Digital Commons Network^™

First Assembly Of A Draft Genome Of The Critically Endangered Northern Muriqui ( Brachyteles Hypoxanthus , Primates, Atelidae) Including Non‐Invasive Genotyping Strategies For The Species, Amanda Alves De Melo-Ximenes, Romina Batista, Leonardo Carlos Jeronimo Corvalán, Tomas Marques-Bonet, Lukas Kuderna, Kyle Farh, Jeffrey Rogers, Mariane Da Cruz Kaizer, Jean Philippe Boubli, Fabiano Rodrigues De Melo, Rhewter Nunes, Mariana Pires De Campos Telles

Faculty, Staff and Students Publications

Genomic resources, such as draft genomes, are vital for biodiversity monitoring and conservation. For endangered species, they enable the development of tools like organellar genomes and molecular markers, which are crucial for population genetics. Advances in sequencing technologies now allow high‐throughput genotyping with detailed amplicon sequences, enhancing genetic variation studies. The northern muriqui ( Brachyteles hypoxanthus ), a critically endangered primate endemic to Brazil's Atlantic Forest, currently lacks both nuclear and mitochondrial genome data and species‐specific microsatellite markers for population genetic studies. We assembled a 2.52 Gb draft genome for B. hypoxanthus with 202,243 contigs (N50 = 29,134 bp), and …

Mechanisms Underlying Atrial Fibrillation In Chronic Kidney Disease, Jose Alberto Navarro-Garcia, Joshua A Keefe, Jia Song, Na Li, Xander H T Wehrens

Faculty, Staff and Students Publications

Chronic kidney disease (CKD) is a serious and progressive worldwide health problem affecting 15 % of the global population. CKD is associated with higher mortality rates due to secondary complications such as cardiovascular disease. Common cardiovascular complications found in CKD patients include left ventricular hypertrophy, heart failure, and cardiac arrhythmias. The most common type of cardiac arrhythmia in CKD patients is atrial fibrillation (AF). Proper management of AF is important due to its high risk of cardiovascular complications and stroke. The incidence of AF remains higher in CKD patients than in the healthy population, highlighting the need to improve our …

Dynamic Mode Decomposition Of Geostrophically Balanced Motions From Swot Cal/Val In The Separated Gulf Stream, Takaya Uchida, Badarvada Yadidya, Karl E. Lapo, Xiaobiao Xu, Jeffrey J. Early, Brian K. Arbic, Dimitris Menemenlis, Luna Hiron, Eric P. Chassignet, Jay F. Shriver, Maarten C. Buijsman

Faculty Research, Scholarly, and Creative Activity

The decomposition of oceanic flow into its geostrophically balanced and unbalanced motions carries theoretical and practical significance for the oceanographic community. These two motions have distinct dynamical characteristics and affect the transport of tracers differently from one another. The launch of the Surface Water and Ocean Topography (SWOT) satellite provides a prime opportunity to diagnose the surface balanced and unbalanced motions on a global scale at an unprecedented spatial resolution. Here, we apply dynamic-mode decomposition (DMD), a linear-algebraic data-driven method, to tidally-forced idealized and realistic numerical simulations at submesoscale-permitting resolution and one-day-repeat SWOT observations of sea-surface height (SSH) in the …

Community-Engaged Medical Student Elective To Improve Knowledge And Attitudes Toward Individuals With Intellectual And Developmental Disabilities, Kathryn J Kemere, Nital Appelbaum, Priya Chandan, Elisha Acosta

Faculty, Staff and Students Publications

Individuals with intellectual and developmental disabilities (IDD) face multiple barriers to inclusion throughout life. One barrier is the medical knowledge and biases of adult healthcare providers with diagnoses traditionally associated with childhood. Medical school curricula have limited content related to IDD, and students have limited opportunities to engage with community organizations during their clinical years. Methods: We created a one-month clinical elective to address medical students' attitudes and knowledge regarding individuals with IDD using experiential learning. Students saw adult patients in our primary care clinic with a variety of IDD diagnoses and spent 30% of their time at community sites …

