Digital Commons Network^™

Identifying Risk Factors For Interstate Crashes Using Spatial Statistics, Kaitlin Gibson, Matthew Heaton

Journal of Undergraduate Research

The goal of systemic highway safety improvement is to identify road characteristics, called risk factors, associated with a higher prevalence of crashes, so that the roads can be modified to avoid these characteristics. However, the statistical analyses these improvement projects are based on generally use methods which are not appropriate for the data. Our project implements novel spatial statistical methodology which is appropriate and state-of-the-art to identify these risk factors.

An Algorithm For Multiple Regression Variable Selection For Biochemical Oxygen Demand, Zach White, Dr. William Christensen

Journal of Undergraduate Research

Biochemical Oxygen Demand (BOD) is used to measure of the amount of oxygen required by aerobic bacteria and other microorganisms to stabilize decomposable organic matter. It is run as a laboratory based biodegradation test and relies upon the presence of a thriving microbial community that may be naturally present in the sample or artificially introduced by addition of a seed, commonly a known volume of sewage effluent of known BOD. A standard BOD test is run in the dark at a temperature of 20 degrees Celsius for 5 days. This is defined as a five-day BOD (BOD5), which is the …

Utilizing The Power Of Graphical Processing For Dna Mapping: A Comparison Of Gnumap And Barracuda, Cole Lyman, Mark Clement

Journal of Undergraduate Research

Recent advances in genome sequencing technologies have resulted in a large increase in the amount of genetic data available. Large Genome Wide Association Studies (GWAS) have the potential to identify the causes of cancer, Alzheimer’s disease, heart failure and many other diseases if the large quantities of data that are becoming available can be analyzed effectively. Next-generation read mapping software, a crucial step in analyzing genetic data, is slow while trying to achieve high mapping accuracy. One approach to speeding up next-generation read mapping focuses on using Graphical Processing Units (GPUs). This project compared the effectiveness of two genome mappers, …

Sedentary Behavior Research Network (Sbrn) – Terminology Consensus Project Process And Outcome, Mark S. Tremblay, Salomé Aubert, Joel D. Barnes, Travis J. Saunders, Valerie Carson, Amy E. Latimer-Cheung, Sabastien F.M. Chastin, Teatske M. Altenburg, Mai J.M. Chinapaw, Neil E. Peterson

Faculty Publications

Background

The prominence of sedentary behavior research in health science has grown rapidly. With this growth there is increasing urgency for clear, common and accepted terminology and definitions. Such standardization is difficult to achieve, especially across multi-disciplinary researchers, practitioners, and industries. The Sedentary Behavior Research Network (SBRN) undertook a Terminology Consensus Project to address this need.

Method

First, a literature review was completed to identify key terms in sedentary behavior research. These key terms were then reviewed and modified by a Steering Committee formed by SBRN. Next, SBRN members were invited to contribute to this project and interested participants reviewed …

Trace Element Analysis Of Quartz Grains In The Wah Wah Springs Tuff And Granodiorite Intrusion, Joel Barker, Dr. Eric Christiansen

Journal of Undergraduate Research

The Wah Wah Springs tuff and cogenetic granodiorite were part of the creation of the Indian Peak-Caliente Caldera Complex, which lies on the Nevada-Utah border (Skidmore, 2013). The complex formed during the middle Cenozoic (36-18 Ma) during an episode of explosive silicic activity (Best et al., 2013). Rollback of the subducting lithosphere likely caused the silicic activity, evidenced by the migration of magmatism southward (Best et al., 2013). The dehydration of the subducting oceanic lithosphere caused mafic magmas high in water to rise and fractionate in continental crust before eruption (Skidmore, 2013). Over twenty-four different ignimbrites have been found in …

Seeing The World Through New Eyes: Implementing Map-Based Mobile Apps In Field Trips And Research, Mariah Chambers, Ron Harris

Journal of Undergraduate Research

Mobile apps are a resource that can aid in field trip instruction and enhance students’ learning. Because the specific location of the field trip is often an important element in overall understanding, map-based learning materials can be used to integrate information with the place, providing context for the concepts that will be learned on the field trip. The purpose of this project was twofold. One purpose was to provide professors with information and instructions for using map-based mobile apps to prepare students for, and provide resources during, field trips and study abroad experiences. A second purpose was to implement the …

