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9,882 results for “Scale”
Codes and datasets associated with the paper "Day-ahead Wind Power Predictions at Regional Scales: Post-processing Operational Weather Forecasts with a Hybrid Neural Network"
<p>The jupyter notebooks and datasets associated with the EEM20 forecasts are available here. More details will be provided shortly. </p> <p>Please check the EEM20 website (<a href="https://eem20.eu/forecasting-competition/">https://eem20.eu/forecasting-competition/</a>) for the details of the forecasting competition. </p>
Estimating individual level plant traits at scale
<p>Derived prediction of traits for ~5 million trees at two NEON sites (OSBS and TALL)</p>
Multi-scale optical coherence tomography imaging and visualization of Vermeer's Girl with a Pearl Earring
<p>The data sets, software, and figures accompany the publication:</p> <p>"Multi-scale optical coherence tomography imaging and visualization of Vermeer's Girl with a Pearl Earring", Optics Express 28, 26239 (2020) <a href="https://doi.org/10.1364/OE.390703">https://doi.org/10.1364/OE.390703</a></p> <ul> <li>Fig4_largescaleOCT.pdf, high resolution image of figure 4 of the manuscript</li> <li>Fig5_mediumscaleOCT.pdf, high resolution image of figure 5 of the manuscript</li> <li>Fig6_smallscaleOCT.pdf, high resolution image of figure 6 of the manuscript</li> <li>GWPE_DEMO_V5.zip<br> Zip file of a Windows executable of the virtual rendering of the Girl with the Pearl Earring. The readme file describes the operation of the virtual rendering.</li> <li>Stitching_README.txt Describes the stitching software and the accompanying data sets</li> <li>MS-OCT surface data: <ul> <li>SurfaceStitchedKwadrant11.npy</li> <li>SurfaceStitchedKwadrant12.npy</li> <li>SurfaceStitchedKwadrant21.npy</li> <li>SurfaceStitchedKwadrant22.npy</li> <li>UpperInterfaceMatrixRawdataKwadrant11.npy</li> </ul> </li> <li>MS-OCT thickness data <ul> <li>FullResGlazeStratigraphyThicknessKwadrant11.npy</li> <li>FullResGlazeStratigraphyThicknessKwadrant12.npy</li> <li>FullResGlazeStratigraphyThicknessKwadrant21.npy</li> <li>FullResGlazeStratigraphyThicknessKwadrant22.npy</li> </ul> </li> <li>MS-OCT Scattering strength data <ul> <li>FullResScatteringStrengthKwadrant11.npy</li> <li>FullResScatteringStrengthKwadrant12.npy</li> <li>FullResScatteringStrengthKwadrant21.npy</li> </ul> </li> <li>Main.py, DataAnalysisFunctionsRepository.py, and ReadAndCombineKwadrantData.py are Python files for stitching the four quadrants of data together. Runs in Python >3.5. Full stitching image takes more than an hourFullResScatteringStrengthKwadrant22.npy</li> <li>Plot_measure.py and plot_fit.py<br> Analysis of the BRDF measurements of the black underlayer background (RU1) and glaze layer (RU5). Runs in Python > 3.5</li> <li>Visualization1.ave<br> Video of the multi-scale multi-parameter OCT data set of the Girl</li> <li>Visualization2.mp4<br> Video showing an impression of the interactive demo of the Girl <ul> </ul> </li> </ul>
Introgression across evolutionary scales suggests reticulation contributes to Amazonian tree diversity
<p>Hybridisation has the potential to generate or homogenize biodiversity and is a particularly common phenomenon in plants, with an estimated 25% of plant species undergoing inter-specific gene flow. However, hybridisation in Amazonia's megadiverse tree flora was assumed to be extremely rare despite extensive sympatry between closely related species, and its role in diversification remains enigmatic because it has not yet been examined empirically. Using members of a dominant Amazonian tree family (<i>Brownea</i>, Fabaceae) as a model to address this knowledge gap, our study recovered extensive evidence of hybridisation among multiple lineages across phylogenetic scales. More specifically, using targeted sequence capture our results uncovered several historical introgression events between <i>Brownea </i>lineages and indicated that gene tree incongruence in <i>Brownea</i> is best explained by reticulation, rather than solely by incomplete lineage sorting. Furthermore, investigation of recent hybridisation using ~19,000 ddRAD loci recovered a high degree of shared variation between two <i>Brownea </i>species that co-occur in the Ecuadorian Amazon.</p> <p>Our analyses also showed that these sympatric lineages exhibit homogeneous rates of introgression among loci relative to the genome-wide average, implying a lack of selection against hybrid genotypes and persistent hybridisation. Our results demonstrate that gene flow between multiple Amazonian tree species has occurred across temporal scales, and contrasts with the prevailing view of hybridisation's rarity in Amazonia. Overall, our results provide novel evidence that reticulate evolution influenced diversification in part of the Amazonian tree flora, which is the most diverse on Earth.</p>
