Digital Commons Network^™

An Ameliorated Prediction Of Drug–Target Interactions Based On Multi-Scale Discrete Wavelet Transform And Network Features, Cong Shen, Yijie Ding, Jijun Tang, Xinying Xu, Fei Guo

Faculty Publications

The prediction of drug–target interactions (DTIs) via computational technology plays a crucial role in reducing the experimental cost. A variety of state-of-the-art methods have been proposed to improve the accuracy of DTI predictions. In this paper, we propose a kind of drug–target interactions predictor adopting multi-scale discrete wavelet transform and network features (named as DAWN) in order to solve the DTIs prediction problem. We encode the drug molecule by a substructure fingerprint with a dictionary of substructure patterns. Simultaneously, we apply the discrete wavelet transform (DWT) to extract features from target sequences. Then, we concatenate and normalize the target, drug, …

Distribution And Potential Impact Of Microplastics In The Ribbed Marsh Mussel Geukensia Demissa, Matthew Byron Khan

Theses, Dissertations and Culminating Projects

Human activities have generated large quantities of plastics that are actively dumped or indirectly deposited into oceans. In particular, the use of single-use packaging and microplastics in cosmetics and manufacturing has led to significant increases of these contaminants in coastal waters. These plastics, because of their size, can be ingested by filter-, suspension-, and deposit-feeding organisms who coincidentally consume them as potential food sources. As a result, organisms may experience marked reductions in growth and/or health due to the accumulation of these plastics in their digestive tracts. While research has concentrated on the commercially harvested blue mussel Mytilus edulis, none …

Evasion Of Foreign Taxes For Wildlife Exports As A Violation Of The Lacey Act, Audrey Elzerman

Sea Grant Law Fellow Publications

This study considers whether violations of foreign export duty requirements for live wildlife shipments can be prosecuted under United States law. The next section introduces the Lacey Act, which offers a potent enforcement tool against wildlife trafficking and related offenses. The study then considers whether and how export duty fraud violates the Lacey Act and the possible penalties that apply to such violations. Finally, it uses the Philippines as a case study to illustrate the utility of exporting country laws for Lacey Act prosecution of these cases.

The Experience Of Parents And Adolescents With The Medical Care For The Condition Of Cleft Lip And Palate: A Phenomenological Study., Sarah Breseke

Dissertations

The purpose of this qualitative study was to explore the experiences of adolescents born with cleft lip and/or palate and parents of adolescents with the condition. Individuals born with this condition experience extensive medical treatment from birth to late adolescence with impacts on both individuals and families. This study utilized a phenomenological design to explore and describe participants’ experiences of the impact of this condition, its medical treatment, as well as coping mechanisms utilized in adjusting to the condition. Criterion sampling was utilized to recruit adolescents between the ages of 12 and 18 and parents of this age group, all …

A Leptin-Regulated Circuit Controls Glucose Mobilization During Noxious Stimuli, Jonathan N. Flak, Deanna M. Arble, Warren Pan, Christa Patterson, Thomas Lanigan, Paulette B. Goforth, Jamie Sackner, Maja Joosten, Donald A. Morgan, Margaret B. Allison, John Hayes, Eva Feldman, Randy J. Seeley, David P. Olson, Kamal Rahmouni, Martin G. Myers Jr.

Biological Sciences Faculty Research and Publications

Adipocytes secrete the hormone leptin to signal the sufficiency of energy stores. Reductions in circulating leptin concentrations reflect a negative energy balance, which augments sympathetic nervous system (SNS) activation in response to metabolically demanding emergencies. This process ensures adequate glucose mobilization despite low energy stores. We report that leptin receptor–expressing neurons (LepRb neurons) in the periaqueductal gray (PAG), the largest population of LepRb neurons in the brain stem, mediate this process. Application of noxious stimuli, which often signal the need to mobilize glucose to support an appropriate response, activated PAG LepRb neurons, which project to and activate parabrachial nucleus (PBN) …

Catalase Is A Determinant Of The Colonization And Transovarial Transmission Of Rickettsia Parkeri In The Gulf Coast Tick Amblyomma Maculatum, Khemraj Budachetri, Deepak Kumar, Shahid Karim

