Digital Commons Network^™

Identification Of Structures For Ion Channel Kinetic Models, Kathryn E. Mangold, Wei Wang, Eric K. Johnson, Druv Bhagavan, Jonathan D. Moreno, Jeanne M. Nerbonne, Jonathan R. Silva

Open Access Publications

Markov models of ion channel dynamics have evolved as experimental advances have improved our understanding of channel function. Past studies have examined limited sets of various topologies for Markov models of channel dynamics. We present a systematic method for identification of all possible Markov model topologies using experimental data for two types of native voltage-gated ion channel currents: mouse atrial sodium currents and human left ventricular fast transient outward potassium currents. Successful models identified with this approach have certain characteristics in common, suggesting that aspects of the model topology are determined by the experimental data. Incorporating these channel models into …

Urine Tumor Dna Detection Of Minimal Residual Disease In Muscle-Invasive Bladder Cancer Treated With Curative-Intent Radical Cystectomy: A Cohort Study, Pradeep S. Chauhan, Kevin Chen, Ramandeep K. Babbra, Wenjia Feng, Nadja Pejovic, Armaan Nallicheri, Peter K. Harris, Katherine Dienstbach, Andrew Atkocius, Lenon Maguire, Faridi Qaium, Jeffrey J. Szymanski, Brian C. Baumann, Li Ding, Dengfeng Cao, Melissa A. Reimers, Eric H. Kim, Zachary L. Smith, Vivek K. Arora, Aadel A. Chaudhuri

Open Access Publications

BACKGROUND: The standard of care treatment for muscle-invasive bladder cancer (MIBC) is radical cystectomy, which is typically preceded by neoadjuvant chemotherapy. However, the inability to assess minimal residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. Here, we sought to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis.

METHODS AND FINDINGS: We applied urine Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq), a targeted next-generation sequencing (NGS) method for detecting utDNA, to urine cell-free DNA (cfDNA) samples acquired between April 2019 and November 2020 on the day of curative-intent radical cystectomy from 42 patients with localized …

The Alternative Serotonin Transporter Promoter P2 Impacts Gene Function In Females With Irritable Bowel Syndrome, Sandra Mohr, Gregory Sayuk, Et Al

Open Access Publications

Irritable bowel syndrome (IBS) is a gut-brain disorder in which symptoms are shaped by serotonin acting centrally and peripherally. The serotonin transporter gene SLC6A4 has been implicated in IBS pathophysiology, but the underlying genetic mechanisms remain unclear. We sequenced the alternative P2 promoter driving intestinal SLC6A4 expression and identified single nucleotide polymorphisms (SNPs) that were associated with IBS in a discovery sample. Identified SNPs built different haplotypes, and the tagging SNP rs2020938 seems to associate with constipation-predominant IBS (IBS-C) in females. rs2020938 validation was performed in 1978 additional IBS patients and 6,038 controls from eight countries. Meta-analysis on data from …

Dietary Compliance In A Randomized Double-Blind Infant Feeding Trial During Infancy Aiming At Prevention Of Type 1 Diabetes, Suvi M Virtanen, Marilyn Tanner-Blasiar, Et Al

Open Access Publications

The international Trial to Reduce IDDM in the Genetically at Risk (TRIGR) tested the hypothesis whether extensively hydrolyzed casein-based versus regular cow's milk-based infant formula reduces the risk of type 1 diabetes. We describe dietary compliance in the trial in terms of study formula intake, feeding of nonrecommended foods, and serum cow's milk antibody concentration reflecting intake of cow's milk protein among 2,159 eligible newborn infants with a biological first-degree relative affected by type 1 diabetes and with HLA-conferred susceptibility to type 1 diabetes. The participating infants were introduced to the study formula feeding at the median age of 15 …

Non-Motor Phenotypic Subgroups In Adult-Onset Idiopathic, Isolated, Focal Cervical Dystonia, Megan E Wadon, Joel S Perlmutter, Et Al

Open Access Publications

BACKGROUND: Non-motor symptoms are well established phenotypic components of adult-onset idiopathic, isolated, focal cervical dystonia (AOIFCD). However, improved understanding of their clinical heterogeneity is needed to better target therapeutic intervention. Here, we examine non-motor phenotypic features to identify possible AOIFCD subgroups.

