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Cell Of Origin Identification Using Methylation Signatures From Seminal Cell-Free Dna And Heterogenous Cellular Mixtures, Ryan Barney Nov 2023

Cell Of Origin Identification Using Methylation Signatures From Seminal Cell-Free Dna And Heterogenous Cellular Mixtures, Ryan Barney

Theses and Dissertations

Infertility is an issue for approximately 12% of couples attempting to have a child. Of this group, 50% of the cases are due to male factor infertility. There are many reasons for decreased fecundity in men, but there remains 10% to 15% of infertile men that are diagnosed with the most severe form of infertility, non-obstructive azoospermia (NOA). A diagnosis of NOA implies the lack of sperm cells in the ejaculate with no physiological reason. The current diagnostic test and treatment consist of microscopic examination of seminal fluid and a biopsy to extract any viable sperm from the testis. This …

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Analog Artificial Neurons And Digital Amplifiers: Challenging The Roles Of Analog And Digital Circuit Architectures In Modern Cmos Processes, Taylor S. Barton Nov 2023

Analog Artificial Neurons And Digital Amplifiers: Challenging The Roles Of Analog And Digital Circuit Architectures In Modern Cmos Processes, Taylor S. Barton

Theses and Dissertations

As complimentary metal-oxide semiconductor (CMOS) technologies scale and field-effect transistor (FET) architectures change, the factors in deciding to utilize analog or digital transistor behaviors evolve. This thesis examines three case studies where traditionally analog or digital circuitry has dominated published works but I show that the opposite regime has significant benefits in scaled CMOS technologies. I present a highly digital operational amplifier (traditionally analog) and two artificial neurons (traditionally digital). In Chapters 2 and 3 I present a highly-digital five-stage zero-crossing-based amplifier which breaks the trade-off between slew rate and settling accuracy. I investigate the optimal charge pump design by …

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Developing 3d Printed Integrated Microfluidic Devices For Microchip Electrophoresis Separation Of Preterm Birth Biomarkers, Joule E. Esene Nov 2023

Developing 3d Printed Integrated Microfluidic Devices For Microchip Electrophoresis Separation Of Preterm Birth Biomarkers, Joule E. Esene

Theses and Dissertations

Preterm birth is a global health challenge and the leading cause of neonatal mortality. Each year, about 15 million babies are born preterm globally. Traditional tools that have been exploited for the detection of preterm birth biomarkers are expensive, time consuming, or lack multiplexing capabilities. The work described in this dissertation highlights techniques developed to detect preterm birth biomarkers rapidly and accurately in the effort to mitigate preterm birth risk. In this dissertation, I first demonstrated the use of stereolithography digital light processing-based 3D printing and microfluidics for the development of microfluidic devices that had microvalves for fluid control. I …

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A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett Nov 2023

A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett

Faculty Publications

The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, …

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Changes In Rna Expression Of Hut78 Cells Resulting From The Hiv-1 Viral Protein R R77q Mutation, Joshua S. Ramsey Oct 2023

Changes In Rna Expression Of Hut78 Cells Resulting From The Hiv-1 Viral Protein R R77q Mutation, Joshua S. Ramsey

Theses and Dissertations

Human immunodeficiency virus type 1 (HIV-1) is the causative virus for acquired immunodeficiency syndrome (AIDS). AIDS is characterized by chronic inflammation and reduction of CD4+ T-cells in the blood. This leads to the patient becoming immunocompromised and much more susceptible to disease in general. Different phenotypes in the progression of AIDS have been observed in patients in either progressing to AIDS faster as a Rapid Progressor (RP), or slower as a Long-Term Non-Progressor (LTNP). Researching elements that result in the LTNP phenotype is of interest as it has the potential to offer alternative treatments and therapies to those suffering from …

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Facial Motion Augmented Identity Verification With Deep Neural Networks, Zheng Sun Oct 2023

Facial Motion Augmented Identity Verification With Deep Neural Networks, Zheng Sun

