Digital Commons Network^™

A Hybrid Cloud Data Lake Architecture Supporting The Integration Of Clinical And Genomics Data, Apollo Mcowiti, Heidi Dowst, Fei Zheng, Susan Hilsenbeck, Christopher Amos

Center for Medical Ethics and Health Policy Staff Publications

Objective: Cancer centers must quickly integrate clinical genomics data from different vendors for oncology operations and research. Clinical data warehouse architectures are costly to construct and brittle, and they are not readily amenable to the rapid changes in oncology research. We introduce a cost-effective hybrid cloud Data Lake architecture for storing clinical genomic data from different vendors, aiding both clinical and research workflows.

Methods: We created a Data Lake architecture based on the zone architecture, with four layers: ingestion, storage, transformation, and interaction. The layers are implemented with a hybrid cloud architecture. Rich metadata created from patient and genomic data …

When Families Bridge The Research-Clinical Divide: An Exploration Of Values Regarding Cascade Screening In Genomic Research, Katherine E Bonini, Lauren R Desrosiers-Battu, Ann Katherine M Foreman, Nuriye N Sahin-Hodoglugil, Mary A Majumder, Candice R Finnila, Stephanie A Kraft, Laura M Amendola, Eimear E Kenny, Stephanie M Fullerton, Sara L Ackerman, Benjamin S Wilfond, Amy L Mcguire, Hadley Stevens Smith

Center for Medical Ethics and Health Policy Staff Publications

Purpose: Genetic results are important for both patients and their biological relatives. However, cascade screening (CS) uptake is low, especially when testing occurs through research programs and not clinical care. Ethical guidance is needed for CS implementation when individuals receive clinical genetic results through research.

Methods: We conducted focus groups with 3 groups of individuals in the Clinical Sequencing Evidence-Generating Research Consortium: clinicians, patient representatives, and scholars of the ethical, legal, and social implications of genomics. We used inductive thematic and comparative analyses to analyze data within and across the groups.

Results: All participants (n = 27) agreed that …

Leukocyte Infiltration Profiles At The Site Of Intradermal Injection Of Silikon-1000 In Scleroderma-Prone Ucd200/206 And Healthy White Leghorn Chickens, Katee L. Johnson, Jossie M. Santamaria, Chrysta N. Beck, Gisela F. Erf

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

Intradermal injections of silicone-based fillers for the face and body may cause chronic inflammation and fibrotic reactions in some individuals. Chickens from the UCD 200/206 White Leghorn (WL) line spontaneously develop a fibrotic autoimmune disease known as scleroderma/systemic sclerosis (SSc). Using the SSc-prone UCD and healthy WL chickens, a longitudinal study was conducted to examine the cellular inflammatory responses to intradermal (i.d.) injections of sterile SILIKON-1000. Specifically, the pulp (a skin derivative) of growing feathers (GFs) was i.d. injected with sterile SILIKON-1000 or phosphate-buffered saline (PBS) as injection control (8 and 3 birds/line, respectively; 10 µL/GF; 20 GFs/bird). Two GFs …

Temporal Patterns Of The Introduced Sponge Hymeniacidon Perlevis (Montagu, 1814) In The Elkhorn Slough, California, Usa, Jackson T. Hoeke, Kerstin Wasson, Amanda S. Kahn

Faculty Research, Scholarly, and Creative Activity

Hymeniacidon perlevis is a cosmopolitan sponge with a seasonal life cycle. We investigated seasonal and interannual dynamics of H. perlevis in Elkhorn Slough estuary, where it is an introduced species, and explored correlations between sponge cover and environmental conditions. We used sponge cover to estimate the potential effects of H. perlevis on its environment, and how those could vary across its seasonal life cycle. We found that recruitment is currently restricted to the upper estuary and while it varies annually, the frequency and density of sponge recruits have generally increased from 2007 to 2023. A seasonal life cycle was confirmed …

Physiological Effects Of Research Handling On The Northern Elephant Seal (Mirounga Angustirostris), Lauren A. Cooley, Allyson G. Hindle, Cassondra L. Williams, Paul J. Ponganis, Shawn M. Hannah, Holger Klinck, Markus Horning, Daniel P. Costa, Rachel R. Holser, Daniel E. Crocker, Birgitte I. Mcdonald

