44 Works

Data from: Understanding the loss of maternal care in avian brood parasites using preoptic area transcriptome comparisons in brood parasitic and non-parasitic blackbirds

Kathleen S. Lynch, Lauren A. O'Connell, Matthew I.M. Louder, Christopher N. Balakrishnan & Eva K Fischer
Parental care is critical for offspring survival in many species. However, parental behaviors have been lost in roughly 1% of avian species known as the obligate brood parasites. To shed light on molecular and neurobiological mechanisms mediating brood parasitic behavior, we compared brain gene expression patterns between two brood parasitic species and one closely related non-parasitic Icterid (blackbird) species. Our analyses focused on gene expression changes specifically in the preoptic area (POA), a brain region...

Data from: Reduced signal for polygenic adaptation of height in UK Biobank

Jeremy J. Berg, Arbel Harpak, Nasa Sinnott-Armstrong, Anja Moltke Joergensen, Hakhamanesh Mostafavi, Yair Field, Evan August Boyle, Xinjun Zhang, Fernando Racimo, Jonathan K. Pritchard & Graham Coop
Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used height effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based on the the UK Biobank (UKB), a large, independent dataset. We find that the signals of selection using UKB effect estimates are strongly attenuated or absent. We also provide evidence that previous analyses were confounded by population stratification. Therefore, the conclusion...

Data from: Local interactions and their group-level consequences in flocking jackdaws

Hangjian Ling, Guillam E. McIvor, Kasper Van Der Vaart, Richard T. Vaughan, Alex Thornton & Nicholas T. Ouellette
As one of nature’s most striking examples of collective behaviour, bird flocks have attracted extensive research. However, we still lack an understanding of the attractive and repulsive forces that govern interactions between individuals within flocks and how these forces influence neighbours’ relative positions and ultimately determine the shape of flocks. We address these issues by analysing the three-dimensional movements of wild jackdaws (Corvus monedula) in flocks containing 2 to 338 individuals. We quantify the social...

2010 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2015 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2016 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: The prevalence of MS in the United States: a population-based estimate using health claims data

Mitchell T. Wallin, William J. Culpepper, Jonathan D. Campbell, Lorene M. Nelson, Annette Langer-Gould, Ruth Ann Marrie, Gary R. Cutter, Wendy E. Kaye, Laurie Wagner, Helen Tremlett, Stephen L. Buka, Piyameth Dilokthornsakul, Barbara Topol, Lie H. Chen & Nicholas G. LaRocca
Objective: To generate a national multiple sclerosis (MS) prevalence estimate for the United States by applying a validated algorithm to multiple administrative health claims (AHC) datasets. Methods: A validated algorithm was applied to private, military, and public AHC datasets to identify adult cases of MS between 2008 and 2010. In each dataset, we determined the 3-year cumulative prevalence overall and stratified by age, sex, and census region. We applied insurance-specific and stratum-specific estimates to the...

Data from: Covariation of diet and gut microbiome in African megafauna

Tyler R. Kartzinel, Julianna C. Hsing, Paul M. Musili, Bianca R. P. Brown & Robert M. Pringle
A major challenge in biology is to understand how phylogeny, diet, and environment shape the mammalian gut microbiome. Yet most studies of non-human microbiomes have relied on relatively coarse dietary categorizations and have focused either on individual wild populations or on captive animals that are sheltered from environmental pressures, which may obscure the effects of dietary and environmental variation on microbiome composition in diverse natural communities. We analyzed plant and bacterial DNA in fecal samples...

Precision mapping of snail habitat provides a powerful indicator of human schistosomiasis transmission

Chelsea Wood, Susanne Sokolow, Isabel Jones, Andrew Chamberlin, Kevin Lafferty, Armand Kuris, Merlijn Jocque, Skylar Hopkins, Grant Adams, Julia Buck, Andrea Lund, Ana Garcia-Vedrenne, Evan Fiorenza, Jason Rohr, Fiona Allan, Bonnie Webster, Muriel Rabone, Joanne Webster, Lydie Bandagny, Raphael Ndione, Simon Senghor, Anne-Marie Schacht, Nicolas Jouanard, Gilles Riveau & Giulio De Leo
Recently, the World Health Organization recognized that efforts to interrupt schistosomiasis transmission through mass drug administration have been ineffective in some regions; one of their new recommended strategies for global schistosomiasis control emphasizes targeting the freshwater snails that transmit schistosome parasites. We sought to identify robust indicators that would enable precision targeting of these snails. At the site of the world’s largest recorded schistosomiasis epidemic—the Lower Senegal River Basin in Senegal—intensive sampling revealed positive relationships...