Theses and Dissertations

Identity verification is ubiquitous in our daily life. By verifying the user's identity, the authorization process grants the privilege to access resources or facilities or perform certain tasks. The traditional and most prevalent authentication method is the personal identification number (PIN) or password. While these knowledge-based credentials could be lost or stolen, human biometric-based verification technologies have become popular alternatives in recent years. Nowadays, more people are used to unlocking their smartphones using their fingerprint or face instead of the conventional passcode. However, these biometric approaches have their weaknesses. For example, fingerprints could be easily fabricated, and a photo or …

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The Effects Of A High-Carbohydrate Versus A High-Fat Shake On Biomarkers Of Metabolism And Glycemic Control When Used To Interrupt A 38-Hour Fast: A Randomized Crossover Study, Landon S. Deru Oct 2023

The Effects Of A High-Carbohydrate Versus A High-Fat Shake On Biomarkers Of Metabolism And Glycemic Control When Used To Interrupt A 38-Hour Fast: A Randomized Crossover Study, Landon S. Deru

Theses and Dissertations

Purpose: The primary aim of this study was to determine the impact of various fast-interrupting shakes on markers of glycemic control including glucose, β-hydroxybutyrate (BHB), insulin, glucagon, GLP-1, and GIP. Methods: Twenty-seven adults (12 female, 15 male) completed all three conditions of this study. One condition consisted of a 38-hour water-only fast, and the other two conditions were similar but the fasts were interrupted at 24 hours by either a high carbohydrate/low fat (HC/LF) or a low carbohydrate/high fat (LC/HF) shake. Results: The water only fast resulted in 135.3% more BHB compared to the HC/LF condition (t = 7.77, p < 0.0001) and 69.6% more compared to the LC/HF condition (t = 5.12, p < 0.0001). Conversely, the LC/HF condition exhibited a 38.8% higher BHB level than the HC/LF condition (t = 2.70, p = 0.0086). Additionally, the area under the curve (AUC) for glucose was 14.2% higher in the HC/LF condition than in the water condition (t = 6.23, p < 0.0001) and 6.9% higher compared to the LC/HF condition (t = 3.14, p = 0.0024), with the LC/HF condition yielding 7.8% more glucose than the water condition (t = 3.21, p = 0.0020). At the 25-hour mark, insulin and glucose-dependent insulinotropic polypeptide (GIP) were significantly elevated in the HC/LF condition compared to the LC/HF condition (F = 3.84, p = 0.0002 and F = 2.27, p = 0.0244, respectively) and compared to the water condition (F = 7.00, p < 0.0001 and F = 9.96, p < 0.0001, respectively). Furthermore, insulin, glucagon-like peptide-1 (GLP-1), and GIP were increased in the LC/HF condition compared to the water condition at 25 hours (F = 3.19, p = 0.0016, F = 2.43, p = 0.0158, and F = 12.13, p < 0.0001, respectively). Notably, glucagon concentrations at the 25-hour mark decreased in the HC/LF group compared to the LC/HF condition (F = 3.37, p = 0.0009). However, by the 38-hour time point, no statistically significant differences were observed among the conditions for any of the analyzed hormones. Conclusions: While a LC/HF shake does not mimic a fast completely, it does preserve some of the metabolic changes including elevated BHB and glucagon, and decreased glucose and insulin compared to a HC/LF shake.

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Integrating Clinical Cancer And Ptm Proteomics Data Identifies A Mechanism Of Ack1 Kinase Activation, Eranga R. Balasooriya, Deshan Madhusanka, Tania P. López-Palacios, Riley J. Eastmond, Dasun Jayatunge, Jake J. Owen, Jack S. Gashler, Christina M. Egbert, Chanaka Bulathsinghalage, Lu Liu, Stephen R. Piccolo, Joshua L. Andersen Oct 2023

