Digital Commons Network^™

Assessing The Performance And Efficiency Of Environmental Dna/Rna Capture Methodologies Under Controlled Experimental Conditions, Anastasija Zaiko, Ulla Von Ammon, Jacqui Stuart, Kirsty F. Smith, Richard Yao, Melissa Welsh, Xavier Pochon, Holly A. Bowers

Faculty Research, Scholarly, and Creative Activity

Growing interest and affordability of environmental DNA and RNA (eDNA and eRNA) approaches for biodiversity assessments and monitoring of complex ecosystems have led to the emergence of manifold protocols for nucleic acids (NAs) isolation and processing. Although there is no consensus on a standardized workflow, the common practice for water samples is to concentrate NAs via filtration using varying pore size membranes. Using the smallest pore is assumed to be most efficient for NAs capture from a wide range of material (including sub-cellular particles); however, a trade-off must occur between detection of a meaningful molecular signal and cost/time effort when …

Disease Surveillance By Artificial Intelligence Links Eelgrass Wasting Disease To Ocean Warming Across Latitudes, Lillian R. Aoki, Brendan Rappazzo, Deanna S. Beatty, Lia K. Domke, Ginny L. Eckert, Morgan E. Eisenlord, Olivia J. Graham, Leah Harper, Timothy L. Hawthorne, Margot Hessing-Lewis, Kevin A. Hovel, Zachary L. Monteith, Ryan S. Mueller, Angeleen M. Olson, Carolyn Prentice, John J. Stachowicz, Fiona Tomas, Bo Yang, For Full Author List, See Comments Below

Faculty Research, Scholarly, and Creative Activity

Ocean warming endangers coastal ecosystems through increased risk of infectious disease, yet detection, surveillance, and forecasting of marine diseases remain limited. Eelgrass (Zostera marina) meadows provide essential coastal habitat and are vulnerable to a temperature-sensitive wasting disease caused by the protist Labyrinthula zosterae. We assessed wasting disease sensitivity to warming temperatures across a 3500 km study range by combining long-term satellite remote sensing of ocean temperature with field surveys from 32 meadows along the Pacific coast of North America in 2019. Between 11% and 99% of plants were infected in individual meadows, with up to 35% of plant tissue damaged. …

Mir-181a Promotes Multiple Protumorigenic Functions By Targeting Tgfβr3, Vida Chitsazzadeh, Tran N Nguyen, Alvaro De Mingo Pulido, Bruna B Bittencourt, Lili Du, Charles H Adelmann, Ivannie Ortiz Rivera, Kimberly A Nguyen, Leah D Guerra, Andrew Davis, Marco Napoli, Wencai Ma, Richard Eric Davis, Kimal Rajapakshe, Cristian Coarfa, Elsa R Flores, Kenneth Y Tsai

Faculty, Staff and Students Publications

Cutaneous squamous cell carcinoma (cSCC) comprises 15‒20% of all skin cancers and has a well-defined progression sequence from precancerous actinic keratosis to invasive cSCC. To identify targets for chemoprevention, we previously reported a cross-species analysis to identify the transcriptional drivers of cSCC development and identified miR-181a as a potential oncomiR. We show that the upregulation of miR-181a promotes multiple protumorigenic properties by targeting an understudied component of TGFβ signaling, TGFβR3. miR-181a and TGFβR3 are upregulated and downregulated, respectively, in cSCC. miR-181a overexpression (OE) and TGFβR3 knockdown (KD) significantly suppresses UV-induced apoptosis in HaCaT cells and in primary normal human epidermal …

Why Evolution Does Not Make The Problem Of Evil Worse, Rope Kojonen

Faith and Philosophy: Journal of the Society of Christian Philosophers

No abstract provided.