Characterizing The Design Space Of Oscillatory Biological Networks, Leanne Lunsford, Denise Stephens, Eric Hintz

Journal of Undergraduate Research

Characterizing the relevant parameters of a design space in order to satisfy a specific behavior criterion is an important problem throughout all of science and engineering. In this project we proposed to apply model reduction to the case of biological oscillations involving Michaelis-Menten reactions. By removing irrelevant parameters from a fully connected network we were able to reduce a known problem in systems biology to a more general model. Furthermore, significant progress has been made in applying Manifold Boundary Approximation Method (MBAM) to oscillatory models in systems biology.

Multi-Fidelity Model Predictive Control Of Upstream Energy Production Processes, Ammon Nephi Eaton

Theses and Dissertations

Increasing worldwide demand for petroleum motivates greater efficiency, safety, and environmental responsibility in upstream oil and gas processes. The objective of this research is to improve these areas with advanced control methods. This work develops the integration of optimal control methods including model predictive control, moving horizon estimation, high fidelity simulators, and switched control techniques applied to subsea riser slugging and managed pressure drilling. A subsea riser slugging model predictive controller eliminates persistent offset and decreases settling time by 5% compared to a traditional PID controller. A sensitivity analysis shows the effect of riser base pressure sensor location on controller …

Active Control Of Cylindrical Shells Using The Weighted Sum Of Spatial Gradients (Wssg) Control Metric, Pegah Aslani

Theses and Dissertations

Cylindrical shells are common structures that are often used in industry, such as pipes, ducts, aircraft fuselages, rockets, submarine pressure hulls, electric motors and generators. In many applications it is desired to attenuate the sound radiated from the vibrating structure. There are both active and passive methods to achieve this purpose. However, at low frequencies passive methods are less effective and often an excessive amount of material is needed to achieve acceptable results. There have been a number of works regarding active control methods for this type of structure. In most cases a considerable number of error sensors and secondary …

Sedimentology And Taphonomy Of The Abydosaurus Mcintoshi Quarry, (Naturita Formation, Early Cretaceous, Latest Albian), Dinosaur National Monument, Utah, Aaron Daniel Holmes

Theses and Dissertations

The holotypic locality of the brachiosaurid titanosauriform sauropod, Abydosaurus mcintoshi, is quarry DNM-16, located in Dinosaur National Monument. The bones are preserved near the base of a heterolithic, trough cross stratified to planar bedded sandstone channel complex. The trough cross to planar bedded sandstones mark times of variable flow with times of high flow velocity based on bones whose upper surfaces were eroded before final burial. The abundance of mud with the dominant medium to fine sand, and poorly confined sandstone channels indicate the bones were transported and buried in medial to distal intermittent flows of a distributive fluvial …

Anthrax, Matrix Biology, And Angiogenesis: Capillary Morphogenesis Gene 2 Mediates Activity And Uptake Of Type Iv Collagen-Derived Anti-Angiogenic Peptides, Jordan Grant Finnell

Theses and Dissertations

Capillary Morphogenesis Gene 2 (CMG2) is a type I transmembrane, integrin-like receptor. It was originally identified as one of several genes upregulated during capillary formation. It was subsequently identified as one of two physiological anthrax toxin receptors, where CMG2 serves as a cell-surface receptor for anthrax toxin and mediates entry of the toxin into cells via clathrin-dependent endocytosis. Additionally, loss-of-function mutations in CMG2 cause the genetic disorder hyaline fibromatosis syndrome (HFS), where the core symptom is dysregulation of extracellular matrix homeostasis (ECM), including excessive accumulation of proteinaceous hyaline material; HFS clearly indicates that CMG2 plays an essential function in ECM …

An Analysis Of Enabling Techniques For Highly-Accessible Low-Cost Virtual Reality Hardware In The Collaborative Engineering Design Process, Joshua Q. Coburn

Theses and Dissertations

While there currently exists a great deal of research in the literature demonstrating various engineering applications for virtual reality (VR) and the benefits of these applications, VR adoption has been slow in part because of the high cost and resources required to setup and maintain the hardware for these applications. However, in the last 5 years, a new generation of VR hardware has emerged with cost and resource requirements which are a small fraction of previous hardware. This work begins with a survey of this newly available hardware summarizing recent advances for providing virtual input to all of the five …