Integrating Clinical Cancer And Ptm Proteomics Data Identifies A Mechanism Of Ack1 Kinase Activation, Eranga R. Balasooriya, Deshan Madhusanka, Tania P. López-Palacios, Riley J. Eastmond, Dasun Jayatunge, Jake J. Owen, Jack S. Gashler, Christina M. Egbert, Chanaka Bulathsinghalage, Lu Liu, Stephen R. Piccolo, Joshua L. Andersen

Faculty Publications

Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML …

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Evaluating A Large Language Model’S Ability To Solve Programming Exercises From An Introductory Bioinformatics Course, Stephen R. Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H. Payne, Perry G. Ridge Sep 2023

Evaluating A Large Language Model’S Ability To Solve Programming Exercises From An Introductory Bioinformatics Course, Stephen R. Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H. Payne, Perry G. Ridge

Faculty Publications

Life scientists frequently write computer code when doing research. Computer programming can aid researchers in performing tasks that are not supported by existing tools. Programming can also help researchers to implement analytical logic in a way that documents their steps and thus enables others to repeat those steps. Many educational resources are available to teach computer programming, but this skill remains challenging for many researchers and students to master. Artificial-intelligence tools like OpenAI’s ChatGPT are able to interpret human-language requests to generate code. Accordingly, we evaluated the extent to which this technology might be used to perform programming tasks described …

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Streamlining The Detection Of Human Thyroid Receptor Ligand Interactions With Xl1-Blue Cell-Free Protein Synthesis And Beta-Galactosidase Fusion Protein Biosensors, J. Porter Hunt, Tyler J. Free, Jackelyn Galiardi, Kevin M. Watt, David W. Wood, Bradley Charles Bundy Sep 2023

Streamlining The Detection Of Human Thyroid Receptor Ligand Interactions With Xl1-Blue Cell-Free Protein Synthesis And Beta-Galactosidase Fusion Protein Biosensors, J. Porter Hunt, Tyler J. Free, Jackelyn Galiardi, Kevin M. Watt, David W. Wood, Bradley Charles Bundy

Faculty Publications

Thyroid receptor signaling controls major physiological processes and disrupted signaling can cause severe disorders that negatively impact human life. Consequently, methods to detect thyroid receptor ligands are of great toxicologic and pharmacologic importance. Previously, we reported thyroid receptor ligand detection with cell-free protein synthesis of a chimeric fusion protein composed of the human thyroid receptor beta (hTRβ) receptor activator and a β-lactamase reporter. Here, we report a 60% reduction in sensing cost by reengineering the chimeric fusion protein biosensor to include a reporter system composed of either the full-length beta galactosidase (β-gal), the alpha fragment of β-gal (β-gal-α), or a …

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Improving Behavior In An Alternative High School Summer Program Using Class‑Wide Function‑Related Intervention Teams: A Pilot Study, Paul Caldarella, Erika J. Richards, Leslie Williams, Emily J. Warburton Sep 2023

Improving Behavior In An Alternative High School Summer Program Using Class‑Wide Function‑Related Intervention Teams: A Pilot Study, Paul Caldarella, Erika J. Richards, Leslie Williams, Emily J. Warburton

Faculty Publications

Effective interventions are needed to help alternative high school teachers manage challenging student behaviors. One such intervention, class-wide function-related intervention teams (CWFIT), is a classroom management program based on positive behavior interventions and supports principles. CW-FIT involves teaching appropriate classroom behavioral expectations (social skills), using high behavior-specific praise-to-reprimand ratios, and an interdependent group contingency to provide differential reinforcement of appropriate classroom behavior and eliminate potential reinforcement of problem behavior. In this pilot study, four alternative high school teachers implemented CW-FIT during a summer school program. A series of single subject A-B designs were used over a 3-week period. Results supported …

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A Probabilistic View Of Protein Stability, Conformational Specificity, And Design, Jacob A. Stern, Tyler J. Free, Kimberlee L. Stern, Spencer Gardiner, Nicholas A. Dalley, Bradley Charles Bundy, Joshua L. Price, David Wingate, Dnnis Della Corte Sep 2023

