Digital Commons Network^™

Wormbase 2024: Status And Transitioning To Alliance Infrastructure, Paul W Sternberg, Tim Schedl, Et Al.

2020-Current year OA Pubs

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate …

Examining The Gateway Hypothesis And Mapping Substance Use Pathways On Social Media: Machine Learning Approach, Yunhao Yuan, Erin Kasson, Jordan Taylor, Patricia Cavazos-Rehg, Munmun De Choudhury, Talayeh Aledavood

2020-Current year OA Pubs

BACKGROUND: Substance misuse presents significant global public health challenges. Understanding transitions between substance types and the timing of shifts to polysubstance use is vital to developing effective prevention and recovery strategies. The gateway hypothesis suggests that high-risk substance use is preceded by lower-risk substance use. However, the source of this correlation is hotly contested. While some claim that low-risk substance use causes subsequent, riskier substance use, most people using low-risk substances also do not escalate to higher-risk substances. Social media data hold the potential to shed light on the factors contributing to substance use transitions.

OBJECTIVE: By leveraging social media …

Tradeoffs Between Bite Force And Gape In Eulemur And Varecia, Myra F. Laird, Taylor A. Polvadore, Gabrielle A. Hirschkorn, Julie C. Mckenney, Callum F. Ross, Andrea B. Taylor, Claire E. Terhune, Jose Iriate-Diaz

Anthropology Faculty Publications and Presentations

In 1974, Sue Herring described the relationship between two important performance variables in the feeding system, bite force and gape. These variables are inversely related, such that, without specific muscular adaptations, most animals cannot produce high bite forces at large gapes for a given sized muscle. Despite the importance of these variables for feeding biomechanics and functional ecology, the paucity of in vivo bite force data in primates has led to bite forces largely being estimated through ex vivo methods. Here, we quantify and compare in vivo bite forces and gapes with output from simulated musculoskeletal models in two craniofacially …

Stereospecific Nanog Pest Stabilization By Pin1, Josephine C Ferreon, Hai Minh Ta, Hyosuk Yun, Kyoung-Jae Choi, My Diem Quan, Phoebe S Tsoi, Choel Kim, Chul Won Lee, Allan Chris M Ferreon

Faculty, Staff and Students Publications

NANOG protein levels correlate with stem cell pluripotency. NANOG concentrations fluctuate constantly with low NANOG levels leading to spontaneous cell differentiation. Previous literature implicated Pin1, a phosphorylation-dependent prolyl isomerase, as a key player in NANOG stabilization. Here, using NMR spectroscopy, we investigate the molecular interactions of Pin1 with the NANOG unstructured N-terminal domain that contains a PEST sequence with two phosphorylation sites. Phosphorylation of NANOG PEST peptides increases affinity to Pin1. By systematically increasing the amount of cis PEST conformers, we show that the peptides bind tighter to the prolyl isomerase domain (PPIase) of Pin1. Phosphorylation and cis Pro enhancement …

Viroporin Activity From Rotavirus Nonstructural Protein 4 Induces Intercellular Calcium Waves That Contribute To Pathogenesis, J Thomas Gebert, Francesca J Scribano, Kristen A Engevik, Asha A Philip, Takahiro Kawagishi, Harry B Greenberg, John T Patton, Joseph M Hyser

Faculty, Staff and Students Publications

Acute gastroenteritis remains the second leading cause of death among children under the age of 5 worldwide. While enteric viruses are the most common etiology, the drivers of their virulence remain incompletely understood. We recently found that cells infected with rotavirus, the most prevalent enteric virus in infants and young children, initiate hundreds of intercellular calcium waves that enhance both fluid secretion and viral spread. Understanding how rotavirus triggers intercellular calcium waves may allow us to design safer, more effective vaccines and therapeutics, but we still lack a mechanistic understanding of this process. In this study, we used existing virulent …

Transmuting Childhood Trauma: A Case Study Exploring The Impact Of Childhood Trauma On The Career Choice And Teaching Experiences Of Special Education Teachers, Monica Bester

Electronic Theses and Dissertations Archive

In recent years, there has been a growing body of research on childhood trauma and its potential effects on the development of a child into adulthood. The findings of this research indicate that those who have undergone traumatic experiences might demonstrate effects in their behavior, interactions with others, management of stressful situations, and even in their career decisions as they mature in age. As research on the impact of trauma on career choices continues to expand, this study looks at trauma’s impact on the experiences and decisions of Special Education Teachers. This qualitative case study uses Contemporary Trauma Theory as …