It's Not You, It's Me: Shame And Misrepresentation In Online Dating, Diedrah Todd

Research Psychology Theses

In the U.S. public opinion about online dating is overall positive with 54% of Americans reporting that relationships that start online through an app or dating site are just as successful as relationships that begin in-person. In dating, success is linked to desirable characteristics such as resources or physical appearance. However, feelings of external shame, which is when a person perceives themselves as existing negatively in the mind of another person is a powerful motivator for avoiding being seen as socially unacceptable. Being seen as socially undesirable as a result of feeling as though oneself is lacking in desirable characteristics …

Elevated Serum Levels Of Interleukin-15 In Pemphigus Vulgaris Patients: A Potential Therapeutic Target, Maedeh Kheirodin, Zohreh Tehranchinia, Yasaman Ketabi, Soheil Tavakolpour, Sahar Dadkhahfar, Masoomeh Faghankani, Hassan Vahidnezhad, Nikoo Mozafari

Department of Dermatology and Cutaneous Biology Faculty Papers

Introduction: Pemphigus vulgaris (PV) is a rare autoimmune disease that causes painful blistering. Interleukin-15 (IL-15) as a member of the immunoregulatory cytokines family is associated with the development of the chronic inflammatory or autoimmune disease. There is not much information available in the literature on the exact role IL-15 plays in PV. Objectives: The goal of this study was to evaluate the serum levels of IL-15 in patients with PV and assess the association of IL-15 with anti-desmoglein antibodies and the severity of the disease. Methods: Fifty-three individuals affected with active PV and 38 age- and gender-matched healthy controls were …

Increased Signal-To-Noise Ratios Within Experimental Field Trials By Regressing Spatially Distributed Soil Properties As Principal Components, Jeffrey C. Berry, Mingsheng Qi, Balasaheb V. Sonawane, Amy Sheflin, Asaph Cousins, Jessica Prenni, Daniel P. Schachtman, Peng Liu, Rebecca S. Bart

Department of Agronomy and Horticulture: Faculty Publications

Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is deter-mined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum …

Relationships Among Sleep, Physical Activity, And Weight Status In Children And Adolescents, Agnes Bucko

Theses and Dissertations

Sleep and physical activity are both associated with multiple behavioral and metabolic health outcomes, and both behaviors have been linked to the development of weight status. Recent estimates suggest that many children are not meeting sleep recommendations or participating in adequate levels of physical activity, which may be related to the high prevalence of childhood overweight and obesity. Much of the research assessing these relationships has focused on adults and older children, and has relied on parent- or child-reported, cross-sectional research in predominantly White samples. Little work has focused on these relationships in very young children. Although more research has …

“No Tits In The Pits!”: An Exploratory Analysis Of The Experiences Of Female Decision Makers In Motorsports In The United States, Alexia Pedo Lopes

Theses and Dissertations

This study explored the lived experiences of sixteen women who have decision-making roles in motorsports in the United States. The purpose was to shed light on the experiences of women who broke the glass ceiling in this unexplored male-dominated industry (Glass & Cook, 2016). The challenges these women encountered along with the mechanisms they employed to navigate those, and finally their motivation to continue pursuing a career in this industry, were assessed via in-depth semi-structured interviews and then the data was analyzed following a constant comparison thematic analysis. Challenges and coping mechanisms were classified according to the four levels, namely …

Middle School Transition: The Influence Of An Academy Approach And The Role Of Leadership, Kimberly Calhoun Odom

Theses and Dissertations

Students entering middle school frequently encounter challenges in their transition as they leave the comforts of elementary school. Traditionally, fifth grade students experience their last year in elementary school in a similar fashion to the previous five years of elementary school. They are in self-contained classrooms with one teacher for the majority of their school day. This study’s objective is to determine best practices and strategies that support fifth grade students in transitioning to the rigors of middle school. More specifically, the research focuses on the impact of an Academy structure in the elementary setting that models the transitions of …

Structure Preserving Reduced-Order Models Of Hamiltonian Systems, Megan Alice Mckay

Theses and Dissertations

Large-scale dynamical systems are expensive to simulate due to the computational cost accrued y the substantial number of degrees of freedom. To accelerate repeated numerical simulations of the systems, proper orthogonal decomposition reduced order models (POD-ROMs) have been developed. When applied to Hamiltonian systems, however, special care must be taken when performing the reduced order modeling to keep their energy-preserving nature. This work presents a survey of several structure-preserving reduced order models (SP-ROMs). In addition, this work employs the discrete empirical interpolation method (DEIM) and develops an SP-DEIM model for nonlinear Hamiltonian systems. The wave equation is considered as a …

Molecular And Morphological Investigations Of Grouper (Serranidae) Biodiversity In Saudi Arabia, Mohammad Saeed Al Jazza Alqahtani

Theses and Dissertations

Chapter 1: The seas surrounding the Arabian Peninsula, which represent the northernmost portion of the Indian Ocean, are considered to have the highest aquatic biodiversity among the worlds marine regions. Seas that surround the Arabian Peninsula include the Red Sea, the Gulf of Aden, the Arabian Sea, the Gulf of Oman, and the Arabian Gulf. In aggregate, this area harbors a large number of endemic and more widespread marine species, including fishes, echinoderms, and corals.