A Probabilistic View Of Protein Stability, Conformational Specificity, And Design, Jacob A. Stern, Tyler J. Free, Kimberlee L. Stern, Spencer Gardiner, Nicholas A. Dalley, Bradley Charles Bundy, Joshua L. Price, David Wingate, Dnnis Della Corte

Faculty Publications

Various approaches have used neural networks as probabilistic models for the design of protein sequences. These "inverse folding" models employ different objective functions, which come with trade-offs that have not been assessed in detail before. This study introduces probabilistic definitions of protein stability and conformational specificity and demonstrates the relationship between these chemical properties and the p(stucture|seq) Boltzmann probability objective. This links the Boltzmann probability objective function to experimentally verifiable outcomes. We propose a novel sequence decoding algorithm, referred to as “BayesDesign”, that leverages Bayes’ Rule to maximize the p(stucture|seq) objective instead of the p(seq|structure) objective common in inverse folding …

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Spatial And Temporal Distribution Of Phalaropes (Phalaropus Spp.) And Adult Brine Flies (Ephydra Spp.) Are Linked On Great Salt Lake, Utah, Maureen G. Frank, Michael R. Conover Sep 2023

Spatial And Temporal Distribution Of Phalaropes (Phalaropus Spp.) And Adult Brine Flies (Ephydra Spp.) Are Linked On Great Salt Lake, Utah, Maureen G. Frank, Michael R. Conover

Western North American Naturalist

Great Salt Lake (GSL), Utah, is home to some of the world’s largest concentrations of Wilson’s Phalaropes (Phalaropus tricolor), Red-necked Phalaropes (Phalaropus lobatus), American Avocets (Recurvirostra americana), and Black-necked Stilts (Himantopus mexicanus). These birds spend several weeks on GSL feeding on larvae, pupae, and adult brine flies (Ephydra spp.) before migrating to their wintering grounds in Central and South America. Unfortunately, GSL is shrinking in size and becoming more saline due to water diversions and climate change. Assessing how a smaller and more saline GSL will affect adult brine flies is …

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Recent Breakthroughs In Using Quantum Dots For Cancer Imaging And Drug Delivery Purposes, Aisha Hamidu, William G. Pitt, Ghaleb A. Husseini Sep 2023

Recent Breakthroughs In Using Quantum Dots For Cancer Imaging And Drug Delivery Purposes, Aisha Hamidu, William G. Pitt, Ghaleb A. Husseini

Faculty Publications

Cancer is one of the leading causes of death worldwide. Because each person’s cancer may be unique, diagnosing and treating cancer is challenging. Advances in nanomedicine have made it possible to detect tumors and quickly investigate tumor cells at a cellular level in contrast to prior diagnostic techniques. Quantum dots (QDs) are functional nanoparticles reported to be useful for diagnosis. QDs are semiconducting tiny nanocrystals, 2–10 nm in diameter, with exceptional and useful optoelectronic properties that can be tailored to sensitively report on their environment. This review highlights these exceptional semiconducting QDs and their properties and synthesis methods when used …

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Combining Expert Opinions To Assess Risk Of Change In Earth Systems: Permafrost Collapse, Global Wildfire, And Water Security, Sayedeh Sara Sayedi Sep 2023

Combining Expert Opinions To Assess Risk Of Change In Earth Systems: Permafrost Collapse, Global Wildfire, And Water Security, Sayedeh Sara Sayedi

Theses and Dissertations

In a world of uncertainty and change, leaders should base their decisions on best available scientific evidence. However, history has shown that science is often inadequately incorporated into the decision-making process. This dissertation investigates three environmental issues to identify the challenges of considering Earth system dynamics in policymaking and management. I also propose solutions for improving the two-way exchange of knowledge and values between researchers and policymakers. In chapter one, I investigate subsea permafrost carbon sensitivity to climate change using an expert assessment. The analysis revealed that subsea permafrost contains significant carbon stocks and is already contributing to climate change …

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Oxytocin And Attachment Development, Sage Delamare Sep 2023

Oxytocin And Attachment Development, Sage Delamare

Family Perspectives

No abstract provided.

