20 Works

Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader

Ben Flanagan, Stacy Krueger-Hadfield, Courtney Murren, Chris Nice, Allan Strand & Erik Sotka
Genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during invasions. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution. A survey of 62,285 SNPs for 351...

2018 FaultScan San Jacinto Fault dense array experiment

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This experiment is part of the FaultScan project (UGA, UCSD, USC). It targets the San Jacinto Fault by using passive seismic interferometry measurements across the fault using permanent and dense array stations. This preliminary experiment in 2018 will be followed by longer-term arrays deployments starting 2022.

Congestion reduction via personalized incentives

Ali Ghafelebashi, Meisam Razaviyayn & Maged Dessouky
The purpose of this research is to develop real-time algorithms to reduce traffic congestion and improve routing efficiency via offering personalized incentives to drivers. The incentives and alternative routes should be chosen smartly in order to maximize the probability of acceptance by drivers and to avoid the creation of new congestion in other areas of the network. To this end, we propose to exploit the wide-accessibility of smart communication devices and develop a real-time look-ahead...

Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica

Joanna Griffiths, Kevin Johnson, Kyle Sirovy, Mark Yeats, Francis Pan, Jerome La Peyre & Morgan Kelly
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity. We outplanted oysters to either a low or medium salinity site in Louisiana for two years. We then crossed adult parents using a North Carolina...

DatasetS2 Intramidbrain macroconnection reports for rat

Larry Swanson
This file contains data used to construct connection matrices for network analysis of the rat intra-midbrain axonal connections from one gray matter region to another. The data was expertly collated from the peer-reviewed neuroanatomical literature. The Connection Reports are listed in an Excel Worksheet and are self-explanatory.

Supplementary information for: A biased fossil record can preserve reliable phylogenetic signal

C. Henrik Woolley, Jeffrey Thompson, Yun-Hsin Wu, David Bottjer & Nathan Smith
Abstract.­­––The fossil record is notoriously imperfect and biased in representation, hindering our ability to place fossil specimens into an evolutionary context. For groups with fossil records mostly consisting of disarticulated parts (e.g., vertebrates, echinoderms, plants), the limited morphological information preserved sparks concerns about whether fossils retain reliable evidence of phylogenetic relationships, and lends uncertainty to analyses of diversification, paleobiogeography, and biostratigraphy in Earth history. To address whether a fragmentary past can be trusted, we need...

Food insecurity and brain health in adults: A systematic review

Alan J. McMichael, Bernadette McGuinness, Jinkook Lee, Hoang Van Minh, Jayne V. Woodside & Claire T. McEvoy
Food insecurity has been associated with adverse effects on physical health and well-being in both high and low-income countries, but effects on brain health are not clear. The purpose of this systematic review was to determine the relationship between food insecurity and important brain health outcomes in adults including depression, stroke, cognitive impairment and dementia. Electronic databases were searched to find studies which investigated relations between food insecurity and predefined brain health outcomes. Thirty studies...

Comparing single-species and mixed-species groups in fruit flies: differences in group dynamics but not group formation

Julia Saltz, Anna Girardeau & Brad Foley
Mixed-species groups describe active associations among individuals of two or more species at the same trophic level. Mixed-species groups are important to key ecological and evolutionary processes such as competition and predation; and ignoring the presence of other species risks ignoring a key aspect of the environment in which social behavior is expressed and selected. Despite the defining emphasis of active formation for mixed-species groups, surprisingly little is known about the mechanisms by which mixed-species...

2-back task in split-belt adaptation

Cristina Rossi, Ryan Roemmich, Nicolas Schweighofer, Amy Bastian & Kristan Leech
We studied split-belt treadmill adaptation and savings in young (21±2 y/o) and older (56±6 y/o) adults with or without a secondary 2-back task during adaptation. We here provide here kinematic data for split-belt treadmill walking - specifically, step length asymmetry, double support asymmetry, and limb excursion asymmetry measure. We provide raw response data (button presses and reaction time) for performance in the 2-back cognitive task. We also provide scripts that can be used to analyse...

Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

Caitlin G. Howe, Helen B. Foley, Shohreh F. Farzan, Thomas A. Chavez, Mark Johnson, John D. Meeker, Theresa M. Bastain, Carmen J. Marsit & Carrie V. Breton
Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated...

Recommended fossil calibrators for time-scaled molecular phylogenies of Afrotheria

Steven Heritage, Erik Seiffert & Matthew Borths
A phylogenetic framework provides the necessary evolutionary context for studies of comparative anatomy, life history, behavior, biogeography, systematics, and conservation. Time-scaled phylogenetic analyses require researchers to include calibration ages which are used to fit a model that transforms tree branch lengths into units of time. The inclusion of multiple calibration ages (if they are available) is a best practice that brings all the available evidence to bear on the temporal model. While selecting the appropriate...

Data from: Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios

Erinn Muller, Ashley Dungan, Wyatt Million, Katherine Eaton, Chelsea Petrik, Erich Bartels, Emily Hall & Carly Kenkel
Knowledge of multi-stressor interactions and the potential for trade-offs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here we conducted an aquaria-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered...

Adaptive parameter of standard deviation enhances the power of noninvasive prenatal screens

Li Qu, Qixi Wu, Xiaoke Yang, Weiwei Wang, Bing Xu, Guangyu Shan, Lin Liang, Shaowei Wang & Jingbo Zhang
Traditional Z-test methods during noninvasive prenatal screens (NIPS) use the fixed parameter of standard deviation (SD), which ignores the influence of actual sequencing read counts of a sample on the results. The aim of this study is to eliminate the influence of the sequencing depth of individual samples on the results and enhance the power of NIPS. In this study, we propose an improved NIPS method, which calculates the SD in the Z-score process adaptively...

