41 Works

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

Data sets used in the manuscript titled \"Ecosystem-level energy and water budgets are resilient to canopy mortality in sparse semi-arid biomes\"

Cheng-Wei Huang, Dan Krofcheck, Tomer Duman, Andrew Fox, William Pockman, Christopher Lippit, Cameron McIntire & Marcy Litvak
This data set reports water and energy fluxes, soil water content and sap fluxes measured at two adjacent pinon-juniper woodlands in central New Mexico from January 2009 to December 2016. This data set was used for the analysis in the manuscript titled “Ecosystem-level energy and water budgets are resilient to canopy mortality in sparse semi-arid biomes” submitted to JGR-Biogeosciences.

Do Synthesis Centers Synthesize? A Semantic Analysis of Topical Diversity in Research

Edward Hackett, Erin Leahy, John Parker, Ismael Rafols, Stephanie Hampton, Ugo Corte, Diego Chavarro, John Drake, Bart Penders, Laura Sheble, Niki Vermeulen & Todd Vision
Synthesis centers are a form of scientific organization that catalyzes and supports research that integrates diverse theories, methods and data across spatial or temporal scales to increase the generality, parsimony, applicability, or empirical soundness of scientific explanations. Synthesis working groups are a distinctive form of scientific collaboration that produce consequential, high-impact publications. But no one has asked if synthesis working groups synthesize: are their publications substantially more diverse than others, and if so, in what...

Soil organic carbon in drylands: shrub encroachment and vegetation management effects dwarf those of livestock grazing

Heather Throop, Steven Archer & Mitchel McClaran
Dryland ecosystems occur worldwide and play a prominent, but potentially shifting, role in global biogeochemical cycling. Widespread woody plant proliferation, often associated with declines in palatable grasses, has jeopardized livestock production in drylands and prompted attempts to reduce woody cover by chemical or mechanical means. Woody encroachment also has the potential to significantly alter terrestrial carbon storage. However, little is known of the long-term biogeochemical consequences of woody encroachment in the broader context of its...

Data from: Friction of Longmaxi shale gouges and implications for seismicity during hydraulic fracturing

Mengke An, Fengshou Zhang, Derek Elsworth, Zhengyu Xu, Zhaowei Chen & Lianyang Zhang
Longmaxi formation shales are the major target reservoir for shale gas extraction in the Sichuan Basin, southwest China. Swarms of earthquakes accompanying hydraulic fracturing are observed at depths typified by the Longmaxi formation. Mineral composition varies broadly through the stratigraphic section due to different depositional environments. The section is generally tectosilicate-poor and phyllosilicate-rich with a minor portion (~5 wt.%) the converse. We measure the frictional and stability properties of shale gouges taken from the full...

Data from: Sleep, inflammation, and cognitive behavior of aged wild-type mice subjected to diffuse brain injury and aged 3xTg-AD mice as a model of Alzheimer’s disease

Rachel Rowe, Maha Saber, Sean Murphy & Jonathan Lifshitz
Identifying differential responses between sexes following traumatic brain injury (TBI) can elucidate the mechanisms behind disease pathology. Peripheral and central inflammation in the pathophysiology of TBI can increase sleep in male rodents, but this remains untested in females. We hypothesized that diffuse TBI would increase inflammation and sleep in males more so than in females. Diffuse TBI was induced in C57BL/6J mice and serial blood samples were collected (baseline, 1, 5, 7 days post‐injury [DPI])...

Right ventricular contractility and load in HIV associated pulmonary hypertension

Arun Rajaratnam, Marc Simon, Alison Morris, Sofiya Rehman, Prerna Sharma, Melissa Saul, Rebecca Vanderpool, Mark Gladwin & Vikas Singh
Background: People living with human immunodeficiency virus (PLWH) are at risk of developing pulmonary hypertension (PH) and right ventricular (RV) dysfunction, but understanding of the relationship of RV function to afterload (RV-PA coupling) is limited. We evaluated the clinical and hemodynamic characteristics of human immunodeficiency virus (HIV)-associated PH. Methods: We performed a retrospective review of patients with a diagnosis of HIV undergoing right heart catheterization (RHC) from 2000-2016 in a tertiary care center. Inclusion criteria...

Multiple environmental stressors induce an adaptive maternal effect

Ahva Potticary & Renee Duckworth
Evolution of adaptation requires predictability and recurrence of functional contexts. Yet, organisms live in multi-faceted environments that are dynamic and ever-changing, making it difficult to understand how complex adaptations evolve. This problem is particularly apparent in the evolution of adaptive maternal effects, which are often assumed to require reliable and discrete cues that predict conditions in the offspring environment. One resolution to this problem is if adaptive maternal effects evolve through pre-existing, generalized maternal pathways...