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Reproductively Viable Population Of American Black Bears (Ursus Americanus) In Lowland Chihuahuan Desert Habitat Of Trans-Pecos Texas, Franklin D. Yancey Ii, Stephen Kasper Sep 2023

Reproductively Viable Population Of American Black Bears (Ursus Americanus) In Lowland Chihuahuan Desert Habitat Of Trans-Pecos Texas, Franklin D. Yancey Ii, Stephen Kasper

Western North American Naturalist

During a 6.5-year camera-trap study in Big Bend Ranch State Park (situated in the Trans-Pecos region of West Texas), we documented a persistent breeding population of American black bears (Ursus americanus) in the Solitario region of the park. The habitat in the Solitario, which is an isolated, eroded remnant of volcanic activity, is low-elevation Chihuahuan Desert scrub but includes significant and complex localized topography and prolonged water sources in the form of tinajas. From January 2016 to May 2022, camera traps captured 367,301 photographs. Of these, 868 contained one or more black bears, resulting in 1010 black bear …

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Mass Shootings In The United States, Sydney Livingston Sep 2023

Mass Shootings In The United States, Sydney Livingston

Ballard Brief

High rates of mass shootings are becoming a uniquely American problem; the US makes up 73% of the world’s mass shootings, yet makes up only 4.25% of the world’s population. School shootings, in particular, have increased dramatically in the US since the Columbine High School shooting in 1999, an event many perpetrators have since drawn upon as inspiration. There is a strong divide of opinions in the nation regarding how firearm deaths should be reduced, which has complicated and slowed progress in identifying effective solutions. Each mass shooting causes additional shootings to occur, and each one takes a toll on …

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First Documentation Of Least Chub In The Snake River Drainage In Idaho, Eric J. Billman, Dallin Stokes, Isaac Calderwood, Cody Diehl Aug 2023

First Documentation Of Least Chub In The Snake River Drainage In Idaho, Eric J. Billman, Dallin Stokes, Isaac Calderwood, Cody Diehl

Western North American Naturalist

The Least Chub (Iotichthys phlegethontis) is a small minnow endemic to the Bonneville Basin in Utah, where the current distribution of extant populations is limited to a few small spring complexes. We report on the first documentation of Least Chub in the upper Snake River drainage in Idaho. In June 2021, October 2021, and June 2022, we surveyed for small-bodied fishes in off-channel habitat of lower Henrys Fork in Cartier Slough Wildlife Management Area west of Rexburg, Idaho. Small-bodied fishes were sampled at 17 sites in off-channel habitat; 5 baited minnow traps (galvanized steel) were set for approximately …

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Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras Aug 2023

Utilizing Low-Cost Sensors To Monitor Indoor Air Quality In Mongolian Gers, Callum Flowerday, Jaron C. Hansen, Phil Lundrigan, Christopher Kitras

Faculty Publications

Air quality has important climate and health effects. There is a need, therefore, to monitor air quality both indoors and outdoors. Methods of measuring air quality should be cost-effective if they are to be used widely, and one such method is low-cost sensors (LCS). This study reports on the use of LCSs in Ulaanbataar, Mongolia to measure PM2.5 concentrations inside yurts or “gers”. Some of these gers were part of a non-government agency (NGO) initiative to improve insulating properties of these housing structures. The goal of the NGO was to decrease particulate emissions inside the gers; a secondary result …

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A Feminist Icon Or A Homicidal Coward: Medea’S Revenge On Patriarchy, Beyza Ertugrul Aug 2023

A Feminist Icon Or A Homicidal Coward: Medea’S Revenge On Patriarchy, Beyza Ertugrul

Criterion: A Journal of Literary Criticism

Medea, the alleged epitome of sophistication, does not deserve her title of the flawless feminist icon as she is praised to be. For context, Euripides’ Medea, first performed in 431 BC, portrays a young sorceress whose abusive husband abandons her for another woman and who takes revenge by murdering her own children to spite him. Throughout the tragedy, Medea speaks out on gender inequality, and by definition, such uncommon and advanced statements can be described by the modern term of feminism as the “belief in and advocacy of the political, economic, and social equality of the sexes” (Merriam-Webster). Especially …