There are unique challenges involved in grouper species identification in the Arabian region including ‘familiar’ Arabic species designations that are not standardized in the Arabic …

The Moderating Impact Of Gender And Friendship Quality On The Effects Of Interparental Conflict On Adolescent Internalizing Problems, Jessica Dandan

Theses and Dissertations

In response to escalating concerns about the increasing incidence of adolescent internalizing disorders, several mechanisms have been investigated to understand their etiology. Though genetic predisposition contributes to the risk for psychopathology, its interaction with environmental stressors such as interparental conflict appears to further increase this risk. Girls are more susceptible to stressors and twice as likely as boys to develop internalizing problems. However, friendship quality may buffer some of the adverse effects incurred from exposure to interparental conflict. A recent review of proposed mechanisms through which conflict is associated with youth psychopathology pinpointed the need for further adolescent-focused research including …

Methyltransferase Mystery: Epigenetic Mechanisms Induced By Food Limitation In Daphnia Pule, Trenton C. Agrelius

Theses and Dissertations

Daphnia are ecologically important organisms that have been well studied in the context of evolution, ecology, ecotoxicity, and genomics. Daphnia have strong maternal effects in which the environment experienced by the mother can alter offspring disease resistance, life history traits, and morphology, as well as gene expression and methylation for multiple generations. Coupled with their ability to reduce genetic differences via parthenogenesis, Daphnia are an ideal system for epigenetic studies involving the transmission of maternal effects. Using two clones of Daphnia pulex, we investigated the plasticity of life history and DNA methyltransferase (Dnmt) gene expression with respect to food …

Hybrid Theory-Machine Learning Methods For The Prediction Of Afp Layup Quality, Christopher M. Sacco

Theses and Dissertations

The advanced manufacturing capabilities provided through the automated fiber placement (AFP) system has allowed for faster layup time and more consistent production across a number of different geometries. This contributes to the modern production of large composite structures and the widespread adaptation of composites in industry in general and aerospace in particular. However, the automation introduced in this process increases the difficulty of quality assurance efforts. Industry available tools for predicting layup quality are either limited in scope, or have extremely high computational overhead. With the advent of automated inspection systems, direct capture of semantic inspection data, and therefore complete …

Statistical Methods For Analyzing Dependence Structures With Applications In Single-Cell Experiments, Zhen Yang

Theses and Dissertations

This dissertation focuses on studying methods in dependence structure analysis. In particular, it consists of two topics: (1) modeling dynamic correlation in zero-inflated bivariate count data; and (2) gene co-expression latent factor analysis for cell-type clustering.

In Chapter 2, a zero-inflated negative binomial model for analyzing the dynamic correlation in zero-inflated bivariate count data is proposed. Interactions between biological molecules in a cell are tightly coordinated and often highly dynamic. As a result of these varying signaling activities, changes in gene co-expression patterns could often be observed. The advancements in next-generation sequencing tech-nologies bring new statistical challenges for studying these …

Cognitive Consequences Of Covid-19 Infection And Quarantine-Induced Social Isolation: Hope For The Young And Mildly Infected, Kristin Nickole Kirchner

Theses and Dissertations

Coronavirus disease 2019 (COVID-19) has infected over 539 million individuals worldwide, and initial research supports the possibility that COVID-19 may damage the central nervous system either directly or indirectly. Neurological signs and noted cognitive deficits observed in even mildly infected patients are a cause for concern for those infected by COVID-19; the effect of social isolation on the central nervous system is also of interest. The present study sought to determine the extent of these potential cognitive deficits in a young and mildly infected sample of college students. Participants completed an extensive survey assessing their experience with COVID-19 and any …

Evaluation Of The Throw-Catch Assessment, Bryan Terlizzi

Theses and Dissertations

Motor competence assessment has been characterized by the evaluation of motor skill performance in closed performance contexts that lack task and environmental constraints reflective of real-world contexts. In contrast, the throw-catch (TC) assessment employs a dynamic task environment that allows performers to adapt over multiple trials to evaluate the degree of skilled performance via demonstration of a flexible and adaptable repertoire of both throwing and catching actions. The purpose of this dissertation was to investigate the developmental validity of the TC, as well as the content validity of the TC in terms of assessing throwing skillfulness.

