Digital Commons Network^™

Sequencing The Guts Out Of Covid-19; The Evolution Behind The Covid-19 Pandemic, Madelyn Purnell

Undergraduate Honors Theses

The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and tracking of virus variants. In this paper, we attempted a novel method of sequencing using Large Reverse Transcriptase-based cloning (LRTC). Although our methodology ended up not working due to high amount and fast degradation of RNA, we were able to sequence multiple variants of COVID-19 Positive samples from the BYU Student Health Center and 4 sewage samples to check for variant outbreaks in corresponding times. We were able to find several corresponding variants and track the progression of mutation in our local population.

Nursing Burnout During The Covid-19 Pandemic, Noreen Rizvi

Theoretical Foundation in Advanced Practice Nursing

Nursing burnout continues to rise as the COVID-19 pandemic amplifies environmental stressors in the workplace. This paper explores the application of Callista Roy's adaptation model in preventing nursing burnout during the pandemic using four modes of adaptation: rolefunction, interdependence, physiological/physical, and self-concept or group identity. The presented solution to alleviate nursing burnout examines the implementation of Roy's adaptation model through proposed resiliency initiatives, leadership and management modifications, and state legislature regulation. These interventions aim to reduce anxiety, moral distress, and compassion fatigue, along with increasing support for nurses.

Continuous Fluorescence-Based Endonuclease-Coupled Dna Methylation Assay To Screen For Dna Methyltransferase Inhibitors, Rebecca Switzer, Katie A. Ward, Jessica Medrano

Faculty Journal Articles

DNA methylation, a form of epigenetic gene regulation, is important for normal cellular function. In cells, proteins called DNA methyltransferases (DNMTs) establish and maintain the DNA methylation pattern. Changes to the normal DNA methylation pattern are linked to cancer development and progression, making DNMTs potential cancer drug targets. Thus, identifying and characterizing novel small molecule inhibitors of these enzymes is of great importance. This paper presents a protocol that can be used to screen for DNA methyltransferase inhibitors. The continuous coupled kinetics assay allows for initial velocities of DNA methylation to be determined in the presence and absence of potential …

Variability In The Vertical Distributions Of Mesopelagic Fishes: Effect Of Body Size, Season, And Sampling Strategy On The Characterization Of Diel Vertical Migration, Brandon A. Brule

All HCAS Student Capstones, Theses, and Dissertations

Diel‌ ‌vertical‌ ‌migration,‌ or DVM, ‌is‌ ‌defined‌ ‌as‌ ‌the‌ large-scale changes in the depth distribution of a species or an assemblage with respect to the time of day. DVM‌ ‌is‌ ‌the‌ ‌largest‌ ‌active movement‌ ‌of‌ ‌biomass‌ on Earth, driven by the need for food balanced against predator avoidance and metabolic constraints. Asynchronous‌ ‌diel‌ ‌vertical‌ ‌migration, in the context of this study,‌ ‌refers‌ ‌to‌ the phenomenon where only a portion of a species’ population migrates upwards at night while others remain at depth. ‌The‌ extent that factors such as temporal variation, ontogenic variation, and methodological variation explain this migratory pattern is …

Adaptation And Dosimetric Commissioning Of A Synchrotron-Based Proton Beamline For Flash Experiments, Ming Yang, Xiaochun Wang, Fada Guan, Uwe Titt, Kiminori Iga, Dadi Jiang, Takeshi Takaoka, Satoshi Tootake, Tadashi Katayose, Masumi Umezawa, Emil Schüler, Steven Frank, Steven H Lin, Narayan Sahoo, Albert C Koong, Radhe Mohan, X Ronald Zhu

Faculty, Staff and Student Publications

Objective. Irradiation with ultra-high dose rates (>40 Gy s^-1), also known as FLASH irradiation, has the potential to shift the paradigm of radiation therapy because of its reduced toxicity to normal tissues compared to that of conventional irradiations. The goal of this study was to (1) achieve FLASH irradiation conditions suitable for pre-clinicalin vitroandin vivobiology experiments using our synchrotron-based proton beamline and (2) commission the FLASH irradiation conditions achieved.