The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding
<p>Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multi-hierarchical approach was performed using <span>haplotype-level-COI metabarcoding</span> of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local assemblages were highly distinctive between grasslands and forests, and within each of them showed strong spatial structures and high endemicity at the scale of a few kilometres or less. The local distance-decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was very similar in all three regions, pointing to a significant role of dispersal limitation driving the local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod-diversity on Earth.</p>
Figure 4. Caprella equilibra Say, 1818. Male mouthparts. Scale bar x in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 4. Caprella equilibra Say, 1818. Male mouthparts. Scale bar x (Mx1, Mx2, LMd, Mxp) and y (UL, LL): 0.1 mm.
Figure 7. Caprella mendax Mayer, 1903. Male mouthparts. Scale bar x in Littoral caprellids (Crustacea: Amphipoda) from the Mexican Central Pacific coast, with the description of four new species
Figure 7. Caprella mendax Mayer, 1903. Male mouthparts. Scale bar x (Mx1, Mx2, LMd, RMd, Mxp) and y (UL, LL): 0.1 mm.
Figure 4 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 4. Mean Margalef's species richness and Shannon–Wiener diversity index values per year; 90% confidence intervals are shown.
Figure 3 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 3. Seasonal and inter-annual patterns of total calanoid abundance (individuals per m3) (left scale and bars) and their contribution (%) to total mesozooplankton abundance (right scale and line) over the study period.
Figure 2 in Temporal patterns of the calanoid copepod community in Veliko Jezero, an isolated marine lake (South Adriatic Sea): links to a larger-scale climate changes
Figure 2. Seasonal and inter-annual patterns of hydrographic parameters (temperature and salinity) over the study period.
Associations between socio-environmental factors and landscape-scale biodiversity recovery in naturally regenerating tropical and subtropical forests
<p class="western"><span><span>Natural regeneration is key for large-scale forest restoration, yet it may lead to different biodiversity outcomes depending on socio-environmental context. We combined the results of a global meta-analysis to quantify how biodiversity recovery in naturally regenerating forests deviates from biodiversity values in reference old-growth forests, with structural equation modeling, to identify direct and indirect associations between socioeconomic, biophysical and ecological factors and deviation in biodiversity recovery at a landscape scale. Low deviation within a landscape means higher chances of multiple sites in naturally regenerating forests successfully recovering biodiversity compared to reference forests. Deviation in biodiversity recovery was directly negatively associated with the percentage of cropland, forest cover, and positively associated with the percentage of urban areas in the surrounding landscape. These three factors mediated the indirect associations with rural population size, recent gross deforestation, time since natural regeneration started, mean annual temperature, mean annual water deficit, road density, land opportunity cost, percentage cover of strictly protected forest areas, and human population variation in the surrounding landscape. We suggest that natural forest restoration should be prioritized in landscapes with both low socioeconomic pressures on land use conversion to pasturelands and urban areas, and high percentage of forest cover.</span></span></p>
Anuran accents: Continental-scale citizen science data reveal spatial and temporal patterns of call variability
<p>Data and code associated with the 2020 publication in Ecology and Evolution (doi:10.1002/ece3.6833).</p>
Productivity loss associated with physical impairment in a contemporary small-scale subsistence population