Performance of the TC …

Statistical Methods For Analyzing Multi-Omics Data: Dependence Structure And Missing Values, Wenda Zhang

Theses and Dissertations

The advancements in high-throughput technologies have made it possible to generate a huge number of "omics'' data, including genomics, proteomics, transcriptomics, epigenomics, metabolomics, and microbiomics. Combining multiple data sources and performing joint analyses with all available information and the phenotypic outcome can reflect various aspects in complex biological systems, such as revealing regulation processes, discovering novel associations between biological entities, and identifying relevant biomarkers for certain diseases or phenotypic outcomes. This dissertation focuses on developing statistical models for analyzing multi-omics data. It is comprised of three topics: (1) integrative analysis for multi-omics data with missing observations in intermediate variables; (2) …

Food Insecurity Resilience Of Refugee Families In The United States: A Qualitative Study, Maryam Suliman Alhabas

Theses and Dissertations

Refugee families living in the United States often encounter a number of challenges while trying to build a new home and maintain their household food security. Refugee families at high risk of experiencing food insecurity in the resettlement country. Food insecurity among US refugee families is a major public health concern as it adversely impacts their health and wellbeing, since it affects dietary intake and mental health and associated with illness, poor nutrition, and obesity. Little is known about what happens when refugee families face food insecurity experience, and the role of their social contexts in that experience. The objective …

Dying Of Pestilence: Gender, Stature, And Mortality From The Black Death In 14th Century Kyrgyzstan, David Wayne Hansen Ii

Theses and Dissertations

Bioarchaeological studies have provided important information about mortality patterns during the Second Pandemic of Plague, including the Black Death, but to date have focused exclusively on European contexts. This study represents a temporal and spatial expansion of plague bioarchaeology, focusing on Central Asia, the origin of the Second Pandemic. I examine the relationship between stature, gender, and plague mortality during an outbreak of plague at two fortified settlements in northern Kyrgyzstan in 1338-39, the earliest archaeological sites known to contain victims of the Black Death in Eurasia.

Stature is frequently used in bioarchaeology as a proxy for exposures to developmental …

Long Non-Coding Rna Pvt1 – An Exploratory Study In Ovarian And Endometrial Cancer, Kevin Tabury

Theses and Dissertations

Gynecological cancers, ovarian and endometrial cancer, are still leading causes of cancer-related death in women worldwide. Early detection methods as well as treatment resistance remain a challenge. Long non-coding RNAs (lncRNAs) are emerging as therapeutic targets with diagnostic and prognostic potential with lncRNA PVT1 being one of them.

Here I test and demonstrate the role of PVT1 in ovarian cancer growth and metastasis. PVT1 is amplified and overexpressed in ovarian cancer and has predictive value for survival and response to targeted therapeutics. We find that expression of PVT1 is regulated by tumor cells in response to cellular stress, particularly loss …

Disengagement Of Male Students In Remediated Ela Classes, Joanne Berardi Martin

Theses and Dissertations

The purpose of this action research was to examine the disengagement of male students in remediated English Language Arts (ELA) classes. Male students are disproportionately represented in remediated ELA classes, which indicates that male students are not progressing in their literacy skills at the same rate as females. Data was gathered from an ELA section of male students through a Google survey, a group interview, and two observations of students in a co-taught class. The purpose of these data collection methods was to understand the experiences of male students to determine the source of their disengagement. A focus group with …

Oxidized Graphitic Nano-Amendment Of Cement Composites: Exploring Truly Low Concentrations And Novel Particle Morphologies, Shohana Iffat

Theses and Dissertations

Oxidized graphitic nanoparticles such as multiwalled carbon nanotubes (MWCNTs) and graphene nanoplatelets (GNPs), can produce enhancements in physicomechanical properties of cement composites that are relevant to structural and durability performance, provided that said nanoparticles are well dispersed in the composite. Lower-bound MWCNT concentrations are reported in the literature in the range 0.01-0.05% in weight of cement (wt%). Such concentrations may not be costeffective for practical applications and may also be excessive since they would result in a nanoparticle surface area at or above 105 m2 for 1 m3 of cement paste, or 104.5 m2 for 1 m 3 of concrete, …

