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Data Representation In Machine Learning Methods With Its Application To Compilation Optimization And Epitope Prediction, Yevgeniy Sher

Electronic Theses and Dissertations

In this dissertation we explore the application of machine learning algorithms to compilation phase order optimization, and epitope prediction. The common thread running through these two disparate domains is the type of data being dealt with. In both problem domains we are dealing with categorical data, with its representation playing a significant role in the performance of classification algorithms. We first present a neuroevolutionary approach which orders optimization phases to generate compiled programs with performance superior to those compiled using LLVM's -O3 optimization level. Performance improvements calculated as the speed of the compiled program's execution ranged from 27% for the …

An Sos Conceptual Model, Lvc Simulation Framework, And A Prototypical Implementation Of Unmanned System Interventions For Nuclear Power Plant Disaster Preparedness, Response, And Mitigation, Matthew Davis

Electronic Theses and Dissertations

Nuclear power plant disasters can have severe and far-reaching consequences, thus emergency managers and first responders from utility owners to the DoD must be prepared to respond to and mitigate effects protecting the public and environment from further damage. Rapidly emerging unmanned systems promise significant improvement in response and mitigation of nuclear disasters. Models and simulations (M&S) may play a significant role in improving readiness and reducing risks through its use in planning, analysis, preparation training, and mitigation rehearsal for a wide spectrum of derivate scenarios. Legacy nuclear reactor M&S lack interoperability between themselves and avatar or agent-based simulations of …

Predicting Child Maltreatment Potential In Mothers Who Are Substance-Involved: A Study Of Childhood Adversity, Stress, Affectivity, Emotion Dysregulation, And Emotion Regulation Strategies As Mechanisms Of Action, Amanda Lowell

Electronic Theses and Dissertations

Compared to the general population, parents who are substance-involved are both more likely to have experienced adversity during childhood and to exhibit elevated child maltreatment potential later in life. Within this population, mothers with young children are particularly at-risk. In order to enhance scientific understanding of this phenomenon, this study identified and examined several characteristics that were shown previously to be related to substance misuse and to the experience and perpetration of maltreatment. These characteristics included stress, affectivity, emotion dysregulation, and emotion regulation strategies. The current study examined these variables collectively in order to clarify the mechanisms at play in …

The Effects Of Social Support And Working Alliance On Latino-American Male Combat Veterans, Lloyd Duran

Electronic Theses and Dissertations

The negative effects of traumatic combat experiences on combatants' psychological functioning is well documented in the literature. The Global War on Terrorism (GWOT) has resulted in many veterans returning from deployments with mental health conditions related to trauma exposure, such as posttraumatic stress disorder, depression, general anxiety, and suicidality. Past researchers found significant ethnic differences in psychological functioning, with Latino-American veterans reporting more symptoms of PTSD. Furthermore, Latino-American cultural values place importance on collective orientation and secrecy of mental health concerns which may affect treatment. Thus, this study built on limited research about Latino-American male combat veterans by focusing on …

Consequences Of Altered Short-Chain Carbon Metabolism In Heart Failure, Julie Horton

Electronic Theses and Dissertations

Cardiovascular disease is currently the foremost cause of death within the United States. Heart failure (HF) is a syndrome defined by the inability of the heart to adequately execute requisite pump function in order to deliver nutrients and oxygen to peripheral tissues, irrespective of etiology. One of the most common causes of HF is chronic pressure overload due to hypertension. Ischemic heart disease is also a common driver of HF, often in conjunction with hypertension. Pressure overload initially causes compensatory metabolic changes. Structural changes follow shortly thereafter typically resulting in left ventricular hypertrophy. Eventually, the heart loses the ability to …

Go With The Flow: Patterns Of Connectivity In Low Dispersal Coral Reef Gobies (Coryphopterus Spp.) Throughout The Western Atlantic, Daniel Volk

Electronic Theses and Dissertations

Gene flow is an integral biological process that can mediate speciation. While many consider the ocean to be an open environment, there are many barriers that limit gene flow, particularly in the western Atlantic. I analyzed data from two widespread, coral reef fishes, the bridled goby (Coryphopterus glaucofraenum) and sand-canyon goby (C. venezuelae), throughout their range in the western Atlantic. Using two genetic datasets, mitochondrial DNA (mtDNA) and genomic SNPs, I investigated the evolutionary history of these species and inferred the location and strength of putative barriers. My results suggest that several unique lineages have genetically diverged from one another …