Health And Weather In Unfavourable Environments: Exploring The Historical Dynamics Of Colonial Medical Meteorology In Nineteenth-Century Tropical Asia, Fiona Williamson

Research Collection College of Integrative Studies

Medical meteorology had a long precedent in medical thought across Eastern and Western traditions. This article considers the tradition of medical meteorology that was favoured by Western doctors in the nineteenth century, which was often applied within colonial contexts to the understanding of new climates and how they might impact on human health. Looking at British-held tropical and sub-tropical colonies of the Straits Settlements and Hong Kong respectively, medical meteorology was stimulated by the new pathological and atmospheric conditions that European explorers and settlers now inhabited in the name of the British Empire. They brought with them concepts of disease …

Immune Modulation Affects Olfactory Glomerular Recovery In Zebrafish, Bonnie E. Ebendick

Dissertations

Adult zebrafish regenerate neurons throughout their lifetime and exhibit rapid recovery from neuronal damage with support from their immune system, making them an excellent model for studying neuroinflammation and brain repair mechanisms. When olfactory sensory neurons are lesioned, their cell death stimulates the immune system by activating microglia and other immune cells in the olfactory bulb, initiating tissue repair and neuronal replacement. This dissertation investigates how the immune system influences recovery from neuronal damage, testing the hypothesis that immune perturbation in zebrafish alters neural recovery.

To investigate the link between immune function and neuronal regeneration, zebrafish received a unilateral lesion …

The Development Of High Throughput Assays For Identification And Evaluation Of Small Molecule Modulators Of The Pri-Microrna-18a—Hnrnp A1 Interaction, Emile N. Van Meter

Dissertations

Therapeutics targeting RNA is a rapidly growing field. While only 1.5% of the human genome encodes genes for protein, over 70% o=f the human genome contains the genes for noncoding RNAs that regulate protein expression and function. Expanding the paradigm of small molecule drug discovery from traditional protein targets to include RNA would broaden the therapeutic landscape and provide new methods to modulate previously undruggable targets. miRNAs (miRs) have been found to be aberrantly expressed in many disease states, including neurodegenerative diseases and cancers making them promising therapeutic targets. The production of functional, mature miRs requires multiple proteins in a …

Formation Control Between Leader And Migratory Follower Tissues Allows Coordinated Growth, Toru Kawanishi, Takamichi Sushida, Tony Y-C Tsai, Hiroyuki Takeda, Sean G Megason

2020-Current year OA Pubs

Coordinated growth of multiple tissues is fundamental to shaping our body, but the underlying mechanisms remain underexplored. In zebrafish embryos, midline tissues composed of the notochord, floorplate, and hypochord elongate synchronously with their lengths aligned. We show that floorplate and hypochord cells collectively migrate posteriorly along the nascent notochord extracellular matrix as it extends posteriorly, maintaining the tripartite configuration. Fibroblast growth factor-mediated migration in a spatially graded manner causes cell stretching, which triggers Yap-dependent proliferation and controls floorplate and hypochord growth. Supported by mathematical modeling, we further suggest that their growth is fine-tuned by mechanical tethering to the notochord via …

The Microrna Mir-30a Blocks Adipose Tissue Fibrosis Accumulation In Obesity, Pradip K Saha, Robert Sharp, Aaron R. Cox, Rabie Habib, Michael J. Bolt, Jessica B. Felix, Claudia E. Ramirez Bustamante, Xin Li, Sung Yun Jung, Kang Ho Kim, Kai Sun, Huaizhu Wu, Samuel Klein, Sean M. Hartig

