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 …

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 …

Impact Of Bubble Baths On Stainless Steel Sphere Water Entry, Wesley Robinson

Physics Capstone Projects

Soap Bubbles on the water surface would seem to be an intuitive means for splash suppression, but their presence appears to be a double edged sword. We present on the water entry of hydrophilic spheres where the liquid surface is augmented by the presence of a bubble layer, similar to a bubble bath. While the presence of a bubble layer can diminish splashing upon impact at low Weber numbers, it also induces cavity formation at speeds below the critical velocity. The formation of a cavity generally results in larger Worthington jets and thus, larger amounts of ejected liquid. Bubble layers …

Mathematica Program To Compute Klein Gordon Equation For Generic Black Holes, Brant Smith

Physics Capstone Projects

The goal of this project is to develop a program that will compute the Klein Gordon equation for generic Black Holes through the program Mathematica. This program will be available on Utah State websites for public usage. This project focuses on an understanding of General Relativity and more concretely on theoretical aspects of Black Holes. Developing the program begins with computing the Laplace equation in flat space to understand what it means to have empty space without a Black Hole. The Klein Gordon equation for a Schwarzschild Black Hole is then solved to show what happens once a static, non-rotating …

Ncer Assistance Agreement Annual Progress Report For Grant #83582401 - Assessment Of Stormwater Harvesting Via Manage Aquifer Recharge (Mar) To Develop New Water Supplies In The Arid West: The Salt Lake Valley Example, Ryan Dupont, Joan E. Mclean, Richard C. Peralta, Sarah E. Null, Douglas B. Jackson-Smith

Civil and Environmental Engineering Faculty Publications

The goals of the original proposed project remain the same, that is, to test the hypothesis that Managed Aquifer Recharge (MAR) for stormwater harvesting is a technically feasible, socially and environmentally acceptable, economically viable, and legally feasible option for developing new water supplies for arid Western urban ecosystems experiencing increasing population, and climate change pressures on existing water resources. The project is being carried out via three distinct but integrated components that include: 1) Monitoring of existing distributed MAR harvesting schemes involving a growing number of demonstration Green Infrastructure (GI) test sites; 2) Integrated stormwater/vadose zone/groundwater/ ecosystem services modeling; and …

Imagining Across Disciplines For A Sustainable Future, Emily James

Writing Center Analysis Papers

At present, the words sustainable and sustainability tend to be associated with environmental issues. Yet, the word sustain comes from the Old French sostenier meaning, “hold up, bear; suffer, endure” and Latin’s sustinere that adds, “hold upright; furnish with means of support; undergo.” Latin’s sustinere can further be broken down into the elements sub and tenere, the root of which, ten, means, “to stretch” (Harper). This paper reflects upon the ways in which the concept of sustainability affects my role as a writing tutor and composition instructor as I seek to help students stretch their abilities to develop ideas …

Can The Desiccation Of Great Salt Lake Be Stopped?, Wayne A. Wurtsbaugh, Craig Miller, Sarah E. Null, R. Justin Derose, Peter Wilcock

Watershed Sciences Faculty Publications

Great Salt Lake is a terminal lake, with its watershed in the Wasatch and Uinta Mountains of Utah, Wyoming and Idaho. Like all terminal lakes, the water inflows are balanced only by evaporative loss from its surface—when inflows decrease the lake shrinks until evaporation matches that inflow.

Crystallographic And Computational Characterization Of Methyl Tetrel Bonding In S-Adenosylmethionine-Dependent Methyltransferases, Raymond C. Trievel, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Tetrel bonds represent a category of non-bonding interaction wherein an electronegative atom donates a lone pair of electrons into the sigma antibonding orbital of an atom in the carbon group of the periodic table. Prior computational studies have implicated tetrel bonding in the stabilization of a preliminary state that precedes the transition state in S_N2 reactions, including methyl transfer. Notably, the angles between the tetrel bond donor and acceptor atoms coincide with the prerequisite geometry for the S_N2 reaction. Prompted by these findings, we surveyed crystal structures of methyltransferases in the Protein Data Bank and discovered …

