49 Works

Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska

Joseph Napier, Matias Fernandez, Guillaume De Lafontaine & Feng Sheng Hu
Larix laricina (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether in situ persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new...

Pore scale study of water adsorption and subsequent methane transport in clay in the presence of wettability heterogeneity

Rui Xu, Masa Prodanovic & Christopher Landry

Seismogenesis at Hikurangi Integrated Research Experiment (SHIRE) onshore seismic acquisition field report

Katie Jacobs, Stuart A Henrys, D Okaya, H Van Avendonk, Jenny Black, Dan H. N. Barker, Sapthala C Karalliyadda, E Kurashimo, Wanda R. Stratford, M Savage, R Sullivan, Zane R. Bruce & L Hughes
This report documents the acquisition and archiving of a major controlled source and passive seismic imaging project, the Seismogenesis Hikurangi Integrated Research Experiment (SHIRE). The SHIRE project aims to identify and quantify factors controlling the long-term evolution of the Hikurangi margin and the mode of slip along the subduction megathrust. The components of the data volume were acquired in two phases; between October 2017 – April 2018 (SHIRE I) and February–March 2019 (SHIRE II). The...

A Positive Spin on a Negative Narrative: How the Media Portrays Fraternities and What Fraternities Can Do About It

Zachary Taylor, Jennifer Zamora, Arianne McArdle & Mario Villa

F2R polymorphisms and clopidogrel efficacy and safety in patients with minor stroke or TIA: supplemental figures and tables

Yuesong Pan, Runqi Wangqin, Hao Li, Yilong Wang, Xia Meng, S. Claiborne Johnston, Tabassome Simon, Jinxi Lin, Xingquan Zhao, Liping Liu, David Wang & Yongjun Wang
Objective: To investigate the association between protease-activated receptors-1 (PAR-1) gene F2R polymorphisms and efficacy of clopidogrel for minor stroke or transient ischemic attack (TIA). Methods: Three single-nucleotide polymorphisms (CYP2C19*2 [681G>A, rs4244285], CYP2C19*3 [636G>A, rs4986893] and F2R [IVSn-14 A/T, rs168753] were genotyped among 2,924 patients randomized to clopidogrel plus aspirin (n=1461) or aspirin alone (n=1463). The primary efficacy outcome was new stroke (ischemic or hemorrhagic) and the safety outcome was any bleeding. Results: Overall, 859(29.4%) were...

Data for: Landscape scale variation in the hydrologic niche of California coast redwood

Emily J. Francis, Gregory P. Asner, Katharine J. Mach & Christopher B. Field
Topoclimatic diversity within forest landscapes can underlie variation in water availability, which may correspond to patterns in habitat suitability of tree species with differing hydrologic niches. However, the trade-off between the collection of data at a fine grain size over large spatial extents has limited comprehensive analyses of landscape scale variation in habitat suitability. We present a fine scale analysis of the roles of topographic gradients in moisture availability, soil water storage, and fog frequency...

IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

Jessika Consuegra, Joël Gaffé, Richard E. Lenski, Thomas Hindre, Jeffrey E. Barrick, Olivier Tenaillon & Dominique Schneider
The long-term dynamics of IS elements and their effects on bacteria are poorly understood, including whether they are primarily genomic parasites or important drivers of adaptation by natural selection. Here, we investigate the dynamics of IS elements and their contribution to genomic evolution and fitness during a long-term experiment with Escherichia coli. This data set includes the Rmd file to analyze the genomic and metagenomic data (Tenaillon et al. 2016 and Good et al. 2017)...

Combined-evidence analyses of ultraconserved elements and morphological data: an empirical example in iguanian lizards

Simon Scarpetta
Genomic datasets generated by next-generation sequencing are increasingly prevalent in phylogenetics, but morphological data are required to phylogenetically place fossils, corroborate molecular hypotheses, and date phylogenies. Combined-evidence analyses provide an integrative assessment of tree topology. However, no attempt has been made to simultaneously analyze next-generation genomic datasets and morphological data, and the future of morphology in the context of genomic data is uncertain. I conducted combined-evidence analyses that include genomic and morphological datasets, specifically, with...

