39 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.

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...

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...

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...

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...

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)...

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...

UCE phylogenomics of New World Cryptopone (Hymenoptera: Formicidae) elucidates genus boundaries, species boundaries, and the vicariant history of a temperate-tropical disjunction

Michael G. Branstetter & John T. Longino
The genus Cryptopone Emery contains 25 species of litter and soil ants, 5 of which occur in the Americas. Cryptoponegilva occurs in the southeastern U.S.A. and cloud forests of Mesoamerica, exhibiting an uncommon biogeographic disjunction observed most often in plants. We used phylogenomic data from ultraconserved elements (UCEs), as well as mitogenomes and legacy markers, to investigate phylogenetic relationships, species boundaries, and divergence dates among New World Cryptopone. Species delimitation was conducted using a standard...

Climbing parrots achieve pitch stability using axial-appendicular force couples

David Carrier, Lindsey Reader & David Lee
During vertical climbing, the gravitational moment tends to pitch the animal’s head away from the climbing surface and this may be countered by 1) applying a correcting torque at a discrete contact point, or 2) applying opposing horizontal forces at separate contact points to produce a free moment. We tested these potential strategies in small parrots with an experimental climbing apparatus imitating the fine branches and vines of their natural habitat. The birds climbed on...

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...

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...

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...

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...

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...

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...

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...

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....

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...

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...

Water potential data and model output

Steven Kannenberg
Classifying the diverse ways that plants respond to hydrologic stress into generalizable ‘water-use strategies' has long been an eco-physiological research goal. While many schemes for describing water-use strategies have proven to be quite useful, they are also associated with uncertainties regarding their theoretical basis and their connection to plant carbon and water relations. In this review, we discuss the factors that shape plant water stress responses and assess the approaches used to classify a plant’s...

Learning Interactions of Local and Non-Local Phonotactic Constraints from Positive Input

Aniello De Santo & Alëna Aksënova

CPCP-1: Thermal demagnetization data

Ziaul Haque, John Geissman, Randall Irmis, Paul Olsen, Christophere Lepre, Hesham Buhedma, Ronald Mundil, William Parker, Cornelia Rasmussen & George Gehrels
The Colorado Plateau Coring Project Phase 1 (CPCP-1) acquired three continuous drill cores from Petrified Forest National Park (PFNP), Arizona, U.S.A. Two cores, CPCP-PFNP13-1A and CPCP-PFNP13-2B, hereafter CPCP-1A and CPCP-2B; respectively, intersected the Upper Triassic Chinle Formation, Lower(?)-Middle Triassic Moenkopi Formation (MF) and Permian Coconino Sandstone. We examined CPCP-1A and CPCP-2B cores to construct a high-resolution magnetostratigraphy of Moenkopi Formation strata. These data files contain progressive thermal demagnetization data collected from the specimens from cores...

Data from: Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism

Douglas Booher, Joshua Gibson, Cong Liu, John Longino, Brian Fisher, Milan Janda, Nitish Narula, Evropi Toulkeridou, Alexander Mikheyev, Andrew Suarez & Evan Economo
Evolutionary innovations underlie the rise of diversity and complexity—the two long-term trends in the history of life. How does natural selection redesign multiple interacting parts to achieve a new emergent function? We investigated the evolution of a biomechanical innovation, the latch-spring mechanism of trap-jaw ants, to address two outstanding evolutionary problems: how form and function change in a system during the evolution of new complex traits, and whether such innovations and the diversity they beget...

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