Faculty Research, Scholarly, and Creative Activity

Wildlife researchers must balance the need to safely capture and handle their study animals to sample tissues, collect morphological measurements, and attach dataloggers while ensuring their results are not confounded by stress artifacts caused by handling. To determine the physiological effects of research activities including chemical immobilization, transport, instrumentation with biologgers, and overnight holding on a model marine mammal species, we collected hormone, blood chemistry, hematology, and heart rate data from 19 juvenile northern elephant seals (Mirounga angustirostris) throughout a translocation experiment. Across our six sampling timepoints, cortisol and aldosterone data revealed a moderate hormonal stress response to handling accompanied …

Reelin Regulation Of Striatal Physiology And Cocaine Reward, Kasey Lynn Brida

All ETDs from UAB

Drugs of abuse activate defined neuronal populations in brain reward structures such as the nucleus accumbens (NAc), which are thought to promote the enduring synaptic, circuit, and behavioral consequences of drug exposure. While the molecular and cellular effects arising from experience with drugs like cocaine are increasingly well understood, the mechanisms that sculpt NAc neuron participation are largely unknown. Here, we leveraged unbiased single-nucleus transcriptional profiling to identify expression of the secreted glycoprotein Reelin (encoded by the Reln gene) as a marker of cocaine-activated neurons within the rat NAc. Multiplexed in situ detection confirmed selective expression of the immediate early …

Context-Dependent Functional Connectivity During Attention Orienting And Reorienting: Comparing Individuals With Schizophrenia And Controls, Hyun Freeman

All ETDs from UAB

Attentional deficits are a well-established feature of schizophrenia, impacting various functional domains. Previous research suggested altered connectivity within attention networks may underlie these deficits, but few studies have examined how these net-works dynamically interact during different types of attention processes. In this study, we investigated functional connectivity patterns during attentional orienting and reori-enting to social and nonsocial cues in 25 individuals with schizophrenia and 25 controls. Participants completed a modified Posner spatial cueing task with both social (eyes) and nonsocial (arrows) cues during fMRI scanning. Using generalized psychophysiological interaction analysis with the left lateral occipital cortex (LOC) as a seed …

Stimulation And Quantification Of Dopamine-Associated Behaviors, Hunter Goffinett

All ETDs from UAB

Dopamine (DA) is a neurotransmitter involved in the regulation of essential behaviors, including motor control and reward processing. Alterations in DA levels can significantly modulate these behaviors: increased DA release is associated with heightened locomotion and enhanced preference for rewarding stimuli. Therefore, measuring behavioral changes in vivo provides critical insight into DA release and function. In this study, we quantified DA-associated behaviors by radiolytic stimulation of the Drosophila A-isoform of the transient receptor potential ankyrin type-1 A (dTRPA1(A)) channel and investigated how the human-immunodeficiency virus (HIV) and its secreted protein, the trans-activator of transcription regulatory protein (Tat), alter drug-induced behaviors. …

Occupational Exposure To Cooking Emissions And Evaluation Of Ventilation System In Restaurant Kitchens, Matthew Kaleb Hanvey

All ETDs from UAB

Background: In the restaurant environment, there are many harmful contaminants generated during the cooking process that kitchen workers are potentially exposed to. The purposes of this study were to evaluate the potential exposure to aldehydes and respirable particles among restaurant kitchen workers and to examine the ventilation performance of the kitchen exhaust hoods. Methods: There were three restaurants recruited for this study and they cooked seafood/poultry (Restaurant 1), farm style foods (Restaurant 2), and finger foods (Restaurant 3). The three restaurants had wall-mounted canopy hoods. Restaurant 1 had two hoods, Restaurant 2 had two hoods, and Restaurant 3 had one …

Unveiling The Other: Feminine And Colonial Subjugation In Mary Elizabeth Braddon's England, Kaylie Rastegar

All ETDs from UAB

Just a few years after England experienced major societal shifts, both domestically in the passage of revolutionary women’s rights legislation and internationally in the Indian Mutiny, Mary Elizabeth Braddon’s Lady Audley’s Secret (1862) offered Victorian readers a way to confront their anxieties and uncertainties about the nation’s future. The traditional power structures of British imperialism and patriarchy faced growing resistance as Indian rebels and women’s rights reformers challenged their assumed natural authority. Past scholarship contextualizes the novel within these major historical events, viewing them in relation to each other in which the struggles of Indian colonial subjects equate to those …

