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311 results for “Empirical data”
Data from: Synergism and antagonism of proximate mechanisms enable and constrain the response to simultaneous selection on body size and development time: an empirical test using experimental evolution
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Data associated with: Going round the twist – An empirical analysis of shell coiling in helicospiral gastropods
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Data from: The effect of egg size on hatch time and metabolic rate: theoretical and empirical insights on developing insect embryos
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Data from: Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies
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Data from: Economic uncertainty, geopolitical risk and U.S. energy price risk spillover: An empirical study based on the risk spillover model
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Data from: Crop-to-wild hybridization in cherries – empirical evidence from Prunus fruticosa
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Data from: Conventional analysis of trial-by-trial adaptation is biased: empirical and theoretical support using a Bayesian estimator
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Data from: Empirical and theoretical investigation into the potential impacts of insecticide resistance on the effectiveness of insecticide-treated bed nets
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Data presented in the paper : Consistent theoretical and empirical approaches of at-a-station hydraulic geometry exponents in stream reaches
<p>This dataset contains the data used in the paper.</p> <p> </p> <p>Variables descriptions :</p> <p>ID : reach identifier.</p> <p>Exponent_b : at-a-station hydraulic geometry width exponent (<em>b</em>) (-).</p> <p>Exponent_f : at-a-station hydraulic geometry depth exponent (<em>f</em>) (-).</p> <p>Fr50 : the reach-scale Froude number at the median flow (<em>Fr<sub>50</sub></em>) (-).</p> <p>W50/WQb : the median to bankfull width ratio <em>(W<sub>50</sub></em>/<em>W<sub>Qb</sub></em>) (-).</p> <p>R_theo : the shape parameter (<em>r<sub>theo</sub></em>) (-).</p> <p>Relative_standard_dev._profile : the standard deviation of the bed elevation relative to the bankfull width (<em>σ</em>/<em>W<sub>Qb</sub></em>) (-).</p> <p>Relative_grain_size : the reach-average grain size relative to bankfull width (<em>D</em>/<em>W<sub>Qb</sub></em>) (-).</p> <p>Source : data source.</p> <p>Type : data type.</p> <p>(-) denotes dimensionless quantities.</p>
Data, Code, Models, and Results for 'Empirical estimation of yield variability due to weather shocks using biophysical characteristics for U.S. rainfed and irrigated maize, soybeans, and winter wheat'
<p>Data, Code, Models, and Results for 'Empirical estimation of yield variability due to weather shocks using biophysical characteristics for U.S. rainfed and irrigated maize, soybeans, and winter wheat'</p>
Data from: Plant water potential improves prediction of empirical stomatal models
Climate change is expected to lead to increases in drought frequency and severity, with deleterious effects on many ecosystems. Stomatal responses to changing environmental conditions form the backbone of all ecosystem models, but are based on empirical relationships and are not well-tested during drought conditions. Here, we use a dataset of 34 woody plant species spanning global forest biomes to examine the effect of leaf water potential on stomatal conductance and test the predictive accuracy of three major stomatal models and a recently proposed model. We find that current leaf-level empirical models have consistent biases of over-prediction of stomatal conductance during dry conditions, particularly at low soil water potentials. Furthermore, the recently proposed stomatal conductance model yields increases in predictive capability compared to current models, and with particular improvement during drought conditions. Our results reveal that including stomatal sensitivity to declining water potential and consequent impairment of plant water transport will improve predictions during drought conditions and show that many biomes contain a diversity of plant stomatal strategies that range from risky to conservative stomatal regulation during water stress. Such improvements in stomatal simulation are greatly needed to help unravel and predict the response of ecosystems to future climate extremes.
Data from: Empirical evidence for species-specific export of fish naïveté from a no-take marine protected area in a coastal recreational hook and line fishery
No-take marine protected areas (MPAs) are assumed to enhance fisheries catch via the "spillover" effect, where biomass is exported to adjacent exploited areas. Recent studies in spearfishing fisheries suggest that the spillover of gear-naïve individuals from protected to unprotected sites increases catch rates outside the boundaries of MPAs. Whether this is a widespread phenomenon that also holds for other gear types and species is unknown. In this study, we tested if the distance to a Mediterranean MPA predicted the degree of vulnerability to hook and line in four small-bodied coastal fish species. With the assistance of underwater video recording, we investigated the interaction effect of the distance to the boundary of an MPA and species type relative to the latency time to ingest a natural bait, which was considered as a surrogate of fish naïveté or vulnerability to fishing. Vulnerability to angling increased (i.e., latency time decreased) within and near the boundary of an MPA for an intrinsically highly catchable species (Serranus scriba), while it remained constant for an intrinsically uncatchable control species (Chromis chromis). While all of the individuals of S. scriba observed within the MPA and surrounding areas were in essence captured by angling gear, only one fifth of individuals in the far locations were captured. This supports the potential for the spillover of gear-naïve and consequently more vulnerable fish from no-take MPAs. Two other species initially characterized as intermediately catchable (Coris julis and Diplodus annularis) also had a shorter latency time in the vicinity of an MPA, but for these two cases the trend was not statistically significant. Overall, our results suggest that an MPA-induced naïveté effect may not be universal and may be confined to only intrinsically highly catchable fish species. This fact emphasizes the importance of considering the behavioural dimension when predicting the outcomes of MPAs, otherwise the effective contribution may be smaller than predicted for certain highly catchable species such as S. scriba.