Stability Of Planar Detonations In The Reactive Navier-Stokes Equations, Joshua W. Lytle

Theses and Dissertations

This dissertation focuses on the study of spectral stability in traveling waves, with a special interest in planar detonations in the multidimensional reactive Navier-Stokes equations. The chief tool is the Evans function, combined with STABLAB, a numerical library devoted to calculating the Evans function. Properly constructed, the Evans function is an analytic function in the right half-plane whose zeros correspond in multiplicity and location to the spectrum of the traveling wave. Thus the Evans function can be used to verify stability, or to locate precisely any unstable eigenvalues. We introduce a new method that uses numerical continuation to follow unstable …

Development Of A Performance-Based Procedure To Predict Liquefaction-Induced Free-Field Settlements For The Cone Penetration Test, Mikayla Son Hatch

Theses and Dissertations

Liquefaction-induced settlements can cause a large economic toll on a region, from severe infrastructural damage, after an earthquake occurs. The ability to predict, and design for, these settlements is crucial to prevent extensive damage. However, the inherent uncertainty involved in predicting seismic events and hazards makes calculating accurate settlement estimations difficult. Currently there are several seismic hazard analysis methods, however, the performance-based earthquake engineering (PBEE) method is becoming the most promising. The PBEE framework was presented by the Pacific Earthquake Engineering Research (PEER) Center. The PEER PBEE framework is a more comprehensive seismic analysis than any past seismic hazard analysis …

Student Participation In The Distribution Of Instructional Leadership, Janeel M. Juncker

Theses and Dissertations

This explorative study offers much needed perspective on students' role and development as instructional leaders (Halverson & Clifford, 2013) through answering the following questions: (a) How can students be involved in distributions of instructional leadership in a studio learning environment; (b) What is the value of their contribution; and (c) What patterns of distributed instructional leadership (DIL) facilitate student involvement? I chose an animation studio at a large western university for the setting, on account of its collective-leadership structure involving students. I randomly sampled a pre-recorded data set of participants' studio interactions and participant interviews to use for the study; …

Enzyme Encapsulation, Biosensing Endocrine Disrupting Chemicals, And Bio-Therapeutic Expression Platforms Using Cell-Free Protein Synthesis, Seung Ook Yang

Theses and Dissertations

Cell-free protein synthesis (CFPS) is a powerful protein expression platform where protein synthesis machinery is borrowed from living organisms. Target proteins are synthesized in a reaction tube together with cell extract, amino acids, energy source, and DNA. This reaction is versatile, and dynamic optimizations of the reaction conditions can be performed. The "œopen" nature of CFPS makes it a compelling candidate for many technologies and applications. This dissertation reports new and innovative applications of CFPS including 1) enzyme encapsulation in a virus-like particle, 2) detection of endocrine disrupting chemicals in the presence of blood and urine, and 3) expression of …

Quality Education In Idaho: A Case Study Of Academic Achievement In Three High-Poverty Rural Schools, Christine Brown

Theses and Dissertations

The focus of this research is bridging the achievement gap for students living in poverty through quality education. Such a study is important because the percentage of students affected by poverty is increasing and the persistent gap in achievement evidences that the right to quality education for students in poverty is not being met. This is mixed-methods study of three high-poverty elementary schools in Idaho. Both quantitative (achievement test scores) and qualitative data (interviews of seventeen teachers and principals) are compared and contrasted. The findings provide evidence that quality education for students in poverty requires relatable curriculum, teachers who are …

The Ogcleaner: Detecting False-Positive Sequence Homology, Masaki Stanley Fujimoto

Theses and Dissertations

Within bioinformatics, phylogenetics is the study of the evolutionary relationships between different species and organisms. The genetic revolution has caused an explosion in the amount of raw genomic information that is available to scientists for study. While there has been an explosion in available data, analysis methods have lagged behind. A key task in phylogenetics is identifying homology clusters. Current methods rely on using heuristics based on pairwise sequence comparison to identify homology clusters. We propose the Orthology Group Cleaner (the OGCleaner) as a method to evaluate cluster level verification of putative homology clusters in order to create higher quality …