Faculty Publications

The Gulf Coast tick (Amblyomma maculatum) has evolved as a competent vector of the spotted‐fever group rickettsia, Rickettsia parkeri. In this study, the functional role of catalase, an enzyme responsible for the degradation of toxic hydrogen peroxide, in the colonization of the tick vector by R. parkeri and transovarial transmission of this pathogen to the next tick generation, was investigated. Catalase gene (CAT) expression in midgut, salivary glands and ovarian tissues exhibited a 2–11‐fold increase in transcription level upon R. parkeri infection. Depletion of CAT transcripts using an RNA‐interference approach significantly reduced R. parkeri infection …

Wisp1 Is An Overexpressed Driver Of Glioblastoma, Pushan R. Dasgupta

Dissertations and Theses (Open Access)

Despite current multimodal therapies for glioblastoma (GBM) the prognosis remains very grim. There is a tremendous need to identify new genetic drivers which can serve as potential therapeutic targets. In order to find new drivers, we leveraged genomic datasets to conduct a context specific in vivo functional genomic screen of overexpressed and/or amplified genes in GBM. We identified WISP1, a secreted extracellular matrix protein, to be an overexpressed driver in GBM. Overexpression of WISP1 was able to drive tumor growth in various in vivo models. Knockdown of WISP1 with shRNAs resulted in reduced colony formation in vitro and reduced tumor …

Targeting Epigenetic Regulators For The Treatment Of Diffuse Large B-Cell Lymphoma, Aarthi Goverdhan

Dissertations and Theses (Open Access)

Small-molecule inhibitors of the histone methyltransferase EZH2 hold great promise for the treatment of Germinal Center B-Cell-like Diffuse Large B-Cell Lymphoma (GCB-DLBCL). Compared to a 60% Objective Response Rate (ORR) in Phase I clinical trials, Phase II trial results for the EZH2 inhibitor EPZ-6438 reported an attenuation of response. Mechanisms contributing to lymphoma cell survival and growth after EZH2 ablation are poorly studied. In EZH2-mutant cells, we found that B-Cell Receptor (BCR) signaling was enhanced after EZH2 inhibitor treatment, and associated with an activated B-cell phenotype. Genetic manipulation of BCR, CD19 and CD79A greatly increased sensitivity to the EZH2 inhibitor …

Identifying The Immune Related Metabolic Properties Of Pancreatic Cancer Using Nuclear Magnetic Resonance Spectroscopy And Dynamic Magnetic Resonance Spectroscopic Imaging With Hyperpolarized Pyruvate, Joseph Weygand

Dissertations and Theses (Open Access)

Despite its relatively low incidence, pancreatic cancer was the fourth leading cause of cancer-related death in the US in 2015. This is due in part to pancreatic cancer’s natural resistance to both chemotherapy and radiotherapy. Immunotherapy presents an attractive potential treatment approach, but initial trials in mice have proved ineffective. Because cancer cells exhibit a significant increase in metabolic activity relative to normal tissue, an understanding of the metabolic function of tumors in systems with different levels of immunocompetence is a critical first step to develop an understanding of the immune-related metabolic properties of the tumor, which have potential application …

Investigating The Neural Basis Of Audiovisual Speech Perception With Intracranial Recordings In Humans, Muge O. Sertel

Dissertations and Theses (Open Access)

Speech is inherently multisensory, containing auditory information from the voice and visual information from the mouth movements of the talker. Hearing the voice is usually sufficient to understand speech, however in noisy environments or when audition is impaired due to aging or disabilities, seeing mouth movements greatly improves speech perception. Although behavioral studies have well established this perceptual benefit, it is still not clear how the brain processes visual information from mouth movements to improve speech perception. To clarify this issue, I studied the neural activity recorded from the brain surfaces of human subjects using intracranial electrodes, a technique known …

The Differential Expression Of Gene Cohorts Over The Course Of Development In Type I And Type Ii Layer V Pyramidal Neurons Of The Mouse Medial Prefrontal And Primary Somatosensory Cortex, Ryan Shaun Pevey

