Digital Commons Network^™

Topological Data Analysis For Systems Of Coupled Oscillators, Alec Dunton

HMC Senior Theses

Coupled oscillators, such as groups of fireflies or clusters of neurons, are found throughout nature and are frequently modeled in the applied mathematics literature. Earlier work by Kuramoto, Strogatz, and others has led to a deep understanding of the emergent behavior of systems of such oscillators using traditional dynamical systems methods. In this project we outline the application of techniques from topological data analysis to understanding the dynamics of systems of coupled oscillators. This includes the examination of partitions, partial synchronization, and attractors. By looking for clustering in a data space consisting of the phase change of oscillators over a …

Purification Of Recombinant Spider Silk Protein From Escherichia Coli., Randolph V. Lewis, Justin Jones, Todd Brown

Biology Posters

Spider silk has many applications including human health (sutures, vaccine encapsulations, i.e.) and military usage (underwater Velcro-type fasteners). In order to test these applications, we need large quantities of spider silk protein to use in our experiments. One way to make spider silk is by using Escherichia coli (E. Coli) to produce the protein. E. Coli has many advantages: it can be produced in larger amounts, it is inexpensive to grow, and it can be easily transported. We usually start with a culture mass weighing 4 kg but we are scaling up to produce even greater amounts of product. The …

Geographic Patterns And Possibility Of Predation, Jennica Blasi

Biology Posters

A poster documenting if lizard and feral cats inhabit the same areas in the St. George, UT region.

Dna Methylation Of Regulatory Regions Of Imprinted Genes At Birth And Its Relation To Infant Temperament, Bernard F. Fuemmeler, Chien-Ti Lee, Adelheid Soubry, Edwin S. Iversen, Zhiqing Huang, Amy P. Murtha, Joellen M. Schildkraut, Randy L. Jirtle, Susan K. Murphy, Cathrine Hoyo

Health Policy Publications

Background: DNA methylation of the differentially methylated regions (DMRs) of imprinted genes is relevant to neurodevelopment.

Methods: DNA methylation status of the DMRs of nine imprinted genes in umbilical cord blood leukocytes was analyzed in relation to infant behaviors and temperament (n = 158).

Results: MEG3 DMR levels were positively associated with internalizing (β = 0.15, P = 0.044) and surgency (β = 0.19, P = 0.018) behaviors, after adjusting for birth weight, gender, gestational age at birth, maternal age at delivery, race/ethnicity, education level, smoking status, parity, and a history of anxiety or depression. Higher methylation levels at the …

News Stories Of Intimate Partner Violence: An Experimental Examination Of Participant Sex, Perpetrator Sex, And Violence Severity On Seriousness, Sympathy, And Punishment Preferences, Matthew W. Savage, Jennifer A. Scarduzio, Kate Lockwood Harris, Kellie E. Carlyle, Sarah E. Sheff

Health Policy Publications

This study experimentally examines the effects of participant sex, perpetrator sex, and severity of violence on perceptions of intimate partner violence (IPV) seriousness, sympathy toward the victim, and punishment preferences for the perpetrator. Participants (N = 449) were randomly assigned to a condition, exposed to a composite news story, and then completed a survey. Ratings of seriousness of IPV for stories with male perpetrators were significantly higher than ratings of seriousness for stories with female perpetrators. Men had significantly higher sympathy for female victims in any condition than for male victims in the weak or strong severity of violence …

Using An Epiphytic Moss To Identify Previously Unknown Sources Of Atmospheric Cadmium Pollution, Geoffrey H. Donovan, Sarah E. Jovan, Demetrios Gatziolis, Igor Burstyn, Yvonne L. Michael, Michael C. Amacher, Vicente J. Monleon

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bioindicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting.We collected 346 samples of the moss Orthotrichum lyellii from deciduous trees in December, 2013 using a modified randomized grid-based sampling strategy across Portland, Oregon.We estimated a spatial linear model of moss cadmium levels and predicted cadmium on a 50 m grid …

Burrowing Herbivores Alter Soil Carbon And Nitrogen Dynamics In A Semi-Arid Ecosystem, Argentina, Kenneth L. Clark, Lyn C. Branch, Jose L. Hierro, Diego Villarreal

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Activities of burrowing herbivores, including movement of soil and litter and deposition of waste material, can alter the distribution of labile carbon (C) and nitrogen (N) in soil, affecting spatial patterning of nutrient dynamics in ecosystems where they are abundant. Their role in ecosystem processes in surface soil has been studied extensively, but effects of burrowing species on processes in subsurface soil remain poorly known. We investigated the effects of burrowing and grazing by plains vizcachas (Lagostomus maximus, Chinchilidae), a large colonial burrowing rodent native to South America, on the distribution and dynamics of C and N in …

