Physical Sciences and Mathematics Commons^™

Power In Pairs: Assessing The Statistical Value Of Paired Samples In Tests For Differential Expression, John R. Stevens, Jennifer S. Herrick, Roger K. Wolff, Martha L. Slattery

Mathematics and Statistics Faculty Publications

Background: When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study.

Results: We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of …

Magmatic Response To Subduction Initiation: Part 1. Fore-Arc Basalts Of The Izu-Bonin Arc From Iodp Expedition 352, John W. Shervais, Mark Reagan, Emily A. Haugen, Renat R. Almeev, Julian A. Pearce, Julie Prytulak, Jeffrey G. Ryan, Scott A. Whattam, Marguerite Godard, Timothy Chapman, Hongyan Li, Walter Kurz, Wendy R. Nelson, Daniel Heaton, Maria Kirchenbaur, Kenji Shimizu, Tetsuya Sakuyama, Yibing Li, Scott K. Vetter

Geosciences Faculty Publications

The Izu-Bonin-Mariana (IBM) fore arc preserves igneous rock assemblages that formed during subduction initiation circa 52 Ma. International Ocean Discovery Program (IODP) Expedition 352 cored four sites in the fore arc near the Ogasawara Plateau in order to document the magmatic response to subduction initiation and the physical, petrologic, and chemical stratigraphy of a nascent subduction zone. Two of these sites (U1440 and U1441) are underlain by fore-arc basalt (FAB). FABs have mid-ocean ridge basalt (MORB)-like compositions, however, FAB are consistently lower in the high-field strength elements (TiO2, P2O5, Zr) and Ni compared to MORB, with Na2O at the low …

Sampling Bias Overestimates Climate Change Impacts On Forest Growth In The Southwestern United States, Stefan Klesse, R. Justin Derose, Christopher H. Guiterman, Ann M. Lynch, Christopher D. O’Connor, John D. Shaw, Margaret E.K. Evans

Wildland Resources Faculty Publications

Climate−tree growth relationships recorded in annual growth rings have recently been the basis for projecting climate change impacts on forests. However, most trees and sample sites represented in the International Tree-Ring Data Bank (ITRDB) were chosen to maximize climate signal and are characterized by marginal growing conditions not representative of the larger forest ecosystem. We evaluate the magnitude of this potential bias using a spatially unbiased tree-ring network collected by the USFS Forest Inventory and Analysis (FIA) program. We show that U.S. Southwest ITRDB samples overestimate regional forest climate sensitivity by 41–59%, because ITRDB trees were sampled at warmer and …

Investigation Of An Unusual Thin Layer Descending Through The Upper Stratosphere, Houston D. Bentley

Physics Capstone Projects

Lidar observations on the night of 19-20 February 2004 at Logan, Utah (41.74 N, 111.81 W) revealed a strange thin layer which descended from roughly 55 km to 30 km over seven hours. Approximations are made for the dimensions and descent rate of the layer. Although the particle radius and density are unknown, a range can be determined from the descent rate and reference to the sizes of known particles. Several possible sources for the layer are explored, concluding that an object entering the Earth’s atmosphere was the most probable cause.

Carbene Triel Bonds Between Trr3 (Tr=B, Al) And N-Heterocyclic Carbenes, Zongqing Chi, Wenbo Dong, Qingzhong Li, Xin Yang, Steve Scheiner, Shufeng Liu

Chemistry and Biochemistry Faculty Publications

The carbene triel bond is predicted and characterized by theoretical calculations. The C lone pair of N‐heterocyclic carbenes (NHCs) is allowed to interact with the central triel atom of TrR₃ (Tr = B and Al; R = H, F, Cl, and Br). The ensuing bond is very strong, with an interaction energy of nearly 90 kcal/mol. Replacement of the C lone pair by that of either N or Si weakens the binding. The bond is strengthened by electron‐withdrawing substituents on the triel atom, and the reverse occurs with substitution on the NHC. However, these effects do not strictly follow …