Political Consciousness & The Postcolonial Subject: Toward Revolutionary Education In Pakistan, Ali Mahboob

Electronic Theses and Dissertations Archive

We live in a post-colonial reality. It is a fact of history. A past that determines the present, a present that determines the future. It is not the colonization of land that this project seeks to inquire about, but the colonization of knowledge, for what we know determines who we are. This thesis studies the relationship between the construction of the colonial self and the colonial reality from which it derives consciousness. It is an epistemological examination of a form of knowledge that presupposes the inferiority of the colonial being. This colonization of knowledge is the foundation of Western Humanism …

A Causal-Comparative Study Of Novices And Experts Testing Nielsen's Five User Assumption Within A Learning Technology, Jessica Danielle Gatewood

Electronic Theses and Dissertations Archive

This non-experimental causal-comparative study aims to explore the possible effect of expertise on learning experience design (LXD) deviation identification and the classification of these deviations in alignment with provided learning experience design constructs within a learning technology. Additionally, this study challenges Nielsen’s (1993) Five User Assumption regarding how many novices or experts are needed to identify 80% of LXD deviations within the learning technology. According to Nielsen’s (1993) Five User Assumption, only five participants are required to identify 80% percent of usability problems; however, this assumption has yet to be tested within a learning technology (Nielsen, 1993). A convenience sample …

A Comprehensive Examination Of Historical Events Leading To Disinterment Practices And Repatriation Delays Involving The Muscogee (Creek) Nation And Etowah Mounds, With An Analysis Of The Vermillion Accord As A Framework For Assessing How Repatriation Is Hindered When Institutions Reject Indigenous ‘Respect’ Ideologies That Honor Ancestral Remains, Wendy Butts

Electronic Theses and Dissertations Archive

The impetus for this dissertation was a meeting with several subject matter experts belonging to the Muscogee (Creek) Nation, who shared their interest in garnering enough public support to pressure eleven institutions into returning burial belongings disinterred from the Etowah Mounds. As such, the objective of this historical research was to support the Tribe’s goal by raising public awareness of their decades-long repatriation challenges. In order to accomplish that objective, as a backdrop, this dissertation undertook a comprehensive examination of pertinent pre- and post- contact events surrounding Muskogean-speaking people of the Southeast region, which provided context for why present-day descendants …

Re/Searching (For) Hope: Archives And (Decolonizing) Archival Impressions, Romeo Garcia

The Writing Center Journal

On archives and archival impressions, this essay extends archival research to the elsewhere and otherwise. The essay asks, how do we reposition the contents of archives so that we can position ourselves in relation to it otherwise? It puts forward a theory of (decolonizing) archival impressions.

Multisensory Realm: Architecture For The Visually Impaired, Jennifer Perez

Bachelor of Architecture Theses - 5th Year

According to the World Health Organization, there are approximately 2.2 billion people who have a near or distance vision impairment. Vision has historically been considered the most important of the senses; therefore, when this sense becomes obstructed, an individual’s lifestyle can be harshly impacted. Because their vision becomes obstructed, visually impaired individuals run into various daily life challenges such as having difficulty navigating around independently, stigma in society, leisure, accessibility, and isolation. This can be due to the issue that the built environment has tended to neglect building for all senses. For this reason, an architectural goal has been to …

From Silence To Thriving: Architecture As A Voice For The Wayuu Tribe, Angie Son Pulido

Bachelor of Architecture Theses - 5th Year

This research explores how stories, music, and patterns intersect to shape the built environment, with an emphasis on spotlighting the Wayuu tribe, a resilient culture facing extinction in the arid desert of La Guajira, Colombia. The Wayuu people have endured centuries of adversity, including colonialism, exploitation, drug trafficking, and internal conflict. In this place, water and food are scarce, and child mortality rates are very high. Despite hardships, they preserve a culture of resilience thanks to their tradition of oral storytelling. Drawing from the tradition of storytelling, the works of writer Gabriel García Márquez, particularly his Magical Realism, serve as …

Histone Demethylase Kdm5 Regulates Cardiomyocyte Maturation By Promoting Fatty Acid Oxidation, Oxidative Phosphorylation, And Myofibrillar Organization, Manisha Deogharia, Leslye Venegas-Zamora, Akanksha Agrawal, Miusi Shi, Abhinav K Jain, Kevin J Mchugh, Francisco Altamirano, Ali J Marian, Priyatansh Gurha

Faculty, Staff and Student Publications

Aims: Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.

