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1,034 results for “Empirical”
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>
Replication Package: "When Uncertainty Leads to Unsafety: Empirical Insights into the Role of Uncertainty in Unmanned Aerial Vehicle Safety"
<p>Replication Package of the paper titled "When Uncertainty Leads to Unsafety: Empirical Insights into the Role of Uncertainty in Unmanned Aerial Vehicle Safety"</p>
Dataset for An Empirical Study of Static Analysis Tools for Secure Code Review
Open the record for dataset details and reuse information.
Replication Package of ''Improving the Sustainability of Neural Code Summarization Models: An Empirical Study"
<p>This repository contains the replication package of "Improving the Sustainability of Neural Code Summarization Models: An Empirical Study".</p>
Investigating Economic Growth Catalysts: An Empirical Analysis of Determinants of Domestic Private Investment in Ethiopia
<p>This is the original data that supports the findings of the research entitled "<strong>Investigating Economic Growth Catalysts: An Empirical Analysis of Determinants of Domestic Private Investment in Ethiopia"</strong></p>
RCubed WP3 empirical downscaling results, common ensemble
<p>NetCDF4 files containing the seasonal output of empirically downscaled GCM data under the RCP8.5 trajectory, has been produced in the Norwegian Research Council Project RCubed, work package 3, using a hybrid dynamical-statistical downscling approach. The data covers most of South Norway, and is available in a lat-lon projection with a resolution of 0.1° in longitude and 0.05° in latitude. The data is produced using the R software package <a href="https://github.com/metno/esd/wiki">esd</a>. The downscaled variables are seasonal mean 2-meter temperature (T2), seasonal wet-day mean (mu - the precipitation intensity on rainy (>1 mm) days), and seasonal wet-day frequency (fw - the frequency of days where precipitation is 1 mm or more). The data here is the common ensemble, that is GCM model runs which were used for downscaling T2, mu, and fw. From mu and fw seasonal mean precipitation (excluding days where precipitation is less than 1 mm) is derived. The data is also available from MET Norway's thredds server with <em>OPeNDAP</em> <a href="http://thredds.met.no/thredds/catalog/metusers/helenebe/catalog.html">http://thredds.met.no/thredds/catalog/metusers/helenebe/catalog.html</a></p> <p>The data is downscaled using ouput from a dynamical downscaling (see Pontoppidan, 2018) as reference data. This means that the data may contain biases during historical time. The precipitation fields inter-annual variation is not fully captured at the fine grid scale for which the data is produced, so we recommend applying some upscaling/areal averaging if the inter-annual correlation is of importance. The long-term trend is likely captured for the fields at the resolution of the data. An article describing the work behind the data is underway, and will be added here once published.</p> <p>Pontoppidan, M., Kolstad, E. W., Sobolowski, S., & King, M. P. ( 2018). Improving the reliability and added value of dynamical downscaling via correction of large‐scale errors: A Norwegian perspective. <em>Journal of Geophysical Research: Atmospheres</em>, 123, 11,875– 11,888. <a href="https://doi.org/10.1029/2018JD028372">https://doi.org/10.1029/2018JD028372</a></p> <p> </p> <p>The GCM runs downscaled:</p> <p>"1" "ACCESS13_r1i1p1"<br> "2" "bcccsm11_r1i1p1"<br> "3" "CanESM2_r1i1p1"<br> "4" "CanESM2_r2i1p1"<br> "5" "CanESM2_r3i1p1"<br> "6" "CanESM2_r4i1p1"<br> "7" "CanESM2_r5i1p1"<br> "8" "CCSM4_r1i1p1"<br> "9" "CCSM4_r2i1p1"<br> "10" "CCSM4_r3i1p1"<br> "11" "CCSM4_r4i1p1"<br> "12" "CCSM4_r5i1p1"<br> "13" "CCSM4_r6i1p1"<br> "14" "CESM1BGC_r1i1p1"<br> "15" "CESM1CAM5_r1i1p1"<br> "16" "CNRMCM5_r10i1p1"<br> "17" "CNRMCM5_r1i1p1"<br> "18" "CNRMCM5_r2i1p1"<br> "19" "CNRMCM5_r4i1p1"<br> "20" "CNRMCM5_r6i1p1"<br> "21" "CSIROMk360_r10i1p1"<br> "22" "CSIROMk360_r1i1p1"<br> "23" "CSIROMk360_r3i1p1"<br> "24" "CSIROMk360_r5i1p1"<br> "25" "CSIROMk360_r6i1p1"<br