30 Works

Data from: Effects of fertilizer on inorganic soil N in East Africa maize systems: vertical distributions and temporal dynamics

Katherine L. Tully, Jonathan Hickman, Madeline McKenna, Christopher Neill & Cheryl A. Palm
Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0–200 kg N/ha/yr. Soil profiles were collected...

Data from: Publication and reporting of clinical trial results: cross sectional analysis across academic medical centers

Ruijun Chen, Nihar R. Desai, Joseph S. Ross, Weiwei Zhang, Katherine H. Chau, Brian Wayda, Karthik Murugiah, Daniel Y. Lu, Amit Mittal & Harlan M. Krumholz
Objective: To determine rates of publication and reporting of results within two years for all completed clinical trials registered in ClinicalTrials.gov across leading academic medical centers in the United States. Design: Cross sectional analysis. Setting: Academic medical centers in the United States. Participants: Academic medical centers with 40 or more completed interventional trials registered on ClinicalTrials.gov. Methods: Using the Aggregate Analysis of ClinicalTrials.gov database and manual review, we identified all interventional clinical trials registered on...

Data from: Long-distance dispersal suppresses introgression of local alleles during range expansions

C. E. G. Amorim, T Hofer, N Ray, M Foll, A Ruiz-Linares & L Excoffier
During range expansions, even low levels of interbreeding can lead to massive introgression of local alleles into an invader's genome. Nonetheless, this pattern is not always observed in human populations. For instance, European Americans in North America are barely introgressed by Amerindian genes in spite of known contact and admixture. With coalescent spatially explicit simulations, we examined the impact of long-distance dispersal (LDD) events on introgression of local alleles into the invading population using a...

Data from: Sexual and natural selection in the evolution of extended phenotypes: the use of green nesting material in starlings

Juan G. Rubalcaba, Vicente Polo, Rafael Maia, Dustin R. Rubenstein & José P. Veiga
Although sexual selection is typically considered the predominant force driving the evolution of ritualized sexual behaviors, natural selection may also play an important and often underappreciated role. The use of green aromatic plants among nesting birds has been interpreted as a component of extended phenotype that evolved either via natural selection due to potential sanitary functions, or via sexual selection as a signal of male attractiveness. Here we compared both hypotheses using comparative methods in...

Data from: An auditory illusion reveals the role of streaming in the temporal misallocation of perceptual objects

Anahita H. Mehta, Nori Jacoby, Ifat Yasin, Andrew J. Oxenham & Shihab A. Shamma
This study investigates the neural correlates and processes underlying the ambiguous percept produced by a stimulus similar to Deutsch's ‘octave illusion’, in which each ear is presented with a sequence of alternating pure tones of low and high frequencies. The same sequence is presented to each ear, but in opposite phase, such that the left and right ears receive a high–low–high … and a low–high–low … pattern, respectively. Listeners generally report hearing the illusion of...

Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains

Arno Onken, Jian K. Liu, P. P. Chamanthi R. Karunasekara, Ioannis Delis, Tim Gollisch & Stefano Panzeri
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike...

Data from: The multivariate association between genomewide DNA methylation and climate across the range of Arabidopsis thaliana

Thomas E. Keller, Jesse R. Lasky & Soojin V. Yi
Epigenetic changes can occur due to extracellular environmental conditions. Consequently, epigenetic mechanisms can play an intermediate role to translate environmental signals to intracellular changes. Such a role might be particularly important in plants, which often show strong local adaptation and have the potential for heritable epigenetic states. However, little is currently known about the role of epigenetic variation in the ecological mechanisms of adaptation. Here, we used multivariate redundancy analyses to examine genomewide associations between...

