60 Works

Data from: Functional trait evolution in Sphagnum peat mosses and its relationship to niche construction

Bryan T. Piatkowski & A. Jonathan Shaw
Species in the genus Sphagnum create, maintain, and dominate boreal peatlands through ‘extended phenotypes’ that allow these organisms to engineer peatland ecosystems and thereby impact global biogeochemical cycles. One such phenotype is the production of peat, or incompletely decomposed biomass, that accumulates when rates of growth exceed decomposition. Interspecific variation in peat production is thought to be responsible for the establishment and maintenance of ecological gradients, such as the microtopographic hummock-hollow gradient, along which sympatric...

Data from: Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes

Yang Liu, Matthew G. Johnson, Cymon J. Cox, Rafael Medina, Nicolas Devos, Alain Vanderpoorten, Lars Hedenäs, Neil E. Bell, James R. Shevock, Blanka Aguero, Dietmar Quandt, Norman J. Wickett, A. Jonathan Shaw & Bernard Goffinet
Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30...

Taking a Hard Look at Our Research Data Support Through A Critical Lens

Hilary Davis & Susan Ivey

Data from: Quality and quantity of genetic relatedness data affect the analysis of social structure

Vivienne Foroughirad, Alexis Levengood, Janet Mann & Celine H. Frère
Kinship plays a fundamental role in the evolution of social systems and is considered a key driver of group living. To understand the role of kinship in the formation and maintenance of social bonds, accurate measures of genetic relatedness are critical. Genotype-by-sequencing technologies are rapidly advancing the accuracy and precision of genetic relatedness estimates for wild populations. The ability to assign kinship from genetic data varies depending on a species’ or population’s mating system and...

Character Strengths and Self-Compassion among Young Adults

Jordan Booker & Joshua Perlin
This is a multi-site project addressing the ways multiple aspects of character (curiosity, grit, hope, gratitude, forgiveness) may robustly inform individual differences in self-compassion across college- and community recruited adults, focusing predominantly on young adults from ages 18-to-24 years

Traditional Healers and Mental Health in Nepal: A Scoping Review

Tony Pham, Brandon Kohrt, Bonnie Kaiser, Rishav Koirala, Nawaraj Upadhaya, Sujen Maharjan & Lauren Franz

BabbleCor: A Crosslinguistic Corpus of Babble Development in Five Languages

Meg Cychosz, Amanda Seidl, Elika Bergelson, Marisa Casillas, Gladys Baudet, Anne Warlaumont, Camila Scaff, Lisa Yankowitz & Alejandrina Cristia
BabbleCor is a largescale, cross-linguistic corpus of infant babbling. Each clip has a unique ID. Speaker data can be referenced in the accompanying metadata file.

Conceptualizing Curation: A framework to guide libraries through the research data curation lifecycle

Susan Ivey & Moira Downey
Presentation from the Triangle Research Libraries Network's 2018 Annual Meeting

Healthcare costs of stroke and major bleeding in patients with atrial fibrillation treated with non-vitamin K antagonist oral anticoagulants

Heather M. Rozjabek, Craig I. Coleman, Veronica Ashton, François Laliberté, Paul Oyefesobi, Dominique Lejeune, Guillaume Germain, Jeff R. Schein, Zhong Yuan, Patrick Lefebvre & Eric D. Peterson
Objective: To assess long-term healthcare costs related to ischemic stroke and systemic embolism (stroke/SE) and major bleeding (MB) events in patients with non-valvular atrial fibrillation (NVAF) treated with non-vitamin K antagonist oral anticoagulants (NOACs). Materials and methods: Optum’s Clinformatics Data Mart database from 1/2009–12/2016 was analyzed. Adult patients with ≥1 stroke/SE hospitalization (index date) were matched 1:1 to patients without stroke/SE (random index date), based on propensity scores. Patients with an MB event were matched...

Folk Intuitions and the Conditional Ability to Do Otherwise

Thomas Nadelhoffer, Siyuan Yin & Rose Graves

Convergent evolution in lemur environmental niches

James Herrera
Aim: To test the hypothesis that adaptive convergent evolution of climate niches occurred in multiple independent lemur lineages. Location: Madagascar Taxon: Lemurs Methods: I collected climate and altitude data from WorldClim and summarized the niches of almost all living lemurs (83 species) into phylogenetically-controlled principal components. To test for convergent evolution, I searched for multiple, similar climate optima using multi-peak Ornstein-Uhlenbeck models (surface, l1-ou, bayou). I compared the observed level of climate convergence to that...

Supp_Figs_11_12_13_CELL-METABOLISM-D-19-00134_Williams_et_al

Timothy Koves
Uncropped Blots for CELL-METABOLISM-D-19-00134 Disruption of acetyl-lysine turnover in muscle mitochondria promotes insulin resistance and redox stress without overt respiratory dysfunction

Data from: Comparative genomic analysis of the pheromone receptor Class 1 family (V1R) reveals extreme complexity in mouse lemurs (genus, Microcebus) and a chromosomal hotspot across mammals

Kelsie E Hunnicutt, George P Tiley, Rachel C Williams, Peter A Larsen, Marina B Blanco, Rodin M Rasoloarison, Christopher Ryan Campbell, Kevin Zhu, David W Weisrock, Hiroaki Matsunami & Anne D Yoder
Sensory gene families are of special interest, both for what they can tell us about molecular evolution, and for what they imply as mediators of social communication. The vomeronasal type-1 receptors (V1Rs) have often been hypothesized as playing a fundamental role in driving or maintaining species boundaries given their likely function as mediators of intraspecific mate choice, particularly in nocturnal mammals. Here, we employ a comparative genomic approach for revealing patterns of V1R evolution within...

Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

William Morris
Multiple, simultaneous environmental changes, in climatic/abiotic factors, in interacting species, and in direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate...

NASPSPA/STORK Pre-Conference Workshop on Open Science Practices

Christopher Hill, Keith Lohse, John Mills & Zachary Zenko
Files and materials from the NASPSPA/STORK pre-conference workshop on open science practices.

Data from: Costs and drivers of helminth parasite infection in wild female baboons

Mercy Y. Akinyi, David Jansen, Bobby Habig, Laurence Gesquiere, Susan C. Alberts & Elizabeth A. Archie
1. Helminth parasites can have wide ranging, detrimental effects on host reproduction and survival. These effects are best documented in humans and domestic animals, while only a few studies in wild mammals have identified both the forces that drive helminth infection risk and their costs to individual fitness. 2. Working in a well-studied population of wild baboons (Papio cynocephalus) in the Amboseli ecosystem in Kenya, we pursued two goals, to: (i) examine the costs of...

Methods Synopsis

Laura Warmuth & David Gill

Systematic review of public evaluations of the LENA (TM) software

Alejandrina Cristia, Federica Bulgarelli & Elika Bergelson

Presentations Given by COS

Timothy Errington, Brian Geiger, Brian Nosek, Longze Chen, Fitz Elliott, David Mellor, David Litherland, Zachary Loomas, Yuhuai Liu, Krystal Hahn, Olivia Miske, Alexis Rice, Summer Pearce, Huajin Wang, Briana Wade, Nicole Pfeiffer, Ronald Brooks, Lisa Shaw, Blaine Butler, Doug Corell, Andrew Tyner, Terry Foor, Gretchen Gueguen, Lesley Markham, Whitney Wissinger … & Abram Booth
A collection of slides for virtually all presentations given by Center for Open Science staff since its founding in 2013.

Perceptions of Diversity Statements

Rebecca Ponce de Leon

Monkey Penaltykick

Lun Yin
Data for Latent Goal Models for Dynamic Strategic Interaction by Shariq N. Iqbal, Lun Yin, Caroline B. Drucker, Qian Kuang, Jean-Francois Gariepy, Michael L. Platt, John Pearson, accepted by PLOS Computational Biology

Data from: Diving behavior of Cuvier's beaked whales (Ziphius cavirostris) off Cape Hatteras, North Carolina

Jeanne M. Shearer, Nicola J. Quick, William R. Cioffi, Robin W. Baird, Daniel L. Webster, Heather J. Foley, Zachary T. Swaim, Danielle M. Waples, Joel T. Bell & Andrew J. Read
Cuvier’s beaked whales exhibit exceptionally long and deep foraging dives. The species is relatively little studied due to their deep-water, offshore distribution and limited time spent at the surface. We used LIMPET satellite tags to study the diving behavior of Cuvier's beaked whales off Cape Hatteras, North Carolina from 2014 to 2016. We deployed 11 tags, recording 3,242 hours of behavior data, encompassing 5,926 dives. Dive types were highly bimodal; deep dives (>800m, n=1,408) had...

Data from: A mitochondrial progesterone receptor increases cardiac beta-oxidation and remodeling

Qunsheng Dai, Creighton E Likes, Anthony L Luz, Lan Mao, Jason S Yeh, Zhengzheng Wei, Maragatha Kuchibhatla, Olga R Ilkayeva, Timothy R Koves & Thomas M Price
Progesterone is primarily a pregnancy related hormone, produced in substantial quantities after ovulation and during gestation. Traditionally known to function via nuclear receptors for transcriptional regulation there is also evidence of non-nuclear action. A previously identified mitochondrial progesterone receptor (PR-M) increases cellular respiration in cell models. In these studies, we demonstrated that expression of PR-M in rat H9c2 cardiomyocytes resulted in a ligand-dependent increase in oxidative cellular respiration and beta-oxidation. Cardiac expression in a TET-On...

Data from: Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Yifu Ding, Daniel J Vanselow, Maksim A Yakovlev, Spencer R Katz, Alex Y Lin, Darin P Clark, Phillip Vargas, Xuying Xin, Jean E Copper, Victor A Canfield, Khai C Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B Van Rossum, Patrick La Riviere & Keith Cheng
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Using micro-CT optimized for cellular characterization (histo-tomography), brain nuclei can be computationally segmented and assigned to brain regions....

Data from: Uncovering the genomic signature of ancient introgression between white oak lineages (Quercus)

Andrew A. Crowl, Paul S. Manos, John D. McVay, Alan R. Lemmon, Emily Moriarty Lemmon & Andrew L. Hipp
• Botanists have long recognized interspecific gene flow as a common occurrence within white oaks (Quercus section Quercus). Historical allele exchange, however, has not been fully characterized, and the complex genomic signals resulting from the combination of vertical and horizontal gene transmission may confound phylogenetic inference and obscure our ability to accurately infer the deep evolutionary history of oaks. • Using anchored enrichment, we obtained a phylogenomic dataset consisting of hundreds of single-copy nuclear loci....

Registration Year

  • 2019
    60

Resource Types

  • Dataset
    34
  • Text
    26

Affiliations

  • Duke University
    60
  • University of Notre Dame
    3
  • The University of Texas Southwestern Medical Center
    3
  • University of Minnesota
    2
  • University of Chicago
    2
  • University of Connecticut
    2
  • Michigan State University
    2
  • University of South Dakota
    1
  • University of Liège
    1
  • The Nature Conservancy
    1