Methods and results: KDM5A, B, and C proteins were mainly expressed …

Single Extracellular Vesicle Imaging And Computational Analysis Identifies Inherent Architectural Heterogeneity, Kshipra S Kapoor, Seoyun Kong, Hikaru Sugimoto, Wenhua Guo, Vivek Boominathan, Yi-Lin Chen, Sibani Lisa Biswal, Tanguy Terlier, Kathleen M Mcandrews, Raghu Kalluri

Faculty, Staff and Student Publications

Evaluating the heterogeneity of extracellular vesicles (EVs) is crucial for unraveling their complex actions and biodistribution. Here, we identify consistent architectural heterogeneity of EVs using cryogenic transmission electron microscopy (cryo-TEM), which has an inherent ability to image biological samples without harsh labeling methods while preserving their native conformation. Imaging EVs isolated using different methodologies from distinct sources, such as cancer cells, normal cells, immortalized cells, and body fluids, we identify a structural atlas of their dominantly consistent shapes. We identify EV architectural attributes by utilizing a segmentation neural network model. In total, 7,576 individual EVs were imaged and quantified by …

Regulation Of Neuronal Cell-Type-Specific Transcription By Non-Cg Methylation And Mecp2, James Russell Moore

Arts & Sciences Graduate Student Theses and Dissertations

Modulation of gene expression is fundamental to the exceptional complexity and diversity of cells in the nervous system. Within that last decade, evidence has emerged that neurons utilize unique forms of DNA methylation to regulate transcriptional programs, with multiple types of neurons displaying high levels of cytosine methylation in a non-CG context compared to non-neural cells. This non-CG methylation primarily occurs at CA dinucleotides (mCA) and is read out by methyl-CpG binding protein 2 (MeCP2). Inactivation of MeCP2 results in Rett Syndrome (RTT), a severe neurodevelopmental disorder, while overexpression of MeCP2 results in MeCP2 duplication syndrome, an autism spectrum disorder. …

The Unseen Pen: The Hidden History Of Black Women Writers During The Civil Rights Movement, Serenity Hill

Master's Theses

As taught in standard high-school and general educational courses, integration was a primary goal of the Civil Rights Movement; however, when this era is discussed in classrooms, by historians, and in textbooks there are key perspectives and acknowledgements that are less recognized. The visibility of the Black women who pushed forward the movement is often reduced, overlooked, or overshadowed because of the more celebrated contributions of their male counterparts. Focusing on an era before the internet, with the eloquent writing of activists like Dr. King memorialized, this project aims to showcase how changes in course curriculum can shed light on …

Crizanlizumab For Retinal Vasculopathy With Cerebral Leukoencephalopathy In A Phase Ii Clinical Study, Wilson X. Wang, Dan Spiegelman, P. Kumar Rao, Andria L. Ford, Rajendra S. Apte

2020-Current year OA Pubs

BackgroundRetinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S) is a rare, autosomal dominant, universally fatal disease without effective treatment options. This study explores the safety and preliminary efficacy of crizanlizumab, a humanized monoclonal antibody against P-selectin approved for the prevention of sickle cell crises, in slowing retinal nonperfusion and preserving vision in patients with RVCL-S.METHODSEleven patients with RVCL-S with confirmed exonuclease 3 prime repair exonuclease 1 (TREX1) mutations received monthly crizanlizumab infusions over 2 years. The study measured the nonperfusion index within 3 retinal zones and the total retina with fluorescein angiography, visual acuity, intraocular pressure (IOP), and optical …

Urinary Proteomics And Outcomes In Heart Failure With Preserved Ejection Fraction, Corinne Carland, Ali Javaheri, Douglas L Mann, Et Al.

2020-Current year OA Pubs

BACKGROUND: Although several studies have addressed plasma proteomics in heart failure with preserved ejection fraction, limited data are available on the prognostic value of urinary proteomics. The objective of our study was to identify urinary proteins/peptides associated with death and heart failure admission in patients with heart failure with preserved ejection fraction.

