26 Works

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...

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...

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)...

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....

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...

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.

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...

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...

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.

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...

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...

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...

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...

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....

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: 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...

Video of nest predation of an African Paradise Flycatcher (Terpsiphone viridis) by an Olive Sunbird (Cyanomitra olivacea)

William Newmark & Victor Mkongewa
Nest predation is the dominant cause of nest failure in the tropics. However, our knowledge about tropical nest predator identity and community structure is still quite limited. On 9 January 2019, we video-recorded an Olive Sunbird (Cyanomitra olivacea) removing and flying off with an egg from an African Paradise Flycatcher (Terpsiphone viridis) nest in the East Usambara Mountains, Tanzania. This observation is surprising because the Olive Sunbird is a specialized nectarivore. Nectar, however, is a...

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

Aniello De Santo & Alëna Aksënova

Processes underlying complex patterns of song trait evolution in a Setophaga hybrid zone

Jay Love & Franz Goller
During secondary contact between two species when hybrids are less fit than parents, mating signals are expected to diverge while aggressive signals are expected to converge. If a single signal trait is used in both mating and aggression, then the dynamics between these two forces could influence the evolutionary trajectory of that trait. We studied such a situation in an avian hybrid zone between two Setophaga species, where birdsong is used in both mate attraction...

Data from: Different frequency control mechanisms and the exploitation of frequency space in passerines

Franz Goller, Jay Love & Gabriel Mindlin
1. Birdsong is used in reproductive context and, consequently, has been shaped by strong natural and sexual selection. The acoustic performance includes a multitude of acoustic and temporal characteristics that are thought to honestly reveal the quality of the singing individual. 2. One major song feature is frequency and its modulation. Sound frequency can be actively controlled, but the control mechanisms differ between different groups. Two described mechanisms are pressure-driven frequency changes in suboscines and...

Providing virtual nature experiences to incarcerated men reduces stress and increases interest in the environment

James Ruff, Nalini Nadkarni, Tierney Thys, Allison Anholt, Jeff Treviño, Sara Yeo, Nalini M. Nadkarni, Tierney M. Thys, James S. Ruff & Sara K. Yeo
Humans gain multiple health benef­­­its through contact with the green and blue parts of the world . However, many people do not have access to such places, including more than two million adults who are incarcerated. Building on studies that have shown positive emotional and mood effects when inmates in solitary confinement were exposed to nature videos featuring non-human built environments in their cellblocks, we measured physiological effects of interventions of nature visual imagery and...

Data from: Pathogenic effect of TP73 gene variants in people with amyotrophic lateral sclerosis

Kristi Russell
Objective: To identify novel disease associated loci for amyotrophic lateral sclerosis (ALS), we utilized sequencing data and performed in vitro and in vivo experiments to demonstrate pathogenicity of mutations identified in TP73. Methods: We analyzed exome sequences of 87 sporadic ALS patients and 324 controls, with confirmatory sequencing in independent ALS cohorts of >2,800 patients. For the top hit, TP73, a regulator of apoptosis, differentiation, and a binding partner as well as homolog of the...

Registration Year

  • 2021

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  • University of Utah
  • University of Buenos Aires
  • University of Münster
  • California Academy of Sciences
  • Yale University
  • University of Pennsylvania
  • University of Washington
  • Princeton University
  • Google (United States)
  • Usambara Field Studies Centre