Data from: Invasion of two tick-borne diseases across New England: harnessing human surveillance data to capture underlying ecological invasion processes

Katharine S. Walter, Kim M. Pepin, Colleen T. Webb, Holly D. Gaff, Peter J. Krause, Virginia E. Pitzer & Maria A. Diuk-Wasser
Modelling the spatial spread of vector-borne zoonotic pathogens maintained in enzootic transmission cycles remains a major challenge. The best available spatio-temporal data on pathogen spread often take the form of human disease surveillance data. By applying a classic ecological approach—occupancy modelling—to an epidemiological question of disease spread, we used surveillance data to examine the latent ecological invasion of tick-borne pathogens. Over the last half-century, previously undescribed tick-borne pathogens including the agents of Lyme disease and...

Data from: Selection, constraint and the evolution of coloration in African starlings

Rafael Maia, Dustin R. Rubenstein & Matthew D. Shawkey
Colorful plumage plays a prominent role in evolution of birds, influencing communication (sexual/social selection) and crypsis (natural selection). Comparative studies have focused primarily upon these selective pressures, but the mechanisms underlying color production can also be important by constraining the color gamut upon which selection acts. Iridescence is particularly interesting to study the interaction between selection and color-producing mechanisms because a broad range of colors can be produced with a shared template, and innovations to...

Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates

Mandev S. Gill, Philippe Lemey, Shannon N. Bennett, Roman Biek & Marc A. Suchard
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and...

Data from: A hierarchical model of whole assemblage island biogeography

Jesse R. Lasky, Timothy H. Keitt, Brian C. Weeks & Evan P. Economo
Island systems have long played a central role in the development of ecology and evolutionary biology. However, while many empirical studies suggest species differ in vital biogeographic rates, such as dispersal abilities, quantitative methods have had difficulty incorporating such differences into analyses of whole-assemblages. In particular, differences in dispersal abilities among species can cause variation in the spatial clustering and localization of species distributions. Here, we develop a single, hierarchical Bayes, assemblage-wide model of 252...

Data from: A curated and standardized adverse drug event resource to accelerate drug safety research

Juan M. Banda, Lee Evans, Rami S. Vanguri, Nicholas P. Tatonetti, Patrick B. Ryan & Nigam H. Shah
Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. The publicly available US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) data requires substantial curation before they can be used appropriately, and applying different strategies for...

Data from: Global terrestrial Human Footprint maps for 1993 and 2009

Oscar Venter, Eric W. Sanderson, Ainhoa Magrach, James R. Allan, Jutta Beher, Kendall R. Jones, Hugh P. Possingham, William F. Laurance, Peter Wood, Balázs M. Fekete, Marc A. Levy & James E.M. Watson
Remotely-sensed and bottom-up survey information were compiled on eight variables measuring the direct and indirect human pressures on the environment globally in 1993 and 2009. This represents not only the most current information of its type, but also the first temporally-consistent set of Human Footprint maps. Data on human pressures were acquired or developed for: 1) built environments, 2) population density, 3) electric infrastructure, 4) crop lands, 5) pasture lands, 6) roads, 7) railways, and...

Data from: Transforming water: social influence moderates psychological, physiological, and functional response to a placebo product

Alia J. Crum, Damon J. Phillips, J. Parker Goyer, Modupe Akinola & E. Tory Higgins
This paper investigates how social influence can alter physiological, psychological, and functional responses to a placebo product and how such responses influence the ultimate endorsement of the product. Participants consumed a product, "AquaCharge Energy Water," falsely-labeled as containing 200 mg of caffeine but which was actually plain spring water, in one of three conditions: a no social influence condition, a disconfirming social influence condition, and a confirming social influence condition. Results demonstrated that the effect...

Data from: Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland

Dima Chen, Qingmin Pan, Yongfei Bai, Shuijin Hu, Jianhui Huang, Qibing Wang, Shahid Naeem, James J. Elser, Jianguo Wu & Xingguo Han
1. The rapid loss of global biodiversity can greatly affect the functioning of above-ground components of ecosystems. However, how such biodiversity losses affect below-ground communities and linkages to soil carbon (C) sequestration is unclear. Here we describe how losses in plant functional groups (PFGs) affect soil microbial and nematode communities and net ecosystem exchange (NEE) in a 4-year removal experiment conducted on the Mongolian plateau, the world's largest remaining natural grassland. 2. Our results demonstrated...