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Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) Coupled With An Interferometer For On-Band And Off-Band Detection Of Glyoxal, Callum Flowerday, Jaron Hansen, Ryan Thalman Aug 2023

Broadband Cavity-Enhanced Absorption Spectroscopy (Bbceas) Coupled With An Interferometer For On-Band And Off-Band Detection Of Glyoxal, Callum Flowerday, Jaron Hansen, Ryan Thalman

ScholarsArchive Data

These data are the raw data from the BBCEAS. The "data_" files are the PMT data and the "DualDetection_08_02_2023" files are the spectrograph data. The PMT data are found in column 7 of the sheet. Column 1 is the time stamp.

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Bacterial Extraction And Concentration From Blood Through Filtration Processes, Ryan L. Wood, Rebecca Prymak, Evelyn Welling, Alayna Bedwell, Jordan T. Wood, Damian E. Teasley, Magdalena Crofts, Hope Callister Anderson, Clifton M. Anderson, W Cameron Beard, Jacob Stepan, Alexandra Carter, William G. Pitt Aug 2023

Bacterial Extraction And Concentration From Blood Through Filtration Processes, Ryan L. Wood, Rebecca Prymak, Evelyn Welling, Alayna Bedwell, Jordan T. Wood, Damian E. Teasley, Magdalena Crofts, Hope Callister Anderson, Clifton M. Anderson, W Cameron Beard, Jacob Stepan, Alexandra Carter, William G. Pitt

Faculty Publications

Blood stream infections (BSIs) are challenging to rapidly and precisely diagnose. Current clinical diagnostic methods for BSI identification require culturing the blood sample for many hours prior to identifying the bacteria and possible antibiotic resistance. Removing the culturing step from the bacterial identification process of a BSI provides a significant reduction in the processing time, but shifts the rate-limiting step from the growth time to the concentration procedure, since CFU levels in clinical blood samples can be as low as 10 CFU/mL in blood. This study developed a novel whole blood filtration method to concentrate bacteria from a BSI without …

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Transferrin-Targeted Liposomes In Glioblastoma Therapy: A Review, Paul Kawak, Nour M Al Sawaftah, William G. Pitt, Ghaleb A. Husseini Aug 2023

Transferrin-Targeted Liposomes In Glioblastoma Therapy: A Review, Paul Kawak, Nour M Al Sawaftah, William G. Pitt, Ghaleb A. Husseini

Faculty Publications

Glioblastoma (GBM) is a highly aggressive brain tumor, and its treatment is further complicated by the high selectivity of the blood–brain barrier (BBB). The scientific community is urgently seeking innovative and effective therapeutic solutions. Liposomes are a promising new tool that has shown potential in addressing the limitations of chemotherapy, such as poor bioavailability and toxicity to healthy cells. However, passive targeting strategies based solely on the physicochemical properties of liposomes have proven ineffective due to a lack of tissue specificity. Accordingly, the upregulation of transferrin receptors (TfRs) in brain tissue has led to the development of TfR-targeted anticancer therapeutics. …

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Gene Dive: Assessing The Diversity Of Perchlorate Reducing Genes In Mars Analog Environments, Colin Michael Robinson Aug 2023

Gene Dive: Assessing The Diversity Of Perchlorate Reducing Genes In Mars Analog Environments, Colin Michael Robinson

Theses and Dissertations

Biotic perchlorate reduction, a metabolic process that potentially occurs on Mars, has long been the subject of speculation in astrobiology. To determine whether it could be a viable metabolic strategy on the Red Planet, we sought to determine whether biotic perchlorate reduction could evolve and persist in Mars-analog environments on Earth. In this study, we introduce Gene Dive, a novel computational methodology that leverages profile hidden Markov models, sequence alignment, phylogenetic tree construction, and Faith's phylogenetic diversity to probe the prevalence and diversity of perchlorate reducing genes in metagenomes. To determine whether biotic perchlorate reduction persists in a wide range …