<p>Humans experience unique physical impairments with potentially severe economic consequences. Quantifying the burden of impairment in subsistence populations is critical for understanding selection pressures underlying strategies that minimize risk of production deficits. We examine among forager-horticulturalists whether compromised bone strength (indicated by vertebral fracture and lower bone mineral density, BMD) is associated with diminished subsistence involvement. We estimate the magnitude of productivity losses associated with compromised bone strength. Fracture is associated with cessation of hunting, tree chopping and walking long distances, but not tool manufacture. Age-specific productivity losses from hunting cessation related to fracture and lower BMD are substantial. Productivity loss is thus substantial for high strength and endurance tasks. Determining the extent to which impairment obstructs productivity in contemporary subsistence populations improves the ability to infer consequences of impairment over human evolution.</p>
INCLUDE: A Large Scale Dataset for Indian Sign Language Recognition
<p><strong>Dataset Details</strong>: The INCLUDE dataset has 4292 videos (the paper mentions 4287 videos but 5 videos were added later). The videos used for training are mentioned in train.csv (3475), while that used for testing is mentioned in test.csv (817 files). Each video is a recording of 1 ISL sign, signed by deaf students from St. Louis School for the Deaf, Adyar, Chennai.</p> <p>INCLUDE50 has 766 train videos and 192 test videos.</p> <p><strong>Train-Test Split:</strong> Please download the train-test split for INCLUDE and INCLUDE50 from here: <a href="https://drive.google.com/file/d/1tGjOR9xbk279ZUYnmk3BE-ktcWBdS24w/view?usp=sharing">Train-Test Split</a></p> <p><strong>Publication Link</strong><em>: <a href="https://dl.acm.org/doi/10.1145/3394171.3413528">https://dl.acm.org/doi/10.1145/3394171.3413528</a></em></p> <p><strong>AI4Bharat website</strong><em>: <a href="https://ai4bharat.org/include-dataset">https://sign-language.ai4bharat.org/</a></em></p> <p><strong>Download Instructions</strong></p> <p>For ease of access, we have prepared a Shell Script to download all the parts of the dataset and extract them to form the complete INCLUDE dataset.</p> <p><em>You can find the script here: <a href="http://bit.ly/include_dl">http://bit.ly/include_dl</a></em></p> <p><strong>Paper Abstract:</strong> <em>Indian Sign Language (ISL) is a complete language with its own grammar, syntax, vocabulary and several unique linguistic attributes. It is used by over 5 million deaf people in India. Currently, there is no publicly available dataset on ISL to evaluate Sign Language Recognition (SLR) approaches. In this work, we present the Indian Lexicon Sign Language Dataset - INCLUDE - an ISL dataset that contains 0.27 million frames across 4,287 videos over 263 word signs from 15 different word categories. INCLUDE is recorded with the help of experienced signers to provide close resemblance to natural conditions. A subset of 50 word signs is chosen across word categories to define INCLUDE-50 for rapid evaluation of SLR methods with hyperparameter tuning. The best performing model achieves an accuracy of 94.5% on the INCLUDE-50 dataset and 85.6% on the INCLUDE dataset</em></p>
Figure 7 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 7 BSPs showing NefT (Nef = effective population size; T = generation time) changes over time for P. minor based on Cytb sequences. The upper and lower limits of the blue line represent the 95% confidence intervals of highest posterior densities (HPD) analysis. The solid black line represents median estimates of NefT.
Figure 5 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 5 Matrix of pairwise FST values between 11 P. minor populations based on Cytb sequences. * significant at p < 0.05 by the permutation test, ** extremely significant at p < 0.01 by the permutation test.
Figure 6 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 6 The expected mismatch distributions under a sudden expansion model (solid gray line) and the observed pairwise difference (black bars) of Cytb haplotypes of P. minor.
Figure 4 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 4 Unrooted minimum spanning tree showing the genetic relationships among the Cytb haplotypes of P. minor. Circle sizes are proportional to haplotype frequency. Perpendicular tick marks on the lines joining the haplotypes represent the number of nucleotide substitutions.
Figure 1 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 1 Sampling locations of P. minor. Populations are marked by abbreviations that correspond to Table 1.
Figure 2 from: Li Y, Liu C, Lin L, Li Y, Xiao J, Loh K-H (2020) Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution. ZooKeys 969: 137-154. https://doi.org/10.3897/zookeys.969.52069
Figure 2 Composition and distribution of 22 Cytb haplotypes in the Chinese and Malaysian populations.
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.