The Ages2 (Awards For Geochronology Student Research 2) Program: Supporting Community Geochronology Needs And Interdisciplinary Science, Rebecca M. Flowers, J. Ramón Arrowsmith, Vicki Mcconnell, James R. Metcalf, Tammy M. Rittenour, Blair Schoene

Geosciences Faculty Publications

Geochronology is essential in the geosciences. It is used to resolve the durations and rates of earth processes, as well as test causative relationships among events. Such data are increasingly required to conduct cutting-edge, transformative, earth-science research. The growing need for geochronology is accompanied by strong demand to enhance the ability of labs to meet this pressure and to increase community awareness of how these data are produced and interpreted. For example, a 2015 National Science Foundation (NSF) report on opportunities and challenges for U.S. geochronology research noted: "While there has never been a time when users have had greater …

Logarithmic Hennings Invariants For Restricted Quantum Sl (2), Anna Beliakova, Christian Blanchet, Alexandra Tebbs

Mathematics and Statistics Faculty Publications

We construct a Hennings-type logarithmic invariant for restricted quantum sl (2) at a 2p^th root of unity. This quantum group U is not quasitriangular and hence not ribbon, but factorizable. The invariant is defined for a pair: a 3–manifold M and a colored link L inside M. The link L is split into two parts colored by central elements and by trace classes, or elements in the 0^th Hochschild homology of U, respectively. The two main ingredients of our construction are the universal invariant of a string link with values in tensor powers of U, and the modified …

Parental Habituation To Human Disturbance Over Time Reduces Fear Of Humans In Coyote Offspring, Christopher J. Schell, Julie K. Young, Elizabeth V. Lonsdorf, Rachel M. Santymire, Jill M. Mateo

Wildland Resources Faculty Publications

A fundamental tenet of maternal effects assumes that maternal variance over time should have discordant consequences for offspring traits across litters. Yet, seldom are parents observed across multiple reproductive bouts, with few studies consider‐ ing anthropogenic disturbances as an ecological driver of maternal effects. We ob‐ served captive coyote (Canis latrans) pairs over two successive litters to determine whether among‐litter differences in behavior (i.e., risk‐taking) and hormones (i.e., cortisol and testosterone) corresponded with parental plasticity in habituation. Thus, we explicitly test the hypothesis that accumulating experiences of anthropogenic disturbance reduces parental fear across reproductive bouts, which should have disparate phenotypic …

Chemical Analysis Of Aerosol Particle Surfaces, Hillary Woolf

Fall Student Research Symposium 2018

Aerosol particles are thought to impact climate properties. The ability to probe aerosols to understand their chemical properties has been difficult due to a lack of appropriate analytical techniques. Here we present interface-specific SHS techniques to allow for in situ analysis of aerosol particles. Transportation of aerosols from their collection site to the laboratory disturbs their chemical and physical properties thus making it difficult to take accurate measurements of aerosol particles. We show that using a CCD detector is a more effective option for producing more sensitive results and can greatly reduce sampling time and could possibly detect measurements from …

Assessment Of The Effects Of Climate Change On Evapotranspiration With An Improved Elasticity Method In A Nonhumid Area, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Climatic elasticity is a crucial metric to assess the hydrological influence of climate change. Based on the Budyko equation, this study performed an analytical derivation of the climatic elasticity of evapotranspiration (ET). With this derived elasticity, it is possible to quantitatively separate the impacts of precipitation, air temperature, net radiation, relative humidity, and wind speed on ET in a watershed. This method was applied in the Wuding River Watershed (WRW), located in the center of the Yellow River Watershed of China. The estimated rate of change in ET caused by climatic variables is −10.69 mm/decade, which is close to the …

