80 Works

Data to replicate: Forecasting community reassembly using climate-linked spatio-temporal ecosystem models

James Thorson, Mayumi Arimitsu, Lewis Barnett, Wei Cheng, Lisa Eisner, Alan Haynie, Albert Hermann, Kirstin Holsman, David Kimmel, Mike Lomas, Jon Richar & Elizabeth Siddon
Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring data. To illustrate a new approach, we extend a generalization of empirical orthogonal function (EOF) analysis, which involves a spatio-temporal ecosystem model that approximates coupled physical, biological, and human...

Supplemental material for: NINDS consensus diagnostic criteria for Traumatic Encephalopathy Syndrome

Douglas Katz, Charles Bernick, David Dodick, Jesse Mez, Megan Mariani, Charles Adler, Michael Alosco, Laura Balcer, Sarah Banks, William Barr, David Brody, Robert Cantu, Kristen Dams-O'Connor, Yonas Geda, Barry Jordan, Thomas McAllister, Elaine Peskind, Ronald Petersen, Jennifer Wether, Ross Zafonte, Eimear Foley, Debra Babcock, Walter Koroshetz, Ann McKee, Martha Shenton … & Robert Stern
Objective: To develop evidence-informed, expert consensus research diagnostic criteria for Traumatic Encephalopathy Syndrome (TES), the clinical disorder associated with neuropathologically diagnosed Chronic Traumatic Encephalopathy (CTE). Methods: A panel of 20 expert clinician-scientists in neurology, neuropsychology, psychiatry, neurosurgery, and physical medicine and rehabilitation, from 11 academic institutions, participated in a modified Delphi procedure to achieve consensus, initiated at the First NINDS Consensus Workshop to Define the Diagnostic Criteria for TES, April, 2019. Prior to consensus, panelists...

Data from: On the comparative biology of mammalian telomeres: telomere length co-evolves with body mass, lifespan and cancer risk

Michael Le Pepke & Dan T. A. Eisenberg
Telomeres, the short repetitive DNA sequences that cap the ends of linear chromosomes, shorten during cell division and are implicated in senescence in most species. Telomerase can rebuild telomeres but is repressed in many mammals that exhibit replicative senescence, presumably as a tumor suppression mechanism. It is therefore important to understand the co-evolution of telomere biology and life-history traits that has shaped the diversity of senescence patterns across species. Gomes et al. (2011) produced a...

Shifting trends: detecting changes in cetacean population dynamics in shifting habitat

Charlotte Boyd & Andre Punt
The ability to monitor population dynamics and detect major changes in population trend is essential for wildlife conservation and management. However, this is often challenging for cetaceans as surveys typically cover only a portion of a population’s range and conventional stock assessment methods cannot then distinguish whether apparent changes in abundance reflect real changes in population size or shifts in distribution. We developed and tested methods for estimating population size and trend and detecting changes...

Genomic and immunogenic changes of Piscine novirhabdovirus (Viral hemorrhagic septicemia virus) over its evolutionary history in the Laurentian Great Lakes

Carol Stepien, Megan Niner, Carol Stepien, Douglas W. Leaman & Bartolomeo Gorgoglione
A unique and highly virulent subgenogroup (VHSV-IVb) of Piscine novirhabdovirus, also known as Viral Hemorrhagic Septicemia Virus (VHSV), suddenly appeared in the Laurentian Great Lakes, causing large mortality outbreaks in 2005 and 2006, and affecting >32 freshwater fish species to date. Periods of apparent dormancy have punctuated smaller and more geographically-restricted outbreaks in 2007, 2008, and 2017. In this study, we conduct the largest whole genome sequencing analysis of VHSV-IVb to date, evaluating its evolutionary...