Approach. To achieve these suitable FLASH conditions, we made a series of adaptations to our proton beamline, including modifying the spill length …

Small Group Interventions For Students From Single Parent Households, Gerrit Immink

Masters Projects

Research shows that children raised by a single parent often exhibit increased behavioral problems, anxiety, loneliness, stress, and aggressiveness. Divorce, the death of a parent, and parental incarceration are all prominent factors that can lead to children being raised in single parent homes. Small group counseling interventions that focus on these unique situations have been shown to increase self-concept and self-esteem, as well as self-confidence. These interventions have also shown to increase students positive coping skills and decrease feelings of depression and anxiety. This project is a guide to be used by school counselors to build and facilitate counseling small …

Asymmetric Synthesis Of Nortropanes Via Rh-Catalyzed Allylic Arylation, Yan Zhang, F Wieland Goetzke, Kirsten E Christensen, Stephen P Fletcher

Faculty, Staff and Student Publications

Tropane derivatives are extensively used in medicine, but catalytic asymmetric methods for their synthesis are underexplored. Here, we report Rh-catalyzed asymmetric Suzuki–Miyaura-type cross-coupling reactions between a racemic N-Boc-nortropane-derived allylic chloride and (hetero)aryl boronic esters. The reaction proceeds via an unexpected kinetic resolution, and the resolved enantiopure allyl chloride can undergo highly enantiospecific reactions with N-, O-, and S-containing nucleophiles. The method was applied in a highly stereoselective formal synthesis of YZJ-1139(1), a potential insomnia treatment that recently completed Phase II clinical trials. Our report represents an asymmetric catalytic method for the synthesis of YZJ-1139(1) and related compounds.

Counseling Active-Duty Female Service Members Who Have Experienced Sexual Assault: A Guide For Professional Counselors, Rebekah Cole, Rebecca Cowan, Taqueena Quintana

Journal of Social, Behavioral, and Health Sciences

Sexual assault is a prevailing problem for active duty women in the United States military. We explore the unique nature of military culture and explain the military’s dual pathway process for reporting sexual assault. In addition, we describe, in depth, evidence-based theoretical approaches applicable for counselors to use in their work with female service members who are survivors of sexual assault. Finally, we discuss sexual assault resources available to military clients and the steps counselors can take to engage in advocacy for and with this population.

Altered High-Energy Phosphate And Membrane Metabolism In Pelizaeus-Merzbacher Disease Using Phosphorus Magnetic Resonance Spectroscopy, Jeremy J. Laukka, Kevin M. Kain, Anirudha S. Rathnam, Jasloveleen Sohi, Dalal Khatib, John Kamholz, Jeffrey A. Stanley

Student Publications

Pelizaeus-Merzbacher disease is an X-linked recessive leucodystrophy of the central nervous system caused by mutations affecting the major myelin protein, proteolipid protein 1. The extent of the altered in vivo neurochemistry of protein, proteolipid protein 1 duplications, the most common form of Pelizaeus-Merzbacher disease, is, however, poorly understood. Phosphorus magnetic resonance spectroscopy is the only in vivo technique that can assess the biochemistry associated with high-energy phosphate and membrane phospholipid metabolism across different cortical, subcortical and white matter areas. In this cross-sectional study, whole-brain, multi-voxel phosphorus magnetic resonance spectroscopy was acquired at 3 T on 14 patients with Pelizaeus-Merzbacher disease …

Lipopolysaccharide-Induced Interferon Response Networks At Birth Are Predictive Of Severe Viral Lower Respiratory Infections In The First Year Of Life, James F. Read, Michael Serralha, Danny Mok, Barbara J. Holt, Mark Cruickshank, Yuliya V. Karpievitch, David I. Broadhurst, Peter D. Sly, Deborah H. Strickland, Stacey N. Reinke, Patrick G. Holt, Anthony Bosco

Research outputs 2022 to 2026

Appropriate innate immune function is essential to limit pathogenesis and severity of severe lower respiratory infections (sLRI) during infancy, a leading cause of hospitalization and risk factor for subsequent asthma in this age group. Employing a systems biology approach to analysis of multi-omic profiles generated from a high-risk cohort (n = 50), we found that the intensity of activation of an LPS-induced interferon gene network at birth was predictive of sLRI risk in infancy (AUC = 0.724). Connectivity patterns within this network were stronger among susceptible individuals, and a systems biology approach identified IRF1 as a putative master regulator of …

