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1,079 results for “source data”
New insights into the patterns and drivers of avian altitudinal migration from a growing crowdsourcing data source
Altitudinal migration is a common and important but understudied behavior in birds. Difficulty in characterizing avian altitudinal migration has prevented a comprehensive understanding of this behavior. To address this, we investigated the altitudinal migration patterns and explored potential drivers for a major proportion (~70%) of the entire resident bird community along an almost 4,000 m elevational gradient on the main island of Taiwan. Based on the occurrence records collected by citizen scientists, we examined the seasonal shifts in the center and the upper and lower boundaries of elevational distributions for 104 individual species. We then built phylogeny-controlled regression models to investigate the associations between the birds' seasonal distribution shifts and seven of their traits, and examined whether the observed shifts can be explained by three main hypotheses on potential drivers. Results showed that at least 60 species (58%) seasonally changed their distributions along elevations. While most of them (42 species) tended to move downhill in winter, a considerable number of species (14) tended to move uphill. While the species breeding at high or low elevations tended to move downhill in winter, those breeding at medium-low elevations tended to move or extend their distributions to higher elevations. Our regression models suggested that seasonal variations in climates and food availability could be major drivers of the behavior. However, the three hypotheses can only partially explain the observed downhill migration patterns and none of them can well explain the uphill patterns, indicating an important knowledge gap. This study investigated avian altitudinal migration from a new perspective with a novel and generalizable approach, and revealed interesting patterns that could be difficult to identify with conventional approaches. It demonstrated the power of citizen science data to provide new insights into this behavior by characterizing the general patterns and mechanisms across a large number of species.
Source Data - Ilzhofer et al. - Phase coherence in out-of-equilibrium supersolid states of ultracold dipolar atoms
<p>Source data for following publication:</p> <p>"Phase coherence in out-of-equilibrium supersolid states of ultracold dipolar atoms" (2019)</p> <p>P. Ilzhofer and M. Sohmen and G. Durastante and Claudia Politi and A. Trautmann and G. Morpurgo and T. Giamarchi and L. Chomaz and M. Mark and F. Ferlaino</p> <p>Institut f ̈ur Quantenoptik und Quanteninformation, ̈Osterreichische Akademie der Wissenschaften, 6020 Innsbruck, Austria</p> <p>Institut f ̈ur Experimentalphysik und Zentrum f ̈ur Quantenoptik,Universit ̈at Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria</p> <p>DQMP, University of Geneva, 24 Quai Ernest-Ansermet, CH-1211 Geneva, Switzerland</p>
Key input and output data for the multi-model analysis "Open Source Energiewende"
<p>This repository contains key input and output data of the multi-model analysis carried out in the project "Open Source Energiewende", financed by the German Federal Ministry for Economic Affairs and Energy.</p> <p>The results are presented and discussed in the paper "Power sector effects of cheaper stationary batteries: insights from an open multi-model analysis".</p> <p>The model codes are availabe in individual repositories, which are provided in the paper.</p>
Source code for models of floral initiation in pea and gene expression data extracted from published sources
<p>The dataset contains the source code for computational models of a gene network controlling transition to flowering in pea (<em>Pisum sativum</em>). The models were based on ordinary differential equations (ODE) or neural networks. It also includes data on the expression dynamics of genes involved in the network, which was used for model fitting. The expression data was extracted from the following papers: </p> <p>Hecht, V., Laurie, R. E., Schoor, K. Vander, Ridge, S., Knowles, C. L., Liew, L. C., Sussmilch, F. C., et al. (2011). The Pea GIGAS Gene Is a FLOWERING LOCUS T Homolog Necessary for Graft-Transmissible Specification of Flowering but Not for Responsiveness to Photoperiod. 23, 147–161. doi:10.1105/tpc.110.081042</p> <p>Sussmilch, F. C., Berbel, A., Hecht, V., Schoor, K. Vander, Ferrándiz, C., Madueño, F., et al. (2015). Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound In fl orescence Development. 27, 1046–1060. doi:10.1105/tpc.115.136150</p> <p>The source code of the DEEP software used for parameter optimization in the model fitting can be found in the Gitlab repository (https://gitlab.com/mackoel/deepmethod/-/tree/master).</p> <p>The files are the supplement to the following manuscript, submitted to Frontiers in Genetics:</p> <p>"Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in <em>Pisum sativum</em>" by Polina Pavlinova, Maria G. Samsonova, and Vitaly V. Gursky.</p> <p>All possible questions can be sent to: Polina Pavlinova (polina.pavlina1004@gmail.com), Vitaly Gursky (gursky@math.ioffe.ru).</p>
Remote near infrared identification of pathogens with multiplexed nanosensors - source data file for Nißler et al. 2020 (Nat. Commun.)