Usu-Csu Na Lidar Data, Tao Yuan

Browse all Datasets

The naturally existing mesospheric Na layer, overlapping the upper mesosphere and lower thermosphere, provides an excellent tracer for lidar remote sensing. The Na Doppler lidar technique is designed to measure neutral temperature and wind profiles in the mesopause region (~ 80-110 km) by observing the thermal broadening and Doppler shift of the atomic Na fluorescence spectrum. Relocated from Colorado State University (CSU), the Na lidar at Utah State University (USU) has been operating since the summer of 2010, for roughly 1000 hours per year. Enabled by a pair of Faraday filters, it has a unique daytime observation capability to study …

Wild Bees Of Grand Staircase-Escalante National Monument: Richness, Abundance, And Spatio-Temporal Beta-Diversity, Olivia Messinger Carril, Terry Griswold, James Haefner, Joseph S. Wilson

All PIRU Publications

Interest in bees has grown dramatically in recent years in light of several studies that have reported widespread declines in bees and other pollinators. Investigating declines in wild bees can be difficult, however, due to the lack of faunal surveys that provide baseline data of bee richness and diversity. Protected lands such as national monuments and national parks can provide unique opportunities to learn about and monitor bee populations dynamics in a natural setting because the opportunity for large-scale changes to the landscape are reduced compared to unprotected lands. Here we report on a 4-year study of bees in Grand …

Developmental Parameters Of A Southern Mountain Pine Beetle (Coleoptera: Curculionidae) Population Reveal Potential Source Of Latitudinal Differences In Generation Time, Anne E. Mcmanis, James A. Powell, Barbara J. Bentz

Mathematics and Statistics Faculty Publications

Mountain pine beetle (Dendroctonus ponderosae, Hopkins) is a major disturbance agent in pine ecosystems of western North America. Adaptation to local climates has resulted in primarily univoltine generation time across a thermally diverse latitudinal gradient. We hypothesized that voltinism patterns have been shaped by selection for slower developmental rates in southern populations inhabiting warmer climates. To investigate traits responsible for latitudinal differences we measured lifestage-specific development of southern mountain pine beetle eggs, larvae and pupae across a range of temperatures. Developmental rate curves were fit using maximum posterior likelihood estimation with a Bayesian prior to improve fit stability. …

Rectifying Garbage-In Equals Garbage-Out Using A Secondary Electron Yield Materials Database, Phil Lundgreen, Jr Dennison

Presentations

No abstract provided.

Sediment Dynamics In The Bear River-Mud Lake-Bear Lake System, Patrick Belmont, Mitchell Donovan, Janice Brahney, Lindsay Capito, Zach Burgert

Watershed Sciences Faculty Publications

The overarching goal of this project was to compile and analyze a variety of existing datasets, and generate several new datasets, to advance our understanding of how the Bear River Mud Lake-Bear Lake system functions, how it has, or is expected to change, identify which components are degraded or vulnerable to degradation, and determine if/where critical data and/or knowledge gaps exist. We conducted a series of analyses to evaluate changes in hydrology and suspended sediment, collected sediment cores from nine locations in Mud Lake to evaluate how sedimentation rates, sediment sources and water quality have changed over time, and utilized …

Kinetic Characterization Of The Shigella Type Three Secretion System Atpase Spa47 Using Α-32p Atp, Heather B. Case, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

ATPases represent a diverse class of enzymes that utilize ATP hydrolysis to support critical biological functions such as driving ion pumps, providing mechanical work, unfolding/folding proteins, and supporting otherwise thermodynamically unfavorable chemical reactions. We have recently shown that the Shigella protein Spa47 is an ATPase that supports protein secretion through its specialized type three secretion apparatus (T3SA), supporting infection of human host cells. Characterizing ATPases, such as Spa47, requires a means to accurately determine enzyme activity (ATP hydrolysis) as a function of time, reaction conditions, and potential cofactors, regulators, inhibitors, etc. Here, we describe a detailed protocol for characterizing …

An Introduction To Quantile-Quantile Plots For The Experimental Physicist, Allen Andersen, Jr Dennison

Journal Articles

No abstract provided.