Identification Of The Nrf2 Transcriptional Network As A Therapeutic Target For Trigeminal Neuropathic Pain, Chirag Vasavda, Risheng Xu, Jason Liew, Ruchita Kothari, Ryan S Dhindsa, Evan R Semenza, Bindu D Paul, Dustin P Green, Mark F Sabbagh, Joseph Y Shin, Wuyang Yang, Adele M Snowman, Lauren K Albacarys, Abhay Moghekar, Carlos A Pardo-Villamizar, Mark Luciano, Judy Huang, Chetan Bettegowda, Shawn G Kwatra, Xinzhong Dong, Michael Lim, Solomon H Snyder

Duncan NRI Faculty and Staff Publications

Trigeminal neuralgia, historically dubbed the "suicide disease," is an exceedingly painful neurologic condition characterized by sudden episodes of intense facial pain. Unfortunately, the only U.S. Food and Drug Administration (FDA)-approved medication for trigeminal neuralgia carries substantial side effects, with many patients requiring surgery. Here, we identify the NRF2 transcriptional network as a potential therapeutic target. We report that cerebrospinal fluid from patients with trigeminal neuralgia accumulates reactive oxygen species, several of which directly activate the pain-transducing channel TRPA1. Similar to our patient cohort, a mouse model of trigeminal neuropathic pain also exhibits notable oxidative stress. We discover that stimulating the …

An Auto-Inhibited State Of Protein Kinase G And Implications For Selective Activation, Rajesh Sharma, Jeong Joo Kim, Liying Qin, Philipp Henning, Madoka Akimoto, Bryan Vanschouwen, Gundeep Kaur, Banumathi Sankaran, Kevin R Mackenzie, Giuseppe Melacini, Darren E Casteel, Friedrich W Herberg, Choel Kim

Faculty, Staff and Students Publications

Cyclic GMP-dependent protein kinases (PKGs) are key mediators of the nitric oxide/cyclic guanosine monophosphate (cGMP) signaling pathway that regulates biological functions as diverse as smooth muscle contraction, cardiac function, and axon guidance. Understanding how cGMP differentially triggers mammalian PKG isoforms could lead to new therapeutics that inhibit or activate PKGs, complementing drugs that target nitric oxide synthases and cyclic nucleotide phosphodiesterases in this signaling axis. Alternate splicing of PRKG1 transcripts confers distinct leucine zippers, linkers, and auto-inhibitory (AI) pseudo-substrate sequences to PKG Iα and Iβ that result in isoform-specific activation properties, but the mechanism of enzyme auto-inhibition and its alleviation …

Developmental Trajectories Of Cortical Thickness By Functional Brain Network: The Roles Of Pubertal Timing And Socioeconomic Status, Ashley F. P. Sanders, Graham L. Baum, Michael P. Harms, Sridhar Kandala, Susan Y. Bookheimer, Mirella Dapretto, Leah H. Somerville, Kathleen M. Thomas, David C. Van Essen, Essa Yacoub, Deanna M Barch

2020-Current year OA Pubs

The human cerebral cortex undergoes considerable changes during development, with cortical maturation patterns reflecting regional heterogeneity that generally progresses in a posterior-to-anterior fashion. However, the organizing principles that govern cortical development remain unclear. In the current study, we characterized age-related differences in cortical thickness (CT) as a function of sex, pubertal timing, and two dissociable indices of socioeconomic status (i.e., income-to-needs and maternal education) in the context of functional brain network organization, using a cross-sectional sample (n = 789) diverse in race, ethnicity, and socioeconomic status from the Lifespan Human Connectome Project in Development (HCP-D). We found that CT generally …

Disease-Associated Mutations Within The Yeast Dnajb6 Homolog Sis1 Slow Conformer-Specific Substrate Processing And Can Be Corrected By The Modulation Of Nucleotide Exchange Factors, Ankan K Bhadra, Michael J Rau, Jil A Daw, James A J Fitzpatrick, Conrad C Weihl, Heather L True