Data from: Biomass resilience of Neotropical secondary forests

Lourens Poorter, Frans Bongers, T. Mitchell Aide, Angélica M. Almeyda Zambrano, Patricia Balvanera, Justin M. Becknell, Vanessa Boukili, Pedro H. S. Brancalion, Eben N. Broadbent, Robin L. Chazdon, Dylan Craven, Jarcilene S. De Almeida-Cortez, George A. L. Cabral, Ben H. J. De Jong, Julie S. Denslow, Daisy H. Dent, Saara J. DeWalt, Juan M. Dupuy, Sandra M. Durán, Mario M. Espírito-Santo, María C. Fandino, Ricardo G. César, Jefferson S. Hall, José Luis Hernandez-Stefanoni, Catarina C. Jakovac … & Danaë M. A. Rozendaal
Land-use change occurs nowhere more rapidly than in the tropics, where the imbalance between deforestation and forest regrowth has large consequences for the global carbon cycle1. However, considerable uncertainty remains about the rate of biomass recovery in secondary forests, and how these rates are influenced by climate, landscape, and prior land use2, 3, 4. Here we analyse aboveground biomass recovery during secondary succession in 45 forest sites and about 1,500 forest plots covering the major...

Data from: Do community-weighted mean functional traits reflect optimal strategies?

Robert Muscarella & María Uriarte
The notion that relationships between community-weighted mean (CWM) traits (i.e. plot-level trait values weighted by species abundances) and environmental conditions reflect selection towards locally optimal phenotypes is challenged by the large amount of interspecific trait variation typically found within ecological communities. Reconciling these contrasting patterns is a key to advancing predictive theories of functional community ecology. We combined data on geographical distributions and three traits (wood density, leaf mass per area and maximum height) of...

Data from: Late Oligocene caviomorph rodents from Contamana, Peruvian Amazonia

Myriam Boivin, Laurent Marivaux, Adriana M. Candela, Maëva J. Orliac, François Pujos, Rodolfo Salas-Gismondi, Julia V. Tejada-Lara & Pierre-Olivier Antoine
The Deseadan South American Land Mammal Age (late Early Oligocene – Late Oligocene) attests to a time of great diversification in the caviomorph rodent fossil record. Nevertheless, Deseadan rodent-bearing localities in Neotropical lowlands are few and poorly known. Here we describe the rodent assemblages from two Late Oligocene localities, near Contamana, Loreto, Peru. Seven taxa are new to science: Palaeosteiromys amazonensis gen. et sp. nov., Plesiosteiromys newelli gen. et sp. nov., Loretomys minutus gen. et...

Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis

Paul Riccio, Cristina Cebrian, Hui Zong, Simon Hippenmeyer & Frank Costantini
Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive...

Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Francine Kershaw, Inês Carvalho, Jacqueline Loo, Cristina Pomilla, Peter B. Best, Ken P. Findlay, Salvatore Cerchio, Tim Collins, Marcia H. Engel, Gianna Minton, Peter Ersts, Jaco Barendse, P. G. H. Kotze, Yvette Razafindrakoto, Solange Ngouessono, Michael Meӱer, Meredith Thornton & Howard C. Rosenbaum
Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample,...

Data from: HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels

Petter Holland, Helene Knævelsrud, Kristiane Søreng, Benan John Mathai, Alf Håkon Lystad, Serhiy Pankiv, Gunnveig T. Bjørndal, Sebastian W. Schultz, Viola H. Lobert, Robin B. Chan, Bowen Zhou, Knut Liestøl, Sven R. Carlsson, Thomas J. Melia, Gilbert Di Paolo & Anne Simonsen
A fundamental question is how autophagosome formation is regulated. Here we show that the PX domain protein HS1BP3 is a negative regulator of autophagosome formation. HS1BP3 depletion increased the formation of LC3-positive autophagosomes and degradation of cargo both in human cell culture and in zebrafish. HS1BP3 is localized to ATG16L1- and ATG9-positive autophagosome precursors and we show that HS1BP3 binds phosphatidic acid (PA) through its PX domain. Furthermore, we find the total PA content of...