2020-Current year OA Pubs

White adipose tissue (WAT) fibrosis occurring in obesity contributes to the inflammatory and metabolic comorbidities of insulin resistance and type 2 diabetes, yet the mechanisms involved remain poorly understood. Here, we report a role for the broadly conserved miRNA miR-30a as a regulator of WAT fibrosis and systemic glucose metabolism. Mice modified to express miR-30a at elevated levels in adipose tissues maintain insulin sensitivity coupled with reduced fatty liver disease when fed a high-fat diet. These effects were attributable to cell-autonomous functions of miR-30a that potently increase expression of adipocyte-specific genes. Proteomic screening revealed miR-30a limits profibrotic programs in subcutaneous …

The Upcoming Moral Crisis In Primitive Artificial Intelligence, Justin E. Edens

Graduate Theses and Dissertations

As we continue to develop artificially intelligent systems, there is an increasingly high chance that we will develop a system that is both conscious and capable of suffering. Furthermore, it is likely that the development of this conscious machine will be entirely unintentional. While this machine will have moral status, identifying it will be extremely difficult, leading to it being treated the same as its inert predecessors. For these reasons I believe that a crisis in ethics is looming. This paper aims to argue that it is possible for a machine to have moral status, that the first such machine …

Resilience Redefined: Exploring The Impact Of Childhood Trauma On The Value Systems Of High-Achieving Corporate Men, Lana B. Henry

Graduate Theses and Dissertations

This qualitative study employed Interpretive Phenomenological Analysis (IPA) to explore how childhood trauma influences the value systems of high-achieving corporate men. In contemporary corporate culture, where stoicism, performance, and independence are often rewarded, little attention is paid to how early adversity informs internal frameworks of meaning, leadership, and success. Semi-structured interviews were conducted with six high-achieving men, all executives and leaders in high-performing industries, who self-identified as having experienced childhood trauma. Data were analyzed using a six-step IPA process and interpreted through the lens of Schwartz’s Theory of Basic Human Values and social constructivism. Findings revealed that childhood trauma deeply …

Effects Of Multi-Sensory Training In Physical Activity On Reaction Time And Fitness In Elementary Students., Sarah Anne Trout

Graduate Theses and Dissertations

Abstract This study examined the effects of multi-sensory Neuroplasticity training (MSNP™) using the ROXPro system on the psychomotor abilities of third-grade students in a Midwestern elementary school. The research aimed to determine whether the integration of interactive sensory-reactive technology in physical education could improve reaction time, agility, and explosive power compared to standard PE instruction. A total of 49 participants were assigned to either a control group or an intervention group, with the latter engaging in six weeks of ROX-based drills. A pretest-posttest design was employed, and data were analyzed using ANCOVA, repeated measures ANOVA, and independent t-tests to assess …

Effect Of Marination And Storage Time On The Properties And Meat Quality Of Broiler Breast, Mayra Mabel Herrera Rivera

Graduate Theses and Dissertations

Abstract The poultry industry has implemented numerous methods, as marination and aging, to improve meat quality and satisfy consumer demands. Three experiments were developed to assess the effects of vacuum tumble marination and aging on the proteins of chicken breast. These experiments utilized 0.75 % sodium chloride, 0.45 % phosphate, and water in a marinade. In experiment one, 270 fillets were allocated into six treatment groups, each comprising 45 fillets. Six days of storage time were used, marinating and storing the fillets in each group at a temperature of 4°C. Following each day of storage period, the fillets underwent a …

Visual Analog Of Temporal Envelope Benefits Speech Processing In Cochlear Implant Users: A Pilot Functional Near-Infrared Spectroscopy Study On The Associations Between Audiovisual Benefit, Listening Environment, And Peripheral Neural Health, Zi Gao, Yi Yuan, Christopher R. Mueller, Ross A. Aiello, Yingying Wang, Shuman He

Faculty Research, Scholarly, and Creative Activity

Objectives: This study compared the benefit of visual analog of temporal envelope for speech processing across listening environments in postlingually deafened adult cochlear implant users. Associations between cortical activities and peripheral neural health were explored. Design: Speech perception was measured using Harvard/IEEE sentences in quiet and noise with a visually presented sphere whose size was synchronized with the temporal envelope of the sentences. Cortical activities were recorded concurrently using functional near-infrared spectroscopy. Audiovisual benefit was evaluated using sentence scores, activation additivity, and functional connectivity. Peripheral neural health was measured using electrically evoked compound action potentials. Results: Behavioral results showed the …