Quantifying The Impact Of Climate Change And Human Activities On Streamflow In A Semi-Arid Watershed With The Budyko Equation Incorporating Dynamic Vegetation Information, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Understanding hydrological responses to climate change and land use and land cover change (LULCC) is important for water resource planning and management, especially for water-limited areas. The annual streamflow of the Wuding River Watershed (WRW), the largest sediment source of the Yellow River in China, has decreased significantly over the past 50 years at a rate of 5.2 mm/decade. Using the Budyko equation, this study investigated this decrease with the contributions from climate change and LULCC caused by human activities, which have intensified since 1999 due to China’s Grain for Green Project (GFGP). The Budyko parameter that represents watershed characteristics …

Calculating The Cohomology Of A Lie Algebra Using Maple And The Serre Hochschild Spectral Sequence, Jacob Kullberg

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Lie algebra cohomology is an important tool in many branches of mathematics. It is used in the Topology of homogeneous spaces, Deformation theory, and Extension theory. There exists extensive theory for calculating the cohomology of semi simple Lie algebras, but more tools are needed for calculating the cohomology of general Lie algebras. To calculate the cohomology of general Lie algebras, I used the symbolic software program called Maple. I wrote software to calculate the cohomology in several different ways. I wrote several programs to calculate the cohomology directly. This proved to be computationally expensive as the number of differential forms …

Rfviz: An Interactive Visualization Package For Random Forests In R, Christopher Beckett

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

Random forests are very popular tools for predictive analysis and data science. They work for both classification (where there is a categorical response variable) and regression (where the response is continuous). Random forests provide proximities, and both local and global measures of variable importance. However, these quantities require special tools to be effectively used to interpret the forest. Rfviz is a sophisticated interactive visualization package and toolkit in R, specially designed for interpreting the results of a random forest in a user-friendly way. Rfviz uses a recently developed R package (loon) from the Comprehensive R Archive Network (CRAN) to create …

Improving Accuracy Of The Edgebox Approach, Kamna Yadav

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Object region detection plays a vital role in many domains ranging from self-driving cars to lane detection, which heavily involves the task of object detection. Improving the performance of object region detection approaches is of great importance and therefore is an active ongoing research in Computer Vision. Traditional sliding window paradigm has been widely used to identify hundreds of thousands of windows (covering different scales, angles, and aspect ratios for objects) before the classification step. However, it is not only computationally expensive but also produces relatively low accuracy in terms of the classifier output by providing many negative samples. Object …

The Advanced Mesospheric Temperature Mapper: Remote Sensing Of The Nighttime Oh Layer During The Deepwave Campaign, Pattilyn Mclaughlin

All Graduate Plan B and other Reports, Spring 1920 to Spring 2023

The Advanced Mesospheric Temperature Mapper [AMTM] is a remote sensing instrument developed at Utah State University to map temperature structures in the hydroxyl airglow emission at ~87 km. These maps can then be used to quantify wave field characteristics and to observe general climatology trends. Two recent campaigns that it has been involved with are the DEEPWAVE campaign in Lauder, New Zealand and the Super Soaker campaign in Fairbanks, Alaska.

The Deep Propagating Gravity Wave Experiment, “DEEPWAVE” was an international measurement and modeling program intended to characterize the generation and propagation of a broad range of atmospheric gravity waves with …

New Ca-Id-Tims Detrital Zircon Constraints On Middle Neoproterozoic Sedimentary Successions, Southwestern United States, Abigail R. Bullard

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Three related sedimentary successions located in Arizona, Utah, and California were deposited in basins on proto-North America during the early rifting of Rodinia (~780 Mya). Previous detrital zircon U-Pb maximum ages for the units are inexact, making it difficult to piece together what happened at this point in Earth history.