Riparian Trees And Aridland Streams Of The Southwestern United States: An Assessment Of The Past, Present, And Future, D. Max Smith, Deborah M. Finch

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Riparian ecosystems are vital components of aridlands within the southwestern United States. Historically, surface flows influenced population dynamics of native riparian trees. Many southwestern streams has been altered by regulation, however, and will be further affected by greenhouse warming. Our analysis of stream gage data revealed that decreases in volume of annual discharge and mean peak discharge and a shift to earlier peak discharge will occur in the Southern Rockies region of Colorado, New Mexico, and Utah. These changes will likely decrease rates of reproduction and survival of cottonwood (Populus fremontii and Populus deltoides ssp. wislizenii), Goodding's willow …

Review Of Broad-Scale Drought Monitoring Of Forests: Toward An Integrated Data Mining Approach, Steven P. Norman, Frank H. Koch, William W. Hargrove

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Efforts to monitor the broad-scale impacts of drought on forests often come up short. Drought is a direct stressor of forests as well as a driver of secondary disturbance agents, making a full accounting of drought impacts challenging. General impacts can be inferred from moisture deficits quantified using precipitation and temperature measurements. However, derived meteorological indices may not meaningfully capture drought impacts because drought responses can differ substantially among species, sites and regions. Meteorology-based approaches also require the characterization of current moisture conditions relative to some specified time and place, but defining baseline conditions over large, ecologically diverse regions can …

Conditions Inside Fisher Dens During Prescribed Fires; What Is The Risk Posed By Spring Underburns?, Craig M. Thompson, Kathryn L. Purcell

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

The use of spring prescribed fires to reduce accumulated fuel loads in western forests and facilitate the return of natural fire regimes is a controversial topic. While spring burns can be effective at reducing fuel loads and restoring heterogeneous landscapes, concerns exist over the potential impacts of unnaturally timed fires to native species. To protect native wildlife from disturbance during critical periods, limited operating periods (LOPs) are often implemented. However when LOPs for multiple species are combined into an integrated management plan, very few time windows for implementing prescribed fires remain. The use of spring burns is often effectively eliminated, …

Refined Forest Land Use Classification With Implications For United States National Carbon Accounting, John W. Coulston, Christopher W. Woodall, Grant M. Domke, Brian F. Walters

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

The United States provides annual estimates of carbon sources and sinks as part of its National Green-house Gas Inventory (NGHGI). Within this effort, carbon stocks and fluxes are reported for six land use categories that are relevant to economic sectors and land use policy. The goal of this study is to develop methodologies that will allow the US to align with an internationally agreed upon forest land use definition which requires forest to be able to reach 5 m in height at maturity. Models to assess height potential are available for a majority of US forests except for woodland ecosystems. …

Inhibition Of Dna Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity, Yanchun Pan, Takuji Daito, Yo Sasaki, Yong Hee Chung, Xiaoyun Xing, Santhi Pondugula, S. Joshua Swamidass, Ting Wang, Albert H. Kim, Hiroko Yano

Open Access Publications

No abstract provided.

Predicting All-Cause Mortality From Basic Physiology In The Framingham Heart Study, William B. Zhang, Zachary Pincus

Open Access Publications

No abstract provided.

Changes In The Relative Abundance Of Two Saccharomyces Species From Oak Forests To Wine Fermentations, Sofia Dashko, Ping Liu, Helena Volk, Lorena Butinar, Jure Piškur, Justin C. Fay

Open Access Publications

No abstract provided.

Genseed-Hmm: A Tool For Progressive Assembly Using Profile Hmms As Seeds And Its Application In Alpavirinae Viral Discovery From Metagenomic Data, João M.P. Alves, Andre L. De Oliveira, Tatiana O.M. Sandberg, Jaime L. Moreno-Gallego, Marcelo A.F. De Toledo, Elisabeth M.M. De Moura, Liliane S. Oliveira, Alan M. Durham, Dolores U. Mehnert, Paolo M. De A. Zanotto, Alejandro Reyes, Arthur Gruber

Open Access Publications

No abstract provided.

Genome-Wide Association Study Of Lifetime Cannabis Use Based On A Large Meta-Analytic Sample Of 32,330 Subjects From The International Cannabis Consortium, A C. Heath, Et Al

Open Access Publications

No abstract provided.

Critical Evaluation Of The Expression Of Gastrin-Releasing Peptide In Dorsal Root Ganglia And Spinal Cord, Devin M. Barry, Hui Li, Xian-Yu Liu, Kai-Feng Shen, Xue-Ting Liu, Zhen-Yu Wu, Admire Munanairi, Xiao-Jun Chen, Jun Yin, Yan-Gang Sun, Yun-Qing Li, Zhou-Feng Chen

Open Access Publications

No abstract provided.