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"The Trees Act Not As Individuals"--Learning To See The Whole Picture In Biology Education And Remote Sensing Research, Rebeka A.F. Greenall Aug 2023

"The Trees Act Not As Individuals"--Learning To See The Whole Picture In Biology Education And Remote Sensing Research, Rebeka A.F. Greenall

Theses and Dissertations

To increase equity and inclusion for underserved and excluded Indigenous students, we must make efforts to mitigate the unique barriers they face. As their knowledge systems have been historically excluded and erased in Western science, we begin by reviewing the literature on the inclusion of Traditional Ecological Knowledge (TEK) in biology education and describe best practices. Next, to better understand how Native Hawaiian and other Pacific Islander (NHPI) students integrate into the scientific community, we used Social Influence Theory as a framework to measure NHPI student science identity, self-efficacy, alignment with science values, and belonging. We also investigated how students …

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Phosphorus Sorption And Kinetics Across The Sediment-Water Interface Of Utah Lake, A Shallow Eutrophic Lake, Forrest Fielding Stretch Jarvis Jarvis Aug 2023

Phosphorus Sorption And Kinetics Across The Sediment-Water Interface Of Utah Lake, A Shallow Eutrophic Lake, Forrest Fielding Stretch Jarvis Jarvis

Theses and Dissertations

Internal sediment phosphorus (P) cycling may regulate harmful algal blooms (HABs) in shallow eutrophic lakes. Utah Lake frequently experiences HABs despite its high alkalinity and P-rich sediment. Phosphorus cycling between the lakebed and the water column is dependent upon stable P-sorption with organic matter (OM) and mineral species, which can vary with substrate availability, P-concentrations, temperature, redox, pH, and microbial activity. A full biogeochemical analysis of the water and sediment across seven sites shows Utah Lake to be spatially well-mixed in terms of composition and sorption, with few exceptions. Sediment P-concentrations (avg. 677 mg-P kg-1) primarily correlate with redox-sensitive iron …

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Food Web Of Icy Strait, Alaska: Comparison Of Position, Size, And Overlap Of Trophic Niche Among Fish Species, Andrew D. Suchomel Aug 2023

Food Web Of Icy Strait, Alaska: Comparison Of Position, Size, And Overlap Of Trophic Niche Among Fish Species, Andrew D. Suchomel

Theses and Dissertations

The Icy Strait of southeast Alaska, USA is an ideal system to study how ecological diversity is maintained. This area has historical ecological significance and supports diverse assemblages of fish species that are easily sampled. We used stable isotope analysis using δ13C and δ15N stable isotope ratios. Using these isotope ratios, we quantified trophic niche position, size, and overlap and compared how those trophic niche metrics varied using ecological and evolutionary perspectives. For ecological variation, mean total length, and δ13C trophic niche position has positive relationships with trophic niche size while total percent trophic niche overlap had a strong negative …

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Designed For Better Control: Using Kinematic And Dynamic Metrics To Optimize Robot Manipulator Design, John R. Morrell Aug 2023

Designed For Better Control: Using Kinematic And Dynamic Metrics To Optimize Robot Manipulator Design, John R. Morrell

Theses and Dissertations

In the field of control theory, optimal performance is generally defined as the best possible controlled performance given a static, unchangeable plant system. However, principled design of the underlying system can make designing effective controllers easier and dramatically improve the final control performance beyond what any finely tuned controller could achieve alone. This work develops performance metrics for serial robot arms which help guide the design and optimization of the structure of the arm to achieve greater final performance. First, a kinematic (motion-based) metric called the Actuator Independence Metric (AIM) measures the uniqueness of the movement capabilities of the different …

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End Matter, Vol. 83 No. 2 Aug 2023

End Matter, Vol. 83 No. 2

Western North American Naturalist

No abstract provided.

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