Master's Theses

Two of the most challenging problems in neuroscience may be the characterization of different neuron types and determining the various decision points over the course of development that defines those different cell types. Part of the problem is that for the clear majority of neuron types, no single gene so far has been shown to act as a type marker. Instead it seems that signatures involving multiple genes are necessary to define each type. The identity of the genes in these signatures remains an important gap in our knowledge. However, recent developments in bioinformatics have produced population level transcript sequencing …

How Did We Get Here? An Inquiry Into Pop Culture, Pop Culture Icons, And America's Support Of The Degradation Of Humanity Through Mass Media Consumption, Thomas Steele

Master's Theses

This thesis focuses on the contemporary human condition associated with the consumption of current entertainment media. Sampling on modes of thought from anthropological, biological, psychological, sociological, and biographical points of view I sought to define what it means to be uniquely human. Furthermore, I sought to compare and contrast contemporary human interactions as described through research studies associated with tabloid news sources, and the entertainment industry. The results of this study were then articulated through four works of art that visually describe that which was found amongst a variety of resources. They describe the rise and fall of the careers …

Life-Shortening Wolbachia Infection Reduces Population Growth Of Aedes Aegypti, Eunho Suh, David R. Mercer, Stephen L. Dobson

Entomology Faculty Publications

Wolbachia bacteria are being introduced into natural populations of vector mosquitoes, with the goal of reducing the transmission of human diseases such as Zika and dengue fever. The successful establishment of Wolbachia infection is largely dependent on the effects of Wolbachia infection to host fitness, but the effects of Wolbachia infection on the individual life-history traits of immature mosquitoes can vary. Here, the effects of life-shortening Wolbachia (wMelPop) on population growth of infected individuals were evaluated by measuring larval survival, developmental time and adult size of Aedes aegypti in intra- (infected or uninfected only) and inter-group (mixed with …

Comparing Adult Attachment Styles Among Hispanic And Non-Hispanic Undergraduate College Students Using The Experiences In Close Relationships Revised Structures (Ecr-Rs), Guadalupe Flores Valdez

Dissertations

Research on attachment in adult relationships has included minimal studies to encompass a Hispanic population. Mexican Americans have specific characteristics grounded in historical, demographic, and family contexts which are different from other groups. Therefore, cross-cultural validation of instruments to assess family relationships increases the clinical usefulness of the instruments. The purpose of this study was to compare the equivalence of the factor structure of a widely used family attachment assessment, the Experiences in Close Relationships-Revised Structures Questionnaire (ECR-RS; Donbaek & Elklit, 2014; Parker et al., 2011). This study used principal components factor analysis with maximum likelihood extraction to compare the …

Genome Wide Association And Next Generation Sequencing Approaches To Map Determinants Of Ascites In Broiler Chickens, Shatovisha Dey

Graduate Theses and Dissertations

These studies have investigated different candidate genomic regions for their contributions to ascites in broilers. Ascites syndrome is a manifestation of idiopathic pulmonary arteriole hypertension that concerns the poultry industry worldwide. Investigations have demonstrated the disease to be genetically regulated and to exhibit moderate to high heritabilities. Although previous studies have indicated a few chromosomes to be involved with ascites, no genes have been identified to date with direct links to the disease. This dissertation presents a collection of studies that determine the genomic and genetic interactions for regions on chromosome 2 and 9 for ascites phenotypes in broiler chickens. …

Studies In Blackberry: Development And Implementation Of A Phenotyping Protocol For Blackberry Seedling Populations And Impact Of Time Of Day Of Harvest On Red Drupelet Reversion For University Of Arkansas Blackberry Genotypes, Melinda Yin

Graduate Theses and Dissertations

There are two major public blackberry (Rubus L. subgenus rubus Watson) breeding programs in the United States: one at the University of Arkansas (UA) and another at the U.S. Department of Agriculture Agricultural Research Service Horticultural Crops Research Unit (USDA-ARS HCRU) based in Corvallis, OR. The germplasm and breeding objectives of these two breeding programs are diverse, but frequent collaboration necessitated a standardized method of characterizing plant and fruit traits. A phenotyping protocol for blackberry was developed at UA and implemented for two years on UA seedling populations. The protocol included plant traits (health, vigor, estimated crop load, peak bloom …

Models And Methodologies To Address Emerging Needs In Network And Supply Chain Optimization, Forough Enayaty Ahangar

Graduate Theses and Dissertations

In this dissertation, we model three different security scenarios and propose solution methodologies to address each problem.