METHODS: Participants diagnosed with AOIFCD were recruited via specialist neurology clinics (dystonia wales: n = 114, dystonia coalition: n = 183). Non-motor assessment included psychiatric symptoms, pain, sleep disturbance, and quality of life, assessed using self-completed questionnaires or face-to-face assessment. Both cohorts were analyzed independently using Cluster, and Bayesian multiple mixed model phenotype analyses to investigate the relationship between …

Decreased Antiviral Immune Response Within The Central Nervous System Of Aged Mice Is Associated With Increased Lethality Of West Nile Virus Encephalitis, Kristen E Funk, Artem D Arutyunov, Pritesh Desai, James P White, Allison L Soung, Sarah F Rosen, Michael S Diamond, Robyn S Klein

Open Access Publications

West Nile virus (WNV) is an emerging pathogen that causes disease syndromes ranging from a mild flu-like illness to encephalitis. While the incidence of WNV infection is fairly uniform across age groups, the risk of lethal encephalitis increases with advanced age. Prior studies have demonstrated age-related, functional immune deficits that limit systemic antiviral immunity and increase mortality; however, the effect of age on antiviral immune responses specifically within the central nervous system (CNS) is unknown. Here, we show that aged mice exhibit increased peripheral organ and CNS tissue viral burden, the latter of which is associated with alterations in activation …

Inclusivity In Practice: A Queer Examination Of The Acceptance Of Trans Communities From The Standpoints Of Trans University Students, Sean Maulding

Electronic Theses, Projects, and Dissertations

Despite attending the same universities and working toward the same degrees, trans students and cisgender students do not always have the same experiences during their college years. In addition to the hardships associated with being a university student, members of trans communities often also face gender-based discrimination and challenges that their cisgender counterparts do not. Although the mid-size Southern California university at which this research took place has taken steps toward fostering an accepting climate for all students, the transmale, gender nonconforming, and gender nonbinary students who participated in this study continue to experience a layer of rejection due to …

Mental Health Awareness Training Manual: For Faculty To Help Students, Ricardo Vega

Electronic Theses, Projects, and Dissertations

Mental health issues and stigma can affect students in many ways. The teacher-student relationship can be affected by the fear and inconsistent thoughts to be successful in college settings caused by mental health issues. First-generation college students face mental health issues due to support, education degree expectations, inhibition of uncertainty, and resources (Pascarella et al., 2004). This project is about providing communication strategies for faculty to help reduce stigma and provide students with resources to support their mental health.

The Curious Cases Of Cancel Culture, Loydie Solange Burmah

Electronic Theses, Projects, and Dissertations

Cancel culture is a complex phenomenon that challenges our notions of civic practices, perpetuates surveillance practices amongst individuals who encourage digital public shaming and obscures communal ideas regarding accountability. Hence, it is imperative to complicate and nuance “cancel culture” to understand the different meanings derived from its diverse mechanizations. Other matrices such as power, platform governance, decoloniality, and more bolster ideas about the phenomenon’s extensive sociocultural reach. Using a critical digital ethnographic approach, I exemplify with the analysis two cancel culture cases uncovering themes such as selective cancelations, cancelation effectiveness, performative activism, performative wokeness, hypocrisy, victimization, and empathy. This study …

Inducing Proactive Control With High Load Ax-Cpt, Mina Selim

Electronic Theses, Projects, and Dissertations

A central hypothesis of cognitive control is that goal maintenance operates via two distinct modes: proactive control and reactive control (Braver, Gray, & Burgess, 2007). Individuals using a proactive strategy, focus on actively maintaining goal-relevant information in memory, whereas reactive individuals store goal-relevant information and retrieve it when cues are present. This theoretical framework for understanding the sources of variation in cognitive control is termed the dual mechanisms of control (DMC). When compared to high working memory capacity (WMC) individuals, low WMC individuals tend to utilize reactive control more often. However, some factors influence an individuals’ bias towards one type …

Decolonial Lessons From Historical African American Community Leaders: Reconstructing African American Identity As Resistance In Praxis, Rhejean King-Johnson