Multi-scale drivers of soil resistance predict vulnerability of seasonally wet meadows to trampling by pack stock animals in the Sierra Nevada, USA

Joy S. Baccei, Mitchel P. McClaran, Tim J. Kuhn & Stephen C. Hart
Background Meadow ecosystems have important ecological functions and support socioeconomic services, yet are subject to multiple stressors that can lead to rapid degradation. In the Sierra Nevada of the western USA, recreational pack stock (horses and mules) use in seasonally wet mountain meadows may lead to soil trampling and meadow degradation, especially when soil water content is high and vegetation is developing. Methods In order to improve the ability to predict meadow vulnerability to soil...

Defensive structures influence fighting outcomes

Zachary Emberts & John Wiens
In many animal species, individuals engage in fights with conspecifics over access to limited resources (e.g. mates, food, or shelter). Most theory about these intraspecific fights assumes that damage has an important role in determining the contest winner. Thus, defensive structures that reduce the amount of damage an individual accrues during intraspecific competition should provide a fighting advantage. Examples of such damage-reducing structures include the dermal shields of goats, the dorsal osteoderms of crocodiles, and...

Multi-Institutional Approach to Technical Report Literature: Development of the Technical Report Archive & Image Library (TRAIL)

Maliaca Oxnam
While availability and access to more recent technical report literature has greatly improved through electronic delivery, older technical report literature still remains elusive to users. The challenges posed by these collections are two-fold: 1) the diverse nature of distribution and collection building practices across institutions; and, 2) the variability in the selection and acquisition methods used, resulting in incomplete series, confusion in depository and non-depository status, lack of awareness and definition of a “complete collection,”...

Cardinium localization during its parasitoid wasp host’s development provides insights into cytoplasmic incompatibility

Matthew Doremus
Arthropods harbor heritable intracellular symbionts that may manipulate host reproduction to favor symbiont transmission. In cytoplasmic incompatibility (CI), the symbiont sabotages the reproduction of infected males such that high levels of offspring mortality result when they mate with uninfected females. In crosses with infected males and infected females, however, (the “rescue” cross), normal numbers of offspring are produced. A common CI-inducing symbiont, Cardinium hertigii, causes variable levels of CI mortality in the parasitoid wasp, Encarsia...

Genetic variation in parental effects contributes to the evolutionary potential of prey responses to predation risk

Natasha Tigreros
Despite the ubiquity of parental effects and their potential impact on evolutionary dynamics, their contribution to the evolution of predator-prey interactions remains poorly understood. Using quantitative genetics, here we demonstrate that parental effects substantially contribute to the evolutionary potential of larval antipredator responses in a leaf beetle (Leptinotarsa decemlineata). Previous research showed that larger L. decemlineata larvae elicit stronger antipredator responses, and mothers perceiving predators improved offspring responses by increasing intraclutch cannibalism –an extreme form...

Optimal Defense Theory in an ant‐plant mutualism: extrafloral nectar as an induced defense is maximized in the most valuable plant structures

Eduardo Calixto, Denise Lange, Judith Bronstein, Helena Torezan-Silingardi & Kleber Del-Claro
Optimal Defense Theory (ODT) predicts that to maximize the benefits of defense against herbivores while minimizing its costs, plants will invest in defenses to structures according to their value and to the likelihood that they will be attacked. Constitutive defenses are expected in structures of high value, whereas induced defenses are expected in structures of low value. Regarding the biotic defense mediated by extrafloral nectaries (EFNs) and based on ODT, we predicted that under control...

The origins of acoustic communication in vertebrates

Zhuo Chen & John Wiens
Acoustic communication is crucial to humans and many other tetrapods, including birds, frogs, crocodilians, and mammals. However, large-scale patterns in its evolution are largely unstudied. Here, we address several fundamental questions about the origins of acoustic communication in terrestrial vertebrates (tetrapods), using phylogenetic methods. We show that origins of acoustic communication are significantly associated with nocturnal activity. We find that acoustic communication does not increase diversification rates, a surprising result given the many speciation-focused studies...

Leaf size of woody dicots predicts ecosystem primary productivity

Yaoqi Li, Peter Reich, Bernhard Schmid, Nawal Shrestha, Xiao Feng, Tong Lyv, Brian Maitner, Xiaoting Xu, Yichao Li, Dongting Zou, Zheng-Hong Tan, Xiangyan Su, Zhiyao Tang, Qinghua Guo, Xiaojuan Feng, Brian Enquist & Zhiheng Wang
A key challenge in ecology is to understand the relationships between organismal traits and ecosystem processes. Here, with a novel dataset of leaf length and width for 10,480 woody dicots in China and 2,374 in North America, we show that the variation in community mean leaf size is highly correlated with the variation in climate and ecosystem primary productivity, independent of plant life form. These relationships likely reflect how natural selection modifies leaf size across...