We report better maximum age constraints on these units obtained by subjecting detrital zircons to high-precision CA-ID-TIMS analysis, which provide more exact ²⁰⁶Pb/²³⁸U ages. These new data significantly improve the precision for the base of the ChUMP units, with an average age of 775.63 ± 0.27 Ma …

Climate Change Perceptions And Adaptation Among Small-Scale Farmers In Uganda: A Community-Based Participatory Approach, Thomas Derr

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Climate change in the East African country of Uganda is causing severe variations in the once predictable seasonal weather patterns that farmers had come to depend on. This, in combination with social and economic challenges, has significantly increased the vulnerability of farmers who make up the majority of Uganda’s population. Previous knowledge and observations suggest that Ugandan farmers may be reluctant or slow to change their practices in response to the changing climate. Strategies are therefore needed to identify challenges and sustainable solutions. This research used qualitative data collection methods known as participatory rural appraisal (PRA) and participatory action research …

Historical Channel Change Caused By A Century Of Flow Alteration On Sixth Water Creek And Diamond Fork River, Ut, Jabari C. Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Changes in the amount of water and sediment that enter a river can change its shape and size. The way that rivers change is affected by a variety of factors, including the size of the sediment in the river, and past changes to the river. The Diamond Fork River in central Utah has been altered by water delivered from the Colorado River system for over a century. Beginning in 1915, water used for irrigation was delivered through a tributary, Sixth Water Creek, with daily summer flows that were much larger than natural flows. This caused drastic change to the rivers, …

Sensitivity Of The Opal Instrument For Gravity Wave Detection, Kenneth I. Zia

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Knowing what goes on in the upper atmosphere (∼80-140 km) is very important to the space science community. There are several competing forces that influence the temperature and densities of neutral molecules in that region. OPAL (Optical Profiling of the Atmospheric Limb) is funded by the National Science Foundation (NSF) to measure the temperature there using light from oxygen molecules (∼760 nm). To accomplish this,OPAL is built into a CubeSat (a satellite the size of a loaf of bread) to be launched from the International Space Station (ISS) at an altitude of about 400 km. This vantage point is needed …

Sheaf Theory As A Foundation For Heterogeneous Data Fusion, Seyed M-H Mansourbeigi

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

A major impediment to scientific progress in many fields is the inability to make sense of the huge amounts of data that have been collected via experiment or computer simulation. This dissertation provides tools to visualize, represent, and analyze the collection of sensors and data all at once in a single combinatorial geometric object. Encoding and translating heterogeneous data into common language are modeled by supporting objects. In this methodology, the behavior of the system based on the detection of noise in the system, possible failure in data exchange and recognition of the redundant or complimentary sensors are studied via …

The Development Of Hydrodynamic And Kinetic Models For The Plasmasphere Refilling Problem Following A Geomagnetic Storm, Kausik Chatterjee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The objective of this dissertation is the development of computer simulation-based models for the modeling of upper ionosphere, starting from the first principles. The models were validated by exact analytical benchmarks and are seen to be consistent with experimentally obtained results. This area of research has significant implications in the area of global communication. In addition, these models would lead to a better understanding of the physical processes taking place in the upper ionosphere.

The Influence Of Mechanical Stratigraphy On Thrust-Ramp Nucleation And Propagation Of Thrust Faults, Sarah S. Wigginton

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Our current understanding of thrust fault kinematics predicts that thrust faults nucleate on low angle, weak surfaces before they propagate upward and forms a higher angle ramp. While this classic kinematic and geometric model serves well in some settings, it does not fully consider the observations of footwall deformation beneath some thrust faults. We examine an alternative end-member model of thrust fault formation called “ramp-first” fault formation. This model hypothesizes that in mechanically layered rocks, thrust ramps nucleate in the structurally strong units, and that faults can propagate both upward and downward into weaker units forming folds at both fault …

Mesospheric Gravity Wave Climatology And Variances Over The Andes Mountains, Jonathan Rich Pugmire

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Look up! Travelling over your head in the air are waves. They are present all the time in the atmosphere all over the Earth. Now imagine throwing a small rock in a pond and watching the ripples spread out around it. The same thing happens in the atmosphere except the rock is a thunderstorm, the wind blowing over a mountain, or another disturbance. As the wave (known as a gravity wave) travels upwards the thinning air allows the wave to grow larger and larger. Eventually the gravity wave gets too large – and like waves on the beach – it …

Energy And Risk: Discourse, Framing, And Content, Temis Gardner Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This research examined how people communicate and create knowledge about energy-related risks. Analysis of the discourse, frames, and content surrounding unconventional energy policy and development in the Western United States was conducted using three case studies. The results contribute to an understanding of energy-related risk perceptions in social and historical contexts.