Chapter 2 presents a large-scale optimization approach for solving a dynamic bi-level network interdiction problem (NIP) in which interdiction activities must be scheduled in order to minimize the cumulative maximum flow over a finite time horizon. A logic-based decomposition (LBD) approach is proposed that utilizes constraint programming to exploit the scheduling nature of this dynamic NIP. Chapter 3 considers a set of centers to which content (e.g., data or smuggled items), are assigned to ensure availability. An interdictor (e.g., border security officials) attempts …

Comprehensive Assessments Of The Genetic Determinants In Salmonella Typhimurium For Fitness Under Host Stressors: Oxidative Stress And Iron Restriction, Sardar Abdullah

Graduate Theses and Dissertations

Salmonella is an intracellular pathogen that infects a wide range of hosts. The infected host utilizes reactive oxygen species (ROS) and iron-restriction to eliminate the pathogen. We used proteogenomics to determine the candidate genes and proteins that have a role in resistance of S. Typhimurium to H2O2. For Tn-seq, a highly saturated Tn5 library was grown in vitro under either 2.5 (H2O2L) or 3.5 mM H2O2 (H2O2H). We identified two sets of overlapping genes that are required for resistance of S. Typhimurium to H2O2L and H2O2H, and the results were validated via phenotypic evaluation of 50 selected mutants. The enriched …

Vol 62 #4, Melanie Argo

MPLA Newsletter

No abstract provided.

Ltc Newsletter, University Of Dayton. Ryan C. Harris Learning Teaching Center

LTC Newsletter

Fall 2017

Nutrinews, Volume 31, August, 2017, Department Of Nutrition And Dietetics, University Of North Florida

NutriNews

This issue features Iodide Supplementation and Preemies, What not to do: Alcohol and Caffeine, Oats appear safe for patients with Celiac Disease, Marmite and Brain Functioning, Is Soda Bad for Your Brain?

Bayesian Approach On Short Time-Course Data Of Protein Phosphorylation, Casual Inference For Ordinal Outcome And Causal Analysis Of Dietary And Physical Activity In T2dm Using Nhanes Data., You Wu

Electronic Theses and Dissertations

This dissertation contains three different projects in proteomics and causal inferences. In the first project, I apply a Bayesian hierarchical model to assess the stability of phosphorylated proteins under short-time cold ischemia. This study provides inference on the stability of these phosphorylated proteins, which is valuable when using these proteins as biomarkers for a disease. in the second project, I perform a comparative study of different confounding-adjusted to estimate the treatment effect when the outcome variable is ordinal using observational data. The adjusted U-statistics method is compared with other methods such as ordinal logistic regression, propensity score based stratification and …

Preparing For Racial Discrimination : The Role Of Cognition And Emotion In The Proactive Coping Process Of African American College Students., Ryan Christopher Tyler Delapp

Electronic Theses and Dissertations

Traditionally, conceptual models of racial discrimination have characterized the reactive experiences of African Americans, particularly identifying how African Americans cognitively, emotionally, and behaviorally respond to racial stress. The current study extends beyond the reactive coping experience and identifies nuances in the anticipatory and preparatory coping processes associated with racial discrimination. Methods: 62 African American college students participated in a stress induction experiment that prompted anticipatory judgments of discrimination. The full sample completed quantitative self-report questionnaires about their anticipatory thoughts (SAM; Peacock & Wong, 1990; Roesch & Rowley, 2005), state-based affect (PANAS-X; Watson & Clark, 1994), and proactive coping behaviors (PPCB; …

Characterization Of Porphyromonas Gingivalis Mfa1 Fimbriae., Jae Yong Lee

Electronic Theses and Dissertations

Porphyromonas gingivalis, an obligate anaerobic bacterium associated with chronic periodontitis, utilizes various virulence factors to achieve pathogenicity, one of which is the Mfa1 fimbriae. As a surface structure comprising Mfa1 major subunit along with accessory fimbrial proteins Mfa2-5, the Mfa1 fimbriae has been shown to mediate the adherence of P. gingivalis to antecedent bacterial colonizers of the oral cavity to cause increased virulence. However, the spatial relationships amongst the individual subunits and their assembly mechanism have remained unclear. Through immuno-electron microscopy, Mfa1-4 were localized on the surface of P. gingivalis with Mfa1 localizing throughout the fimbriae and Mfa2 in …