2020-Current year OA Pubs

Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. Dominant mutations within DNAJB6 (Hsp40)-an Hsp70 co-chaperone-lead to a protein aggregation-linked myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights into the molecular basis of LGMDD1. Here, we show how mutations analogous to those found in LGMDD1 affect Sis1 (a functional homolog of human DNAJB6) function by altering the structure of client …

Exploring The Use Of A Restoration Step To Detect Mosaic Chromosomal Alterations In Prostate Samples, Ayanna N. Woodberry, Justin W. Wong, Paul A. Scheet

Summer Experience 2022

Department of Epidemiology

Muscle Activation Patterns Of The Proximal Medial And Distal Biceps Femoris And Gluteus Maximus Among 6 Hip Extension And Knee Flexion Exercises In Trained Women., Bryn M. Stevens, Ben R. Nichols, Holly I. Doty, John Adam Korak

International Journal of Exercise Science

International Journal of Exercise Science 15(1): 1179-1189, 2022. The biceps femoris (BF) is a double-jointed muscle that performs both hip extension and knee flexion, making it a challenging muscle to train during common resistance training movements. An imbalance between the posterior and anterior chain increases the risk of lower-extremity injury. The purpose of this study was to compare BF proximal (BFprox), BF medial (BFmed), and BF distal (BFdist) peak and mean muscle activation among four hip hinging movements and two knee flexion movements. A secondary variable was gluteus maximus (GMax) muscle activation among the same six movements. Fifteen trained females …

Ndwae Ngone Mwaitu: A Postmodern Cultural Phenomenon Of Dowry Among The Akamba And Its Influence On Spousal Violence, Telesia Kathini Musili

Journal of International Women's Studies

Dowry, also referred to as bride wealth or bride price, is a consultative, amicable, and quantifiable summation of goods exchanged between the groom’s and bride’s families. Traditionally, dowry (ngasya) payment among the Akamba was an obligation for the parents-in-law (husband’s parents), but that has in the recent past transitioned to the husband paying the dowry himself. An emerging trend is, however, catching up with married women budding together and opting to pay the dowry for themselves, which is not only a cultural shock and an empowering paradigm shift but also a ceremony that could be riddled and clouded …

Women, Security, And Gender-Based Violence In The Northeast, Nigeria, Abidemi Abiola Isola, Adeogun Tolulope

Journal of International Women's Studies

Gender-based violence is inevitable in every armed conflict zone. To survive, every human being, including women and girls, requires security. In armed conflict zones, however, women and girls are more vulnerable to the dangers of insecurity. These difficulties may influence them physically, psychologically, economically, and educationally. They may also have to live with the effects of their trauma for the rest of their lives. The effects of the Boko Haram insurgency on women’s security in Nigeria’s northeast are the subject of this study. This investigation relied on structural violence theory. It’s a meta-analytical study based on secondary sources like books, …

Affirming The Traditional Teaching Of Imbusa As A Tool Against Gender-Based Violence, Sylvia Mukuka

Journal of International Women's Studies

The main objective of this paper is to provide light on the traditional teaching of Imbusa, which is utilized to combat the problem of gender-based violence. Violence against women has increased to incredible rates in modern societies, to the point where many women continue to perpetuate anguish in the form of physical abuse, assaults, and molestation, and all these social evils have left women badly devastated, scared, disoriented, and defenceless. Violence entails the use of physical force, such as sexual assault, to injure, mutilate, or kill humans, and occasionally to ruin an individual's life. This paper examines several forms of …

Covid-19 And Ubuntu Disruptions: Curbing The Violence Against Women And Girls With Disabilities Through African Women’S Theology Of Disability, Sinenhlanhla S. Chisale

Journal of International Women's Studies

The COVID-19 restrictions that require the lockdown of public and economic activities heighten the levels of sexual and gender-based violence against women and girls with disabilities. As the COVID-19 pandemic spreads across the globe, particularly in Africa, women and girls with disabilities become vulnerable to sexual and gender-based violence, highlighting that the home is no longer a safe space for the vulnerable. The restrictions have eroded the community structures that are promoted by Ubuntu to protect vulnerable community members from violence and different forms of abuse. This article grapples with the question of African women’s theology of disability and Ubuntu …