Electronic Theses, Projects, and Dissertations

This study analyzes the communication praxis for the purposes of decolonization of four community leaders, Frederick Douglass, W.E.B. DuBois, Ida B. Wells and Malcolm X in efforts to reconstruct African American (AA) identity by exposing the inhumane speech, behavior and thought of white supremacy. Their work employs specific communication strategies such as descriptive narrative, allegory, two-ness, anaphora, and metaphors to address the oppressive white-centric representation of AA identity and provide a decolonial shift in U.S. Eurocentric ideology. Through a close reading and textual analysis of representative works such as, Frederick Douglass’s book, “Narrative of the Life of Frederick Douglass” (2005), …

Athlete Monitoring Program In Division I Collegiate Female Soccer, Ai Ishida

Electronic Theses and Dissertations

The objectives of this dissertation include 1) to review athlete monitoring strategies and the physical performance demands of female soccer match-play and to provide practical application of athlete monitoring programs, 2) to examine individual and group relationship between training load (TL) and subjective recovery and stress state and neuromuscular performance, and 3) to investigate acute effects of match-play on neuromuscular and subjective recovery and stress state in National Collegiate Association Athlete (NCAA) division I collegiate female soccer. TL was assessed using 10Hz Global Navigation Satellite System units. Subjective recovery and stress state was measured using the Short Recovery and Stress …

Exposure To Parasitic Infections Determines Features And Phenotypes Of Active Convulsive Epilepsy In Africa, Nelson K. Langat, Symon M. Kariuki, Gathoni Kamuyu, Angelina Kakooza-Mwesige, Seth Owusu-Agyei, Kenneth Ae-Ngibise, Anne Wang'ombe, Anthony Ngugi, Honorati Masaja, Ryan G. Wagner

Population Health, East Africa

Background: Epilepsy affects 70 million people worldwide, 80% of whom are in low-and-middle income countries (LMICs). Infections of the central nervous system (CNS) contribute considerably to the burden of epilepsy in LMICs, but the nature and presentation of epilepsy following these infections is not fully understood. We examined if epilepsy foutcomes are associated with the exposure to parasitic infections.
Methods: This was a case-comparison study nested in a cross-sectional survey of people with active convulsive epilepsy, with cases as those exposed to parasitic infections, and comparison as those unexposed. Associations of exposure to parasites with clinical and electroencephalographic …

Deeper Learning And District-Level Curriculum Leadership: A Case Study Of One Large Public School District, Jonathan Warren Cooney

Dissertations

A key element within school accountability frameworks across the United States is student performance as measured by standardized assessments. Scholars have argued that these types of assessments and accountability systems have narrowed the curriculum to emphasize students' development of discrete, specialized skills. Researchers have recently suggested that deeper learning approaches will better support students in building the skills and understanding needed for life and work. Unfortunately, deeper learning has not commonly been observed at the school-wide level. Recent research suggested that a prevailing culture of district-level curriculum leadership serves as a potential barrier to the enactment of deep learning in …

Drug Repurposing For Covid-19 Using Molecular Docking Tools, Deniz Yasar Oztas

Computational and Data Sciences (MS) Theses

Since severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious and mortal, finding a treatment is time critical. Drug repurposing is probably the quickest and safest approach in our arsenal. However, testing every drug in a brute force manner would require a lot of resources, and a more sophisticated method is required to filter possible candidates. Since several molecules have already been shown to be effective against SARS-CoV-2 in wet-lab experiments, choosing drugs with similar characteristics would increase our chances of success. In this study, we compare the molecular docking results of FDA-approved drugs from the ZINC database against …

Application Of A Dna Mini-Barcoding System Based On The Mitochondrial Control Region For The Identification Of Raw And Processed Tuna Products, Jiahleen Roungchun

Food Science (MS) Theses

Accurate species identification methods are needed to combat tuna fraud, improve tuna stock regulation, and mitigate health risks associated with mislabeled tuna products. The objective of this study was to conduct a market survey of raw and processed tuna products using a DNA mini-barcoding system based on the mitochondrial control region (CR). A total of 80 samples of raw, dried, and canned tuna products were collected at the retail level for CR mini-barcoding analysis. The samples underwent DNA extraction, polymerase chain reaction (PCR), and DNA sequencing of the 236-bp CR mini-barcode. The resulting sequences were searched against GenBank using the …

Modeling Of Hydrogen Sulfide Generation And Rates Of Microbial Induced Concrete Corrosion In Manhole Shafts, Sunakshi Hada

