36 Works

Machine Learning meets Library Archives

Harish Maringanti, Dhanushka Samarakoon, Bohan Zhu & Brian McBride
This is the slide presentation from the 2018 LYRASIS Leaders Summit documenting the University of Utah Catalyst Fund project - Machine Learning Meets Library Archives.

Parasitic cnidarians (Myxozoa) do not retain key oxygen-sensing and homeostasis tool-kit genes: Transcriptome assemblies

Allie Graham & Felipe Barreto
For aerobic organisms, both the Hypoxia-Inducible Factor (HIF) pathway and the mitochondrial genomes are key players in regulating oxygen homeostasis. However, recent work has suggested that these mechanisms are not as highly conserved as previously thought, prompting more thorough surveys across animal higher taxonomic levels, which would in turn permit testing of hypotheses about the ecological conditions that may have facilitated evolutionary loss of such genes. The phylum Cnidaria is known to harbor wide variation...

Did shell-crushing predators drive the evolution of ammonoid septal shape?

Erynn Johnson, Briana DiMarco, David Peterman, Aja Carter & Warren Allmon
For centuries, paleontologists have sought functional explanations for the uniquely complex internal walls (septa) of ammonoids, extinct shelled cephalopods. Ammonoid septa developed increasingly complex fractal margins, unlike any modern shell morphologies, throughout more than 300 million years of evolution. Some have suggested these morphologies provided increased resistance to shell-crushing predators. We perform the first physical compression experiments on model ammonoid septa using controlled, theoretical morphologies generated by computer-aided design and 3D printing. These biomechanical experiments...

Atmospheric pollutant concentrations and leaf chemistry variables collected along gradients of median household income and traffic density in Salt Lake Valley, UT

LaShaye Cobley, Diane Pataki, Frederick Adler & Sarah Jack Hinners
We utilize traffic density and Convolvulus arvensis leaf chemistry to understand spatial patterns linking atmospheric pollution and household income in the Salt Lake City metropolitan area, USA. We hypothesize that traffic density will explain variation in atmospheric NOx and O3 concentrations. In addition, we expect foliar %N and nitrogen isotope ratios (δ15N) to be elevated and carbon isotope ratios (δ13C) to be depleted on high traffic density roads. These hypotheses were supported: we found the...

Adaptive introgression of the beta-globin cluster in two Andean waterfowl

Allie Graham & Kevin McCracken
Introgression of alleles has emerged as an important avenue for genetic adaptation in both plant and animal populations. In vertebrates, adaptation to hypoxic high-altitude environments involves the coordination of multiple molecular and cellular mechanisms, including selection on the Hypoxia-Inducible Factor (HIF) pathway and the blood-O2 transport protein hemoglobin (Hb). In two Andean duck species, a striking DNA sequence similarity reflecting identity by descent is present across the ~20 kb b-globin cluster including both embryonic (HBE)...

Diarrhea etiology prediction validation dataset - Bangladesh and Mali

Daniel Leung, Ben Brintz & Stephanie Garbern
Background: Diarrheal illness is a leading cause of antibiotic use for children in low- and middle-income countries. Determination of diarrhea etiology at the point-of-care without reliance on laboratory testing has the potential to reduce inappropriate antibiotic use. Methods: This prospective observational study aimed to develop and externally validate the accuracy of a mobile software application (“App”) for the prediction of viral-only etiology of acute diarrhea in children 0-59 months in Bangladesh and Mali. The App...

ENIGMA Pediatric msTBI diffusion MRI supplemental data

Emily Dennis
Objective: Our study addressed aims: (1) test the hypothesis that moderate-severe TBI in pediatric patients is associated with widespread white matter (WM) disruption; (2) test the hypothesis that age and sex impact WM organization after injury; and (3) examine associations between WM organization and neurobehavioral outcomes. Methods: Data from ten previously enrolled, existing cohorts recruited from local hospitals and clinics were shared with the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Pediatric msTBI working group. We...

Biogeography and diversification of Old World buntings (Aves: Emberizidae): radiation in open habitats

Tianlong Cai, Guiyou Wu, Sun Lu, Yu Zhang, Zhaojie Peng, Yanqing Guo, Xinyue Liu, Tao Pan, Jiang Chang, Zhonglou Sun & Baowei Zhang
The Old World buntings (Aves: Emberizidae) mainly inhabit open habitats in Eurasia and Africa. It has long been debated whether the group originated in the New World or the Old World and whether their radiation is related to the expansion of open habitats and shifts in migratory behaviours. To answer these questions, we reconstructed their biogeographic histories and analysed their diversification patterns in terms of time, space and traits using a near-complete phylogeny. We found...