Geomx® Digital Spatial Profiling (Dsp) As An Important Tool To Study Immune Landscape Of Tumors, Natalia Alaniz, Sharia Hernandez, Wei Lu, Khaja B. Khan, Larisa V. Kostousov, Sean W. Barnes, Mei Jiang, Ignacio Wistuba, Luisa M. Solis Soto, Mario Luiz Marques-Piubelli

Summer Experience 2022

Translational Molecular Pathology

The Covid-19 Pandemic In South Asia: A Comprehensive Review Of The Genomic Variations, Epidemiological Features, Diagnosis, Treatment And Preventive Schemes, Abdullah Al Noman, Jannatul Efte Ekra, Rima Islam Meem, Sujan Islam, Fariha Sharzana, Shofiqul Islam, Samiron Sana, Masnoon Kabir, Niaz Mahmud, Abdullah Al Mahedi, Taufique Joarder

Journal of Health Research

Background: The purpose of the study was to outline the genomic and epidemiological characteristics of COVID-19 in South Asian countries as well as the diagnosis, treatments, and prevention approaches undertaken by these countries to tackle the COVID-19 pandemic.

Methods: We searched electronic databases such as Google Scholar, PubMed, and Scopus as well as various national and international COVID-19 websites, WHO databases, and electronic media. 63 articles were included from databases and 34 articles from various other sources.

Results: Scientists observed genomic variations including common mutations in ORF1ab, ORF1a, ORF3a, and S genes, while several unique mutations exist in most isolates …

How Area Health Management Leads To Improved Equity In Health: A Scoping Review, Methinee Intarates, Teerapon Dhippayom, Nilawan Upakdee, Vinai Leesmidt, Jain Weraphong, Mukdarut Bangpan

Journal of Health Research

Background: The scoping review of published studies aims to explore what practices and processes can improve equity (horizontal and vertical) in countries that adopted Area Health Management (AHM) utilizing the “Six Building Blocks Plus” (SBBP) concept.

Method: An electronic search was conducted from the inception to January 27, 2021, from 6 databases (Embase, Social Sciences, Web of Science, PubMed, CINAHL, and WHO) and the gray literature. The inclusion criteria were AH, SBBP, and equity. Data extraction was using a standardized data collection form.

Results: This scoping review includes 63 full-text studies. SBBP are identical in the horizontal and vertical equity. …

Factors That Influence Individual And Community Behavioural Change Regarding Environmental Health, Obadia Kyetuza Bishoge, Ademola Kabir Aremu, Dickson Dare Ajayi, Sayoki Godfrey Mfinanga

Journal of Health Research

Background: Increased environmental health problems have led to a rise in concern among individuals, as well as government and non-governmental organizations to tackle them. To achieve this, there is a need for behavioural change among individuals and the community on environmental health at local to international levels. The purpose of this paper is to critically explore the factors that influence personal and community behavioural change regarding environmental health.

Method: The study is a systematic review of the literature on the factors that influence personal behavioural change regarding environmental health based on the relevant studies published between 2005 and 2020. We …

Depression And Related Factors Among Health Science Students In Da Nang, Vietnam: A Cross-Sectional Study, Ngoc Thi Nhu Hoang, Ann Jirapongsuwan, Sukhontha Siri

Journal of Health Research

Background: This paper aimed to investigate the prevalence of depression and related factors among health science students in Da Nang, Vietnam.

Method: A cross-sectional study was undertaken among 401 undergraduate students. Depression was measured using the Centre for Epidemiological Studies Short Depression Scale. Bivariate and multivariate logistic regression was applied to identify any associations.