Transient Absorption Studies Of Cdse Nanocluster Passivated With Phenyldithiocarbamate Ligands., Yizhou Xie

Electronic Theses and Dissertations

Semiconductor nanocluster (SCNC) research is a rapidly growing field driven by the promising fact that properties of such materials can be tailored by modifying their size, shape, and structure. Combination of nanocluster and organic ligands provides even wider possibilities of design and development of effective and task-specific nanostructures. Understanding of and, eventually, control of energetics, interfacial interaction, and photoinduced processes in such highly heterogeneous structures is critical to invention of novel materials including those in photovoltaic devices. In the newly established Ultrafast Laser Facility (ULF), transient absorption pump-probe spectroscopy (TAPPS) has been employed to investigate the electron transfer (ET) and …

Engineering Applications Of Organic Surfactant Modified Bentonite In Sorptive Soil Barriers., Sadra Javadi

Electronic Theses and Dissertations

Earthen barriers such as CCLs and GCLs have been employed in geotechnical practices to provide a low permeability hydraulic barrier since long time ago. These types of barriers exhibited satisfactory performance for many applications such as landfills. The performance of low permeability barriers is based on the swelling potential of their component, which is mostly Na-bentonite, in contact with polar fluids such as water. However, the acceptable range of conductivity cannot be achieved by traditional earthen barriers when they are permeated by non-polar fluids such as gasoline. This phenomenon occurs due to the incompatibility of earthen barrier constituent with non-polar …

Gene Expression Of Ammonium Transporters In Ustilago Maydis And Their Role In Pathogenicity And Virulence., Kirsten Richardson

Electronic Theses and Dissertations

The fungus, Ustilago maydis, a plant pathogen of Zea mays, is capable of a dimorphic switch, e.g., a transition between a yeast-like form and a filamentous form. This switch is activated when U. maydis cells are starved for their preferred nitrogen source - ammonium. U. maydis has two important genes that play a role in this switch, ump1 and ump2. Each gene is responsible for the uptake of ammonium and the latter is responsible for the filamentous response in the absence of ammonium. Ump2 deletion mutants are unable to filament in response to low ammonium while ump1 deletion …

The Role Of Hemodynamic Force On Development Of The Mouse Embryonic Heart, Samantha Jean Fredrickson

Graduate Theses/Dissertations

The most common type of birth defects are congenital heart defects (or CHDs). Though a few cases of CHDs have been attributed to genetic defects specific to the heart, substance exposure, or to maternal disease, the cause of most CHDs is unknown. Thus, further research is needed to determine how CHDs form. Very few studies have investigated how physiological factors like perturbations of blood flow can affect normal heart development. For instance, increasing or decreasing the resistance to blood flow can alter development of the heart in both zebrafish and chicken embryos. This could be one mechanism to explain CHD …

Summer 2017: Dangerous Science Draws Film Crew To Campus, St. Norbert College

St. Norbert College Magazine 2013-2018

St. Norbert biology professor Adam Brandt will appear in an Australian TV series on dangerous animals, highlighting his research on the rare, venomous Hispaniolan solenodon and aiming to involve students in conservation efforts.

Clinical And Therapeutic Significance Of Obesity In Melanoma, Jennifer L. Mcquade

Dissertations and Theses (Open Access)

While the FDA approval of targeted and immune therapies in metastatic melanoma (MM) have dramatically improved outcomes in this disease, de novo and/or acquired resistance can limit the clinical benefit of these agents. The IGF-1/PI3K/AKT pathway has been implicated in resistance to both targeted and immune therapy. The IGF-1/PI3K/AKT pathway has also been shown to play a key role in the pathogenesis of obesity in other malignancies. To date, the impact of energy balance on clinical outcomes and therapeutic response in MM has not been studied. I hypothesized that energy balance would impact the molecular biology, behavior, and drug sensitivity …