Uncovering The Role Of Heparanase-Armed Extracellular Vesicles In Sepsis-Associated Vascular Endotheliopathy, Robert Patrick Richter

All ETDs from UAB

Sepsis remains one of the most frequent causes of mortality and life-altering morbidity in humans of all ages globally. Though sepsis pathobiology is incompletely understood, it is clear that a unifying feature of all sepsis phenotypes is systemic vascular endotheliopathy and damage to the luminal glycocalyx of endothelial cells, or eGC, that leads to organ injury. While prior work has established that heparan sulfate (HS) is an especially important eGC constituent that helps regulate a host of endothelial cell (EC) functions, its role in promoting endotheliopathy during sepsis has not been fully characterized. Additionally, previous studies in the context of …

Chronic Pain And Resilience: Associations And Interactions With Diet, Asia Wiggins

All ETDs from UAB

Chronic pain is a significant issue globally, affecting millions of people. One relatively new way mechanism to reduce pain is to promote resilience. Yet, the effect of resilience on chronic pain may differ by sociodemographic factors (like racialized group). Furthermore, access to therapies that promote resilience may be limited across populations. However, the utilization of diet interventions for chronic pain symptoms has also been well-examined. In addition, research has shown that diets can be related to psychological resilience. Therefore, beneficial diets could potentially be utilized as a catalyst to, not only promote resilience, but also reduce pain (in combination with …

Use Of Machine Learning Models To Predict Microaspiration Measured By Tracheal Pepsin A., Annette Bourgault, Ilana Logvinov, Chang Liu, Rui Xie, Jan Powers Phd, Rn, Ccrn, Mary Lou Sole

Nursing Publications, Posters, & Presentations

BACKGROUND: Enteral feeding intolerance, a common type of gastrointestinal dysfunction leading to underfeeding, is associated with increased mortality. Tracheal pepsin A, an indicator of microaspiration, was found in 39% of patients within 24 hours of enteral feeding. Tracheal pepsin A is a potential biomarker of enteral feeding intolerance.

OBJECTIVE: To identify predictors of microaspiration (tracheal or oral pepsin A). It was hypothesized that variables predicting the presence of tracheal pepsin A might be similar to predictors of enteral feeding intolerance.

METHODS: In this secondary analysis, machine learning models were fit for 283 adults receiving mechanical ventilation who had tracheal and …

Data Literacy Competencies In Context: Employee Perspectives From The Workplace, Patricia Condon, Wendy G. Pothier

Faculty Publications

Data literacy is essential in today’s workplace, and professionals across roles and experience levels recognize its value. This article reports on findings from interviews with 16 supply chain and logistics professionals. The study examines how seven proposed data literacy competencies align with workplace needs, how employees address the data literacy gap, and how librarians can support workforce readiness. Findings highlight opportunities for libraries to bridge the data literacy gap through instruction and resources development that integrate technical and non-technical data skills with information literacy.

A Collaborative Assessment Of Coastal Ocean Acidification Monitoring In Maine & Standard Operating Procedures And Best Practices For The Collection Of Continuous Ph Data In Coastal Marine Environments, Christopher W. Hunt, Curtis Bohlen, Mike Doan, Jeremy Miller

Faculty Publications

The ‘Sensor Squad’ of the Maine Ocean Climate Collaborative is the product of a 2023 Maine Coastal and Marine Climate Action Fund grant to conduct “A two-year pilot project designed to address and overcome technological barriers to ocean acidification data collection, develop protocols to elevate quality assurance and ensure comparable data, and meet regularly to discuss project results and data compilation”. The Squad consists of representatives from Friends of Casco Bay (FOCB), Wells National Estuarine Research Reserve (WNERR), and the University of New Hampshire (UNH). This report is a summary of their efforts to assess affordable, repeatable means of continuously …

The Chatgpt Fact-Check: Exploiting The Limitations Of Generative Ai To Develop Evidence-Based Reasoning Skills In College Science Courses, Ursula Holzmann, Sulekha Anand, Alexander Y. Payumo

