaging System (ISIIS) that addressed some shortcomings of other imaging systems by allowing for the simultaneous sampling of both abundant (e.g., copepods, appendicularians, marine snow) and rare (e.g., fish larvae, medusae, ctenophores) members of the plankton community. The main objectives of this study were 1) to describe the physical …

Apoptotic Regulation Of B Cell Development And Autoimmunity, Jacqueline A. Wright

Open Access Dissertations

Misguided immune reactions against self can cause autoimmunity. Although multiple factors are likely involved, a common feature is altered lymphocyte homeostasis due to dyregulated apoptosis. Here, we show that the integration of signals from the BCR and BAFF-R promotes survival of T2 cells that have passed the self-reactivity checkpoint. BCR engagement produces NF-κB2 protein, a substrate used by the BAFF-R for the activation of the alternative NF-κB pathway. In contrast, pre-checkpoint T1 cells fail to integrate BCR and BAFF-R signals and remain sensitive to BCR-mediated-apoptosis. Btk and c-Rel are critical in this signal integration and B-cell survival. Importantly, BAFF-R promotes …

Ddx24 Negatively Regulates Cytosolic Rna Mediated Innate Immune Signaling, Zhe Ma

Open Access Dissertations

Innate immunity is characterized by production of type I interferon which is necessary for the stimulation of effective anti-viral host defense. Upon recognition of cytosol viral dsRNA species, RIG-I-Like Receptors (RLRs), as well as many co-regulators, are recruited to adaptor protein IPS-1 and trigger innate immune responses. FADD (Fas associated with death domain) and RIP1 (receptor-interacting protein 1), have been reported to be recruited to this IPS-1 complex during viral infection and essential for optimal RLR signaling. Here we reported a novel type I interferon inducible DExD/H family helicase DDX24, which was found and confirmed to specifically associate with FADD …

Improving Reuse In Software Development For The Life Sciences, Nicholas Vincent Iannotti

Open Access Dissertations

The last several years have seen unprecedented advancements in the application of technology to the life sciences, particularly in the area of data generation. Novel scientific insights are now often driven primarily by software development supporting new multidisciplinary and increasingly multifaceted data analysis. However, despite the availability of tools such as best practice frameworks, the current rate of software development is not able to keep up with the needs of scientists. This bottleneck in software development is largely due to code reuse generally not being applied in practice.

This dissertation presents Legwork, a class library of reuse-optimized design pattern implementations …

Observation-Based Algorithm Development For Subsurface Hydrology In Northern Temperate Wetlands, Chun-Mei Chiu

Open Access Dissertations

This study investigates wetland subsurface hydrology, as well as biogeochemistry - which is strongly influenced by water and temperature dynamics - as these interactions are expected to be highly significant, yet remain poorly represented in current ecosystem and climate models.

Northern wetlands have received widespread public attention due to steadily increasing summer mean global temperatures, extreme precipitation events and higher rates of natural greenhouse gas emissions, as well as the significant impacts on them due to human activities. The goal of my graduate research has been to improve quantification of the role of subsurface hydrology in northern wetlands by using …

Genes With Physiological Roles In Callipyge Muscle Hypertrophy, Hui Yu

Open Access Dissertations

Callipyge sheep is an excellent model to study genes regulation in muscle growth since the up-regulation of DLK1 and/or RTL1 results in extreme postnatal muscle hypertrophy in loin and hindquarters. DLK1 and/or RTL1 are the primary inducers of muscle hypertrophy due to the inheritance model for the callipyge phenotype. The overall aim of this dissertation is to study the physiological pathways responding to the up-regulation of DLK1 and / or RTL1 in the hypertrophied muscles. Microarray analysis of gene expression identified 375 genes that were differentially expressed in callipyge semimembranosus. Twenty-five transcripts were further verified by quantitative PCR in two …

Maternal Sensitivity, Maternal Mind-Mindedness, And Infant Socioemotional Functioning: An Examination Of Concurrent Associations, Nancy Ignacia Longoria

Open Access Dissertations

Associations between maternal sensitivity, maternal mind-mindedness, and infant socioemotional (SE) functioning were examined in a sample of 40 mother-infant dyads. Semi-structured home observations were conducted to assess maternal sensitivity and collect maternal ratings of maternal depression and infant SE functioning. Mind-mindedness was assessed during free play and teaching interactions during the home visit. Sensitivity at home was positively associated with mind-mindedness during a free play interaction, but not during a teaching interaction. Neither sensitivity nor mind-mindedness was significantly associated with total infant SE scores, or scores on 3 SE subscales (adaptive functioning, self-regulation, and interaction with people). A trend between …