Reversible diffusion-weighted imaging lesions in acute ischemic stroke: a systematic review

Nandakumar Nagaraja, John Forder, Steven Warach & Jośe Merino
Supplemental data: NNagaraja_12292019_DWI_Reversal_In_AIS_Review_Supplemental_File Supplemental Figure e-1: DWI reversal in acute ischemic stroke Supplemental Table e-1: Search Strategy Supplemental Table e-2: Variables extracted for the review Supplemental Table e-3: Imaging protocols for included studies Supplemental Table e-4: DWIR definitions used in the selected studies Supplemental Table e-5: Imaging characteristics of patients Supplemental Table e-6: QUADAS-2 tool for quality assessment of diagnostic accuracy studies by evaluating risk of bias and applicability concerns.

Lost in Translation

Z.W. Taylor
As our world becomes increasingly globalized in social, economic, and political contexts, U.S. students choose to study abroad to develop their international communication skills, cross-cultural competencies, and second or third languages (NAFSA, 2017). However, an under-researched element of the international education enrollment process is how readable and translated international admissions instructions are, especially for language-minority students whose first language is not English, comprising over 92 million people living in the U.S. (Dillinger, 2017). Examining the...

Cassowary gloss and a novel form of structural color in birds

Chad Eliason & Julia Clarke
One of the two lineages of extant birds resulting from its deepest split, Palaeognathae, has been reported not to exhibit structural coloration in feathers, affecting inferences of ancestral coloration mechanisms in extant birds. Structural coloration in facial skin and eggshells have been shown in the lineage, but not feathers. Here, we report the first evidence for two distinct mechanisms of structural color in palaeognath feathers. One extinct volant clade, Lithornithidae, shows evidence of elongate melanin-containing...

Data from: A new dissorophoid temnospondyl from the Allegheny Group (Late Westphalian, Carboniferous) of Five Points, Mahoning County, Ohio (USA)

Rainer Schoch, Amy Henrici & Robert Hook
A small temnospondyl skull from the Upper Carboniferous Allegheny Group of Five Points, Ohio, is referred to a new dissorophoid, Palodromeus bairdi n. gen n. sp. The complete skull with mandibles is preserved in counterparts. It is characterized by (1) elongated slit-like choana, (2) postfrontal, postorbital, and supratemporal bearing a distinct ridge, and (3) reduced parietal only two-thirds the length of the frontal. Phylogenetic analysis confirms a dichotomy between amphibamiforms and olsoniforms and places Palodromeus...

Switchgrass v5 4-way (AP13 x DAC, WBC x VS16) genetic map

John Lovell, Adam Healey, Jeremy Schmutz & Thomas Juenger
Here we present the genetic map construction methods for the switchgrass 4-way mapping population. The map spans 750 recombinant 4-way (pseudo F2) progeny genotyped at 4700 markers. These data are formatted for simple input into R/qtl and most other QTL mapping programs.

Reversible Diffusion Weighted Imaging Lesion in Acute Ischemic Stroke – A Systematic Review

Nandakumar Nagaraja, John Forder, Steven Warach & Jośe Merino
Supplemental data: NNagaraja_12292019_DWI_Reversal_In_AIS_Review_Supplemental_File Supplemental Figure e-1: DWI reversal in acute ischemic stroke Supplemental Table e-1: Search Strategy Supplemental Table e-2: Variables extracted for the review Supplemental Table e-3: Imaging protocols for included studies Supplemental Table e-4: DWIR definitions used in the selected studies Supplemental Table e-5: Imaging characteristics of patients Supplemental Table e-6: QUADAS-2 tool for quality assessment of diagnostic accuracy studies by evaluating risk of bias and applicability concerns.