Faculty Research, Scholarly, and Creative Activity

Generative large language models (LLMs) like ChatGPT can quickly produce informative essays on various topics. However, the information generated cannot be fully trusted, as artificial intelligence (AI) can make factual mistakes. This poses challenges for using such tools in college classrooms. To address this, an adaptable assignment called the ChatGPT Fact-Check was developed to teach students in college science courses the benefits of using LLMs for topic exploration while emphasizing the importance of validating their claims based on evidence. The assignment requires students to use ChatGPT to generate essays, evaluate AI-generated sources, and assess the validity of AI-generated scientific claims …

Identification Of Salt Tolerance And Stress Response In Us Department Of Agriculture Tomato Germplasm At The Seedling Stage, Ibtisam Alatawi, Haizheng Xiong, Kenani Chiwina, Hanan Alkabkabi, Qun Luo, Neelendra K. Joshi, Xiaolun Sun, Xuan Zhuang, Kai-Shi Ling, Ainong Shi

Horticulture Faculty Publications and Presentations

Soil salinity is a significant abiotic factor that impedes sustainable crop production in key agricultural regions worldwide. Saline cultivation adversely affects soil quality, whereas the use of saline water for irrigation disrupts the physiological and biochemical processes of plants. Continuous irrigation with high salt concentrations leads to a gradual buildup of soil salinity, thus hindering optimal plant growth and development. Consequently, there is a growing emphasis on breeding salinity-tolerant cultivars of various crops. In this study, 71 tomato accessions sourced from 20 countries and provided by the US Department of Agriculture were evaluated under controlled greenhouse conditions and subjected to …

Robust Mitigation Strategy For Misleading Pheromone Trails In Foraging Robot Swarms, Ryan Luna, Qi Lu

Computer Science Faculty Publications

This study advances the security of swarm robotics by examining the resilience of stigmergic communication in foraging robot swarms against deceptive strategies. We specifically investigate the swarm’s vulnerability to attacks via misleading pheromone trails laid by detractor robots, which significantly hinder foraging performance. Through simulations, we evaluated the adverse effects of such attacks on resource collection and forager capture rates, highlighting a notable decline as the percentage of detractors increases. To counter these threats, we implement a robust defense mechanism utilizing DBSCAN for density-based clustering of pheromone trails, complemented by a cluster grouping method that effectively isolates batches of detractors …

Congestion Mitigation For Foraging Robot Swarms Using Spiral Path Strategies, Arturo Gonzalez, Qi Lu

Computer Science Faculty Publications

Swarm robotics offers robust and scalable solutions for tasks such as foraging, but congestion near central collection zones remains a critical challenge, especially with increasing swarm sizes. Traditional solutions, such as static path planning or local repulsion-based methods, often fail to prevent interrobot collisions or bottlenecks near the collection zones. This research presents a comparative study of three strategies to mitigate congestion when returning resources to the central collection zone. The research herein focuses on tightly packed environments where, in theory, robots should follow a preplanned spiral, either ad-hoc, square, or circular, with congestion detection as described in the first …

Challenging The Law, Steven Arrigg Koh

Faculty Scholarship

Frédéric Mégret’s engaging contribution, A Look Back at The Women’s Hague Peace Conference: What Contribution To International Law Today?, exposes a legal duality. On one hand, the legalist perspective: law is a closed system. From this perspective, law is objective, hard, universal, and bounded. On the other hand, the sociocultural perspective: law is a human practice. From this perspective, law is subjective, organic, particular, and porous. This Essay reads Mégret’s analysis of the 1915 International Congress of Women in The Hague as a “sociocultural challenge,” disrupting the legalist perspective on international law, war, and peace during World War I. …

The B3 Scholar Seal: Designing And Implementing An Alternative To The Sobl At A Hispanic-Serving Institution In South Texas, Katherine Christoffersen, Dania López García

Writing and Language Studies Faculty Publications

This chapter describes how the Bilingualism, Biculturalism, and Biliteracy (B3) Institute at the University of Texas Rio Grande Valley (UTRGV) developed the B3 Scholar Seal. Since its founding, UTRGV has provided a rare example of dual language education at the university level, offering courses taught bilingually or in Spanish across diverse disciplines. However, the language of these courses was not formally recognized upon graduation. The B3 Institute developed the B3 Scholar Seal to acknowledge students who successfully complete five courses, including at least three courses taught in Spanish or bilingually and at least one course, including culturally sustaining pedagogy. In …