2012 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2017 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

2018 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Software and Calibration for Photothermal Threshold Quantum Yield

David Hanifi
This is code used to process and apply calibrations to photothermal threshold quantum yields taken, with our specific spectrometer. The calibrations included will not work for any other optics path or components, but this serves as a guide to calibrate one built in any other lab. This code is written in Matlab2018b.

Data from: Direct measurement of swimming and diving kinematics of giant Atlantic bluefin tuna (Thunnus thynnus)

Adrian C. Gleiss, Robert S. Schallert, Jonathan J. Dale, Steven G. Wilson & Barbara A. Block
Tunas possess a range of physiological and mechanical adaptations geared towards high performance swimming that are of considerable interest to physiologists, ecologists and engineers. Advances in biologging have provided significant improvements in understanding tuna migrations and vertical movement patterns, yet our understanding of the locomotion and swimming mechanics of these fish under natural conditions is limited. We equipped Atlantic bluefin tuna (Thunnus thynnus) with motion sensitive tags and video cameras to quantify the gaits and...

Data from: No evidence that gut microbiota impose a net cost on their butterfly host

Alison Ravenscraft, Nicole Kish, Kabir Peay & Carol Boggs
Gut microbes are believed to play a critical role in most animal life, yet fitness effects and cost benefit-tradeoffs incurred by the host are poorly understood. Unlike most hosts studied to date, butterflies largely acquire their nutrients from larval feeding, leaving relatively little opportunity for nutritive contributions by the adult’s microbiota. This provides an opportunity to measure whether hosting gut microbiota comes at a net nutritional price. Since host and bacteria may compete for sugars,...

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity

Kevin Leempoel, Elizabeth Hadly & Trevor Hebert
Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed...

Body size, sampling completeness, and extinction risk in the marine fossil record

Jonathan Payne & Noel Heim
Larger body size has long been assumed to correlate with greater risk of extinction, helping to shape body size distributions across the tree of life, but lack of comprehensive size data for fossil taxa have left this hypothesis untested for most higher taxa across the vast majority of evolutionary time. Here we assess the relationship between body size and extinction using a dataset comprising the body sizes, stratigraphic ranges, and occurrence patterns of 9,408 genera...

2013 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: Revised Airlie House consensus guidelines for design and implementation of ALS clinical trials

Leonard H Van Den Berg, Eric Sorenson, Gary Gronseth, Eric A. Macklin, Jinsy Andrews, Robert H. Baloh, Michael Benatar, James D. Berry, Adriano Chio, Philippe Corcia, Angela Genge, Amelie K. Gubitz, Catherine Lomen-Hoerth, Christopher J. McDermott, Erik P. Pioro, Jeffrey Rosenfeld, Vincenzo Silani, Martin R. Turner, Markus Weber, Benjamin Rix Brooks, Robert G. Miller & Hiroshi Mitsumoto
Objective: To revise the 1999 Airlie House consensus guidelines for the design and implementation of preclinical therapeutic studies and clinical trials in amyotrophic lateral sclerosis (ALS). Methods: A consensus committee comprising 140 key members of the international ALS community (ALS researchers, clinicians, patient representatives, research funding representatives, industry and regulatory agencies) addressed nine areas of need within ALS research: 1. Pre-clinical studies; 2. Biological and phenotypic heterogeneity; 3. Outcome measures; 4. Disease-modifying and symptomatic interventions;...

Data from: Patterned frequency-modulated oral stimulation in preterm infants: a multicenter randomized controlled trial

Dongli Song, Priya Jegatheesan, Suhas Nafday, Kaashif A. Ahmad, Jonathan Nedrelow, Mary Wearden, Sheri Nemerofsky, Sunshine Pooley, Diane Thompson, Daniel Vail, Tania Cornejo, Zahava Cohen & Balaji Govindaswami
Objective To evaluate the effect of patterned, frequency-modulated oro-somatosensory stimulation on time to full oral feeds in preterm infants born 26 - 30 weeks gestation. Study Design This is a multicenter randomized controlled trial. The experimental group (n = 109) received patterned, frequency-modulated oral stimulation via the NTrainer system through a pulsatile pacifier and the control group (n = 101) received a non-pulsatile pacifier. Intent-to-treat analysis (n = 210) was performed to compare the experimental...