Software code for simulations and analyses concerning the calculation of canopy stomatal conductance at eddy covariance sites

Richard Wehr & Scott Saleska
These software codes compare different methods of calculating canopy stomatal conductance based on eddy covariance measurements of the latent heat flux. The R code "CanopyGsErrorSim.R" simulates true and measured canopy stomatal conductance and assesses errors when using the various methods. The Igor Pro code "AmeriFluxHo1gsCalc.ipf" calculates canopy stomatal conductance by the various methods based on real data from the Howland Forest as reported in the Ameriflux eddy covariance site data archive (Hollinger, D.: AmeriFlux US-Ho1...

Agriculture creates subtle genetic structure among migratory and non-migratory populations of burrowing owls throughout North America

Alberto Macías-Duarte, Courtney Conway & Melanie Culver
Population structure across a species distribution primarily reflects historical, ecological and evolutionary processes. However, large-scale contemporaneous changes in land use have the potential to create changes in habitat quality and thereby cause changes in gene flow, population structure, and distributions. As such, land-use changes in one portion of a species range may explain declines in other portions of their range. For example, many burrowing owl populations have declined or become extirpated near the northern edge...

Data from: Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks

Paul D. Blischak, Michael S. Barker & Ryan N. Gutenkunst
Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are...

Data from: Carnivorous mammals from the middle Eocene Washakie Formation, Wyoming, USA, and their diversity trajectory in a post-warming world

Susumu Tomiya, Shawn Zack, Michelle Spaulding & John J. Flynn
The middle Eocene Washakie Formation of Wyoming, USA, provides a rare window, within a single depositional basin, into the faunal transition that followed the early Eocene warming events. Based on extensive examination, we report a minimum of 27 species of carnivorous mammals from this formation, more than doubling the previous taxic count. Included in this revised list are a new species of carnivoraform, Neovulpavus mccarrolli, and up to ten other possibly new taxa. Our cladistic...

Data from: Identifying 'useful' fitness models: balancing the benefits of added complexity with realistic data requirements in models of individual plant fitness

Trace Martyn, Daniel Stouffer, Oscar Godoy, Ignasi Bartomeus, Abigail Pastore & Margaret Mayfield
Direct species interactions are commonly included in individual fitness models used for coexistence and local-diversity modeling. Though widely considered important for such models, direct interactions alone are often insufficient for accurately predicting fitness, coexistence or diversity outcomes. Incorporating higher-order interactions (HOIs) can lead to more accurate individual fitness models, but also adds many model terms, which can quickly result in model over-fitting. We explore approaches for balancing the trade-off between tractability and model accuracy that...

Phenological changes offset the warming effects on biomass production in an alpine meadow on the Qinghai-Tibetan Plateau

Hasbagan Ganjurjav, Hasbagan Ganjurjav, Elise Gornish, Guozheng Hu, Jianshuang Wu, Yunfan Wan, Yue Li & Qingzhu Gao
1. Phenology is an important indicator of plant response to environmental changes and is closely correlated with biomass production. However, how changes of phenological events affect plant biomass production when exposed to changing temperature and precipitation remains unclear. 2. We conducted a four-year manipulative experiment of warming and precipitation addition to explore phenology-biomass interactions under climate change in a dry alpine meadow on the central Qinghai-Tibetan Plateau from 2015 to 2018. 3. In dry and...

Nocturnal bees feed on diurnal leftovers and pay the price of day–night lifestyle transition

Hema Somanathan, Shivani Krishna, Elsa Mini Jos, Vishwas Gowda, Almut Kelber & Renee Borges
Bees exemplify flights under bright sunlight. A few species across bee families have evolved nocturnality, displaying remarkable adaptations to overcome limitations of their daylight-suited apposition eyes. Phase inversion to nocturnality in a minority of bees that co-exist with diurnal bees provide a unique opportunity to study ecological benefits that mediate total temporal niche shifts. While floral traits and sensory modalities associated with the evolution of classical nocturnal pollination syndromes, e.g. by bats and moths, are...

The Comparative Cytotoxicity of Riddelliine in Primary Mouse, Rat and Chick Hepatocytes

Bryan L. Stegelmeier, William S. Resager & Steven M. Colegate
Dehydropyrrolizidine alkaloid (DHPA) producing plants commonly poison livestock, wildlife and humans. Poisoning occurs when DHPAs are ingested as feed or food, or when they contaminate medicinal or herbal products. Direct toxicologic comparison of individual DHPAs is essential to estimate their actual health risks. This has been problematic due to varying models and difficulties in DHPA isolation or synthesis. In contrast, the macrocyclic DHPA riddelliine is readily isolated and it has been used as a benchmark...

Increasing Survey Data Quality Using Screening Validity Questions

Lucas Schalewski, Jamie Utt & Bryant Valant

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text


  • University of Arizona
  • Agricultural Research Service
  • Peking University
  • Chinese Academy of Sciences
  • University of California, Irvine
  • University of California, Merced
  • Utah State University
  • Leiden University
  • University of Sao Paulo
  • Donald Danforth Plant Science Center