256 Works

Embracing Heterogeneity in Modern GPUs

Xulong Tang
Graphics Processing Units is one of the most widely adopted parallel computing engines for modern applications. However, due to the “memory wall”, the scaling of GPUs is lagging behind the ever-growing complexity of application algorithms and ever-increasing data volume of inputs. Near-data computing (NDC) is a widely-acknowledged computing paradigm that alleviates the memory wall problem by offloading computation to data instead of conventional fetching data to computation. While the NDC GPU architectures have been proposed...

Coastal rivers: the missing link in source to sink understanding of sediment flux in a changing world

John Gardner
Rivers connect continents to coasts moving sediment needed to sustain coastal ecosystems. Slow moving, coastal rivers are known to be “bottlenecks” that control how much sediment actually reaches coasts. Yet, coastal rivers are typically ignored in estimates of riverine sediment delivery to coasts and few approaches are able to measure the influence of coastal rivers. We developed a satellite remote sensing method to measure suspended sediment concentration spatially along rivers. We will use this method...

Determining gene expression control during neural differentiation through coupled protein localization and RNA-seq in single cells

Sarah Hainer
Although the primary sequence of the eukaryotic genome is largely invariant across cells in an organism, the expression of genes is tightly regulated: specific complements and levels of expressed genes define the identity and function of cells. A primary mechanism of gene expression control is at the level of access to DNA sequences that can direct expression of individual genes. Access to these DNA regulatory elements is established and maintained by the combinatorial binding of...

Understanding Polarizing Community Perspectives on Harm Reduction Strategies

Stephanie L. Creasy, Jessica R. Thompson, Christina F. Mair & Jessica G. Burke
Introduction: Rural communities face barriers to opioid treatment and overdose prevention including concerns about stigma and lack of harm reduction services. Purpose: The aim of this study was to explore community perspectives and understanding of harm reduction approaches to opioid use and overdose in a high-risk Northern Appalachian case community in Pennsylvania. Methods: A small town approximately 10 miles from Pittsburgh was identified as the community with the greatest predicted probabilities of epidemic outbreak using...

Data from: Genetic mapping and phylogenetic analysis reveal intraspecific variation in sex chromosomes of the Virginian strawberry

Na Wei, Rajanikanth Govindarajulu, Jacob A. Tennessen, Aaron Liston & Tia-Lynn Ashman
With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted...

Data from: Parallel genetic adaptation across environments differing in mode of growth or resource availability

Caroline B. Turner, Christopher W. Marshall & Vaughn S. Cooper
Evolution experiments have demonstrated high levels of genetic parallelism between populations evolving in identical environments. However, natural populations evolve in complex environments that can vary in many ways, likely sharing some characteristics but not others. Here we ask whether shared selection pressures drive parallel evolution across distinct environments. We addressed this question in experimentally evolved populations founded from a clone of the bacterium Burkholderia cenocepacia. These populations evolved for 90 days (approximately 600 generations) under...

Data from: The index case is not enough: variation among individuals, groups, and social networks modify bacterial transmission dynamics

Carl N. Keiser, Noa Pinter-Wollman, Michael J. Ziemba, Krishna S. Kothamasu & Jonathan N. Pruitt
1.The traits of the index case of an infectious disease outbreak, and the circumstances for their etiology, potentially influence the trajectory of transmission dynamics. However, these dynamics likely also depend on the traits of the individuals with whom the index case interacts. 2.We used the social spider Stegodyphus dumicola to test how the traits of the index case, group phenotypic composition, and group size interact to facilitate the transmission of a GFP-labeled cuticular bacterium. We...

Data from: Invasion status and phylogenetic relatedness predict cost of heterospecific pollen receipt: implications for native biodiversity decline

Gerardo Arceo-Gómez & Tia-Lynn Ashman
Understanding the mechanisms by which invasive species affect native plants is a central challenge. Invasive plants have been shown to reduce pollinator visitation to natives and increase pollen quantity limitation. However, visitation and conspecific pollen delivery are only two components of the pollination process; post-pollination interactions on the stigma (heterospecific pollen [HP] receipt) could intensify pre-pollination responses to invasion. Here we used meta-analysis to test the hypotheses that invasive plants are more detrimental as HP...

Data from: In a long-term experimental demography study, excluding ungulates reversed invader’s explosive population growth rate and restored natives

Susan Kalisz, Rachel B. Spigler & Carol C. Horvitz
A major goal in ecology is to understand mechanisms that increase invasion success of exotic species. A recent hypothesis implicates altered species interactions resulting from ungulate herbivore overabundance as a key cause of exotic plant domination. To test this hypothesis, we maintained an experimental demography deer exclusion study for 6 y in a forest where the native ungulate Odocoileus virginianus (white-tailed deer) is overabundant and Alliaria petiolata (garlic mustard) is aggressively invading. Because population growth...

