500 Works

Shale Network database – Production, Injection, and Flowback Water Geochemistry in shale gas development area in the northeastern USA as of March 2021

T. Wen & S.L. Brantley
This data set is a subset of the Shale Network database (https://doi.org/10.4211/his-data-shalenetwork). The Shale Network (http://www.shalenetwork.org/) is a project funded by the National Science Foundation to help scientists and other stakeholders store data for water resources that may be affected by gas exploitation in shale in the U.S.A. Our primary focus currently is the northeastern U.S.A. We want to enable the generation of knowledge from water chemistry and flow data collected in areas of extraction...

Scale Model Equations and Optimization for Annular Flow of Non-Newtonian Fluids Between Eccentric and Rotating Cylinders

Wei Zhang, Pooya Khodaparast, Amin Mehrabian & Amir Shojaei
A broad range of engineering applications involves helical flow of non-Newtonian fluids between two eccentric cylinders. These applications often require estimation of the frictional pressure losses along the axes of the cylinders. Laboratory flow loops are commonly used to study the flow characteristics at smaller scales of investigation. This study uses the laws of similarity and dimensional analysis to obtain a set of scaling equations between the laboratory and prototype scales of the described annular...

Idealized atmospheric boundary layer and tornado simulations for Wang et al. (2022) two-layer-model study.

A. Wang, Y. Pan, G. Bryan & P. Markowski
This dataset contains the numerical simulations used in the Wang et al. (2022) study of two-layer-model in an idealized atmospheric boundary layer and an idealized tornado. That work modifies a wall model from the engineering community known as two-layer model (TLM) to a widely used atmospheric LES mode, Cloud Model 1 (CM1). LES of an idealized, neutral atmospheric boundary layer are performed first, in order to validate the implementation of the TLM in CM1. Next,...

Model Input, Analysis Code, and Select Model Output for the Murdzek et al. (2022) Ordinary Convection Sensitivity Study

S. Murdzek, P. Markowski, Y.P. Richardson & M.R. Kumjian
This dataset contains all relevant Cloud Model 1 (CM1) input files, python analysis code, and select CM1 output for the Murdzek et al. (2022, MWR) study that explores how the sensitivity of simulated ordinary convection changes in environments with different lifting condensation levels (LCLs). Enough CM1 output is provided to recreate most of the figures from Murdzek et al. (2022), and the rest of the output can be recreated using the supplied input files.

Data from: Neonicotinoid insecticide travels through a soil food chain, disrupting biological control of non-target pests and decreasing soya bean yield

Margaret R. Douglas, Jason R. Rohr & John F. Tooker
1. Neonicotinoids are the most widely used insecticides world-wide, but their fate in the environment remains unclear, as does their potential to influence non-target species and the roles they play in agroecosystems. 2. We investigated in laboratory and field studies the influence of the neonicotinoid thiamethoxam, applied as a coating to soya bean seeds, on interactions among soya beans, non-target molluscan herbivores and their insect predators. 3. In the laboratory, the pest slug Deroceras reticulatum...

Data from: Symbiodinium glynnii sp. nov., a species of stress-tolerant symbiotic dinoflagellates from pocilloporid and montiporid corals in the Pacific Ocean

Drew C. Wham, Gang Ning & Todd C. LaJeunesse
A formal Symbiodinium species taxonomy enhances understanding of the physiology and ecology of coral–dinoflagellate symbioses. Here we formally define a new species of stress tolerant Symbiodinium in Clade D, Symbiodinium glynnii sp. nov. This species exhibits high host specificity for members of the stony coral genus Pocillopora in the Pacific Ocean and can also be found in symbiosis with the coral genera Seriatopora and Montipora. Symbiodinium glynnii is especially common in the Eastern Tropical and...

Data from: Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis)

Derek E. Lee, Douglas R. Cavener & Monica L. Bond
Polymorphic phenotypes of mammalian coat coloration have been important to the study of genetics and evolution, but less is known about the inheritance and fitness consequences of individual variation in complex coat pattern traits such as spots and stripes. Giraffe coat markings are highly complex and variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against visually hunting predators. We quantified complex coat pattern traits of...