Mechanisms And Impact Of Hypoxia Regulated Inhibins In Cancer, Ben Allen Horst

Theses and Dissertations

Inhibins are heterodimeric ligands within the TGFβ superfamily, comprised of an α-subunit (INHA) and a β-subunit (either INHBA or INHBB) with emergent roles in cancer. Inhibins are biomarkers of disease burden and prognosis in a subset of cancers and utilize the coreceptors betaglycan (TGFBR3) and endoglin (ENG) for physiological or pathological outcomes. Previously, we found inhibin promotes angiogenesis in ovarian cancer however no mechanism of regulation for inhibin expression in cancer has been established. Hypoxia, a driver of tumor growth and metastasis, regulates angiogenic pathways that are targets for vessel normalization and ovarian cancer management. …

Qualitative Action Research Into The Planning Between The Classroom Teacher And Reading Interventionist, Russell Derrial Clark

Theses and Dissertations

Students reading below grade level need intense intervention. Reading is an active development that requires close collaboration by all the teachers involved in supporting struggling students. Understanding the needs of students with reading deficiencies can present challenges for teachers that are unable to work collectively to support the students. Teachers and interventionists need time to reflect on their attitudes and perceptions of planning and collaborating if they are going to help students achieve reading goals. Through the intervention of this study, the development and implementation of collaborative planning, teachers will be better prepared to meet the needs of their students. …

The Effect Of Pulsed Field Dc Electrophoresis And Field Amplified Sample Stacking On The Microchip Electrophoretic Separation Of Organic Dyes, Travis Geoffrey Stewart

Theses and Dissertations

The utility of field amplified sample stacking and pulsed field electrophoresis toward improving electrophoretic outcomes was studied with regards to the electrophoretic separation of three organic dyes rhodamine B, 2’,7’-dichlorofluorescein, and fluorescein salt in microchip electrophoresis conditions. In this study, there were four experimental groups: nonstacking nonpulsed, nonstacking pulsed, sample stacking nonpulsed, and sample stacking pulsed.

Electrophoretic outcomes were evaluated by examining the electrophoretic separations under an epifluoresence detection method, plotting the signal intensities vs. time, and comparing separation resolutions and signal-to-noise ratios between experimental groups. From this it was shown that sample stacking nonpulsed conditions yielded the best outcome …

In Vivo And In Vitro Investigations Of Mammalian Stem Cell Development: Neurogenesis And Pituitary Progenitors, Allison Culver

Theses and Dissertations

Human development is tightly regulated by complex mechanisms to pattern the early embryo and form specialized tissues. Understanding this regulation is of fundamental importance and can help further understand disease pathologies. Because it is difficult to observe the processes of interest, researchers must rely on the use of model systems. Our research goal is to combine both animal models and in vitro stem cell cultures to address key questions about the mechanisms of development for both the pituitary gland and brain. It is estimated that there are 290-455 cases per million of congenital hypopituitarism. In addition, autism spectrum disorder (ASD) …

“We Make A Life By What We Give”: The Impact Of A High School Mentoring Program On The Perceptions And Academic Achievement Of Black Males, Brandon R. Ross

Theses and Dissertations

This action research study describes how a high school mentoring program impacts the academic achievement and postsecondary planning of Black male students. It further explores the perception Black male students have on school and their White teachers. The theoretical frameworks that support this research are social bonding theory (SBT) and critical race theory (CRT). This study used a qualitative design through a survey to examine the following research questions: “How does a high school mentoring program impact the academic achievement and perception of school for Black male students?” The study further examined “How a high school mentoring program impacts the …

Integrated Behavioral Health And Primary Care: Refining A Determinant Framework, Ariel Michelle Domlyn

Theses and Dissertations

The integration of behavioral health and primary care is a best practice to improve patient outcomes and achieve health equity. However, the process of integrating is opaque, requiring organizational change and sometimes a complete system overhaul. Implementation science offers useful ideas for helping healthcare organizations to implement care. This field has identified potential environmental conditions and determinants of successful implementation; however, much is still unknown about how these factors may be relevant for organizations seeking to integrate care. To address the limited existing knowledge in this area, this dissertation gathers practice-based evidence using exploratory methods. Results are translated into an …