Data from: Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation

Carol Goodwillie, Risa D. Sargent, Susan Kalisz, Richard H. Ree, David A. Moeller, Mario Vallejo-Marin, Christopher G. Eckert, Alice A. Winn, Elizabeth Elle, Monica A. Geber & Mark O. Johnston
Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and...

Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection

Matthew J. Robak & Corinne L. Richards-Zawacki
Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to...

Data from: Persistent social interactions beget more pronounced personalities in a desert-dwelling social spider

Andreas P. Modlmeier, Kate L. Laskowski, Alex E. DeMarco, Anna Coleman, Katherine Zhao, Hayley A. Brittingham, Donna R. McDermott & Jonathan N. Pruitt
The social niche specialization hypothesis predicts that repeated social interactions will generate social niches within groups, thereby promoting consistent individual differences in behaviour. Current support for this hypothesis is mixed, probably because the importance of social niches is dependent upon the ecology of the species. We test whether repeated interactions among group mates generate consistent individual differences in boldness in the social spider, Stegodyphus dumicola. In support of the social niche specialization hypothesis, we found...

Data from: The potential for mass ratio and trait divergence effects to explain idiosyncratic impacts of nonnative invasive plants on carbon mineralization of decomposing leaf litter

Sara E. Kuebbing & Mark A. Bradford
1. Invasive plant effects on litter decomposition tend to be idiosyncratic among species and ecosystems, which may arise from variation in the invader’s relative abundance (mass ratio effect), its relative functional difference to other species (trait divergence effect), and/or from species’ litter mixing that causes non-additive decomposition rates relative to single-species decomposition. 2. We use experimental microcosms to quantify the potential for mass ratio and trait divergence to explain effects of invasive litters on carbon...

Data from: Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: is disturbance an alternative explanation?

Eric A. Griffin, Joshua G. Harrison, Steven W. Kembel, Alyssa A. Carrell, S. Joseph Wright & Walter P. Carson
1. Bacterial endophytes may be fairly host specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community-wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. 2. We tested the following four non-mutually exclusive hypotheses: 1. The Host Identity Hypothesis: endophytes vary substantially among different host plant species. 2. The Core Microbiome Hypothesis: a subset of...

Data from: Individual personalities shape task differentiation in a social spider

Lena Grinsted, Jonathan N. Pruitt, Virginia Settepani & Trine Bilde
Deciphering the mechanisms involved in shaping social structure is key to a deeper understanding of the evolutionary processes leading to sociality. Individual specialization within groups can increase colony efficiency and consequently productivity. Here, we test the hypothesis that within-group variation in individual personalities (i.e. boldness and aggression) can shape task differentiation. The social spider Stegodyphus sarasinorum (Eresidae) showed task differentiation (significant unequal participation) in simulated prey capture events across 10-day behavioural assays in the field,...

Data from: Personality composition is more important than group size in determining collective foraging behaviour in the wild

Carl N. Keiser & Jonathan N. Pruitt
Describing the factors that shape collective behaviour is central to our understanding of animal societies. Countless studies have demonstrated an effect of group size in the emergence of collective behaviours, but comparatively few have accounted for the composition/diversity of behavioural phenotypes, which is often conflated with group size. Here, we simultaneously examine the effect of personality composition and group size on nest architecture and collective foraging aggressiveness in the social spider Stegodyphus dumicola. We created...

Data from: Individual differences in boldness influence patterns of social interactions and the transmission of cuticular bacteria among group-mates

Carl N. Keiser, Noa Pinter-Wollman, David A. Augustine, Michael J. Ziemba, Lingran Hao, Jeffrey G. Lawrence & Jonathan N. Pruitt
Despite the importance of host attributes for the likelihood of associated microbial transmission, individual variation is seldom considered in studies of wildlife disease. Here, we test the influence of host phenotypes on social network structure and the likelihood of cuticular bacterial transmission from exposed individuals to susceptible group-mates using female social spiders (Stegodyphus dumicola). Based on the interactions of resting individuals of known behavioural types, we assessed whether individuals assorted according to their behavioural traits....

Data from: Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

Rajanikanth Govindarajulu, Aaron Liston & Tia-Lynn Ashman
We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be inherited maternally, but the chromosome that houses the sex-determining region differs. Thus, we asked whether (1) the cytotypic composition of hybrid populations represents one or...

Data from: Rapid divergence of wing volatile profiles between subspecies of the butterfly Pieris rapae (Lepidoptera: Pieridae)

Eden W. McQueen & Nathan I. Morehouse
Complex signaling traits such as pheromone profiles can play an important role in the early stages of reproductive isolation between populations. These signals can diverge along multiple trait axes, and signal receivers are often sensitive to subtle differences in signal properties. In the Lepidoptera, prior research has highlighted that natural selection can drive rapid chemical signal divergence, for instance via mate recognition to maintain species boundaries. Much less is known about the occurrence of such...