A Survey Of Sparse Channel Estimation In Aeronautical Telemetry, Christopher James Hogstrom

Theses and Dissertations

Aeronautical telemetry suffers from multipath interference, which can be resolved through the use of equalizers at the receiver. The coefficients of data-aided equalizers are computed from a channel estimate. Most channels seen in aeronautical telemetry are sparse, meaning that most of the coefficients of the channel are zero or nearly zero. The maximum likelihood (ML) estimate does not always produce a sparse channel estimate. This thesis surveys a number of sparse estimation algorithms that produce a sparse channel estimate and compares the post-equalizer bit error rates (BER) using these sparse estimates with the post-equalizer BER using the ML estimate. I …

Flexible Micro-N-Line Probe And Apparatus To Characterize Electronic Conductivity Of Li-Ion Battery Electrode Films, Derek Van Clement

Theses and Dissertations

A key metric that affects Li-ion battery cell performance is the electronic conductivity of the electrode films. Previous research has found that the conductivity of electrodes is not homogeneous throughout the entirety of the deposited film area. To further characterize the non-homogeneity of the conductivity of electrode films, a micro-N-line probe and a micro-flex-line probe were developed to take micro-scale conductivity measurements of thin-film battery electrodes in a non-destructive manner. These devices have been validated by comparing test results to those of it's predecessor, the micro-four-line probe, on various commercial-quality Li-ion battery electrodes. Results show that there is significant variation …

Formation Of Rapakivi Feldspars In The Deer Isle Granite Complex, Coastal Maine: In Situ Lead Isotope And Trace Element Analysis, William Desmond Obrien

Theses and Dissertations

Rapakivi and alkali feldspar phenocrysts from the Deer Isle Granite Complex were investigated using in situ trace element and Pb isotope geochemistry to see if magma mixing or isothermal decompression was responsible for their formation. Pb isotope and trace element profiles, along with CL imagery of quartz phenocrysts, indicate compositional changes in the magma chamber occurred during rapakivi and alkali feldspar growth. Repeated episodes of magma mixing/replenishment by relatively isotopically primitive and LREE enriched magmas (along with hybridized variations with the host magma) created localized disequilibration. Alkali feldspar phenocrysts proximal to these zones of thermal perturbation were first resorbed and …

Using Multiview Annotation To Annotate Multiple Images Simultaneously, Timothy C. Price

Theses and Dissertations

In order for a system to learn a model for object recognition, it must have a lot of positive images to learn from. Because of this, datasets of similar objects are built to train the model. These object datasets used for learning models are best when large, diverse and have annotations. But the process of obtaining the images and creating the annotations often times take a long time, and are costly. We use a method that obtains many images of the same objects in different angles very quickly and then reconstructs those images into a 3D model. We then use …

The Racial Politics Of Secularity: Rethinking African-American Religiosity Through New Paradigms In Secularization Theory, Diana Christine Brown

Theses and Dissertations

Revisions to secularization theory over the past two decades call for reconceptualization of the relation between race and secularity. Structural theories— depicting secularization as the linear, straightforward decline of religion in modernity— commonly explain the tenacity of African-American religiosity as resulting from their marginalization in modern society, a product of educational and economic disparities. However, recent theories address the secular as a historically contingent, incidental phenomenon, what has been called an "accomplishment"; it merits substantive study in itself, carrying the distinct values, beliefs, and understandings of a particular social history. This new framework invites analysis of the racial assumptions embodied …

Informing The Use Of Hyper-Parameter Optimization Through Meta-Learning, Samantha Corinne Sanders

Theses and Dissertations

One of the challenges of data mining is finding hyper-parameters for a learning algorithm that will produce the best model for a given dataset. Hyper-parameter optimization automates this process, but it can still take significant time. It has been found that hyperparameter optimization does not always result in induced models with significant improvement over default hyper-parameters, yet no systematic analysis of the role of hyper-parameter optimization in machine learning has been conducted. We propose the use of meta-learning to inform the decision to optimize hyper-parameters based on whether default hyper-parameter performance can be surpassed in a given amount of time. …