METHODS AND RESULTS: The study population included participants enrolled in TOPCAT (Treatment of Preserved Cardiac Function Heart Failure With an Aldosterone Antagonist Trial). The relationship between urine protein levels and the risk of death or heart failure admission was assessed using Cox regression, in both nonadjusted analyses and …

Geothermal Exploration Using Lineament Density Analysis At Rajabasa Volcano, South Lampung, Dwi Wahyu Hardiyanto, Agung Setianto

Jurnal Pendidikan Geografi: Kajian, Teori, dan Praktek dalam Bidang Pendidikan dan Ilmu Geografi

The research is located around Rajabasa Volcano, South Lampung Regency, Lampung Province, Indonesia. The research areas have unique geological conditions and arrangements. It is part of the caldera body estimated to have centralized geothermal potential. Identification of potential geothermal areas can be made using remote sensings such as lineament density analysis, slope, and land surface temperature with areas of approximately 190 square Kilometers. Manually extraction of lineament density is dominated by the NW-SE direction with an anomaly of only 20 percent. While the lineament density process is automatically controlled in the NE-SW order, it is estimated that the anomaly density …

The Production Of Upstream Space (Area) Of River As Tourism Site In Economic Recovery Post-Covid-19, Muhammad Nur Hidayat, Nieke Rudyanty Winanda

Jurnal Pendidikan Geografi: Kajian, Teori, dan Praktek dalam Bidang Pendidikan dan Ilmu Geografi

This study seeks to explore and analyze the production of the upstream area of the river on the western Anjasmoro flank as a tourism site in economic recovery post-COVID-19. The focus of this research is on the spatial practice, representations of space, and representational spaces carried by the migrants on the flanks of Mount Anjasmoro. The informants were determined using the snowball technique with a subject of seven informants consisting of three key informants and four supporting informants. The results showed that the spatial practice was observed from the method by which migrants obtained the place they desired, and the …

State-Sanctioned Violence Against Civilian Protests, Mariyam Syed

COD Library Student Research and Award Symposium

State-sanctioned violence to suppress political dissidents and minorities, especially during protests, is a pertinent issue across both democratic and authoritarian nations. International governing bodies and human rights organizations examine the causes and dynamics of state violence, the primary governmental actors, the civilian victims, and seek worldwide solutions, such as disarmament.

Faculty Sponsor: David Goldberg

Analysis Of The Online Disinhibition Effect Through Activist Groups Black Lives Matter And All Lives Matter/Blue Lives Matter, Alyssa Marie Cordero

COD Library Student Research and Award Symposium

With the tides of modernity, the internet offers people the chance to communicate to their friends, families and to the world. Through the growing influence of social media, information is easily accessible in various forms such as articles, advertisements and memes, thus predisposing their social biases. In order to promote inspiration and change, activists use social media to awaken social media users by highlighting the national and global inequalities. However, Rider University professor Dr. John Suler speculates the online disinhibition effect, the unrestrained means of online communication, strengthens social polarization and online deception. To find the extent of the online …

Improving Ethics Surrounding Collegiate-Level Hacking Education: Recommended Implementation Plan & Affiliation With Peer-Led Initiatives, Shannon Morgan, Dr. Sanjay Goel

Military Cyber Affairs

Cybersecurity has become a pertinent concern, as novel technological innovations create opportunities for threat actors to exfiltrate sensitive data. To meet the demand for professionals in the workforce, universities have ramped up their academic offerings to provide a broad range of cyber-related programs (e.g., cybersecurity, informatics, information technology, digital forensics, computer science, & engineering). As the tactics, techniques, and procedures (TTPs) of hackers evolve, the knowledge and skillset required to be an effective cybersecurity professional have escalated accordingly. Therefore, it is critical to train cyber students both technically and theoretically to actively combat cyber criminals and protect the confidentiality, integrity, …

Using Digital Twins To Protect Biomanufacturing From Cyberattacks, Brenden Fraser-Hevlin, Alec W. Schuler, B. Arda Gozen, Bernard J. Van Wie

Military Cyber Affairs

Understanding of the intersection of cyber vulnerabilities and bioprocess regulation is critical with the rise of artificial intelligence and machine learning in manufacturing. We detail a case study in which we model cyberattacks on network-mediated signals from a novel bioreactor, where it is important to control medium feed rates to maintain cell proliferation. We use a digital twin counterpart reactor to compare glucose and oxygen sensor signals from the bioreactor to predictions from a kinetic growth model, allowing discernment of faulty sensors from hacked signals. Our results demonstrate a successful biomanufacturing cyberattack detection system based on fundamental process control principles.