Climate Drives Genetic Diversity Loss In American Pika (Ochotona Princeps) Populations In The Great Basin, Emily N. Kulig, Jane Van Gunst, Michael J. Hernandez, Yvonne Luong, Monica Villaseñor, Rachel S. Crowhurst, Clinton W. Epps, Jessica A.Castillo Vardaro

Faculty Research, Scholarly, and Creative Activity

American pikas (Ochotona princeps) are small, thermally sensitive mammals that primarily live in montane and alpine environments. The Sierra Nevada lineage (O. p. schisticeps) has experienced numerous local extinctions, most of which occurred in hotter, drier regions such as the Great Basin. Few genetic studies have assessed these at-risk populations. This study aims to fill that gap by conducting fine-scale genetic analyses on populations in low-elevation Great Basin habitat in northwestern Nevada. Specifically, we: (i) quantified genetic diversity and structure among populations within O. p schisticeps, with particular focus on northwestern Nevada; and (ii) assessed the influence of primary productivity …

Cognitive And Affective Factors Related To Geoscience Academic And Career Choice, Amanda Diane Manzanares

Dissertations

Recruitment and retention continue to be a challenge for Science, Technology, Engineering, and Math (STEM) fields. Research shows that both cognitive and affective factors influence student learning, which can then shape academic and career choice. Therefore, my alternatively formatted dissertation includes three articles examining two STEM disciplines: geosciences and Interdisciplinary Environmental and Sustainability programs adding to prior research and further uncovering specific factors that could predict student educational and professional aspirations.

Regarding cognition, students often begin STEM courses with pre-existing mental frameworks, also referred to as schemas that are formed by their prior experiences. These schemas may conflict with established …

Updates To Administrative Coding Systems Limits Longitudinal Study Of Patients With Congenital Heart Disease., Natalie Jayaram, Dhaval Chauhan, Matt Hall, Janelle R. Noel-Macdonnell Phd, Philip M. Allen, Brett R. Anderson

Manuscripts, Articles, Book Chapters and Other Papers

No abstract provided.

Female Preference And Prezygotic Isolation In The Fundulus Notatus Species Complex, Emilee K. Holderness

Master's Theses

Understanding how reproductive isolation arises between closely related species is central to evolutionary research. Hybridization is widespread across taxa and shaped by interactions among environmental factors, evolutionary history, genetic compatibility, and behavior. These forces often operate nonlinearly across space and time, yet mate choice is frequently assessed under artificial conditions that may not reflect natural behavior. To address this limitation, female mate preference was investigated within the Fundulus notatus species complex, where F. notatus and F. olivaceus hybridize at varying rates across replicate contact zones. Using a free-choice design, behavioral trials were conducted with individuals from populations characterized by high …

Endotherm Energetics Under Environmental And Physiological Constraints, Zachary Andrew David

Biological Sciences Theses & Dissertations

Metabolic rate governs how animals allocate energy toward maintenance, activity, growth, and reproduction, linking physiology to environmental context. This dissertation investigates how two endothermic mammals regulate metabolic rate in response to environmental variability, focusing on thermoregulatory flexibility and physiological constraints. Using flow-through respirometry, I measured resting metabolic rates (RMRs) in two complementary systems: tropical bears housed in semi-natural outdoor enclosures and marsh rice rats (Oryzomys palustris) exposed to controlled thermal treatments. Asiatic black bears (Ursus thibetanus) exhibited unexpectedly low mass-specific metabolic rates even under high ambient temperatures, yet their RMR increased with temperature, suggesting proximity to their …

Truth, Justice, And The American Way: Negotiating Identity Among Superhero Cosplayers At International Comic Book Conventions, James Scanlan