Civil Engineering Dissertations - Archive

Manhole shafts can undergo infrastructure failure due to microbially induced concrete corrosion (MICC). Deterioration of the sewer systems by MICC process occurs due to the volatilization of hydrogen sulfide into the gas phase. The volatized hydrogen sulfide gas reacts with oxygen to form sulfuric acid, resulting in concrete corrosion. If optimum conditions are present, 24 mm of concrete loss can occur in 31 months, and the cost of fixing can range from $10-$30 per square foot. Also, if the manholes are not properly maintained, they can cause serious safety hazards, such as manhole lids falling through the structure, streets giving …

Effectiveness Of Recycled Plastic Pin For Improving Bearing Capacity Of Embankment Over Soft Soil, Md Azijul Islam

Civil Engineering Dissertations - Archive

Construction of embankment over soft foundation soils is incredibly a challenging task due to the risk of bearing failure and excessive settlement of foundation soil. Most of the available conventional methods for addressing these problems are either expensive or time-consuming or both. Therefore, research has been striving to develop a sustainable alternative to the current conventional methods. A noble approach to improve the soft foundation soil could be the use of Recycled Plastic Pins (RPP) in combination with geosynthetics. The load transfer efficiency of a geosynthetic-reinforced and RPP supported embankment is influenced by interactions among embankment fill, geosynthetics, and foundation …

Performance Of Recycled Plastic Pins For Increasing Bearing Capacity Of Foundation Soil, Faria Fahim Badhon

Civil Engineering Dissertations - Archive

Mechanically Stabilized Earth (MSE) walls constructed on unsuitable foundation soil are prone to large deformation and bearing capacity failure. A variety of techniques can be applied to address this issue, such as removal and replacement of existing soil with competent soil, staged construction, dynamic compaction, stone columns, geosynthetic reinforcement. One common traditional approach followed by Texas Department of Transportation (TxDOT) for the improvement of unsuitable foundation soil is removal of the in-situ soil and replacement with suitable fill material. However, this method can be time-consuming and expensive. A pile-supported system in combination with geosynthetic reinforcement can provide a sustainable solution …

Agent-Based Model Simulation For Police Deployment Decision-Making In Patrol Operations, Yasaman Ghasemi

Industrial, Manufacturing, and Systems Engineering Dissertations - Archive

Police patrolling plays a key role in responding to 911 calls and reducing crimes. The effectiveness of patrol operations heavily depends on the deployment of police officers – e.g., the number of officers assigned to specific policing districts or beats. The complex nature of the policing system – dynamic and stochastic criminal behavior, compounded with limited policing resources, render current (traditional) police operations, which are often managed in a reactive and stationary manner – often makes it very challenging to manage and control. This study develops an agent-based simulation framework to address the dynamically changing environment in police operations and …

Altared Bodies: Evangelical Purity Rhetorics In The Age Of Sexual Politics, Victoria G. Houser

All Dissertations

This dissertation argues that rhetorical strategies of contemporary evangelical purity movements create and perpetrate systems of sexual violence, heterosexist ideologies, and reproductive violence in the US. Purity culture is a term that references a recently public movement to declare one’s dedication to sexual abstinence before marriage. In 1994, over 210,00 young adults participated in a nationally broadcasted True Love Waits purity rally hosted on the Washington Mall, where they signed purity pledges in front of national news organizations. Altared Bodies: Evangelical Purity Rhetorics in the Age of Sexual Politics maps the shifting popularity of purity culture in public political discourse …

Standardizing New Diagnostic Tests To Facilitate Rapid Responses To The Covid-19 Pandemic, Xiao Dong

Dissertations and Theses (Open Access)

In order to enhance the data interoperability, an expeditious and accurate standardization solution is highly desirable for naming rapidly emerging novel lab tests, and thus diminishes confusion in early responses to pandemic outbreaks. This is a preliminary study to explore the roles and implementation of medical informatics technology, especially natural language processing and ontology methods, in standardizing information about emerging lab tests during a pandemic, thereby facilitating rapid responses to the pandemic. The ultimate goal of this study is to develop an informatics framework for rapid standardization of lab testing names during a pandemic to better prepare for future public …

An Examination Between Laryngeal Physiology And Parkinson’S Disease: Severity And Treatment, Jillian Pelikan