Data from: The utility of climatic water balance for ecological inference depends on vegetation physiology assumptions

Derek Young, Sean Jeronimo, Derek Churchill, Van Kane & Andrew Latimer
This repository contains the data and code supporting the analyses in the corresponding paper in Global Ecology and Biogeography (GEB). The abstract of the paper is as follows: Background: In modeling and explaining spatial vegetation patterns, ecologists have increasingly favored the use of climatic water balance variables, including actual evapotranspiration (AET) and climatic water deficit (CWD), for representing the hydrologic and energetic environment experienced by plants. Much of the interest in these variables lies in...

Data from: Effects of Bark Beetle Outbreaks on Forest Landscape Pattern in the Southern Rocky Mountains, U.S.A.

Kyle Rodman, Robert Andrus, Cori Butkiewicz, Teresa Chapman, Nathan Gill, Brian Harvey, Dominik Kulakowski, Niko Tutland, Thomas Veblen & Sarah Hart
Since the late 1990s, extensive outbreaks of native bark beetles (Curculionidae: Scolytinae) have affected coniferous forests throughout Europe and North America, driving changes in carbon storage, wildlife habitat, nutrient cycling, and water resource provisioning. Remote sensing is a crucial tool for quantifying the effects of these disturbances across broad landscapes. In particular, Landsat time series (LTS) are increasingly used to characterize outbreak dynamics, including the presence and severity of bark beetle-caused tree mortality, though broad-scale...

Neonatal exposure to BPA, BDE-99, and PCB produces persistent changes in hepatic transcriptome associated with gut dysbiosis in adult mouse livers

Joe Lim, Moumita Dutta, Joseph Dempsey, Hans-Joachim Lehmler, James MacDonald, Theo Bammler, Cheryl Walker, Terrance Kavanagh, Haiwei Gu, Sridhar Mani & Julia Cui
Background. Recent evidence suggests that multigenic and complex environmentally modulated diseases result from early life exposure to toxicants at least partly via gut microbial influences. Environmental toxicants, polybrominated diphenyl ethers (PBDEs), and polychlorinated biphenyls (PCBs) are breast milk-enriched persistent organic pollutants (POPs) and thus remain a continuing threat to human health despite being banned from production. Recent findings focused on the liver developmental reprogramming capabilities from neonatal BPA exposure; however, little is known on how...

Wind Tunnel Mosquito Trajectory Data

Jeff Riffell
Mosquitoes track odors, locate hosts, and find mates visually. The color of a food resource, such as a flower or warm-blooded host, can be dominated by long wavelengths of the visible light spectrum (green to red for humans) and is likely important for object recognition and localization. However, little is known about the hues that attract mosquitoes or how odor affects mosquito visual search behaviors. We use a real-time 3D tracking system and wind tunnel...

Genotypes for herring samples collected from Chinook salmon gut contents

Eleni Petrou, Joshua Chamberlin, Will Duguid, Russel Barsh, Francis Juanes, Jessica Qualley & Lorenz Hauser
Dynamic prey resources influence foraging opportunities for consumers. In coastal food webs, forage fish abundance and seasonal reproduction mediate foraging opportunities for mobile consumers. Recent declines in Chinook salmon productivity have prompted efforts to determine whether poormarine survival is caused by limited feeding opportunities. To establish the importance of phenological diversity in Pacific herring for Chinook salmon, we used genetic stock identification to assign individual herring collected from the guts of juvenile and adult Chinook...

Data from: New approaches to ceramic use and discard: cooking pottery from the Peruvian Andes in ethnoarchaeological perspective

John A. Hildebrand & Melissa B. Hagstrum
Ethnoarchaeological data from contemporary Wanka villages in the Mantaro Valley of the Peruvian Andes provide new perspectives on the use and discard of ceramic cooking vessels. We present a regional survey of ceramic vessel use and discard with household consumption as the focus of study. A mathematical model determines vessel uselife from the age distribution of in-use vessels. We examine the number of vessels per household, their volume, their uselife, and their reported discard. A...