<p>source data file for Nißler et al. 2020 (Nat. Commun.)</p> <p>entitled: </p> <p>Remote near infrared identification of pathogens with multiplexed nanosensors</p>
Data from: Integration and harmonization of trait data from plant individuals across heterogeneous sources
<p>Trait data represent the basis for ecological and evolutionary research and have relevance for biodiversity conservation, ecosystem management and earth system modelling. The collection and mobilization of trait data has strongly increased over the last decade, but many trait databases still provide only species-level, aggregated trait values (e.g. ranges, means) and lack the direct observations on which those data are based. Thus, the vast majority of trait data measured directly from individuals remains hidden and highly heterogeneous, impeding their discoverability, semantic interoperability, digital accessibility and (re-)use. Here, we integrate quantitative measurements of verbatim trait information from plant individuals (e.g. lengths, widths, counts and angles of stems, leaves, fruits and inflorescence parts) from multiple sources such as field observations and herbarium collections. We develop a workflow to harmonize heterogeneous trait measurements (e.g. trait names and their values and units) as well as additional information related to taxonomy, measurement or fact and occurrence. This data integration and harmonization builds on vocabularies and terminology from existing metadata standards and ontologies such as the Ecological Trait-data Standard (ETS), the Darwin Core (DwC), the Thesaurus Of Plant characteristics (TOP) and the Plant Trait Ontology (TO). A metadata form filled out by data providers enables the automated integration of trait information from heterogeneous datasets. We illustrate our tools with data from palms (family Arecaceae), a globally distributed (pantropical), diverse plant family that is considered a good model system for understanding the ecology and evolution of tropical rainforests. We mobilize nearly 140,000 individual palm trait measurements in an interoperable format, identify semantic gaps in existing plant trait terminology and provide suggestions for the future development of a thesaurus of plant characteristics. Our work thereby promotes the semantic integration of plant trait data in a machine-readable way and shows how large amounts of small trait data sets and their metadata can be integrated into standardized data products.</p>
data postprocessing for the EMEP local city source contribution
<p>- First edition by A. Valdebenito (Norwegian Meteorological Institute)</p> <p>similar codes were used in the country source contribution calculations: https://doi.org/10.5194/gmd-13-1787-2020</p> <p>-updated for the analysis and the publication by M. Pommier</p> <p> </p>
Standard Bouguer anomaly model achieved by multi-source Bouguer gravity anomaly Bayesian data fusion algorithm in Sichuan-Yunnan region
<p>* Method: Based on the equivalent source inversion and Bayesian uncertainty quantization theory, a new multi-source gravity data fusion algorithm is developed, which effectively solves the multi-source data fusion problem with different noise and datum.</p> <p>* Standard Bouguer anomaly is Fused from WGM2012 Bouguer gravity anomaly model and 394 gravity profile data measured in Sichuan-Yunnan region. Fusion anomaly results can eliminate datum draft between multi-source gravity and reduce incoherent noise.</p> <p>* Spatial resolution of the standard Bouguer anomaly is about 20 kilometers.</p> <p>* Correcting deviations means the difference between the fused standard Bouguer anomaly model and the WGM2012 Earth gravity model.</p>
Data from: The sources of variation for individual prey-to-predator size ratios
<p>The relative body size at which predators are willing to attack prey, a key trait for predator-prey interactions, is usually considered invariant. However, this ratio can vary widely among individuals or populations. Identifying the range and origin of such variation is key to understanding the strength and constraints on selection in both predators and prey. Still, these sources of variation remain largely unknown. We filled this gap by measuring the genetic, maternal and environmental variation of the maximum prey-to-predator size ratio (PPSRmax) in juveniles of the wolf spider Lycosa fasciiventris using a paternal half-sib split brood design, in which each male was paired with two different females and the offspring reared in two different food environments: poor and rich. Each juvenile spider was then sequentially offered crickets of decreasing size and the maximum prey size killed was determined. We also measured body size and body condition of spiders upon emergence and just before the trial. We found low, but significant heritability (h2=0.069) and dominance and common environmental variance (d2+4c2=0.056). PPSRmax was also partially explained by body condition (during trial) but there was no effect of the rearing food environment. Finally, a maternal correlation between body size early in life and PPSRmax indicated that offspring born larger were less predisposed to feed on larger prey later in life. Therefore, PPSRmax, a central trait in ecosystems, can vary widely and this variation is due to different sources, with important consequences for changes in this trait in the short and long terms.</p>
