66 Works

Data from: Environmental filtering structures fungal endophyte communities in tree bark

Peter Pellitier, Donald Zak & Sydney Salley
The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage...

The Flint MDT Study (March 2014- January 2016)

Robin Pott
The Flint MDT Study is one of the projects of the the National Quality Improvement Center on the Representation of Children in Child Welfare (QIC-ChildRep). The Study partnered with a group of five lawyers-guardian ad litem to observe and evaluate a multidisciplinary approach to representing children in child protection proceedings. The study provided the LGALs two social workers and randomly assigned cases to be either represented by the attorney/social worker team or by the attorney...

A new species of croton (Euphorbiaceae) from a Madagascan lineage discovered in coastal Kenya

Veronicah Ngumbau, Mwadime Nyange, Neng Wei, Benjamin Van Ee, Paul Berry, Itambo Malombe, Guang-Wan Hu & Qing-Feng Wang
Croton kinondoensis, a new species from Kenya, is described and illustrated here with photographs. It is found in the sacred Kaya Kinondo Forest, one of the last remaining coastal forests patches in Kenya. Its morphology and systematic position based on ITS and trnL-F DNA sequence data clearly place it within the Adenophorus Group of Croton, a clade of ca. 15 species otherwise known only from Madagascar and the Comoros Archipelago. Its closest affinities appear to...

Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China

Xiaolei Xie, Zhenyu Wang, Kai Zhang, Yang Li, Yachen Hu, Zhiming Pan, Xiang Chen, Qiuchun Li & Xinan Jiao
CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: – isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34...

Pig as a reservoir of CRISPR type TST4 Salmonella enterica serovar Typhimurium monophasic variant during 2009–2017 in China

Xiaolei Xie, Zhenyu Wang, Kai Zhang, Yang Li, Yachen Hu, Zhiming Pan, Xiang Chen, Qiuchun Li & Xinan Jiao
CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: – isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34...

A Paleocene (Danian) marine osteoglossid (Teleostei, Osteoglossomorpha) from the Nuussuaq Basin of Greenland, with a brief review of Palaeogene marine bonytongue fishes

Alessio Capobianco, Ethan Foreman & Matt Friedman
The early Palaeogene represents a key interval in the evolution of modern marine fish faunas. Together with the first appearances of many familiar fish lineages characteristic of contemporary marine environments, early Palaeogene marine deposits worldwide feature the occurrence of osteoglossid bonytongues. Their presence in marine rocks is surprising, as these fishes are strictly associated with freshwater environments in modern settings and other parts of the fossil record. Despite its possible relevance to faunal recovery after...

Belowground competition can influence the evolution of root traits

Sara Colom & Regina Baucom
Although root traits play a critical role in mediating plant-plant interactions and resource acquisition from the soil environment, research examining if and how belowground competition can influence the evolution of root traits remains largely unexplored. Here we examine the potential that root traits may evolve as a target of selection from interspecific competition using Ipomoea purpurea and I. hederacea, two closely related morning glory species that commonly co-occur in the United States as a model...

Shared morphological consequences of global warming in North American migratory birds

Brian Weeks, David Willard, Marketa Zimova, Aspen Ellis, Max Witynski, Mary Hennen & Ben Winger
Increasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four‐decade specimen series of 70 716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40‐year period predicts consistent reductions in body size across these diverse taxa. Concurrently, wing length – an index of body shape that impacts numerous aspects of avian ecology...