The Paths Less Traveled: Movement Of Gopher Tortoises Along Roads And Railways, Rhett Rautsaw

Electronic Theses and Dissertations

Urbanization and an expanding human population have led to a large degree of habitat destruction and fragmentation. These, in turn, reduce biodiversity and wildlife population sizes on a global scale. Transportation infrastructure, such as roads and railways, are some of the largest contributors to habitat fragmentation. Roads are well-established to negatively impact wildlife, but some studies suggest a potential use in habitat connectivity by functioning as wildlife corridors to connect distant populations. Railways are similarly known to impact wildlife by increasing mortality rates as well as provide unique risks such as electrocution and entrapment when compared to roads. However, the …

Two-Component Covalent Inhibitors (Tcci) Of The Human Immunodeficiency Virus Reverse Transcriptase (Hiv-Rt), Carlos Ledezma

Electronic Theses and Dissertations

The traditional design of nucleoside reverse transcriptase inhibitors (NRTI's) involves the synthesis of chain-terminated nucleoside analogs. HIV-RT has relatively low fidelity which facilitates mutations that confer resistance towards NRTI's, also, drug promiscuity from NRTI's result in various side-effects that lead to poor patient adherence to treatment. We designed and tested two-component covalent inhibitors against HIV-RT. Our inhibitor design results in higher specificity due to its binary approach, which has previously been used in biosensing applications, where both components are necessary for therapeutic effect, and lower chances for mutagenesis because of its inhibitory action. The TCCI approach results in up to …

The Impact Of Automation And Stress On Human Performance In Uav Operation, Jinchao Lin

Electronic Theses and Dissertations

The United States Air Force (USAF) has increasing needs for unmanned aerial vehicle (UAV) operators. Automation may enable a single operator to manage multiple UAVs at the same time. Multi-UAV operation may require a unique set of skills and the need for new operators calls for targeting new populations for recruitment. The objective of this research is to develop a simulation environment for studying the role of individual differences in UAV operation under different task configurations and investigate predictors of performance and stress. Primarily, the study examined the impact of levels of automation (LOAs), as well as task demands, on …

The Effects Of Sprint Interval Training And Maturity Status On Metabolic And Neuromuscular Fatigue Thresholds In Adolescents, Kyle Beyer

Electronic Theses and Dissertations

Purpose: To examine the maturity-related differences in the adaptations to systemic and localized fatigue thresholds (FTs) in response to sprint interval training (SIT) amongst adolescent male athletes. Methods: Twenty-seven adolescent male athletes, 11-17 years of age, completed pre-testing, six weeks of SIT, and post-testing. Participants were grouped according to their number of years from peak height velocity (PHV), an estimation of somatic maturity status, into PRE ( < -1.5yr), PERI (between -1.5 to +1.5yr) and POST ( > +1.5yr) PHV groups. Each testing session consisted of a ramp exercise protocol on a cycle ergometer. During the protocol, three systemic FTs, gas exchange threshold, ventilatory threshold, and respiratory compensation point were calculated …

A Preliminary Assessment Of Steroid Reproductive Hormones In Archaeological Human Hair Utilizing A Modified Enzyme-Linked Immunosorbent Assay (Elisa) Technique, Elisha Tisdale

Electronic Theses and Dissertations

Hair has become an invaluable resource in forensic, clinical, and bioarchaeological research. The unique interaction between the growing hair fiber, the hair follicle, and the endocrine system inundates the growing hair fiber with an incremental record of many of the discreet physiological processes of the body. Recently, a novel study by Webb et al. (2010) demonstrated that endogenous records of cortisol, the "stress hormone", are capable of being extracted from archaeological human hair through a modified enzyme-linked immunosorbent assay (ELISA) technique, thus providing insight into the "invisible" stress experiences of an individual that would otherwise not be detectable through skeletal …

The Bovine Rumen Microbiome Revealed By Different Fractions Of Rumen Contents, Ashlee Breakstone, Jiangchao Zhao

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

The bovine rumen microbiota is very important in terms of animal functionality and digestion. The fermentative capability of the rumen provides means for the digestion of complex plant material that is indigestible by humans. The rumen microbiota is made up of billions of microorganisms, primarily bacteria, that digest and ferment feed into volatile fatty acids and bacterial protein for the animal’s energy and protein needs, respectively. Changes to the rumen microbiota can have a direct measure on animal growth, health, and performance. The possibility of productivity boosts in the cattle industry make the rumen microbiome a hot topic in the …