Flatfish exon-capture

Calder Atta
This dataset contains alignments used to study phylogenetic relationships of flatfishes based on exon-capture data. The samples in this dataset represent 89 species: 86 flatfishes and 3 outgroup Carangidae. 57 samples were extracted and assembled from tissues collected for this project, while 39 were sourced from previously assembled data that were prepared as part of the FishLife project. For this study we targeted 4,434 markers developed by Jiang et al. (2019) for capture efficiency in...

Wildfire smoke affects detection of birds in Washington state

Olivia Sanderfoot
Wildfire smoke is likely to have direct health effects on birds, as well as influence movement, vocalization, and other avian behaviors. These behavioral changes may affect if and how birds are observed in the wild, although research on the effects of wildfire smoke on bird behavior is limited. To evaluate how wildfire smoke affects detection of birds, we combined data from eBird, an online community science program, with data from an extensive network of air...

Benzalkonium Chloride Disinfectants Induce Apoptosis, Inhibit Proliferation, and Activate the Integrated Stress Response in a 3-D in Vitro Model of Neurodevelopment

Josi Herron, Libin Xu, Hideaki Tomita, Collin White & Terrance Kavanagh
We previously found that the widely used disinfectants, benzalkonium chlorides (BACs), alter cholesterol and lipid homeostasis in neuronal cell lines and in neonatal mouse brains. Here we investigate the effects of BACs on neurospheres, an in vitro three-dimensional model of neurodevelopment. Neurospheres cultured from mouse embryonic neural progenitor cells (NPCs) were exposed to increasing concentrations (1 to 100 nM) of a short-chain BAC (BAC C12), a long-chain BAC (BAC C16), and AY9944 (a known DHCR7...

Tactile active sensing in an insect-plant pollinator

Tanvi Deora, Mahad Ahmed, Thomas Daniel & Bingni Brunton
The interaction between insects and the flowers they pollinate has driven the evolutionary diversity of both insects and flowering plants, two groups with the most numerous species on Earth. Insects use vision and olfaction to localize host plants, but we know relatively little about how they find the tiny nectary opening in the flower, which can be well beyond their visual resolution. Especially when vision is limited, touch becomes crucial in successful insect–plant pollination interactions....

Appendix: Association between hemostatic profile and migraine: a Mendelian randomization analysis

Yanjun Guo, Pamela Rist, Maria Sabater-Lleal, Paul De Vries, Nicholas Smith, Paul Ridker, Tobias Kurth & Daniel Chasman
Objective: To assess support for a causal relationship between hemostatic measures and migraine susceptibility using genetic instrumental analysis. Methods: Two-sample Mendelian randomization (MR) instrumental leveraging available genome-wide association study (GWAS) summary statistics was applied to hemostatic measures as potential causal for migraine and its subtypes, migraine with aura (MA) and migraine without aura (MO). Twelve blood-based measures of hemostasis were examined, including plasma level or activity of eight hemostatic factors and two fibrinopeptides together with...

Data for: A size principle for recruitment of Drosophila leg motor neurons

Anthony Azevedo, Evyn Dickinson, Pralaksha Gurung, Lalanti Venkatasubramanian, Richard Mann & John Tuthill
To move the body, the brain must precisely coordinate patterns of activity among diverse populations of motor neurons. In many species, including vertebrates, the motor neurons innervating a given muscle fire in a specific order that is determined by a gradient of cellular size and electrical excitability. This hierarchy allows premotor circuits to recruit motor neurons of increasing force capacity in a task-dependent manner. However, it remains unclear whether such a size principle also applies...

The hidden influence of communities in collaborative funding of clinical science

Kishore Vasan & Jevin West
Every year the National Institutes of Health allocates $10.7 billion (one-third of its funds) for clinical science research while the pharmaceutical companies spend $52.9 billion (90% of its annual budget). However, we know little about funder collaborations and the impact of collaboratively funded projects. As an initial effort towards this, we examine the cofunding network, where a funder represents a node and an edge signifies collaboration. Our core data include all papers that cite and...