2018 Update to “An impact assessment of Great Lakes aquatic nonidigenous species”

Rochelle A. Sturtevant, El Lower, Nicholas Boucher, Peter Alsip, Kylan Hopper, Susannah Iott, Doran M. Mason, Ashley Elgin & Felix A. Martinez
NOAA Technical Memorandum GLERL ; 161b

Data from: A phylogenomic framework for pelagiarian fishes (Acanthomorpha: Percomorpha) highlights mosaic radiation in the open ocean

Matthew Friedman, Kara Feilich, Hermione Beckett, Michael Alfaro, Brant Faircloth, David Černý, Masaki Miya, Thomas Near & Richard Harrington
The fish clade Pelagiaria, which includes tunas as its most famous members, evolved remarkable morphological and ecological variety in a setting not generally considered conducive to diversification: the open ocean. Relationships within Pelagiaria have proven elusive due to short internodes subtending major lineages suggestive of rapid early divergences. Using a novel sequence dataset of over 1000 ultraconserved DNA elements (UCEs) for 94 of the 286 species of Pelagiaria (more than 70% of genera), we provide...

Documentation for the IRIS UMETRICS 2019 Data Release

Natsuko Nicholls, Lindsay Uberseder & Jason Owen-Smith
This is the full data documentation prepared for the IRIS UMETRICS 2019 Data Release. This documentation is only accessible within the IRIS Virtual Data Enclave. It provides detailed descriptions about the third annual IRIS UMETRICS dataset released in April 2019.

Data from: Nocturnal flight-calling behaviour predicts vulnerability to artificial light in migratory birds

Benjamin M. Winger, Brian C. Weeks, Andrew Farnsworth, Andrew W. Jones, Mary Hennen & David E. Willard
Understanding interactions between biota and the built environment is increasingly important as human modification of the landscape expands in extent and intensity. For migratory birds, collisions with lighted structures are a major cause of mortality, but the mechanisms behind these collisions are poorly understood. Using 40 years of collision records of passerine birds, we investigated the importance of species’ behavioral ecologies in predicting rates of building collisions during nocturnal migration through Chicago, IL and Cleveland,...

Data from: Differential changes in bone strength of two inbred mouse strains following administration of a sclerostin-neutralizing antibody during growth

Noah J. Mathis, Emily N. Adaniya, Lauren M. Smith, Alexander G. Robling, Karl J. Jepsen & Stephen H. Schlecht
Administration of sclerostin-neutralizing antibody (Scl-Ab) treatment has been shown to elicit an anabolic bone response in growing and adult mice. Prior work characterized the response of individual mouse strains but did not establish whether the impact of Scl-Ab on whole bone strength would vary across different inbred mouse strains. Herein, we tested the hypothesis that two inbred mouse strains (A/J and C57BL/6J (B6)) will show different whole bone strength outcomes following sclerostin-neutralizing antibody (Scl-Ab) treatment...

2011 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: Heterochrony in chimpanzee and bonobo spatial memory development

Alexandra G. Rosati
Objectives: The emergence of human-unique cognitive abilities has been linked to our species' extended juvenile period. Comparisons of cognitive development across species can provide new insights into the evolutionary mechanisms shaping cognition. This study examined the development of different components of spatial memory, cognitive mechanisms that support complex foraging, by comparing two species with similar life history that vary in wild ecology: bonobos (Pan paniscus) and chimpanzees (Pan troglodytes). Materials and methods: Spatial memory development...

Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record

Caroline Parins-Fukuchi, Elliot Greiner, Laura M. MacLatchy & Daniel C. Fisher
Probabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary patterns by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary...

Data from: Flexible gaze-following in rhesus monkeys

Rosemary Bettle & Alexandra G. Rosati
Humans are characterized by complex social cognitive abilities that emerge early in development. Comparative studies of nonhuman primates can illuminate the evolutionary history of these social capacities. We examined the cognitive skills that rhesus monkeys (Macaca mulatta) use to follow gaze, a foundational skill in human social development. While rhesus monkeys can make inferences about others’ gaze when competing, it is unclear how they think about gaze information in other contexts. In study 1, monkeys...