Design And Deployment Of A Compact Rov For Deep-Sea Research And Exploration, Joshua F. Wood

Open Access Master's Theses

The scientific community has utilized unmanned underwater vehicles for ocean exploration since the mid-twentieth century, resulting in a well-cultivated and ever-changing discipline of ocean technology. The deep-sea environment, specifically, presents unique and harsh criteria due to the increased pressure found at depth and the vehicle components necessary to overcome it. The size and weight of underwater vehicles typically increase as operational depth increases, resulting in physically large systems with high operational costs to accommodate deep-sea research. This project first characterized the effect of length and diameter on carbon fiber pressure housing’s depth tolerance. It then leveraged this data to reduce …

Minimalistic Communication-Based Swarm Slam, Felix B. Koch

Open Access Master's Theses

This study presents and validates Range of Communication Swarm SLAM(RCS-SLAM), a novel SLAM approach designed for multi-robot systems using minimal hardware. Unlike traditional methods that rely on range or bearing measurements, RCS-SLAM only uses the identifiers of nearby robots within communication range. In the front-end, each robot constructs an individual pose graph based on its own odometry, while recording communication events with neighboring robots. The key novelty lies in the use of one-hop communication, where robots not only detect nearby peers but also relay received identifiers, effectively acting as transmitters themselves. This mechanism extends the communication graph and enables the …

Develop A Cross-Platform Toolset For In Situ Deep-Sea Coral Propagation, Joe Bevilacqua

Open Access Master's Theses

Mesophotic and deep-sea gorgonian octocorals in the Gulf of Mexico were significantly damaged following the Deepwater Horizon oil spill, prompting a major federal investment in developing restoration techniques for these fragile, slow-growing communities. Asexual, in-situ coral propagation offers a biologically viable path for restoration at depth. However, current ROV systems are not optimized for the delicate, fine-scale interactions required to perform this process reliably. The objective of this research was to design, prototype, and evaluate a ROV-mountable toolset capable of preparing octocoral fragments for potting in epoxy substrate, with the additional goal of integrating the toolset into URI’s Coral Carousel …

An Evidence-Based Consensus For The Use Of Neurostimulation For The Treatment Of Non-Surgical Low Back Pain: The Neuron Group., Timothy Ray Deer, Jason E Pope, Erika A Petersen, Rany T Abdallah, Kasra Amirdelfan, Nomen Azeem, Vishal Bansal, Kaku Barkoh, Kenneth B Chapman, Daniel R Denis, Michael J Dorsi, Alexander Escobar, Steven Michael Falowski, Rosa Amelia Garcia, Jonathan M Hagedorn, Robert D Heros, Whitney S James, Hemant Kalia, Todd Lansford, Mark N Malinowski, Suzanne Marie Manzi, Pankaj Mehta, Robert Z Moghim, Gregory Anthony Moore, Soriaya Lizette Motivala, Yeshvant A Navalgund, Raj G Patel, Julie G Pilitsis, Michael E Schatman, Philip Michael Shumsky, Natalie Holmes Strand, Nestor D Tomycz, James J Yue, Dawood Sayed

Neuroscience Articles

INTRODUCTION: The use of electrical neuromodulation has often been limited to those with previous back surgery, peripheral neuropathy, and complex regional pain syndrome. Many patients with severe intractable low back pain were thought to be candidates for spinal cord stimulation (SCS), dorsal root ganglion stimulation, or peripheral nerve stimulation but did not meet the criteria. Recently, additional high-level data has supported the use of SCS in non-surgical low back pain (NSLBP), and United States Food and Drug Administration approval has been granted. The American Society of Pain and Neuroscience (ASPN) executive committee realized an unmet need to develop criteria for …

Real-World Clinical Utility Of A Multi-Protein, Blood-Based Biomarker Assay For Disease Activity Assessments In Multiple Sclerosis., Angela Sanchez, Elisa Sheng, Sarah Eagleman, James L Eubanks, Patricia Izbicki, Shannon Mccurdy, Matt Burril, Ferhan Qureshi, Ati Ghoreyshi, Mitzi Joi Williams, Megan Weigel, William Kilgo, Jacqueline Nicholas, Annette Okai, Martin Belkin, Julie Burnham, Yasir Jassam, Michael Sy, Taylor Gonyou

Neuroscience Articles

BACKGROUND: Blood-based biomarkers have emerged as promising tools to optimize treatment decisions in multiple sclerosis (MS) including initiation, switch, or cessation of disease modifying therapies.