Graduate Theses and Dissertations

Cosplay performances in convention spaces, and the increasing commercialization and commodification of both, remain largely unexplored domains that are rapidly expanding into global phenomena. The influx of capital internationally and the growing popularity of cosplay and conventions offers the opportunity to document and describe processes of performance, identity construction, and negotiation of the global phenomena within local contexts (“glocalization”) in non-Western spaces. I conducted ethnographic research at more than half a dozen research sites throughout Europe, the Middle East, South Asia, East Asia, and South and Central America, photographing convention spaces and cosplayers and conducting interviews with cosplayers. By focusing …

Freezing And Shipping Optimization To Increase Quality And Profitability Of Meat E-Commerce, Paul Olaoluwaniyi Dahunsi

Graduate Theses and Dissertations

Freezing remains one of the most reliable methods for preserving meat quality and extending shelf life. However, quality deterioration can still occur due to structural and biochemical changes activated during freezing, thawing, and distribution. Since the COVID-19 pandemic, consumers’ preference for bulk purchasing and online meat shopping has increased, raising questions about the best strategies to balance both quality maintenance and profitability. This thesis aimed to evaluate two key stages where frozen beef is most vulnerable to quality degradation: consumer-level freezing and post-purchase shipping. The objectives were (1) to determine the effects of product size and subsequent consumer freezing practices …

Onward, Christian Soldiers: The Material Rhetoric Of Becoming Fascist In Parachurch Scouting Organizations, Madeline Aubrey Studebaker

Graduate Theses and Dissertations

This thesis provides a material rhetorical analysis of Trail Life USA and American Heritage Girls, two Christian nationalist scouting organizations that aim to renew and restore their cultural dominance across America. In examining how these programs route children’s bodies through ritual and affective indoctrination, I find that a fascist becoming underpins these groups’ (re)production of perfect, patriotic children. The first chapter discusses how boys enrolled in Trail Life USA become fascist as self-defense against American boyhood’s perceived eradication. Trail Life USA restores masculinity through rituals of autogenetic sovereignty, returns to originality through homosocial and affective intensity, and invocations of exceptional …

The Case Against Finean Essentialism, Miles Thibodeaux

Graduate Theses and Dissertations

In this thesis, I survey, critique, and add to recent arguments against Finean Essentialism: the view that all de re modal facts are metaphysically explained by essences. Arguments against Finean Essentialism generally fall into two categories: (a) Finean Essentialism risks contradicting commonly held views or suppositions, or (b) Finean Essentialism involves an explanatory gap, vicious circularity, or a vicious regress. While the details of the arguments within each category differ significantly, it is useful to group them in this way given the relevant implications they have for one another. I will argue that the proposed critiques from category (a) are …

Developing Targets To Control Multiple Pest Fly Species: Violet Polyester Targets Effectively Attract Tsetse (Diptera: Glossinidae), Stable Flies (Diptera: Muscidae), And House Flies (Diptera: Muscidae), Michael N. Okal, Sheillah J. Akinyi, Roger D. Santer

All Peer-Reviewed Publications

Tsetse (Glossina spp.), stable (Stomoxys spp.), and house flies (Musca domestica L.) impact humans and animals through bites and/or disease transmission. Tsetse are controlled using insecticide-coated fabric targets that are traditionally blue and/or black, but a violet polyester has now been engineered for greater attractiveness. Here, we investigate whether violet targets are also effective against stable and house flies. We sampled flies by electrocution at 1.0 (H) × 0.5 m (W) targets in Kenya, comparing catches at violet targets, and blue and black targets made from polyesters used in commercial traps and targets. Catches of female but not male Glossina …

Invited Review: Effects Of Management On Performance Of Stocker Cattle And Subsequent Feedlot Performance: A Review Within Applied Animal Science, M.A. Snider, M.S. Gadberry, J.D. Rivera