Data from: Longitudinal cognitive and biomarker changes in dominantly inherited Alzheimer disease

Eric McDade, Guoqiao Wang, Brian Andrew Gordon, Jason Hassenstab, Tammie L.S. Benzinger, Virginia Buckles, Anne M. Fagan, David M. Holtzman, Nigel J. Cairns, Alison M. Goate, Daniel S. Marcus, John C. Morris, Katrina Paumier, Chengjie Xiong, Ricardo Allegri, Sarah B. Berman, William Klunk, James Nobel, John Ringman, Bernardino Ghetti, Martin Farlow, Reisa Anne Sperling, Jasmeer Chhatwal, Stephen Salloway, Neil R. Graff-Radford … & Randall J. Bateman
Objective: To assess the onset, sequence and rate of progression of comprehensive biomarker and clinical measures across the spectrum of Alzheimer disease using the Dominantly Inherited Alzheimer Network (DIAN) study and compare these to cross-sectional estimates. Methods: We conducted longitudinal clinical, cognitive, cerebrospinal fluid (CSF) and neuroimaging assessments (mean of 2.7 (+/- 1.1) visits) in 217 DIAN participants. Linear mixed effects models were used to assess changes in each measure relative to individuals’ estimated years...

Data from: Behavioral hypervolumes of predator groups and predator-predator interactions shape prey survival rates and selection on prey behavior

Jonathan N. Pruitt, Kimberley Howell, Shaniqua Gladney, Yusan Yang, James L. L. Lichtenstein, Michelle Elise Spicer, Sebastian A. Echeverri & Noa Pinter-Wollman
Predator-prey interactions often vary on the basis of the traits of the individual predators and prey involved. Here we examine whether the multidimensional behavioral diversity of predator groups shapes prey mortality rates and selection on prey behavior. We ran individual sea stars (Pisaster ochraceus) through three behavioral assays to characterize individuals’ behavioral phenotype along three axes. We then created groups that varied in the volume of behavioral space that they occupied. We further manipulated the...

Data from: Proximity to agriculture is correlated with pesticide tolerance: evidence for the evolution of amphibian resistance to modern pesticides

Rickey D. Cothran, Jenise M. Brown & Rick A. Relyea
Anthropogenic environmental change is a powerful and ubiquitous evolutionary force, so it is critical that we determine the extent to which organisms can evolve in response to anthropogenic environmental change and whether these evolutionary responses have associated costs. This issue is particularly relevant for species of conservation concern including many amphibians, which are experiencing global declines from many causes including widespread exposure to agrochemicals. We used a lab toxicity experiment to assess variation in sensitivity...

Data from: Dissecting pollinator responses to a ubiquitous ultraviolet floral pattern in the wild

Matthew H. Koski & Tia-Lynn Ashman
1. Color patterns on flowers can increase pollinator visitation and enhance foraging behavior. Flowers uniform in color to humans, however, can appear patterned to insects due to spatial variation in UV-reflectance on petals. A UV ‘bullseye’ pattern that is common among angiosperms—UV-absorbing petal bases and reflective apices—purportedly functions as a nectar guide, enhancing pollinator orientation, and experimental evidence suggests that UV reflectance increases apparency to pollinators. 2. We test the pollinator-attracting and -orienting functions of...

Hepatic estrogen sulfotransferase distantly sensitizes mice to hemorrhagic shock-induced acute lung injury

Yang Xie, Anne Barbosa, Meishu Xu, Patrick Oberly, Songrong Ren, Robbert Gibbs, Samuel Poloyac, Wenchao Song, Jie Fan & Wen Xie
Hemorrhagic shock (HS) is a potential life-threatening condition that may lead to injury to multiple organs, including the lung. The estrogen sulfotransferase (EST, or SULT1E1) is a conjugating enzyme that sulfonates and deactivates estrogens. In this report, we showed that the expression of Est was markedly induced in the liver, but not in the lung of female mice subject to hemorrhagic shock and resuscitation (HS/R). Genetic ablation or pharmacological inhibition of Est effectively protected female...

Predicting resistance to amyloid-beta deposition and cognitive resilience in the oldest-old

Beth Snitz
Objective: To explore long-term predictors of avoiding amyloid-beta (Aβ) deposition and maintaining unimpaired cognition as outcomes in the oldest old. Methods: In a longitudinal observational cohort study, N=100 former participants of the Ginkgo Evaluation of Memory Study (GEMS; 2000-2008) completed biannual Pittsburgh Compound B (PiB)-PET imaging and annual clinical-cognitive evaluations beginning in 2010. Most recent Aβ status and cognitive status were selected for each participant. Longitudinal outcomes included change in serial Aβ and cognitive tests....

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  • University of Pittsburgh
  • Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
  • Cluster of Excellence livMatS, Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, 79110 Freiburg, Germany
  • Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany
  • Oregon State University
  • University of Minnesota
  • Massachusetts General Hospital
  • University of Washington
  • University of California, Davis
  • University of Arizona