The Application Of Artificial Neural Networks For Prioritization Of Independent Variables Of A Discrete Event Simulation Model In A Manufacturing Environment, Rebecca Pires Dos Santos

Theses and Dissertations

The high complexity existent in businesses has required managers to rely on accurate and up to date information. Over the years, many tools have been created to give support to decision makers, such as discrete event simulation and artificial neural networks. Both tools have been applied to improve business performance; however, most of the time they are used separately. This research aims to interpret artificial neural network models that are applied to the data generated by a simulation model and determine which inputs have the most impact on the output of a business. This would allow prioritization of the variables …

Estimating Human Intent For Physical Human-Robot Co-Manipulation, Eric Townsend, Erich Mielke, David Wingate, Marc D. Killpack

Faculty Publications

Human teams can be exceptionally efficient at adapting and collaborating during manipulation tasks using shared mental models. However, the same shared mental models that can be used by humans to perform robust low-level force and motion control during collaborative manipulation tasks are non-existent for robots. For robots to perform collaborative tasks with people naturally and efficiently, understanding and predicting human intent is necessary. However, humans are difficult to predict and model. We have completed an exploratory study recording motion and force for 20 human dyads moving an object in tandem in order to better understand how they move and how …

In-Class Participation And Performance Gender Gaps In Introductory Biology Courses: The Instructor Gender Effect, Nicholas Nelson, Liz Bailey

Journal of Undergraduate Research

It is well known that undergraduate women are underrepresented in STEM disciplines, which includes the sciences, technology, engineering, and mathematics (NSF 20011). However, the explanation for this phenomenon is not completely understood. Much research has been done recently and suggests that the “why?” is very complicated and multi-faceted (Smith 2012, Gayles 2014). Reasons can include female students’ sense of belonging, perception of ability, access to a positive mentor, and others (Smith 2012). While biology programs are unique in that female enrollment often exceeds that of males, gender inequities are still seen as postgraduates enter their careers (Handelsman et.al 2005). Because …

Uncertainty Quantification And Propagation Of Errors Of The Lennard-Jones 12-6 Parameters For N-Alkanes, Richard A. Messerly, Thomas A. Knotts Iv, W Vincent Wilding

Faculty Publications

Molecular simulation has the ability to predict various physical properties that are difficult to obtain experimentally. For example, we implement molecular simulation to predict the critical constants (i.e., critical temperature, critical density, critical pressure, and critical compressibility factor) for large n-alkanes that thermally decompose experimentally (as large as C₄₈). Historically, molecular simulation has been viewed as a tool that is limited to providing qualitative insight. One key reason for this perceived weakness in molecular simulation is the difficulty to quantify the uncertainty in the results. This is because molecular simulations have many sources of uncertainty that propagate …

Fossil Mustela Nigripes From Snake Creek Burial Cave, Nevada, And Implications For Black-Footed Ferret Paleoecology, Nathaniel S. Fox, Steven C. Wallace, Jim I. Mead

Western North American Naturalist

Morphometric measurements were used to classify 11 mustelid dentaries from Snake Creek Burial Cave (SCBC), a late Pleistocene to early Holocene–aged paleontological locality in eastern Nevada, that were undifferentiated between Mustela nigripes (black-footed ferret) and Neovison vison (American mink) due to their similar size and morphology. We, therefore, classified the SCBC fossils using 10 linear measurements of the dentary using extant M. nigripes and N. vison as proxy. Discriminant function and principal component analyses grouped the 11 unknown SCBC specimens within extant M. nigripes exclusively. Confirmation of M. nigripes at SCBC is significant because Cynomys spp. (their primary prey source …

A Handy Underwater Solution, Benjamin Murdoch, Matt Ricks, Ales Ball, Jacob Olson, Ethan Durrant, Connor Monson, Lars Watts, Mark Killpack

Journal of Undergraduate Research

Hod Lipson once asked an audience at TED, “Where are the robots?” We’ve been waiting for them a long time now and modern robotics still hasn’t caught up with our hopes and dreams. Through our research we hope to address one of the major topics in robotics: movement (or kinematics), and use this moment of exploration to build a new low cost robotic hand capable of use within the exciting realm of aquatics.