Discourses contained in newspapers and public comments to the Bureau of Land Management presented arguments on the basis of risks to the environment; climate; human health and safety; jobs and economic prosperity; property rights; and local governments. Governments were seen as risks when they were perceived to allow misuse …

Statistical Methods To Account For Gene-Level Covariates In Normalization Of High-Dimensional Read-Count Data, Lauren Holt Lenz

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The goal of genetic-based cancer research is often to identify which genes behave differently in cancerous and healthy tissue. This difference in behavior, referred to as differential expression, may lead researchers to more targeted preventative care and treatment. One way to measure the expression of genes is though a process called RNA-Seq, that takes physical tissue samples and maps gene products and fragments in the sample back to the gene that created it, resulting in a large read-count matrix with genes in the rows and a column for each sample. The read-counts for tumor and normal samples are then compared …

Carbon Monoxide On Demand: Light-Induced Co Release Of Flavonols, Stacey N. Anderson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Carbon monoxide (CO) is an extremely useful molecule with applications in industrial manufacturing, synthetic procedures as a C1 building block, and as a potential pharmaceutical to produce anti-inflammatory effects and vasodilation. However, the toxicity associated with CO has prevented its full utilization. In order to safely handle CO, compounds and molecules have been developed that act as storage materials for the gas. Ideal storage platforms only release CO upon stimulation via a trigger. Light activation is the most desirable trigger as it can be regulated in terms of the intensity and the wavelength of light used. The majority of light-induced …

Identifying Criticality In Market Sentiment: A Data Mining Approach, Vaibhav Sahu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The aim of this thesis is to study and identify time periods of high activity in commodity and stock market sentiment based on a data mining approach. The method is to develop tools to extract relevant information from web searches and Twitter feeds based on the tally of certain keywords and their combinations at regular intervals. Periods of high activity are identified by a measure of complexity developed for analysis of living systems. Experiments were conducted to see if the measure of activity could be applied as a predictor of changes in stock market and commodity prices.

“I Really Don’T Look For Certifications, It All Has To Do With Personal Relationships”: The Construction Of A Meat Philosophy And Innovation Adoption By Culinary Professionals In The Rocky Mountain Region, Kailie B. Leggett

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Demand for new methods of beef production is rising due to concern over potential impacts on human health, animal welfare, and the environment. Researchers at Utah State University have developed a method of beef production from cattle finished on tannin-containing legume forages in the Rocky Mountain Region in order to address those concerns. To ensure success of this product, the demand and marketability needed to be assessed. Food values addressed through new production standards and certifications are communicated through labeling by culinary professionals in the kitchen and behind service counters. This research study utilized qualitative methods to understand how culinary …

Comparing Performance Of Gene Set Test Methods Using Biologically Relevant Simulated Data, Richard M. Lambert

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Today we know that there are many genetically driven diseases and health conditions. These problems often manifest only when a set of genes are either active or inactive. Recent technology allows us to measure the activity level of genes in cells, which we call gene expression. It is of great interest to society to be able to statistically compare the gene expression of a large number of genes between two or more groups. For example, we may want to compare the gene expression of a group of cancer patients with a group of non-cancer patients to better understand the genetic …

Inorganic Electrocatalysts For Innovative Water Splitting And Organic Upgrading, Nan Jiang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The booming worldwide demand for energy and the increasing concerns about global warming due to fossil fuel consumption have urged the development of techniques for storing and converting renewable and clean energy resources. Electrocatlytic or photoelectrocatalytic water splitting to generate green energy carrier H₂ with sustainable energy input, like solar, has been regarded as an attractive strategy for carbon-neutral energy needs. However, the sluggish kinetics for both half reactions (HER and OER), high overpotentials and thermodynamic requirements, and H₂ and O₂ gas crossover have been regarded as the major challenges, which limit its widespread application.

On account …