Data from: An Early Oligocene age for the oldest known monkeys and rodents of South America

Erik Seiffert
The Santa Rosa fossil locality in eastern Perú produced the first Paleogene vertebrate fauna from the Amazon Basin, including the oldest known monkeys from South America. This diverse paleofauna was originally assigned an Eocene age, based largely on the stage of evolution of the site’s caviomorph rodents and marsupials. Here we present new detrital zircon dates that indicate that the maximum composite age of Santa Rosa is 29.6±0.8 Ma (Lower Oligocene), although several zircons from...

Urinary metals and maternal circulating extracellular vesicle microRNA in the MADRES pregnancy cohort

Caitlin G. Howe, Helen B. Foley, Shohreh F. Farzan, Thomas A. Chavez, Mark Johnson, John D. Meeker, Theresa M. Bastain, Carmen J. Marsit & Carrie V. Breton
Exposure to metals increases risk for pregnancy complications. Extracellular vesicle (EV) miRNA contribute to maternal-foetal communication and are dysregulated in pregnancy complications. However, metal impacts on maternal circulating EV miRNA during pregnancy are unknown. Our objective was to investigate the impact of multiple metal exposures on EV miRNA in maternal circulation during pregnancy in the MADRES Study. Associations between urinary concentrations of nine metals and 106 EV miRNA in maternal plasma during pregnancy were investigated...

Food insecurity and brain health in adults: A systematic review

Alan J. McMichael, Bernadette McGuinness, Jinkook Lee, Hoang Van Minh, Jayne V. Woodside & Claire T. McEvoy
Food insecurity has been associated with adverse effects on physical health and well-being in both high and low-income countries, but effects on brain health are not clear. The purpose of this systematic review was to determine the relationship between food insecurity and important brain health outcomes in adults including depression, stroke, cognitive impairment and dementia. Electronic databases were searched to find studies which investigated relations between food insecurity and predefined brain health outcomes. Thirty studies...

Detrital magnetite grains scanned to detect inclusions for cosmogenic 3He exposure dating

Florian Hofmann & Emily Cooperdock
More than 3000 individual detrital magnetite grains from a fanglomerate near Whitewater (California, USA) were scanned using microCT. These data were used to detect mineral inclusion in these magnetite grains, which can contribute significant amounts of 3He. Grains without inclusions were then picked from these analyzed grains and used to calibrate the cosmogenic 3He production rate in magnetite (manuscript submitted to GChron).

Data from: Widespread loss of mammalian lineage and dietary diversity in the early Oligocene of Afro-Arabia

Dorien De Vries, Steven Heritage, Matthew Borths, Hesham Sallam & Erik Seiffert
Diverse lines of geological and geochemical evidence indicate that the Eocene-Oligocene transition (EOT) marked the onset of a global cooling phase, rapid growth of the Antarctic ice sheet, and a worldwide drop in sea level. Paleontologists have established that shifts in mammalian community structure in Europe and Asia were broadly coincident with these events, but the potential impact of early Oligocene climate change on the mammalian communities of Afro-Arabia has long been unclear. Here we...

BAF155 Methylation Drives Metastasis By Hijacking Super-enhancers and Subverting Anti-tumor Immunity

Eui-Jun Kim, Peng Liu, Shengjie Zhang, Kristine Donahue, Yidan Wang, Jennifer Schehr, Serena Wolfe, Amber Dickerson, Li Lu, Lixin Rui, Xuehua Zhong, Kari Wisinski, Min Yu, Aussie Suzuki, Joshua Lang, Irene Ong & Wei Xu
Subunits of the chromatin remodeler SWI/SNF are the most frequently disrupted genes in cancer. However, how post-translational modifications (PTM) of SWI/SNF subunits elicit epigenetic dysfunction remains unknown. Arginine-methylation of BAF155 by coactivator-associated arginine methyltransferase 1 (CARM1) promotes triple negative breast cancer (TNBC) metastasis. Herein, we discovered the dual roles of methylated-BAF155 (me-BAF155) in promoting tumor metastasis: activation of super-enhanceraddicted oncogenes by recruiting BRD4, and repression of interferon / pathway genes to suppress host immune response....

Data from: Ecological and environmental stability in offshore Southern California Marine Basins through the Holocene

Hannah Palmer, Tessa Hill, Esther Kennedy, Peter Roopnarine, Sonali Langlois, Katherine Reyes & Lowell Stott
In the face of ongoing marine deoxygenation, understanding timescales and drivers of past oxygenation change is of critical importance. Marine sediment cores from tiered silled basins provide a natural laboratory to constrain timing and implications of oxygenation changes across multiple depths. Here, we reconstruct oxygenation and environmental change over time using benthic foraminiferal assemblages from sediment cores from three basins across the Southern California Borderlands: Tanner Basin (EW9504-09PC, 1194 m water depth), San Nicolas Basin...

Registration Year

  • 2021
    20

Resource Types

  • Dataset
    20

Affiliations

  • University of Southern California
    20
  • University of California, Davis
    3
  • Queen's University Belfast
    2
  • University of Michigan–Ann Arbor
    2
  • Duke University
    2
  • University of Cambridge
    2
  • Hanoi University
    2
  • Birkbeck, University of London
    2
  • Emory University
    2
  • Imperial College London
    2