Animal Science Faculty Publications and Presentations

Purpose: The purpose of this review is to summarize relevant research from the journal Applied Animal Science (formerly known as The Professional Animal Scientist) between 1995 and 2024, that explores management practices and concepts as they relate to stocker calf performance and subsequent feedlot performance. A secondary objective of this review is to describe research trends and identify knowledge and research gaps within existing literature. Sources: Sources for this article included peer-reviewed scientific literature obtained from the journal Applied Animal Science, formerly known as The Professional Animal Scientist. Literature used in this review included original research, short communications, technical notes, …

Environmental Drivers Of Vegetation Dynamics In Constructed And Natural Wetlands Of The Chihuahuan Desert, Enrique David Garcia

Open Access Theses & Dissertations

Desert wetlands are critical ecosystems that provide water, food, and habitat for many different species at different trophic levels. Additionally, they have the capacity to recharge aquifers, control floods, and purify water, among others. Unfortunately, they have been facing multiple environmental challenges due to different human activities, sometimes with disastrous consequences. There is an urgent need to better understand the structure and function of wetlands of different types and in different biomes in order to conserve, restore, and even create them so we can continue to obtain all the ecological services they provide. In this dissertation, I investigated how environmental …

Cellular And Noncellular Influences On Lipid Nanoparticle Tropism In The Liver, Mario Yomir Mata Corral

Open Access Theses & Dissertations

Hepatocellular carcinoma (HCC) is currently ranked as the second leading cause of cancer-related mortality worldwide, causing more than 700,000 deaths a year. The liver is important in blood filtration and metabolism, and for this reason is a prime target for drug delivery, with lipid nanoparticles (LNPs) showing promise as carriers due to their natural hepatic tropism. However, LNP efficacy is decreased in HCC due to the limited understanding of liver physiology in cancerous environments. This project proposes to address this gap by using a tissue-clearing technique known as CLARITY along with a chemically tagged LNP for comprehensive visualization of LNPs …

Spatial And Thermal Aspects Of The Ecology Of Three Sympatric Rattlesnakes In The Montane Northern Chihuahuan Desert, Joshua James Mead

Open Access Theses & Dissertations

To understand how animals coexist on the landscape, the individual aspects of a species life history must first be understood. Animals need to find locations that provide the resources they need to survive. Movement, microhabitats, and temperature can alter such areas where animals occur. Understanding animal movements provide important information on space use and microhabitats on the landscape. Ectothermic animals must acquiesce to ambient temperatures or use behavioral modifications to alter their body temperature. The ability to maintain suitable body temperature is essential for physiological function, reproduction, and ability to avoid predation. Research on the variation in a species ecology …

Expression Of Glycine Transporter 1 In The Rodent Basal Ganglia: Glial Vs. Neuronal, Rosa Atziri Perez

Open Access Theses & Dissertations

Glycine functions as an inhibitory neurotransmitter in the central nervous system (CNS),and it is mainly involved in autonomic functions. The levels of extracellular glycine are regulated by two membrane transporters, glycine transporter 1 and glycine transporter 2 (GlyT1 and GlyT2, respectively). These transporters differ in function and localization within the CNS. For many years, studies suggested that only GlyT2 served as a neuronal marker; however, GlyT1 has been localized in neurons in recent studies. The expression of GlyT1 is widespread compared to GlyT2; hence, the main objective is to determine the nature of the expression of GlyT1 in areas devoid …

Temporal Partitioning And Coexistence Among Four Sympatric Felid Species In The Northern Jaguar Reserve, Kylie Marie Rezendes

Open Access Theses & Dissertations

Coexistence among sympatric carnivores is shaped by behavioral strategies that mediate competition and mortality risk in heterogeneous landscapes. Understanding how sympatric carnivores, such as felids, use space and time in relation to one another requires models that account for both spatial and temporal overlap across landscapes. Models incorporating time-to-event probabilities provide a powerful framework for detecting behavioral dynamics across shared landscapes. This study evaluated the spatiotemporal responses of two apex predators â?? the jaguar (Panthera onca) and mountain lion (Puma concolor) - and two mesopredators - bobcat (Lynx rufus) and ocelot (Leopardus pardalis) - across five years of camera trap …