Nanomechanical topological insulators with an auxiliary orbital degree of freedom - source data
<p>This data set contains the source data and the matlab scripts applied to obtain the results published in "Nanomechanical topological insulators with an auxiliary orbital degree of freedom". For details of the experimental procedure please refer to the main text of the article, as well as the supplementary information. </p>
Acoustic transfer function data for source and sensor placement
<p>Acoustic transfer function (ATF) data for the codes of source and sensor placement in sound field control. </p> <p>https://github.com/sh01k/SourceSensorPlacementSFC</p> <p>The ATF data in the 2D acoustic field was generated by the finite element method using FreeFem++ (<a href="https://freefem.org/">https://freefem.org/</a>).</p>
Benchmark data for source localization validation
<p>Template data related to the publication :<br> La Fisca et al., A Versatile Validation Framework for ERP and Oscillatory Source Reconstruction Using FieldTrip, 2021</p> <p>Funded by: F.N.R.S - F.R.I.A, Belgium</p>
Data from: Sources of variation in maternal allocation in a long-lived mammal
<p>Life history theory predicts allocation of energy to reproduction varies with maternal age but additional maternal features may be important to the allocation of energy to reproduction. We aimed to characterize age-specific variation in maternal allocation and assess the relationship between maternal allocation and other static and dynamic maternal features. Mass measurements of 531 mothers and pups were used with Bayesian hierarchical models to explain the relationship between diverse maternal attributes and both the proportion of mass allocated by Weddell seal mothers, and the efficiency of mass transfer from mother to pup during lactation as well as the weaning mass of pups. Our results demonstrated that maternal mass was strongly and positively associated with the relative reserves allocated by a mother and a pup's weaning mass but that the efficiency of mass transfer declines with maternal parturition mass. Birthdate was positively associated with proportion mass allocation and pup weaning mass, but mass transfer efficiency was predicted to be highest at the mean birthdate. The relative allocation of maternal reserves declined with maternal age but the efficiency of mass transfer to pups increases, suggestive of selective disappearance of poor-quality mothers. These findings highlight the importance of considering multiple maternal features when assessing variation in maternal allocation.</p>
Data from: Plant community response to switchgrass (Panicum virgatum) population source in establishing prairies
Ecological restoration and revegetation efforts entail the translocation of native plant populations. Risks associated with these efforts include failure of translocated populations to establish or, conversely, such strong establishment that they excessively dominate the recipient community. The role that selective breeding plays in mediating these risks is unclear but of increasing importance as efforts to restore and establish multifunctional grasslands also increase. In a three-year, spatially replicated study, we seeded experimental prairie communities with either domesticated (cultivar) or undomesticated strains of Panicum virgatum (switchgrass), a North American C4 species under development as a biomass crop. We evaluated the composition, performance, and diversity of the recipient plant communities and compared the performance of cultivar and undomesticated switchgrass in those communities. We found little evidence that switchgrass population source affected community response. Switchgrass cultivars modestly exceeded undomesticated strains with respect to stand establishment, third-year stand density, and aboveground biomass; effect size and significance differed among sites. Our results suggest that including cultivars in ecological restorations and multifunctional grasslands may enhance success of switchgrass establishment with little risk of impairing the composition or diversity of plant communities for up to three years, as reflected in the measures used here. However, the incorporation of undomesticated switchgrass into multifunctional grasslands may enhance landscape-scale genetic variation and mitigate risks associated with gene flow between translocated and local wild switchgrass populations; more research on these dynamics is needed.