Data from: Empirical Bayesian elastic net for multiple quantitative trait locus mapping
In multiple quantitative trait locus (QTL) mapping, a high-dimensional sparse regression model is usually employed to account for possible multiple linked QTLs. The QTL model may include closely linked and thus highly correlated genetic markers, especially when high-density marker maps are used in QTL mapping because of the advancement in sequencing technology. Although existing algorithms, such as Lasso, empirical Bayesian Lasso (EBlasso) and elastic net (EN) are available to infer such QTL models, more powerful methods are highly desirable to detect more QTLs in the presence of correlated QTLs. We developed a novel empirical Bayesian EN (EBEN) algorithm for multiple QTL mapping that inherits the efficiency of our previously developed EBlasso algorithm. Simulation results demonstrated that EBEN provided higher power of detection and almost the same false discovery rate compared with EN and EBlasso. Particularly, EBEN can identify correlated QTLs that the other two algorithms may fail to identify. When analyzing a real dataset, EBEN detected more effects than EN and EBlasso. EBEN provides a useful tool for inferring high-dimensional sparse model in multiple QTL mapping and other applications. An R software package 'EBEN' implementing the EBEN algorithm is available on the Comprehensive R Archive Network (CRAN).
Data from: Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities – i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities – from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions.
Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold Model
Conditional strategies are the most common form of discrete phenotypic plasticity. In a conditional strategy, the phenotype expressed by an organism is determined by the difference between an environmental cue and a threshold, both of which may vary among individuals. The Environmental Threshold model (ETM) has been proposed as a mean to understand the evolution of conditional strategies, but has been surprisingly seldom applied to empirical studies. A hindrance for the application of the ETM is that often, the proximate cue triggering the phenotypic expression and the individual threshold are not measurable, and can only be assessed using a related observable cue. We describe a new statistical model that can be applied in this common situation. The Latent Environmental Threshold Model (LETM) allows for a measurement error in the phenotypic expression of the individual environmental cue and a purely genetically determined threshold. We show that coupling our model with quantitative genetic methods allows an evolutionary approach including an estimation of the heritability of conditional strategies. We evaluate the performance of the LETM with a simulation study and illustrate its utility by applying it to empirical data on the size-dependent smolting process for stream-dwelling Atlantic salmon juveniles.
Data from: pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies
Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise. Markers on one chromosome were included simultaneously in a multilocus model and least angle regression was used to select the most potentially associated single-nucleotide polymorphisms (SNPs), whereas the markers on the other chromosomes were used to calculate kinship matrix as polygenic background control. The selected SNPs in multilocus model were further detected for their association with the trait by empirical Bayes and likelihood ratio test. We herein refer to this method as the pLARmEB (polygenic-background-control-based least angle regression plus empirical Bayes). Results from simulation studies showed that pLARmEB was more powerful in QTN detection and more accurate in QTN effect estimation, had less false positive rate and required less computing time than Bayesian hierarchical generalized linear model, efficient mixed model association (EMMA) and least angle regression plus empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model and fast multilocus random-SNP-effect EMMA methods had almost equal power of QTN detection in simulation experiments. However, only pLARmEB identified 48 previously reported genes for 7 flowering time-related traits in Arabidopsis thaliana.
Data for: Fossil samples archive functional diversity in marine ecosystems: An empirical test from a present-day coastal environment (Tyler and Kowalewski)
<p>Data associated with "Fossil samples archive functional diversity in marine ecosystems: An empirical test from a present-day coastal environment" by Carrie L. Tyler and Michal Kowalewski. Data include GPS coordinates for sample localities, variables quantifying multivariate space for all three assemblages, trait data for all species, and the associated R code (Functional Fidelity.zip). Abundance data is available in Tyler and Kowalewski (2023) <a href="https://doi.org/10.7717/peerj.15574">10.7717/peerj.15574</a> at <strong><a href="https://github.com/tylercl/Multi-Taxic-Fidelity">https://github.com/tylercl/Multi-Taxic-Fidelity</a> </strong>(DOI: 10.5281/zenodo.7871639).</p>
Data set for EMPIR project MeDDII Report A2.1.5 D3
<p>Data set for EMPIR project MeDDII Report A2.1.5 D3</p> <p>Validation report on the primary standards developed for the in-line measurement of the dynamic viscosity of Newtonian liquids with a target uncertainty of 2 % (k=2)</p>
Data from: When do species-tree and concatenated estimates disagree? An empirical analysis with higher-level scincid lizard phylogeny
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Data from: Empirical evidence for species-specific export of fish naïveté from a no-take marine protected area in a coastal recreational hook and line fishery
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ScienceDex guides
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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.