Gremlin is a potential target for posterior capsular opacification

Bo Ma, Ruihua Jing, Jie Liu, Tiantian Qi & Cheng Pei
Objective: The present study was conducted to determine the role of gremlin during the development of posterior capsular opacification (PCO) via in vitro and in vivo experiments. Methods: The activation, roles and relationships of the BMPs/Smad1/5, MAPK, FAK and AKT signaling pathways in human lens epithelial cells (HLECs) after gremlin induction were detected by western blotting and real-time PCR. Wound-healing, transwell, capsular bag models and rat PCO models assays were used to test the effects...

Effective Strategies for Recording Interviewer Observations: Evidence from the PASS Study in Germany

Brady T. West & Mark Trappmann

HIF-1α promotes the keloid development through the activation of TGF-β/Smad and TLR4/MyD88/NF-κB pathways

Rui Lei, Jian Li, Feng Liu, Weihan Li, Shizhen Zhang, Yang Wang, Xi Chu & Jinghong Xu
A keloid is defined as an overgrowth of the dense fibrous tissues that form around a wound. Since they destroy the vascular network, keloid tissues often exhibit anoxic conditions. Hypoxia-inducible factor-1α (HIF-1α) is a core factor that mediates hypoxia stress responses and regulates the hypoxic cellular and biological behaviors. In this study, we found that the expression level of HIF-1α in keloid tissue was significantly higher than that in the normal skin tissue. Hypoxia-induced HIF-1α...

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data

Clément Goubert, Jainy Thomas, Lindsay Payer, Jeffrey Kidd, Julie Feusier, W. Scott Watkins, Kathleen Burns, Lynn Jorde & Cédric Feschotte
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alu are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alu and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses...

Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming

Eric Meineri, Kari Klanderud, John Guittar, Deborah Goldberg & Vigdis Vandvik
Understanding the degree to which plant communities are open to seedling recruitment is key to predicting how they will be impacted by climate change. We experimentally assessed whether communities assembled under colder climates were inherently more open to recruitment than warmer-climate communities, after controlling for differences in the current climate under which the communities were growing. We then tested whether variation in openness to recruitment could be explained by community biomass or by the plant...

Sex differences in IV thrombolysis treatment for stroke: a systematic review and meta-analysis

Brent Strong, Lynda Lisabeth & Mathew Reeves
Objective: A prior meta-analysis of reports published between 2000 and 2008 found that women were 30% less likely to receive IV rt-PA treatment for stroke than men; we updated this meta-analysis to determine if this sex difference still persisted. Methods: We identified studies that reported sex-specific IV rt-PA treatment rates for acute ischemic stroke published between 2008 and 2018. Eligible studies included representative populations of ischemic stroke patients from hospital-based, registry-based, or administrative data. Random...

Data from: The contribution of host cell-directed vs. parasite-directed immunity to the disease and dynamics of malaria infections

Nina Wale, Matthew J. Jones, Derek G. Sim, Andrew F. Read & Aaron A. King
Hosts defend themselves against pathogens by mounting an immune response. Fully understanding the immune response as a driver of host disease and pathogen evolution requires a quantitative account of its impact on parasite population dynamics. Here, we use a data-driven modeling approach to quantify the birth and death processes underlying the dynamics of infections of the rodent malaria parasite, Plasmodium chabaudi, and the red blood cells (RBCs) it targets. We decompose the immune response into...

Similar but different: Revealing the relative roles of species‐traits versus biome properties structuring genetic variation in South American marsh rats

Joyce Rodrigues Do Prado, Joyce R. Prado, Alexandre R. Percequillo, Andréa T. Thomaz & L. Lacey Knowles
Aim: Wetland habitats, and the ecological restrictions imposed by them, structure patterns of genetic variation in constituent taxa. As such, genetic variation may reflect properties of the specific biomes species inhabit, or shared life history traits among species may result in similar genetic structure. We evaluated these hypotheses jointly by quantifying the similarity of genetic structure in three South American marsh rat species (Holochilus), and test how genetic variation in each species relates to biome‐specific...

Registration Year

  • 2019

Resource Types

  • Dataset
  • Text


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