Data from: Phylogenomics reveals three sources of adaptive variation during a rapid radiation
Speciation events often occur in rapid bursts of diversification, but the ecological and genetic factors that promote these radiations are still much debated. Using whole transcriptomes from all 13 species in the ecologically and reproductively diverse wild tomato clade (Solanum sect. Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group. Despite widespread phylogenetic discordance due to the sorting of ancestral variation, we date the origin of this radiation to approximately 2.5 million years ago and find evidence for at least three sources of adaptive genetic variation that fuel diversification. First, we detect introgression both historically between early-branching lineages and recently between individual populations, at specific loci whose functions indicate likely adaptive benefits. Second, we find evidence of lineage-specific de novo evolution for many genes, including loci involved in the production of red fruit color. Finally, using a "PhyloGWAS" approach, we detect environment-specific sorting of ancestral variation among populations that come from different species but share common environmental conditions. Estimated across the whole clade, small but substantial and approximately equal fractions of the euchromatic portion of the genome are inferred to contribute to each of these three sources of adaptive genetic variation. These results indicate that multiple genetic sources can promote rapid diversification and speciation in response to new ecological opportunity, in agreement with our emerging phylogenomic understanding of the complexity of both ancient and recent species radiations.
Data from: Novel sources of (co)variation in nestling begging behavior and hunger at different biological levels of analysis
<p>Biological hypotheses predicting patterns of offspring begging typically concern the covariance with hunger and/or development at specific hierarchical levels. For example, hunger drives within-individual patterns of begging, but begging also drives food intake among individuals within broods, and begging and food intake can covary positively or negatively among genotypes or broods. Testing biological phenomena that occur at multiple levels therefore requires the partitioning of covariance between traits of interest to ensure that each level-specific relationship is appropriately assessed. We performed a partial cross-fostering study on a wild population of great tits (Parus major), then used multivariate mixed-models to partition variation and covariation in nestling begging effort and two metrics of nestling hunger within versus among individual nestlings and broods. At the within-individual level, we found that nestlings begged more intensely when hungrier (positive correlation between begging and hunger). However, among individuals, nestlings that were fed more frequently also begged more intensely on average (negative correlation between begging and hunger). Variation in nestling mass did not give rise to the negative correlation between begging and hunger among nestlings, but we did find that lighter nestlings begged more intensely than their heavier biological siblings, suggesting that this effect may be driven by a genetic component linked to offspring size. Our study illustrates how patterns of covariance can differ across biological levels of analysis and addresses biological mechanisms that could produce these previously obscured patterns.</p>
Data from: Animal-mediated organic matter transformation: aquatic insects as a source of microbially bioavailable organic nutrients and energy
1. Animal communities are essential drivers of energy and elemental flow in ecosystems. However, few studies have investigated the functional role of animals as sources of dissolved organic matter (DOM) and the subsequent utilization of that DOM by the microbial community. 2. In a small forested headwater stream, we tested the effects of taxonomy, feeding traits, and body size on the quality and quantity of dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) excreted by aquatic insects. In addition, we conducted steady-state solute additions to estimate instream demand for labile C and compared it to the C excreted by invertebrates. 3. Individual excretion rates and excretion composition varied with body size, taxonomy, and feeding guild. The estimated average community excretion rate was 1.31 μg DOC· per mg insect dry weight (DW)-1·h-1 and 0.33 μg DON·mg DW-1·h-1 and individuals excreted DON at nearly twice the rate of 〖"NH" 〗_"4" ^"+" . This DOM was 2-5 times more bioavailable to microbial heterotrophs than ambient stream water DOM. 4. We estimated that the insect community, conservatively, excreted 1.62 mg of bioavailable DOC·m-2·h-1 and through steady-state additions measured an ambient labile C demand as 3.97±0.67 mg C·m-2·h-1. This suggests that insect-mediated transformation and excretion of labile DOC could satisfy a significant fraction (40±7%) of labile C demand in this small stream. 5. Collectively, our results suggest that animal excretion plays an essential functional role in transforming organic matter into microbially bioavailable forms and may satisfy a variable but significant portion of microbial demand for labile C and N.