Results: Findings indicated that the prevalence of depression among students was 41.6%. Factors associated with the depression were studying in second year (aOR=3.15, 95%CI: 1.24-7.99), studying in third year (aOR=2.60, 95%CI: 1.056-6.42), poor health status (aOR= 2.57, 95%CI: 1.54-4.29), low and moderate parents’ relationships (aOR=12.41, 95%CI: …

Effects Of Dietary Ω-3 Polyunsaturated Fatty Acids (N-3 Pufa) In Light Sensitivity Of Retinas Of Mice Models To Prevent Retinal Damage, Aaron Eugene Rice

Longitudinal Scholar's Project

Light-induced retinal degeneration (LIRD) causes photoreceptor cell death in albino mice after exposure to high intensity light for a set period of time (6-24 hours). This causes retinal photoreceptor cell death through apoptosis. From several previous studies, Dr. Mandal’s lab concluded that de novo biosynthesis of ceramide mediates photoreceptor cell death in a LIRD model. Previous studies in Dr. Mandal’s lab has shown that mouse models with higher endogenous ω-3 Polyunsaturated Fatty Acids (n-3 PUFA) generates less ceramide upon neuronal injury and prevent neurodegeneration (Mol Neurobio 2021). There are currently not many available effective therapies for retinal degeneration in humans …

Medical School Watercooler Newsletter - August 4, 2022, Lindsey Lyle

Watercooler Newsletter

This is the August 4, 2022 edition of the Frederick P. Whiddon College of Medicine's newsletter - Watercooler.

Contents include:

• Register now: Opioid Awareness Summit set for Aug. 26
• Meet a Ph.D. Student: Takreem Aziz
• Alexeyev to present on mitochondrial DNA
• Williams named assistant dean for institutional and academic success
• Department of Urology established at Whiddon College of Medicine; interim chair appointed
• Lin awarded $2.3 million NIH grant to further study cognitive deficits in pneumonia patients

Valuing Angling On Reservoirs Using Benefit Transfer, Richard T. Melstrom, Mark A. Kaemingk, Nicholas W. Cole, John C. Whitehead, Christopher J. Chizinski, Kevin L. Pope

Biology Faculty Publications

Economic assessments are rarely applied to inland recreational fisheries for management purposes, especially when compared to fish, habitat, and creel assessments, yet economic assessments can provide critical information for management decisions. We provide a brief overview of economic value, key terminology, and existing economic techniques to address these issues. Benefit transfer, a technique used to measure economic value when an original analysis is not practicable, is conducted by drawing on existing estimates of economic value in similar contexts. We describe an application of benefit transfer to measure the economic value of several recreational fisheries in Nebraska, USA. We examine two …

Low Levels Of Hybridization Between Sympatric Cold-Water-Adapted Arctic Cod And Polar Cod In The Beaufort Sea Confirm Genetic Distinctiveness, Robert E. Wilson, Sarah A. Sonsthagen, Philip Lavretsky, Andrew Majewski, Einar Árnason, Katrín Halldórsdóttir, Axel W. Einarsson, Kate Wedemeyer, Sandra L. Talbot

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

As marine ecosystems respond to climate change and other stressors, it is necessary to evaluate current and past hybridization events to gain insight on the outcomes and drivers of such events. Ancestral introgression within the gadids has been suggested to allow cod to inhabit a variety of habitats. Little attention has been given to contemporary hybridization, especially within cold-water-adapted cod (Boreogadus saida Lepechin, 1774 and Arctogadus glacialis Peters, 1872). We used whole-genome, restriction-site associated, and mitochondrial sequence data to explore the degree and direction of hybridization between these species where previous hybridization had not been reported. Although nearly identical …

Valuing Angling On Reservoirs Using Benefit Transfer, Richard Melstrom, Mark A. Kaemingk, John C. Whitehead, Nicholas W. Cole, Christopher J. Chizinski, Kevin L. Pope

School of Environmental Sustainability: Faculty Publications and Other Works

Economic assessments are rarely applied to inland recreational fisheries for management purposes, especially when compared to fish, habitat, and creel assessments, yet economic assessments can provide critical information for management decisions. We provide a brief overview of economic value, key terminology, and existing economic techniques to address these issues. Benefit transfer, a technique used to measure economic value when an original analysis is not practicable, is conducted by drawing on existing estimates of economic value in similar contexts. We describe an application of benefit transfer to measure the economic value of several recreational fisheries in Nebraska, USA. We examine two …