Data from: The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

Lei Gao, Itay Gonda, Honghe Sun, Qiyue Ma, Kan Bao, Denise M. Tieman, Elizabeth A. Burzynski-Chang, Tara L. Fish, Kaitlin A. Stromberg, Gavin L. Sacks, Theodore W. Thannhauser, Majid R. Foolad, Maria Jose Diez, Joaquin Canizares, Yimin Xu, Esther Van Der Knaap, Sanwen Huang, Harry J. Klee, James J. Giovannoni & Zhangjun Fei
Modern tomatoes have narrow genetic diversity limiting their improvement potential. We present a tomato pan-genome constructed using genome sequences of 725 phylogenetically and geographically representative accessions, revealing 4,873 genes absent from the reference genome. Presence/absence variation analyses reveal substantial gene loss and intense negative selection of genes and promoters during tomato domestication and improvement. Lost or negatively selected genes are enriched for important traits, especially disease resistance. We identify a rare allele in TomLoxC promoter...

Data from: The significance of prey avoidance behaviour for the maintenance of a predator colour polymorphism

Helena Ajuria Ibarra, Michael Kinahan, Julien Marcetteau, Andrew J.R. Mehigan, Ross O. Ziegelmeier, Tom Reader & Andrew J R Mehigan
The existence of conspicuous colour polymorphisms in animals provides an ideal opportunity to examine the mechanisms which determine genetic and phenotypic variation in populations. It is well known that directional and negative frequency-dependent selection by predators can influence the persistence of colour polymorphisms in their prey, but much less attention has been paid to the idea that prey behaviour could generate selection on predator colour morphs. In this study, we examine the role that avoidance...

Data from: Persistent chaos of measles epidemics in the prevaccination United States caused by a small change in seasonal transmission patterns

Benjamin D. Dalziel, Ottar N. Bjornstad, Willem G. Van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell & Ottar N. Bjørnstad
Epidemics of infectious diseases often occur in predictable limit cycles. Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates, resulting in deterministic chaos. However, persistent deterministic chaos has never been observed, in part because sufficiently large oscillations in transmission rates are uncommon. Where they do occur, the resulting deep epidemic troughs break the chain of transmission, leading to epidemic extinction, even in large cities. Here we demonstrate a new...

Data from: Adaptation to warmer climates by parallel functional evolution of CBF genes in Arabidopsis thaliana

J. Grey Monroe, Cullen McGovern, Jesse R. Lasky, Kelsi Grogan, James Beck & John K. McKay
The evolutionary processes and genetics underlying local adaptation at a specieswide level are largely unknown. Recent work has indicated that a frameshift mutation in a member of a family of transcription factors, C-repeat binding factors or CBFs, underlies local adaptation and freezing tolerance divergence between two European populations of Arabidopsis thaliana. To ask whether the specieswide evolution of CBF genes in Arabidopsis is consistent with local adaptation, we surveyed CBF variation from 477 wild accessions...

Data from:A computational study of cancer hyperthermia based on vascular magnetic nanoconstructs

Mahdi Nabil & Paolo Zunino
The application of hyperthermia to cancer treatment is studied using a novel model arising from the fundamental principles of flow, mass and heat transport in biological tissues. The model is defined at the scale of the tumour microenvironment and an advanced computational scheme called the embedded multiscale method is adopted to solve the governing equations. More precisely, this approach involves modelling capillaries as one-dimensional channels carrying flow, and special mathematical operators are used to model...

Data from: Covariation in abscission force and terminal velocity of wind-borne sibling seeds alters long distance dispersal projections

Brittany J. Teller, James H. Marden & Katriona Shea
1. Despite the fact that seeds are unlikely to be identical—even among siblings within a maternal individual—dispersal models typically use one mean trait value to represent the ability of an entire species to disperse. Previous work has shown that the environmental conditions under which individuals leave the maternal site strongly affect how far seeds will travel. However, less is known about how trait variation within individuals contributes to dispersal or how such variation might interact...

Data from: Ecological effects on metabolic scaling amphipod responses to fish predators in freshwater springs

Douglas S. Glazier, Eric M. Butler, Sara A. Lombardi, Travis J. Deptola, Andrew J. Reese & Erin V. Satterthwaite
Metabolic rate is commonly thought to scale with body mass to the 3/4-power as a result of universal body-design constraints. However, recent comparative work has shown that the metabolic scaling slope may vary significantly among species and higher taxa, apparently in response to different lifestyles and ecological conditions, though the precise mechanisms involved are not well understood. To better understand these under-appreciated ecological effects and their causes, it is important to control for extraneous phylogenetic...

Data from: Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae)

Michael R. McKain, Norman Wickett, Yeting Zhang, Saravanaraj Ayyampalayam, W. Richard McCombie, Mark W. Chase, J. Chris Pires, Claude W. DePamphilis, Jim Leebens-Mack & Claude W. De Pamphilis
PREMISE OF THE STUDY: The stability of the bimodal karyotype found in Agave and closely related species has long interested botanists. The origin of the bimodal karyotype has been attributed to allopolyploidy, but this hypothesis has not been tested. Next Generation transcriptome sequence data were used to test whether a paleopolyploid event occurred on the same branch of the Agavoideae phylogenetic tree as the origin of the Yucca-Agave bimodal karyotype. METHODS: Illumina RNAseq data were...

Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

Gerrit Angst, Kevin E. Mueller, David M. Eissenstat, Susan Trumbore, Katherine H. Freeman, Sarah E. Hobbie, Jon Chorover, Jacek Oleksyn, Peter B. Reich & Carsten W. Mueller
Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and...

Data from: Real-time decision-making during emergency disease outbreaks

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari & Michael J. Tildesley
In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policymakers do not have the luxury of waiting for data to alleviate this state of uncertainty. For policymakers, however, it is the selection...

Data from: Conservation and modification of genetic and physiological toolkits underpinning diapause in bumble bee queens

Etya Amsalem, David A. Galbraith, Jonathan Cnaani, Peter E. A. Teal & Christina M. Grozinger
Diapause is the key adaptation allowing insects to survive unfavorable conditions and inhabit an array of environments. Physiological changes during diapause are largely conserved across species, and are hypothesized to be regulated by a conserved suite of genes (a “toolkit”). Furthermore, it is hypothesized that in social insects, this toolkit was co-opted to mediate caste differentiation between long-lived, reproductive, diapause-capable queens and short-lived, sterile workers. Using Bombus terrestris queens we examined the physiological and transcriptomic...

Data from: Degradation of internal organic matter is the main control on pteropod shell dissolution after death

Rosie L. Oakes, Victoria L. Peck, Clara Manno & Timothy J. Bralower
The potential for preservation of thecosome pteropods is thought to be largely governed by the chemical stability of their delicate aragonitic shells in seawater. However, sediment trap studies have found that significant carbonate dissolution can occur above the carbonate saturation horizon. Here we present the results from experiments conducted on two cruises to the Scotia Sea to directly test whether the breakdown of the organic pteropod body influences shell dissolution. We find that, on the...

Utilizing field collected insects for next generation sequencing: effects of sampling, storage, and DNA extraction methods

Kimberly Ballare, Nathaniel Pope, Antonio Castilla, Sarah Cusser, Richard Metz & Shalene Jha
DNA sequencing technologies continue to advance the biological sciences, expanding opportunities for genomic studies of non-model organisms for basic and applied questions. Despite these opportunities, many next-generation sequencing protocols have been developed assuming a substantial quantity of high molecular weight DNA (>100 ng), which can be difficult to obtain for many study systems. In particular, the ability to sequence field-collected specimens that exhibit varying levels of DNA degradation remains largely unexplored. In this study we...

Enhanced and unified anatomical labeling for a common mouse brain atlas

Uree Chon, Daniel Vanselow, Keith Cheng & Yongsoo Kim
Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin and Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, here we adopt the FP labels into the CCF to merge two labels in...

Identifying and classifying shared selective sweeps from multilocus data

Alexandre Harris & Michael DeGiorgio
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can...

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...

Disentangling the mechanisms underpinning disturbance-mediated invasion data

Luke Lear, Elze Hesse, Katriona Shea & Angus Buckling
Disturbances can play a major role in biological invasions: by destroying biomass, they alter habitat and resource abundances. Previous field studies suggest that disturbance-mediated invader success is a consequence of resource influxes, but the importance of other potential covarying causes, notably the opening up of habitats, have yet to be directly tested. Using experimental populations of the bacterium Pseudomonas fluorescens we determined the relative importance of disturbance-mediated habitat opening and resource influxes, plus any interaction...

Substantial genetic divergence and lack of recent gene flow support cryptic speciation in a colour polymorphic bumble bee (Bombus bifarius) species complex

Guillaume Ghisbain, Jeffrey D. Lozier, Sarthok Rasique Rahman, Briana D. Ezray, Li Tian, Jonah M. Ulmer, Sam D. Heraghty, James P. Strange, Pierre Rasmont & Heather M. Hines
Phenotypic polymorphism can constitute an inherent challenge for species delimitation. This issue is exemplified in bumble bees (Bombus), where species can exhibit high colour variation across their range, but otherwise exhibit little morphological variation to distinguish them from close relatives. We examine the species status of one of the most abundant North American bumble bees, Bombus bifarius Cresson, which historically was comprised of two major taxa, bifarius s.s. (sensu stricto) and nearcticus. These sublineages are...

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  • Pennsylvania State University
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  • United States Department of Agriculture
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