Geographic Variation In Maternal Smoking During Pregnancy In The Missouri Adolescent Female Twin Study (Moafts), Min Lian, Pamela A. Madden, Michael T. Lynskey, Graham A. Colditz, Christina N. Lessov-Schlaggar, Mario Schootman, Andrew C. Heath

Open Access Publications

No abstract provided.

Rna-Seq Of The Caribbean Reef-Building Coral Orbicella Faveolata (Scleractinia-Merulinidae) Under Bleaching And Disease Stress Expands Models Of Coral Innate Immunity, David A. Anderson, Marcus E. Walz, Ernesto Weil, Peter Tonellato, Matthew C. Smith

Open Access Publications

No abstract provided.

Hyperthermic Laser Ablation Of Recurrent Glioblastoma Leads To Temporary Disruption Of The Peritumoral Blood Brain Barrier, Eric C. Leuthardt, Chong Duan, Michael J. Kim, Jian L. Campian, Albert H. Kim, Michelle M. Miller-Thomas, Joshua S. Shimony, David D. Tran

Open Access Publications

No abstract provided.

The Z-Cad Dual Fluorescent Sensor Detects Dynamic Changes Between The Epithelial And Mesenchymal Cellular States, M. J. Toneff, A. Sreekumar, A. Tinnirello, P. Den Hollander, S. Habib, Shunqiang Li, M. J. Ellis, L. Xin, S. A. Mani, J. M. Rosen

Open Access Publications

No abstract provided.

Small Molecule Dual-Inhibitors Of Trpv4 And Trpa1 For Attenuation Of Inflammation And Pain, Patrick Kanju, Yong Chen, Whasil Lee, Michele Yeo, Suk Hee Lee, Joelle Romac, Rafiq Shahid, Ping Fan, David M. Gooden, Sidney A. Simon, Ivan Spasojevic, Robert A. Mook, Rodger A. Liddle, Farshid Guilack, Wolfgang B. Liedtke

Open Access Publications

No abstract provided.

The Fallacy Of Univariate Solutions To Complex Systems Problems, Christina N. Lessov-Schlaggar, Joshua B. Rubin, Bradley L. Schlaggar

Open Access Publications

No abstract provided.

Evolutionary Inactivation Of A Sialidase In Group B Streptococcus, Masaya Yamaguchi, Yujiro Hirose, Masanobu Nakata, Satoshi Uchiyama, Yuka Yamaguchi, Kana Goto, Tomoko Sumitomo, Amanda L. Lewis, Shigetada Kawabata, Victor Nizet

Open Access Publications

No abstract provided.

Endothelial To Mesenchymal Transition Is Common In Atherosclerotic Lesions And Is Associated With Plaque Instability, Gwendalyn J. Randolph, Et Al

Open Access Publications

No abstract provided.

A Disintegrin And Metalloproteinase10 (Adam10) Regulates Notch Signaling During Early Retinal Development, Joseph A. Toonen, Adam Ronchetti, D. J. Sidjanin

Open Access Publications

No abstract provided.

A Critical Evaluation Of The Down Syndrome Diagnosis For Lb1, Type Specimen Of Homo Floresiensis, Karen L. Baab, Peter Brown, Dean Falk, Joan T. Richtsmeier, Charles F. Hildebolt, Kirk Smith, William Jungers

Open Access Publications

No abstract provided.

Reprogrammable Crispr/Cas9-Based System For Inducing Site-Specific Dna Methylation, James I. Mcdonald, Hamza Celik, Lisa E. Rois, Gregory Fishberger, Tolison Fowler, Ryan Rees, Ashley Kramer, Andrew Martens, John R. Edwards, Grant A. Challen

Open Access Publications

No abstract provided.

Mapping Rare, Deleterious Mutations In Factor H: Association With Early Onset, Drusen Burden, And Lower Antigenic Levels In Familial Amd, Erin K. Wagner, Soumya Raychaudhuri, Mercedes B. Villalonga, Anuja Java, Michael P. Triebwasser, Mark J. Daly, John P. Atkinson, Johanna M. Seddon

Open Access Publications

No abstract provided.

Tpl-2 Regulates Macrophage Lipid Metabolism And M2 Differentiation To Control Th2-Mediated Immunopathology, Yashaswini Kannan, Jimena Perez-Lloret, Yanda Li, Lewis J. Entwistle, Hania Khoury, Stamatia Papoutsopoulou, Radma Mahmood, Nuha R. Mansour, Stanley Ching-Cheng Huang, Edward J. Pearce, Luiz Pedro S. De Carvalho, Steven C. Ley, Mark S. Wilson

Open Access Publications

No abstract provided.