A Deoxyribozyme Sensor And Isothermal Amplification For Human Sex Determination, Alexandra Smith

Electronic Theses and Dissertations

Ribozymes are known to catalyze biochemical reactions and behave like enzymes. They are naturally occurring and have very diverse functions within a cell. After investigating ribozymes that next step was to find if DNA can exhibit the same characteristics since RNA and DNA only differ by a ribose 2'-hydroxyl group. This evolution in curiosity gave rise to artificial DNA enzymes that can catalyze certain reactions and have been created by in vitro selection methods. Due to the ability to manipulate and control DNA hybridization, the deoxyribozyme is advantageous to the field of molecular diagnostics. Other hybridization probes like Taqman for …

Chaperonin Containing Tcp1 (Cct) As A Target For Cancer Therapy, Ana Carr

Electronic Theses and Dissertations

Treatments for aggressive cancers like triple negative breast cancer (TNBC) and small-cell lung cancer (SCLC) have not improved and remain associated with debilitating side effects. There is an unmet medical need for better, druggable targets and improved therapeutics. To this end, we investigated the role of Chaperonin-Containing TCP1 (CCT), an evolutionarily conserved protein-folding complex composed of eight subunits (CCT1-8), in oncogenesis. Our laboratory was the first to report that the CCT2 subunit is highly expressed in breast cancer and could be therapeutically targeted. To determine whether CCT is a marker of disease progression in other cancers, we analyzed CCT2 gene …

Novel Cytokine Signaling And Molecular Therapeutic Strategy In Pancreatic Cancer, Sarah Gitto

Electronic Theses and Dissertations

Pancreatic ductal adenocarcinoma (PDAC) is highly chemo-resistant and has a five year survival rate of < 8%. Risk factors of pancreatic cancer, such as chronic pancreatitis, help to elicit a pro-tumor immune response, and highly fibrotic environment that promotes tumorigenesis. To study how chronic pancreatitis promotes cancer initiation, traditional KRasG12D mice and double mutant Akt1Myr/KrasG12D mice were used to model microenvironment changes. Akt1Myr/KrasG12D mice were more susceptible to chronic tissue damage, accelerated tumor development and metastatic disease. These mice exhibited histological changes consistent with immune cell privilege, where M2 macrophages and non-cytotoxic eosinophils were co-localized with fibrotic regions. IL-5 expression was up regulated in pancreatic cells undergoing acinar to ductal metaplasia and then diminished in advanced lesions. Tumor cells treated with IL-5 exhibit increased migration and activation through STAT5 signaling. Collectively, the results suggest that eosinophils, which are responsive to IL-5, are key mediators in the pancreatic environment subjected to chronic inflammation and injury. Current therapeutics fall short in increasing patient survival. There remains an urgent need for innovative treatments and thus we tested difluoromethylornithine (DFMO) in combination with a novel polyamine transport inhibitor, Trimer44NMe, against Gemcitabine-resistant PDAC cells. Prior clinical failures when targeting polyamine biosynthesis with DFMO monotherapy may be due to tumor escape via an undefined polyamine transport system. In pancreatic tumor cells DFMO alone and with Trimer44NMe significantly reduced PDAC cell viability by inducing apoptosis or cell cycle arrest. In vivo orthotopic PDAC growth with DFMO treatment resulted in decreased c-Myc expression, a readout of polyamine pathway dysfunction. Moreover, dual inhibition significantly prolonged survival of tumor-bearing mice, and increased M1 macrophage infiltration and reduced FoxP3 expression. Collectively, these studies demonstrate that targeting polyamine pathways in PDAC is a promising immunomodulating therapy that increases survival.

A Universal Electrochemical Biosensor For The Detection Of Nucleic Acids Based On A Four-Way Junction Structure, Dawn Mills

Electronic Theses and Dissertations

Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode's surface. This dissertation demonstrates that a single probe can be used to analyze several nucleic acid targets of different lengths with high selectivity, low cost and can be regenerated in 30 seconds by a simple water rinse. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode's surface and two adaptor …

Harnessing Spatial Intensity Fluctuations For Optical Imaging And Sensing, Milad Akhlaghi Bouzan

Electronic Theses and Dissertations

Properties of light such as amplitude and phase, temporal and spatial coherence, polarization, etc. are abundantly used for sensing and imaging. Regardless of the passive or active nature of the sensing method, optical intensity fluctuations are always present! While these fluctuations are usually regarded as noise, there are situations where one can harness the intensity fluctuations to enhance certain attributes of the sensing procedure. In this thesis, we developed different sensing methodologies that use statistical properties of optical fluctuations for gauging specific information. We examine this concept in the context of three different aspects of computational optical imaging and sensing. …

Gender Perception Of The Rationales Behind Vegetarianism, Nicholas Tallant

Honors Theses

No abstract provided.