Hybridizations and fruit geography of Solanum jamesii

Bruce Pavlik & Lisbeth Louderback
Premise: Plant domestication can be detected when transport, use and manipulation of propagules impact reproductive functionality, especially in species with self-incompatible breeding systems. Methods: Evidence for human-caused founder effect in the Four Corners potato (Solanum jamesii Torr.) was examined by conducting 526 controlled matings between archaeological and non-archaeological populations from field-collected tubers grown in a greenhouse. Specimens from 24 major herbaria, along with collection records from >160 populations were examined to determine which produced fruits....

Temperature‐associated decreases in demographic rates of Afrotropical bird species over 30 years

Montague H. C. Neate‐Clegg, Thomas R. Stanley, Çağan H. Şekercioğlu & William D. Newmark
Tropical mountains harbor globally significant levels of biodiversity and endemism. Climate change threatens many tropical montane species, yet little research has assessed the effects of climate change on the demographic rates of tropical species, particularly in the Afrotropics. Here, we report on the demographic rates of 21 Afrotropical bird species over 30 years in montane forests in Tanzania. We used mark-recapture analyses to model rates of population growth, recruitment, and apparent survival as functions of...

Integrating venom peptide libraries into a phylogenetic and broader biological framework

Kevin Chase & Maren Watkins
The venomous marine snails are conventionally divided into three groups, the cone snails (family Conidae), the auger snails (family Terebridae) and the turrids (formerly all assigned to a single family, Turridae). In this study, a library of venom peptides from species conventionally assigned to the genus Turris was correlated to a phylogenetic analysis. Nucleotide sequences of multiple genes from transcriptomes were used to assess the phylogenic relationships across a diverse set of species. The resulting...

Horizontal transmission of a murine retrovirus is driven by males within semi-natural enclosures

Douglas Cornwall, James Ruff, Elisabeth Zachary, Chloe Young, Katie Maguire, Rachel Painter, Sophie Truillo & Wayne Potts
1. Transmission is a key component of a pathogen’s life history, but it is often difficult to obtain reliable ecological estimates of the dominant mode(s) of transmission and how host traits, such as sex, influence transmission dynamics. 2. Here, we have developed a robust system pairing the use of semi-natural populations of house mice (Mus musculus) with modern molecular viral titering approaches to evaluate the transmission dynamics of Friend Virus Complex (FVC). 3. Semi-natural populations...

Community characteristics of forest understory birds along an elevational gradient in the Horn of Africa: A multi-year baseline of Afromontane birds

Kyle Kittelberger, Montague Neate-Clegg, Evan Buechley & Çağan Şekercioğlu
Tropical mountains are global hotspots for birdlife. However, there is a dearth of baseline avifaunal data along eleva-tional gradients, particularly in Africa, limiting our ability to observe and assess changes over time in tropical montane avian communities. In this study, we undertook a multi-year assessment of understory birds along a 1,750 m elevational gradient (1,430-3,186 m) in an Afrotropical moist evergreen montane forest within Ethiopia's Bale Mountains. Analyzing 6 years of systematic bird-banding data from...

Supplemental material from: A population-based prevalence of myotonic dystrophy type 1

Nicholas Johnson, Russell Butterfield, Katie Mayne, Tara Newcomb, Carina Imburgia, Diane Dunn, Brett Duval, Marcia Feldkamp & Robert Weiss
Objective: To determine whether the genetic prevalence of the CTG expansion in the DMPK gene associated with myotonic dystrophy (DM1) in an unbiased cohort is higher than previously reported population estimates, ranging from 5-20 per 100,000 individuals. Methods: This study used a cross-sectional cohort of de-identified dried blood spots (DBS) from the newborn screening program in the state of New York, taken from consecutive births from 2013-2014. Blood spots were screened for the CTG repeat...

The past, present, and future of herbivore impacts on savanna vegetation

Ann Carla Staver, Joel Abraham, Gareth Hempson, Allison Karp & J Faith
1) Herbivory is a key process structuring vegetation in savannas, especially in Africa where large mammal herbivore communities remain intact. Exclusion experiments consistently show that herbivores impact savanna vegetation, but effect size variation has resisted explanation, limiting our understanding of the past, present, and future roles of herbivory in savanna ecosystems. 2) Synthesis of vegetation responses to herbivore exclusion shows that herbivory decreased grass abundance by 57.0% and tree abundance by 30.6% across African savannas....