OBJECTIVES: The clinically validated MS disease activity (MSDA) test measures 18 proteins to derive a disease activity score. This study tests the clinical utility of MSDA in real-world practice.

METHODS: Twenty clinicians from 14 clinics conducted a chart review utilizing a retrospective, longitudinal design, with a pre-post component. Chart reviews captured clinician decision-making before and after receipt of each MSDA result, while separate clinician assessments also captured the perceived impact of MSDA on MS management. …

An Operational Field Study: A Comparison Of Piloting Uncrewed Underwater Vehicles And Uncrewed Aircraft Systems, David Thirtyacre, Joseph Cerreta, Pete Miller, Kimberly Luthi, Jolee Thirtyacre

Publications

and operations, the ability to cross-train personnel in both Uncrewed Underwater Vehicles and Small Uncrewed Aircraft System operations has become a focal point for efficiency and workforce optimization. This study presents a comparative analysis of the operational and human factor considerations involved in piloting mini UUV and sUASs, highlighting the key similarities and differences in control methods, environmental influences, navigation, emergency procedures, and situational awareness. A qualitative experimental field study was conducted between July 2024 and October 2024, involving real-world deployments of both systems in maritime and aerial environments. Findings indicated that while UUV and sUAS operators relied on remote …

Scoping Review Of Machine Learning Techniques In Marker-Based Clinical Gait Analysis, Kevin N. Dibbern, Maddalena G. Krzak, Alejandro Olivas, Mark V. Albert, Joseph J. Krzak, Karen M. Kruger

Biomedical Engineering Faculty Research and Publications

The recent proliferation of novel machine learning techniques in quantitative marker-based 3D gait analysis (3DGA) has shown promise for improving interpretations of clinical gait analysis. The objective of this study was to characterize the state of the literature on using machine learning in the analysis of marker-based 3D gait analysis to provide clinical insights that may be used to improve clinical analysis and care. Methods: A scoping review of the literature was conducted using the PubMed and Web of Science databases. Search terms from eight relevant articles were identified by the authors and added to by experts in clinical gait …

Identifying Notch-Regulated Genes Using A Specific Notch Signaling Inhibitor, Hammed Gafar

EWU Masters Thesis Collection

Bone remodeling is a dynamic process that requires a balance between bone resorption by osteoclasts and bone formation by osteoblasts to maintain skeletal integrity. Disruptions to this equilibrium can lead to pathological conditions such as osteoporosis. Osteoclasts originate from macrophages, and their differentiation is regulated by several signaling pathways, notably the notch signaling pathway. Gamma-secretase, an enzyme crucial for initiating notch signaling, can be inhibited by DAPT. However, DAPT also targets non-Notch substrates, complicating the identification of genes specifically regulated by Notch. To address this limitation, this study employed IMR-1A, a selective Notch pathway inhibitor that disrupts the assembly of …

The Effects Of Salinity On The Cutaneous Microbiome And Pathogen Infection On The Pacific Tree Frog (Pseudacris Regilla) In Monterey Bay, California, Usa, Hannah Eunhae Kim

EWU Masters Thesis Collection

Global climate change and infectious diseases are considered a leading cause of amphibian population declines worldwide. Changes in precipitation and salinity have altered watershed systems and microbial communities, reducing habitat availability and physiological performances for amphibian survival. The salt refuge hypothesis, however, is a proposed explanation that higher saline environments may reduce susceptibility to pathogens such as Batrachochytrium dendrobatidis (Bd). The Moro Cojo Slough State Marine Reserve (MCSSMR) (California, USA) is known as an abundant breeding ground for endangered/threatened amphibian species. To test and expand the salt refuge hypothesis, I evaluated Bd prevalence and intensity and the cutaneous microbiome of …