Interfacing Nickel Nitride And Nickel Boosts Both Electrocatalytic Hydrogen Evolution And Oxidation Reactions, Fuzhan Song, Wei Li, Jiaqi Yang, Guanqun Han, Peilin Liao, Yujie Sun

Chemistry and Biochemistry Faculty Publications

Electrocatalysts of the hydrogen evolution and oxidation reactions (HER and HOR) are of critical importance for the realization of future hydrogen economy. In order to make electrocatalysts economically competitive for large-scale applications, increasing attention has been devoted to developing noble metal-free HER and HOR electrocatalysts especially for alkaline electrolytes due to the promise of emerging hydroxide exchange membrane fuel cells. Herein, we report that interface engineering of Ni₃N and Ni results in a unique Ni₃N/Ni electrocatalyst which exhibits exceptional HER/HOR activities in aqueous electrolytes. A systematic electrochemical study was carried out to investigate the superior hydrogen …

Dependence Of Nmr Chemical Shifts Upon Ch Bond Lengths Of A Methyl Group Involved In A Tetrel Bond, Steve Scheiner

Chemistry and Biochemistry Faculty Publications

Four different Lewis acids that might participate in a tetrel bond with a nucleophile (SEt₂Me⁺, NMe₄⁺, SMe₂, NMe₃) are examined. The NMR chemical shifts of the methyl C and H atoms are calculated as the CH bond lengths are systematically stretched and contracted, in the absence of a base. The C shielding diminishes by roughly 2 ppm for a stretch of 0.01 Å, while that of H drops by only 0.3 ppm. The deshieldings caused purely by the bond length changes are far too small to account for the …

Entry Of A Sphere Into A Water-Surfactant Mixture And The Effect Of A Bubble Layer, Nathan B. Spiers, Mohammad M. Mansoor, Randy Craig Hurd, Saberul I. Sharker, W. G. Robinson, B. J. Williams, Tadd T. Truscott

Mechanical and Aerospace Engineering Faculty Publications

A rigid sphere entering a liquid bath does not always produce an entrained air cavity. Previous experimental work shows that cavity formation, or the lack thereof, is governed by fluid properties, wetting properties of the sphere, and impact velocity. In this study, wetting steel spheres are dropped into a water-surfactant mixture with and without passing through a bubble layer first. Surprisingly, in the case of a water-surfactant mixture without a bubble layer, the critical velocity for cavity formation becomes radius dependent. This occurs due to dynamic surface tension effects, with the local surface tension in the splash increasing during surface …

A Novel Shortwave Infrared Proximal Sensing Approach To Quantify The Water Stability Of Soil Aggregates, Azadeh Gholoubi, Hojat Emami, Scott B. Jones, Markus Tuller

Plants, Soils, and Climate Faculty Publications

Soil structure and aggregate stability (AS) are critical soil properties affecting water infiltration, root growth, and resistance to soil and wind erosion. Changes in AS may be early indicators of soil degradation, pointing to low organic matter (OM) content, reduced biological activity, or poor nutrient cycling. Hence, efficient and reliable AS measurement techniques are essential for detection, management, and remediation of degraded soil resources. Here we quantify soil AS by developing a novel proximal sensing technique based on shortwave infrared (SWIR) reflectance measurements. The novel approach is similar to the well-documented high energy moisture characteristic (HEMC) method, which yields a …

Fluted Films, Nathan B. Spiers, Mohammad M. Mansoor, Jesse Belden, Randy Craig Hurd, Zhao Pan, Tadd T. Truscott

Mechanical and Aerospace Engineering Faculty Publications

This paper is associated with a poster winner of a 2017 APS/DFD Milton van Dyke Award for work presented at the DFD Gallery of Fluid Motion. The original poster is available from the Gallery of Fluid Motion, https://doi.org/10.1103/APS.DFD.2017.GFM.P0030

Real-Time Video Processing Of Arcing Events To Determine Coincidence, Jr Dennison, Gregory Wilson, Jonh Mojica Decena, Brian Wood

Posters

No abstract provided.

Real-Time Video Processing Of Arcing Events To Determine Coincidence, Jr Dennison, Gregory Wilson, Jonh Mojica Decena, Brian Wood

Posters

A system has been developed and tested for real-time monitoring of environmentally-induced electrostatic discharge events to test spacecraft component and material survivability. Simultaneous detection by several parallel methods in coincidence, enhances event detection, minimizes false signals, and collects complementary information to determine arc location, intensity, and timing. This research focuses on four computer-interfaced video cameras which provide spatial and temporal detection of visual arcing from the surface of various elements. A real time processing solution was developed which can calculate integrated intensities, sensitively detect intensity threshold events, and store relevant video frames from these threshold events. Post processing of this …