Data from: Why is Amazonia a 'source' of biodiversity? climate-mediated dispersal and synchronous speciation across the Andes in an avian group (Tityrinae)
Amazonia is a 'source' of biodiversity for other Neotropical ecosystems, but which conditions trigger in situ speciation and emigration is contentious. Three hypotheses for how communities have assembled include (1) a stochastic model wherein chance dispersal events lead to gradual emigration and species accumulation, (2) diversity-dependence wherein successful dispersal events decline through time due to ecological limits, and (3) barrier displacement wherein environmental change facilitates dispersal to other biomes via transient habitat corridors. We sequenced thousands of molecular markers for the Neotropical Tityrinae (Aves) and applied a novel filtering protocol to identify loci with high utility for dated phylogenomics. We used these loci to estimate divergence times and model Tityrinae's evolutionary history. We detected a prominent role for speciation driven by barriers including synchronous speciation across the Andes, and found that dispersal increased toward the present. Because diversification was continuous but dispersal was non-random over time, we show that barrier displacement better explains Tityrinae's history than stochasticity or diversity-dependence. We propose that Amazonia is a source of biodiversity because (1) it is a relic of a biome that was once more extensive, (2) environmentally-mediated corridors facilitated emigration, and (3) constant diversification is attributed to a spatially heterogeneous landscape that is perpetually dynamic through time.
Data from: Oyster reefs as carbon sources and sinks
Carbon burial is increasingly valued as a service provided by threatened vegetated coastal habitats. Similarly, shellfish reefs contain significant pools of carbon and are globally endangered, yet considerable uncertainty remains regarding shellfish reefs' role as sources (+) or sinks (−) of atmospheric CO2. While CO2 release is a by-product of carbonate shell production (then burial), shellfish also facilitate atmospheric-CO2 drawdown via filtration and rapid biodeposition of carbon-fixing primary producers. We provide a framework to account for the dual burial of inorganic and organic carbon, and demonstrate that decade-old experimental reefs on intertidal sandflats were net sources of CO2 (7.1 ± 1.2 MgC ha−1 yr−1 (µ ± s.e.)) resulting from predominantly carbonate deposition, whereas shallow subtidal reefs (−1.0 ± 0.4 MgC ha−1 yr−1) and saltmarsh-fringing reefs (−1.3 ± 0.4 MgC ha−1 yr−1) were dominated by organic-carbon-rich sediments and functioned as net carbon sinks (on par with vegetated coastal habitats). These landscape-level differences reflect gradients in shellfish growth, survivorship and shell bioerosion. Notably, down-core carbon concentrations in 100- to 4000-year-old reefs mirrored experimental-reef data, suggesting our results are relevant over centennial to millennial scales, although we note that these natural reefs appeared to function as slight carbon sources (0.5 ± 0.3 MgC ha−1 yr−1). Globally, the historical mining of the top metre of shellfish reefs may have reintroduced more than 400 000 000 Mg of organic carbon into estuaries. Importantly, reef formation and destruction do not have reciprocal, counterbalancing impacts on atmospheric CO2 since excavated organic material may be remineralized while shell may experience continued preservation through reburial. Thus, protection of existing reefs could be considered as one component of climate mitigation programmes focused on the coastal zone.
South African Open Data in Higher Education: Sources, resources and providers
<p>Spreadsheet of data sourced on South African sources, resources and providers of higher education open data. Composed through desk review as principle component of the situational analysis conducted for the 'Use of open data in the governance of South African higher education' research project, in the IDRC/WWWF 'Exploring Emerging Impacts of Open Data in the South' initiative.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.