> "26" "CSIROMk360_r8i1p1"<br> "27" "GFDLCM3_r1i1p1"<br> "28" "GFDLESM2M_r1i1p1"<br> "29" "GISSE2H_r1i1p1"<br> "30" "GISSE2H_r1i1p2"<br> "31" "GISSE2H_r1i1p3"<br> "32" "GISSE2R_r1i1p1"<br> "33" "GISSE2R_r1i1p2"<br> "34" "GISSE2R_r1i1p3"<br> "35" "HadGEM2CC_r1i1p1"<br> "36" "HadGEM2ES_r1i1p1"<br> "37" "HadGEM2ES_r3i1p1"<br> "38" "HadGEM2ES_r4i1p1"<br> "39" "inmcm4_r1i1p1"<br> "40" "IPSLCM5ALR_r1i1p1"<br> "41" "IPSLCM5ALR_r2i1p1"<br> "42" "IPSLCM5ALR_r3i1p1"<br> "43" "IPSLCM5ALR_r4i1p1"<br> "44" "IPSLCM5AMR_r1i1p1"<br> "45" "IPSLCM5BLR_r1i1p1"<br> "46" "MIROC5_r1i1p1"<br> "47" "MIROC5_r2i1p1"<br> "48" "MIROC5_r3i1p1"<br> "49" "MIROCESM_r1i1p1"<br> "50" "MIROCESMCHEM_r1i1p1"<br> "51" "MRICGCM3_r1i1p1"<br> "52" "NorESM1M_r1i1p1"<br> "53" "NorESM1ME_r1i1p1"</p>
Studying the Characteristics of SQL-related Development Tasks: An Empirical Study
<p>This replication package contain datasets and scripts to replicate the results obtained in the paper titled "<strong>Studying the Characteristics of SQL-related Development Tasks: An Empirical Study"</strong>, published in the Empirical Software Engineering Journal (EMSE)</p>
The dataset of the paper titled "Human Value Requirements in AI Systems: Empirical Analysis of Amazon Alexa"
<p>This package includes the dataset (user reviews) of Amazon Alexa and the corresponding labels of human values used in this paper which was submitted to EmpiRE 2023. It also includes the details of the results with some visualizations.</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>
Dataset of the Paper: Practices and Challenges of Using GitHub Copilot: An Empirical Study
<p>This dataset collected from Stack Overflow (SO) and GitHub Discussions was used to conduct an empirical study on the practices and challenges of using GitHub Copilot. A brief description of each document in the dataset is provided below:</p> <p><strong>1. Dataset (SO).xlsx</strong></p> <p>contains the IDs and URLs of the labelled posts which are related to Copilot from Stack Overflow, and the data extracted from these related SO posts.</p> <p><strong>2. Dataset (GitHub).xlsx</strong></p> <p>contains the discussion IDs and discussion URLs in the Copilot category of GitHub Discussions, and the data extracted from all the discussions.</p> <p><strong>3. Extracted Data (SO+GitHub).xlsx</strong></p> <p>contains the final results of data extracted from SO posts and GitHub discussions.</p>
An Empirical Comparison of Ethnic and Gender Diversity of DevOps and non-DevOps Contributions to Open-Source Projects
<p>This is the replication package for the paper titled "An Empirical Comparison of Ethnic and Gender Diversity of DevOps and non-DevOps Contributions to Open-Source Projects." </p> <p>The preview is our online appendix. We encourage you to read the README.md file for more information about the replication package and the folder structure. </p> <p> </p>
Empire State Building
Empire State Building, the world's most iconic building, simply known for once being the world's tallest building for 40 years, from 1931 to 1971 when it was surpassed by the World Trade Center North Tower. It is standing at 1,250 feet tall for the roof and 1,454 feet tall for the overall height with its radio-cast TV antenna. It is located in New York City, at 5th Avenue and between 33rd and 34th Street, near Herald Square. Source: Objaverse 1.0 / Sketchfab
My First Empire State Building
My **first** 3D model building. I thought big for this one and went with the **Empire State Building** which used to be tallest building in the world at one point. Source: Objaverse 1.0 / Sketchfab
Coins of the Achaemenid Empire
The Achaemenid Empire issued coins from 520 to 450 BC to 330 BC. The Persian darik was the first gold coin, which, along with a similar silver coin, siglo represented the first bimetallic monetary standard. Source: Objaverse 1.0 / Sketchfab
Empire State Quick Build
In college, we had to create a quick build Empie State building with no images to help us build. Built in under 30 mins. Source: Objaverse 1.0 / Sketchfab
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.