Mixed-phase orographic cloud microphysics during StormVEx and IFRACS

Douglas Lowenthal, A. Gannet Hallar, Robert O. David, Ian B. McCubbin, Randolph D. Borys & Gerald G. Mace
Wintertime mixed-phase orographic cloud (MPC) measurements were conducted at the Storm Peak Laboratory (SPL) during the Storm Peak Lab Cloud Property Validation Experiment (StormVEx) and Isotopic Fractionation in Snow (IFRACS) programs in 2011 and 2014, respectively. The data include 92 h of simultaneous measurements of supercooled liquid cloud droplet and ice particle size distributions (PSDs). Average cloud droplet number concentration (CDNC), droplet size (NMD), and liquid water content (LWC) were similar in both years, while...

Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti)

Timothy O'Connor, Marissa Sandoval, Jiarui Wang, Jacob Hans, Risa Takenaka, & Noah Whiteman
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, making them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across...

Data from: Testing potential mechanisms of conspecific sperm precedence in Drosophila pseudoobscura

Brooke Peckenpaugh, Dean M. Castillo & Leonie C. Moyle
Drosophila pseudoobscura females that co-occur with sister species D. persimilis show elevated fertilization by conspecific sperm when they mate with both a heterospecific and a conspecific male. This phenomenon, known as conspecific sperm precedence (CSP), has evolved as a mechanism to avoid maladaptive hybridization with D. persimilis. In this study, we assessed pericopulatory (during mating) and postcopulatory (after mating) traits in crosses with sympatric or allopatric D. pseudoobscura females and conspecific or heterospecific males to...

Enhancing research informatics core user satisfaction through agile practices

Andrew Post, Jared Luther, J Loveless, Melanie Ward & Shirleen Hewitt
Objective: The Huntsman Cancer Institute (HCI) Research Informatics Shared Resource (RISR), a software and database development core facility, sought to address a lack of published operational best practices for research informatics cores. It aimed to use those insights to enhance effectiveness after an increase in team size from 20 to 31 full-time equivalents coincided with a reduction in user satisfaction. Materials and Methods: RISR migrated from a water-scrum-fall model of software development to agile software...

A Minimalist Approach to Facilitatory Effects in Stacked Relative Clauses

Aniello De Santo

CCG Supertagging as Top-down Tree Generation

Jakob Prange, Nathan Schneider & Vivek Srikumar

Machine learning meets library archives: Image Analysis to generate descriptive metadata

Harish Maringanti, Dhanushka Samarakoon & Bohan Zhu
$34,700 to develop and test a model for applying machine learning techniques to extract useful information from historical images to assist in and increase the efficiency of metadata creation for archives, libraries and museums of all types.

Flipping the Feedback: Formative Assessment in a Flipped Freshman Circuits Class

Donna H. Ziegenfuss & Cynthia M. Furse
This paper describes the application of formative assessment methods in a flipped freshman engineering circuits course. This student-centered approach provided value for the instructor seeking to improve the learning environment and content in real-time, and for the students who actively participated in the process of course improvement. Three types of assessment were used in this course: online formative course feedback every three weeks; weekly ‘muddiest point’ content feedback; and midterm exam scores. Data were assessed...

Data and code for: Replay of innate vocal patterns during sleep in suboscines

Juan Francisco Döppler, Manon Peltier, Ana Amador, Franz Goller & Gabriel Mindlin
Activation of forebrain circuitry during sleep has been variably characterized as ‘pre- or replay’ and has been linked to memory consolidation. The evolutionary origins of this mechanism, however, are unknown. Sleep activation of the sensori-motor pathways of learned birdsong is a particularly useful model system because the muscles controlling the vocal organ are activated, revealing syringeal activity patterns for direct comparison with those of day-time vocal activity. Here we show that suboscine birds, which develop...

Microhabitats associated with solar energy development alter demography of two desert annuals

Karen Tanner, Kara Moore-O'Leary, Ingrid Parker, Bruce Pavlik, Sophia Haji & Rebecca Hernandez
Political and economic initiatives intended to increase energy production while reducing carbon emissions are driving demand for solar energy. Consequently, desert regions are now targeted for development of large-scale photovoltaic solar energy facilities. Where vegetation communities are left intact or restored within facilities, ground-mounted infrastructure may have negative impacts on desert-adapted plants because it creates novel rainfall runoff and shade conditions. We used experimental solar arrays in the Mojave Desert to test how these altered...

Registration Year

  • 2021

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  • University of Utah
  • University of Buenos Aires
  • University of Münster
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  • California Academy of Sciences
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  • Princeton University