Bakerman Student Research Awards

Larynx; Muscles; Symptomatic Parkinson's disease

Three Distinct Mechanisms, Notch Instructive, Permissive, And Independent, Regulate The Expression Of Two Different Pericardial Genes To Specify Cardiac Cell Subtypes In Drosophila Melanogaster, Panta Manoj

Bakerman Student Research Awards

The development of a complex organ involves the specification and differentiation of diverse cell types. Two major cell types, contractile cardial cells (CCs) and nephrocytic pericardial cells (PCs), comprise the Drosophila heart, with binding sites for Suppressor of Hairless [Su(H)], an integral transcription factor in the Notch signaling pathway, enriched in the enhancers of genes that are specifically expressed in PCs. Here we show three distinct mechanisms regulating the expression of two PC-specific genes, Holes in muscle (Him), and Zn finger homeodomain 1 (zfh1). Him is regulated in a Notch-permissive manner: Su(H) forms a repressor complex with co-repressors that binds …

Subclinical Atherosclerosis Quantified Through Cumulative Shear Measurement, Margaret Lynne Papka

Master's Theses

With the high mortality rate of cardiovascular disease, it is important to study the early signs. The early detection of cardiovascular disease can lead to saved lives. Currently the most prevalent detection methods are the Framingham Risk Score and the carotid intima media thickness, both of which are insufficient. The necessary tool for early detection requires a uniform quantification system. The stimulus leading to endothelial dysfunction, the most significant predictor of a major adverse cardiovascular event (MACE)—and subsequently subclinical atherosclerosis—is reduced shear stress. Increased surface relative roughness affects the flow profile transition from laminar to turbulent resulting in reduced shear …

Multi-Assay Nutritional Metabolomics Profiling Of Low Vitamin A Status Versus Adequacy Is Characterized By Reduced Plasma Lipid Mediators Among Lactating Women In The Philippines: A Pilot Study, Catherine M. Johnson

Master's Theses

Background: A significant portion of lactating women in less developed countries have vitamin A (VA) deficiency. Lactation has substantial effects on a mother’s metabolism and VA is known to be needed in multiple biological processes, including growth, vision, immunity, and reproduction.

Objective: The objective of this pilot study was to utilize metabolomics profiling to conduct a broad, exploratory assessment of differences in plasma metabolites associated with low VA status versus adequacy in lactating women.

Methods: Plasma samples from lactating women who participated in a survey in Samar, Philippines, were selected from a cross-sectional study based on plasma retinol concentrations indicating …

3d Printing For Lab-On-A-Chip, Gregory P. Nordin

BYU Research Development Office Research Networking Conference

3D printed microfluidics, biological and chemical sensors, nanophotonics and integrated optics, micro- and nanofabrication, MEMS, and microfluidics

Understanding Host-Pathogen Interactions, Brett E. Pickett

BYU Research Development Office Research Networking Conference

Gene Expression, Signaling Pathway Analysis, RNA-Sequencing, Drug Repurposing, Infectious Diseases, Diagnostics, Cancer, Comparative Genomics, Machine Learning

Molecular Differences In Skeletal Muscle After 1 Week Of Active Vs. Passive Recovery From High-Volume Resistance Training, Christopher G. Vann, Cody T. Haun, Shelby C. Osbourn, Matthew E. Romero, Paul A. Roberson, Petey W. Mumford, C. Brooks Mobley, Hudson M. Holmes, Carlton D. Fox, Kaelin C. Young, Michael D. Roberts

Faculty Scholarship

Numerous studies have evaluated how deloading after resistance training (RT) affects strength and power outcomes. However, the molecular adaptations that occur after deload periods remain understudied. Trained, college-aged men (n = 30) performed 6 weeks of whole-body RT starting at 10 sets of 10 repetitions per exercise per week and finishing at 32 sets of 10 repetitions per exercise per week. After this period, subjects performed either active (AR; n = 16) or passive recovery (PR; n = 14) for 1 week where AR completed ∼15% of the week 6 training volume and PR ceased training. Variables related to …

Usf Women's Club Yearbook, 2021–2022, Usf Women's Club

USF Women’s Club Collection

Yearbook of the USF Women's Club. Inside is a list of past presidents, officers, committee chairmen, and members for 2021–2022. The booklet also includes a tribute to Grace Allen, interest groups, calendar of events, and a copy of the constitution and by-laws from the handbook.