Data from: Lambda interferon restructures the nasal microbiome and increases susceptibility to Staphylococcus aureus superinfection

Paul J. Planet, Dane Parker, Taylor S. Cohen, Hannah Smith, Justinne D. Leon, Chanelle Ryan, Tobin J. Hammer, Noah Fierer, Emily I. Chen & Alice S. Prince
Much of the morbidity and mortality associated with influenza virus respiratory infection is due to bacterial coinfection with pathogens that colonize the upper respiratory tract such as methicillin-resistant Staphylococcus aureus (MRSA) and Streptococcus pneumoniae. A major component of the immune response to influenza virus is the production of type I and III interferons. Here we show that the immune response to infection with influenza virus causes an increase and restructuring of the upper respiratory microbiota...

Data from: New England cod collapse and the climate

Kyle C. Meng, Kimberly L. Oremus & Steven D. Gaines
To improve fishery management, there is an increasing need to understand the long-term consequences of natural and anthropogenic climate variability for ecological systems. New England’s iconic cod populations have been in decline for several decades and have recently reached unprecedented lows. We find that 17% of the overall decline in Gulf of Maine cod biomass since 1980 can be attributed to positive phases of the North Atlantic Oscillation (NAO). This is a consequence of three...

Data from: Continuum of vasodilator stress from rest to contrast medium to adenosine hyperemia for fractional flow reserve assessment

Nils P. Johnson, Allen Jeremias, Frederik M. Zimmermann, Julien Adjedj, Nils Witt, Barry Hennigan, Bon-Kwon Koo, Akiko Maehara, Mitsuaki Matsumura, Emanuele Barbato, Giovanni Esposito, Bruno Trimarco, Gilles Rioufol, Seung-Jung Park, Hyoung-Mo Yang, Sérgio B. Baptista, George S. Chrysant, Antonio M. Leone, Colin Berry, Bernard De Bruyne, K. Lance Gould, Richard L. Kirkeeide, Keith G. Oldroyd, Nico H. J. Pijls, William F. Fearon … & Nico H.J. Pijls
OBJECTIVES: We compared the diagnostic performance with adenosine-derived fractional flow reserve (FFR) #0.8 of contrast-based FFR (cFFR), resting distal pressure (Pd)/aortic pressure (Pa), and the instantaneous wave-free ratio (iFR). BACKGROUND: FFR objectively identifies lesions that benefit from medical therapy versus revascularization. However, FFR requires maximal vasodilation, usually achieved with adenosine. Radiographic contrast injection causes submaximal coronary hyperemia. Therefore, intracoronary contrast could provide an easy and inexpensive tool for predicting FFR. METHODS: We recruited patients undergoing...

Data from: Cytonuclear incompatibility contributes to the early stages of speciation

Karen B. Barnard-Kubow, Nina So & Laura F. Galloway
Genetic incompatibility is a hallmark of speciation. Cytonuclear incompatibilities are proposed to be among the first genetic barriers to arise during speciation. Accordingly, reproductive isolation (RI) within species should be heavily influenced by interactions between the organelle and nuclear genomes. However, there are few clear examples of cytonuclear incompatibility within a species. Here, we show substantial postzygotic RI in first-generation hybrids between differentiated populations of an herbaceous plant (up to 92% reduction in fitness). RI...

Registration Year

  • 2016

Resource Types

  • Dataset


  • Columbia University
  • Stanford University
  • Ghent University
  • University of Glasgow
  • University of Virginia
  • University of Minnesota
  • Wildlife Conservation Society
  • University of Wisconsin-Madison
  • University of Connecticut
  • University College London