Ten year camera trap dataset of tigers in India

Beth Gardner, Rahel Sollmann, N. Samba Kumar, Devcharan Jathanna & K. Ullas Karanth
1. With continued global changes, such as climate change, biodiversity loss and habitat fragmentation, the need for assessment of long-term population dynamics and population monitoring of threatened species is growing. One powerful way to estimate population size and dynamics is through capture-recapture methods. Spatial capture (SCR) models for open populations make efficient use of capture-recapture data, while being robust to design changes. Relatively few studies have implemented open SCR models and to date, very few...

Detection histories of mesocarnivores in agricultural areas of Southern Chile

Nicolás Gálvez, José Infante, Adrián Fernandez, Jesús Díaz & Lisanne Petracca
We obtained mesocarnivore detection/non-detection data from 180 sampling units (4 km2 each) located in the agricultural landscapes of southern Chile from January-April of 2019. We used single-species occupancy models to investigate the associations of forest fragmentation, forest loss, and private land ownership subdivision (as a measure of human use intensification) with the occurrence of four mesocarnivores (güiña, grey fox, culpeo fox, and Molina’s hog-nosed skunk), and extended this framework to two-species occupancy models to assess...

Variation in the modality of a yeast signaling pathway is mediated by a single regulator

Julius Palme, Jue Wang & Michael Springer
Bimodal gene expression by genetically identical cells is a pervasive feature of signaling networks, and has been suggested to allow organisms to hedge their "bets" in uncertain conditions. In the galactose-utilization (GAL) pathway of Saccharomyces cerevisiae, gene induction is unimodal or bimodal depending on natural genetic variation and pre-induction conditions. Here, we find that this variation in modality arises from regulation of two features of the pathway response: the fraction of cells that show induction,...

Data from: Examining the dynamics of Epstein-Barr virus shedding in the tonsils and the impact of HIV-1 coinfection on daily saliva viral loads

Catherine Byrne, Christine Johnston, Jackson Orem, Fred Okuku, Meei-Li Huang, Habibur Rahman, Anna Wald, Lawrence Corey, Joshua Schiffer, Corey Casper, Daniel Coombs & Soren Gantt
Epstein-Barr virus (EBV) is transmitted by saliva and is a major cause of cancer, particularly in people living with HIV/AIDS. Here, we describe the frequency and quantity of EBV detection in the saliva of Ugandan adults with and without HIV-1 infection and use these data to develop a novel mathematical model of EBV infection in the tonsils. Eligible cohort participants were not taking antiviral medications, and those with HIV-1 infection had a CD4 count >200...

Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger (Squamata: Phrynosomatidae)

Robert Bryson, Jared Grummer, Elizabeth Connors, Joseph Tirpak, John McCormack & John Klicka
Sceloporus subniger Poglaygen & Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting S. subniger may be a composite of several distinct species, we examined in more detail the genetic structure of S. subniger. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing...

Data from: Incomplete convergence of gliding-mammal skeletons

David Grossnickle
Ecology and biomechanics play central roles in the generation of phenotypic diversity. When unrelated taxa invade a similar ecological niche, biomechanical demands can drive convergent morphological transformations. Thus, identifying and examining convergence helps to elucidate the key catalysts of phenotypic change. Gliding mammals are often presented as a classic case of convergent evolution because they independently evolved in numerous clades, each possessing patagia (‘wing’ membranes) that generate lift during gliding. We use phylogenetic comparative methods...

The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos)

Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe & Tereza Jezkova
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here we explore...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of Washington
  • University of Cambridge
  • West China Hospital of Sichuan University
  • Zhejiang University
  • Stanford University
  • Peking University Cancer Hospital
  • Huazhong University of Science and Technology
  • Sichuan University
  • Fudan University
  • Capital Medical University