Open Educational Resource 2017 Textbook List, Zachariah Claybaugh, Chelsea Stone

Librarian Publications

This is an updated, discipline specific OER textbook list for departments at Sacred Heart University, compiled by Zach Claybaugh and Chelsea Stone.

Exploring The Socio-Ecological Dimensions Of Agricultural Expansion In New Hampshire, Jennifer Wilhelm

Doctoral Dissertations

Forest ecosystems and agriculture represent coupled socio-ecological systems that are shaped by human activity. The extensification of agriculture (expansion of food production on the landscape) can cause significant changes in land use, and can contribute to the degradation of biodiverse ecosystems and the services these systems provide. Yet the need to increase food production capacity, either through agricultural intensification or extensification, continues to rise. In this dissertation, I address the critical issue of agricultural extensification from several angles.

The first chapter assesses agricultural expansion through the lens of urban and peri-urban agriculture (UPA) through systematic review of the literature. I …

Development Of Novel Bio- And Heterogeneous Catalysts For The Production Of Bio- And Green Diesel, Ye Deng

Doctoral Dissertations

Diminishing petroleum reserves and increasing environmental awareness has led to an urgent need to develop alternative fuels, such as biodiesel. Enzymatic trans/-esterification of waste cooking oils with a lipase catalyst is a promising environmentally-friendly process to produce biodiesel, compared to the current industrial chemical process. Despite several advantages, there are a few technical and economical obstacles that limit this process, such as insufficient availability of large quantities of inexpensive lipase suitable for catalysis, and bad performance at low temperatures due to biodiesel’s low cetane number. These limitations are addressed in this dissertation using genetic engineering of plants to produce the …

Nature Of Formal Intimate Partner Violence Help Seeking: The Influence Of Individual And Community Characteristics, Desiree Ruth Wiesen-Martin

Doctoral Dissertations

Intimate partner violence is a public health concern, and intimate partner violence victim help seeking is the focus of many intervention/prevention policies and programs. Help seeking by victims of intimate partner violence from formal support services, such as the police, domestic violence shelters, and/or rape crisis centers, is relatively low (Kaukinen 2002; Davies, Block, and Campbell 2007; Campbell 2008; Kaukinen, Meyer, and Akers 2013; Zaykowski 2014), and the research which considers the nature of help seeking among those victims who seek help is quite limited. This dissertation investigates the nature of formal help seeking among intimate partner violence victims who …

Effects Of Alien Shrubs On Caterpillars And Shrubland-Dependent Passerines Within Three Transmission Line Rights-Of-Way In Southeastern New Hampshire, Matthew Tarr

Doctoral Dissertations

By altering plant species composition and reducing plant species richness, invasion of non-native (alien) plants can reduce caterpillar abundance in bird habitats and simplify the bird community, but whether these cascading effects of alien plants extend further to affect bird productivity has not been quantified. This study is the first to quantify how reduced caterpillar abundance associated with alien plant invasion affects the reproductive success of a breeding passerine, the common yellowthroat (Geothlypis trichas trichas). The study was conducted in three transmission line rights-of-way where plant composition in yellowthroat territories was dominated by a near monoculture of alien shrubs (“ALIEN” …

Biophysical Mechanisms Of Rhythm Generation In The Pre-Bötzinger Complex, Ryan S. Phillips

Doctoral Dissertations

The pre-Bötzinger complex (pre-BötC) is an essential rhythmogenic brainstem nucleus located in the ventrolateral medulla. Rhythmic output from the pre-BötC is relayed through premotor and motor neurons to the diaphragm and intercostal muscles to drive the active inspiratory phase of breathing. The specific biophysical mechanisms responsible for generating rhythmic bursting and network synchronization are not well understood and remain a highly debated topic within the field. Through extensive experimental and theoretical work two plausible rhythmogenic mechanisms have emerged. One mechanism is based on a slowly inactivating persistent sodium current (INaP) and the other on a calcium activated non-selective cation current …