Data from: Applying modern coexistence theory to priority effects

Tess Nahanni Grainger, Andrew D. Letten, Benjamin Gilbert & Tadashi Fukami
Modern coexistence theory is increasingly used to explain how differences between competing species lead to coexistence versus competitive exclusion. Although research testing this theory has focused on deterministic cases of competitive exclusion, in which the same species always wins, mounting evidence suggests that competitive exclusion is often historically contingent, such that whichever species happens to arrive first excludes the other. Coexistence theory predicts that historically contingent exclusion, known as priority effects, will occur when large...

Data from: Empowering conservation practice with efficient and economical genotyping from poor quality samples

Meghana Natesh, Ryan W. Taylor, Nathan Truelove, Elizabeth A. Hadly, Stephen Palumbi, Dmitri Petrov & Uma Ramakrishnan
1. Moderate to high density genotyping (100+ SNPs) is widely used to determine and measure individual identity, relatedness, fitness, population structure and migration in wild populations. 2. However, these important tools are difficult to apply when high-quality genetic material is unavailable. Most genomic tools are developed for high quality DNA sources from lab or medical settings. As a result, most genetic data from market or field settings is limited to easily-amplified mitochondrial DNA or a...

Agricultural intensification drives changes in hybrid network robustness by modifying network structure

Beth Morrison, Berry Brosi & Rodolfo Dirzo
Within ecological communities, species engage in myriad interaction types, yet empirical examples of hybrid species interaction networks composed of multiple types of interactions are still scarce. A key knowledge gap is understanding how the structure and stability of such hybrid networks are affected by anthropogenic disturbance. Using 15,169 interaction observations, we constructed 16 hybrid herbivore-plant-pollinator networks along an agricultural intensification gradient to explore changes in network structure and robustness to local extinctions. We found that...

Data from: Species richness change across spatial scales

Jonathan M. Chase, Brian J. McGill, Patrick L. Thompson, Laura H. Antão, Amanda E. Bates, Shane A. Blowes, Maria Dornelas, Andrew Gonzalez, Anne E. Magurran, Sarah R. Supp, Marten Winter, Anne D. Bjorkmann, Helge Bruelheide, Jarrett E.K. Byrnes, Juliano Sarmento Cabral, Robin Ehali, Catalina Gomez, Hector M. Guzman, Forest Isbell, Isla H. Myers-Smith, Holly P. Jones, Jessica Hines, Mark Vellend, Conor Waldock & Mary O'Connor
Humans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in...

Data from: Molecular physiology of chemical defenses in a poison frog

Stephanie N Caty, Aurora Alvarez-Buylla, Gary` D Byrd, Charles Vidoudez, Alexandre B Roland, Elicio E Tapia, Bogdan Bodnik, Sunia A Trauger, Luis A Coloma & Lauren A O'Connell
Poison frogs sequester small molecule lipophilic alkaloids from their diet of leaf litter arthropods for use as chemical defenses against predation. Although the dietary acquisition of chemical defenses in poison frogs is well-documented, the physiological mechanisms of alkaloid sequestration has not been investigated. Here, we used RNA sequencing and proteomics to determine how alkaloids impact mRNA or protein abundance in the Little Devil Frog (Oophaga sylvatica) and compared wild caught chemically defended frogs to laboratory...

Registration Year

  • 2019
    44

Resource Types

  • Dataset
    44

Affiliations

  • Stanford University
    35
  • Hansen Experimental Physics Laboratory, Stanford University
    9
  • Electrical Engineering and Computer Science Department, University of Michigan
    9
  • SUPA School of Physics and Astronomy, University of Glasgow
    9
  • NASA Goddard Space Flight Center
    9
  • Center for Data Science, New York University
    9
  • Lockheed Martin Solar & Astrophysics Laboratory
    9
  • SETI Institute
    9
  • Southwest Research Institute
    7
  • Department of Psychiatry, University of Amsterdam
    7