Data from: Recurrent circuit dynamics underlie persistent activity in the macaque frontoparietal network

Eric Hart & Alexander Huk
During delayed oculomotor response tasks, neurons in the lateral intraparietal area (LIP) and the frontal eye fields (FEF) exhibit persistent activity that reflects the active maintenance of behaviorally relevant information. Despite many computational models of the mechanisms of persistent activity, there is a lack of circuit-level data from the primate to inform the theories. To fill this gap, we simultaneously recorded ensembles of neurons in both LIP and FEF while macaques performed a memory-guided saccade...

White Matter Tractography Viewer

Population Receptive Field (PRF) Surface Viewer

Groundwater recharge in Africa from ground based measurements

Alan MacDonald, Murray Lark, Richard Taylor, Tamiru Abiye, Helen Fallas, Guillaume Favreau, Ibrahim Goni, Seifu Kebede, Bridget Scanlon, James Sorenson, Moshood Tijani, Kirsty Upton & Charles West
This dataset comprises a map of groundwater recharge for Africa and a database of the 134 observations used to generate the map. The map shows long term average annual groundwater recharge in mm per annum relevant to the period 1970 to 2020. It is in the form of a GIS shapefile and is available as a layer package for ESRI and also as a georeferenced TIFF and BIL file for easy exchange with other software....

Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics

Deise Josely Pereira Goncalves, Gustavo H. Shimizu, Edgardo M. Ortiz, Robert K. Jansen & Beryl B. Simpson
PREMISE OF THE STUDY: Despite the fast pace of exploration of the patterns and processes influencing Neotropical plant hyperdiversity, taxa explored are mostly from large groups that are widely distributed, morphologically diverse or economically important. Vochysiaceae is an example of an undersampled taxon, providing an excellent system for investigating Neotropical biogeography. We present a phylogenomic-based hypothesis of species relationships in Vochysiaceae to investigate its evolutionary history through space and time. METHODS: We inferred a phylogeny...

Data from: Bee phenology is predicted by climatic variation and functional traits

Michael Stemkovski, Will Pearse, Sean Griffin, Gabriella Pardee, Jason Gibbs, Terry Griswold, John Neff, Ryan Oram, Molly RightMyer, Cory Sheffield, Karen Wright, Brian Inouye, David Inouye & Rebecca Irwin
Climate change is shifting the environmental cues that determine the phenology of interacting species. Plant-pollinator systems may be susceptible to temporal mismatch if bees and flowering plants differ in their phenological responses to warming temperatures. While the cues that trigger flowering are well-understood, little is known about what determines bee phenology. Using Generalized Additive Models, we analyzed time-series data representing 67 bee species collected over nine years in the Colorado Rocky Mountains to perform the...

Network Neuroscience Visualizer

White Matter Tracts Surface Visualizer

Archives and Special Collections Linked Data: Navigating between Notes and Nodes

Erin Blake, Itza A. Carbajal, Regine Heberlein, Sarah Horowitz, Jason Kovari, VANESSA LACEY, Cory Lampert, Holly Mengel, Cory Nimer, Maria Oldal, Merrilee Proffitt, Nathan Putnam, Arielle Rambo, Elizabeth Roke, Eric de Ruijter, Dan Santamaria, Karen Smith-Yoshimura, Weatherly Stephan, Bruce Washburn & Chela Weber

Tweeting in Greek: How National Fraternities and Sororities Use Twitter

Zachary Taylor & Arianne McArdle

Dataset for the transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory

Rayna Harris, Hsin-Yi Kao, Juan Marcos Alarcon, André Fenton & Hans Hofmann
The hippocampus plays a critical role in storing and retrieving spatial information. By targeting the dorsal hippocampus and manipulating specific “candidate” molecules using pharmacological and genetic manipulations, we have previously discovered that long-term active place avoidance memory requires transient activation of particular molecules in dorsal hippocampus. These molecules include amongst others, the persistent kinases Ca-calmodulin kinase II (CaMKII) and the atypical protein kinase C isoform PKC iota/lambda for acquisition of the conditioned behavior, whereas persistent...

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