Surmounting Challenges In Aggregating Results From Static Analysis Tools, Dr. Ann Marie Reinhold, Brittany Boles, A. Redempta Manzi Muneza, Thomas Mcelroy, Dr. Clemente Izurieta

Military Cyber Affairs

Aggregation poses a significant challenge for software practitioners because it requires a comprehensive and nuanced understanding of raw data from diverse sources. Suites of static-analysis tools (SATs) are commonly used to assess organizational security but simultaneously introduce significant challenges. Challenges include unique results, scales, configuration environments for each SAT execution, and incompatible formats between SAT outputs. Here, we document our experiences addressing these issues. We highlight the problem of relying on a single vendor's SAT version and offer a solution for aggregating findings across multiple SATs, aiming to enhance software security practices and deter threats early with robust defensive operations.

Generative Machine Learning For Cyber Security, James Halvorsen, Dr. Assefaw Gebremedhin

Military Cyber Affairs

Automated approaches to cyber security based on machine learning will be necessary to combat the next generation of cyber-attacks. Current machine learning tools, however, are difficult to develop and deploy due to issues such as data availability and high false positive rates. Generative models can help solve data-related issues by creating high quality synthetic data for training and testing. Furthermore, some generative architectures are multipurpose, and when used for tasks such as intrusion detection, can outperform existing classifier models. This paper demonstrates how the future of cyber security stands to benefit from continued research on generative models.

Determining The Exit State Of Centrifugal Pumps And Compressors, Chase Oliphant

Utah Space Grant Consortium

Meanline performance models have a rich history in the design of radial flow pumps and compressors. These models are typically based on point data, such as static pressures and temperature measurements at walls, along with occasional traverses to capture additional flow field details. These point measurements, while valuable, do not fully characterize the internal flow behavior within the machine. The Two-Zone model, developed by Japikse and others, is a meanline model based on these measurements to predict machine performance. It posits that the flow at the impeller exit consists of two distinct zones: a primary zone assumed to be isentropic …

Creating Models Of Inter-Panel Slipping In Rolled Gossamer Arrays, Nathan Coleman

Utah Space Grant Consortium

Many deployable satellite systems benefit from having low mass and high surface area, which has led to the proliferation of gossamer structures in space-based applications. Gossamer structures are characterized by lightweight, low stiffness membranes, which can flex and roll to compactly stow. An effect of rolling a gossamer structure is that there is tangential separation along adjacent panels as they roll, resulting in relative motion between panels. To aid designers in predicting and accommodating this motion, a method for modeling the slippage between adjacent panels that occurs while rolling is presented. This analytical slippage model and algorithm is a function …

Discovering What Cannot Be Seen: Dust Attenuation Modeling In Early-Type Galactic Nuclei, Nonnie Bash, Benjamin Boizelle

Utah Space Grant Consortium

Black holes (BHs) are believed to reside at the center of every luminous galaxy. Increasingly accurate techniques are now seeking to expand the BH census. Most of these primary techniques account for extended masses by using a stellar luminosity profile derived from optical or near-IR imaging. About 10% of early type galaxies (ETGs) contain a circumnuclear, dusty disk that obscures much of the stellar light originating from behind this thin disk. Few studies have accurately accounted for dust obscuration, or even acknowledged its effect on a BH mass measurement. In this work, we introduce a sample of ETGs with wide …

Chemical Herding: Using Chemical Reactions To Steer Colloidal Particles, Mark N. Mcdonald, Cameron K. Peterson, Douglas R. Tree

Utah Space Grant Consortium

Creating the next generation of dynamic colloidal materials that change their structure based on external stimuli may require the capability to precisely manipulate colloidal particles. Colloidal particles can be manipulated using a variety of forces, such as electric, magnetic, and optical, but so far chemical reactions have received less attention. We consider here a novel paradigm for using a chemically active colloidal particle to interact with other, passive colloids and precisely manipulate colloidal particles in a microfluidic device, a strategy which we dub “chemical herding”. Specifically, we show in simulation that chemical herding can be used to move a small …