Microbial Community And Vibrio Parahaemolyticus Population Dynamics In Relayed Oysters, Michael Anthony Taylor

Doctoral Dissertations

The CDC estimates that 45,000 people are sickened each year by foodborne Vibrio parahaemolyticus in the United States. Filter-feeding bivalve shellfish, such as oysters, are routinely inhabited by human pathogenic V. parahaemolyticus and there currently is not a contaminant management process that effectively reduces concentrations of V. parahaemolyticus in oysters. The transplanting of V. parahaemolyticus -laden oysters to an area with low concentrations or no V. parahaemolyticus, called oyster relay, is one reduction strategy that holds promise for treating live oysters. A key consideration for effective strategies to reduce Vibrio spp. in shellfish is the influence of microbiota in natural …

Nitrogen Dynamics And Retention In The River Network Of A Tropical Forest, Luquillo Mountains, Puerto Rico, Richard Brereton

Doctoral Dissertations

This dissertation identifies gaps in the scientific understanding of nutrient cycling, particularly nitrogen (N) cycling, in streams and riparian zones of tropical montane forests, and addresses several of those gaps with original field-based research using study watersheds in the Luquillo Mountains of Puerto Rico as the model system. The Luquillo Mountains have features typical of mature montane tropical forests, such as high background N concentrations in streams and groundwater relative to streams in other biomes. As a USDA Forest Service Experimental Forest, the Luquillo Mountains are accessible to researchers and have abundant monitoring and experimental datasets from which to build …

A Study Of The Surface Structure Of Polymorphic Graphene And Other Two-Dimensional Materials For Use In Novel Electronics And Organic Photovoltaics, Maxwell Charles Grady

Doctoral Dissertations

For some time there has been interest in the fundamental physical properties of low- dimensional material systems. The discovery of graphene as a stable two-dimensional form of solid carbon lead to an exponential increase in research in two-dimensional and other re- duced dimensional systems. It is now known that there is a wide range of materials which are stable in two-dimensional form. These materials span a large configuration space of struc- tural, mechanical, and electronic properties, which results in the potential to create novel electronic devices from nano-scale heterostructures with exactly tailored device properties. Understanding the material properties at the …

Improving The Understanding Of Different Diets On The Concentration And Metabolism Of The Mammalian Lignan Enterolactone In Dairy Cattle, Caren Paludo Ghedini

Doctoral Dissertations

Flaxseed (Linum usitatissimum) is the richest source of the plant lignan secoisolariciresinol diglucoside (SDG), which is precursor for the synthesis of the mammalian lignans enterolactone (EL) and enterodiol (ED) by the gastrointestinal microbes in mammals. There is a great deal of interest in promoting increased intakes of lignans in humans’ diet due to their potential health benefits, especially in the prevention of cardiovascular diseases, hypercholesterolaemia, breast and prostate cancers, and osteoporosis. Consumption of milk and dairy products enriched in EL could be an excellent strategy to increase the intake of lignans by humans. The first (Chapter II) and second (Chapter …

Patterns And Drivers Of Carbon Fluxes In Temperate Forests, Andrew Ouimette

Doctoral Dissertations

Despite decades of carbon cycling research in terrestrial ecosystems, a complex suite of biotic and abiotic interactions make a complete understanding of the natural carbon cycle elusive. This thesis aims to advance our understanding of the carbon cycle, and stems from several ongoing projects aimed at quantifying carbon dynamics in forest ecosystems across a range of scales, with a specific effort to include both above and belowground components of forest ecosystems. I begin with a project using detailed chemical measurements on specific segments of root systems from two different tree species, in order to help refine methods that quantify the …

Simulation Studies Of Signaling And Regulatory Proteins, Hossein Mohammadiarani

Doctoral Dissertations

I used molecular dynamics (MD) simulations as a primary tool to study folding and dynamics of signaling and regulatory proteins. Specifically, I have studied two classes of proteins: the first part of my thesis reports studies on peptides and receptors of the insulin family, and the second part reports on studies of regulatory proteins from the G-protein coupled receptor family. The first problem that I investigated was understanding the folding mechanism of the insulin B-chain and its mimetic peptide (S371) which were studied using enhanced sampling simulation methods. I validated our simulation approaches by predicting the known solution structure of …