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1,454 results for “large scale”
Data from: Building the avian tree of life using a large-scale, sparse supermatrix
Birds are the most diverse tetrapod class, with about 10,000 extant species that represent a remarkable evolutionary radiation in which most taxa arose during a short period of time. There has been a tremendous increase in the amount of molecular data available from birds, and more than two-thirds of these species have some sequence data available. Here we assembled these available sequence data from birds to estimate a large-scale avian phylogeny. We performed an unconstrained maximum likelihood analysis of a sparse supermatrix comprising 22 nuclear loci and seven mitochondrial regions from 6714 species. We inferred a phylogeny with a backbone remarkably similar to that obtained by detailed analyses of multigene datasets, yet with the addition of thousands of more taxa. All orders were monophyletic with generally high support. While most families and genera were well supported, a number of them, especially within the oscine passerines, had little or no support. This likely reflects problems with the circumscription of these genera and families. Our results indicate that the amount of sequence data currently available is sufficient to produce a robust estimate of the avian tree of life using current methods of inference. The availability of a tree that is unconstrained by prior information, with branch lengths that have a direct connection to the underlying data, should be useful for comparative methods, taxonomic revisions, and prioritizing taxa that should be targeted for additional data collection.
Data from: Reproductive success is driven by local site fidelity despite stronger specialisation by individuals for large scale habitat preference
1. There is widespread evidence that within populations, specialists and generalists can coexist and this is particularly prevalent in marine ecosystems, where foraging specialisations are evident. 2. While individuals may limit niche overlap by consistently foraging in specific areas, site fidelity may also emerge as an artefact of habitat choice but both drivers and fitness consequences of site fidelity are poorly understood. 3. Here we examine an individual metric of site and habitat fidelity, using tracking data collected over 11 years for black-browed albatrosses (Thalassarche melanophris). Fidelity was calculated as the similarity between pairs of foraging zones, quantifying measures for within and between years. Foraging areas were identified using area restricted search, defined as periods during which birds decrease speed and increase turning. 4. Our results demonstrate that birds were considerably more specialised in the habitat in which they forage than the exact location they use within years, and there was a similar pattern between years. However, despite this, it was site fidelity that explained reproductive success. Within a single year, females which were more faithful to a specific location had higher reproductive success than non-specialists and between years there was tendency for both sexes. 5. Our results suggest that black-browed albatrosses are highly faithful in their foraging habitat but it is rather site fidelity that is more clearly associated with reproductive success.
Large scale expression and purification of full length huntingtin Q23 from baculovirus expression system (2016/08/29)
<p>Open lab notebook huntingtin structure function project.<br> </p>
FIGURE 8. Pseudotomias kisarawe n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 8. Pseudotomias kisarawe n. sp. male mounting female showing sexual size dimorphism.
FIGURE 6 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 6. Last instar of female Pseudotomias usambaricus n. sp.
FIGURE 7. Pseudotomias kisarawe n in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 7. Pseudotomias kisarawe n. sp., male (A) and female (B).
FIGURE 2 in The Eastern Arc Mountains and coastal forests of East Africa—an archive to understand large-scale biogeographical patterns: Pseudotomias, a new genus of African Pseudophyllinae (Orthoptera: Tettigoniidae)
FIGURE 2. Male holotype of Pseudotomias usambaricus n. sp., Sigi Trail, East Usambara Mountains.
Figure 1 in Off the scale: a new species of fishscale gecko (Squamata: Gekkonidae: Geckolepis) with exceptionally large scales
Figure 1 Molecular phylogeny and distribution of Geckolepis OTUs based mainly on Lemme et al. (2013). Dotted lines in the phylogeny indicate uncertain placement. The phylogenetic position and distribution of Geckolepis humbloti is inferred from Hawlitschek et al. (2016).
Dataset to reproduce the figures in "Parameterizing the Impact of Unresolved Temperature Variability on the Large-Scale Density Field: Part 2. Modeling." in Journal of Advances in Modeling Earth Systems (JAMES)
Ocean circulation models have systematic errors in large-scale horizontal density gradients due to estimating the grid-cell-mean density by applying the nonlinear seawater equation of state to the grid-cell-mean water properties. In frontal regions where unresolved subgrid-scale (SGS) fluctuations are significant, dynamically relevant errors in the representation of current systems can result. A previous study developed a novel and computationally efficient parameterization of the unresolved SGS temperature variance andresulting density correction. This parameterization was empirically validated but not tested in an ocean model. In this study, we implement deterministic and stochastic variants of this parameterization in the pressure-gradient force term of a coupled ocean-sea ice configuration of CESM-MOM6 and perform a suite of hindcast sensitivity experiments to investigate the ocean response. The parameterization leads to coherent changes in the large-scale ocean circulation and hydrography, particularly in the Nordic Seas and Labrador Sea, which are attributable in large part to changes in the seasonally varying upper-ocean exchange through Denmark Strait. In addition, the separated Gulf Stream strengthens and shifts equatorward, reducing a common bias in coarse-resolution ocean models. The ocean response to the deterministic and stochastic variants of the parameterization is qualitatively, albeit not quantitatively, similar, yet qualitative differences are found in various regions.
Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) - Data Set
<p>GENERAL INFORMATION</p> <p>The data and scripts used for the analysis of the paper "Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) – Towards an improved representation of mountain water resources in global assessments"</p> <p><strong>When using this dataset, please refer to the original publication in addition to this Zenodo repository.</strong></p> <p><strong>Hanus, S., Schuster, L., Burek, P., Maussion, F., Wada, Y., and Viviroli, D.: Coupling a large-scale glacier and hydrological model (OGGM v1.5.3 and CWatM V1.08) – towards an improved representation of mountain water resources in global assessments, Geosci. Model Dev., 17, 5123–5144, https://doi.org/10.5194/gmd-17-5123-2024, 2024.</strong></p> <p>DATA & FILE OVERVIEW</p> <p>please have a look at readme.txt </p> <p>Don't hesitate to contact us in case of any questions (sarah.hanus@geo.uzh.ch)</p>
Data set for "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories"
<p>Data accompanying the paper "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories" </p>
LIVECell A large-scale dataset for label-free live cell segmentation - organised by cell type
<p>This data was originally published in </p><p><a href="https://doi.org/10.1038/s41592-021-01249-6">Edlund, C., Jackson, T.R., Khalid, N. <i>et al.</i> LIVECell—A large-scale dataset for label-free live cell segmentation. <i>Nat Methods</i> <strong>18</strong>, 1038–1045 (2021). https://doi.org/10.1038/s41592-021-01249-6</a></p><p>The instance segmentation annotation data has been downloaded and organised in folders for each cell type to ease its use in demos and courses. Please, refer to the original publication and <a href="https://sartorius-research.github.io/LIVECell/">original data source</a> for further research studies. </p><p><strong>IF YOU USE THIS DATASET, PLEASE ACKNOWLEDGE THE ORIGINAL AUTHORS (Edlund et al., Nat Methods 2021)</strong></p>
Determination of process parameters and precipitation methods for potential large-scale production of sugar beet leaf protein concentrate
<p>Abstract</p> <p><br>BACKGROUND</p> <p>Sugar beet is one of the most produced industrial plants in the world, and during manufacturing, it produces a large quantity of leaf waste. Because this waste is rich in protein, this study aimed to identify an efficient method for producing large-scale protein concentrate from sugar beet leaves.</p> <p><br>RESULTS</p> <p>Results showed that protein extraction from fresh leaves was more effective than dried leaves. Maximum protein extraction was achieved at pH 9, compared with pH 7 or 8. Blanching as a pretreatment reduced protein yield during isoelectric precipitation, with a yield of 2.31% compared to 20.20% without blanching. Consequently, blanching was excluded from the extraction process. After extraction, isoelectric precipitation, heat coagulation, and isoelectric–ammonium sulfate precipitation were compared. Although the latter resulted in the highest protein yield, Fourier transform infrared analysis revealed that excessive salt was not removed during dialysis, making it unsuitable for scale-up due to its additional cost and complexity. Therefore, isoelectric precipitation was selected as the appropriate method for protein precipitation from sugar beet leaves. To increase yield, extractions were assisted by ultrasound or enzyme addition. Ultrasound-assisted extraction resulted in an increased protein yield from 20.20% to 28.60%, while Pectinex Ultra SP-L-assisted extraction was the most effective, increasing protein yield from 20.20% to 38.09%.</p> <p><br>CONCLUSION</p> <p>Proteins were extracted from fresh sugar beet leaves using optimum conditions (50 °C, 30 min, pH 9) and precipitated at the isoelectric point, with enzymatic-assisted extraction yielding the maximum protein recovery.<br><br></p>
Supplementary: Observing the Southern US Honor Culture Using Large-Scale Social Media Analysis
Open the record for dataset details and reuse information.
Data for the article: Residual Flexural Performance of Large-Scale Ferronickel Slag Alkali-Activated Concrete Slabs After Fire Exposure
<p>Figures and related data for the article Residual Flexural Performance of Large-Scale Ferronickel Slag Alkali-Activated Concrete Slabs After Fire Exposure</p>
Improved snow darkening coefficient for large-scale albedo modelling with Crocus
<p><strong>Description</strong></p> <p>Light-absorbing particles (LAPs) deposited at the snow surface significantly reduce its albedo and strongly affect the snow melt dynamics. The explicit simulation of these effects with advanced snow radiative transfer models can be associated with a large computational cost. Consequently, many albedo schemes used in snowpack models still rely on empirical parameterizations that do not account for the spatial variability of LAP deposition. In Gaillard et al. (2024), a new strategy of intermediate complexity that includes the effects of spatially variable LAP deposition on snow albedo was tested with the snowpack model Crocus. It relies on an optimization of the snow darkening coefficient that controls the evolution of snow albedo in the visible range. A global dataset of LAP-informed and spatially variable values of the snow darkening coefficient was constructed. The revised snow darkening coefficient improved snow albedo simulations at the ten sites considered in the study by 10%, with the largest improvements found in the Arctic (more than 25%). The uncertainties in the values of the snow darkening coefficient resulting from the inter-annual variability of LAP deposition on snow were also computed.</p> <p>The data are distributed in a NetCDF file (gamma<em>_tot_publish_v2.nc</em>). More details about the dataset and the file format are given in the file <em>readme_gamma_v2.pdf</em>. </p>
Large-scale statistical learning for mass transport prediction in porous materials using 90,000 artificially generated microstructures
<p>Dataset and code used in B Prifling, et al, "Large-scale statistical learning for mass transport prediction in porous materials using 90,000 artificially generated microstructures", published in Frontiers in Materials. In this work, we investigate relationships between 3D microstructure and effective diffusivity and permeability, based on a dataset of 90,000 structures and using analytical formulas, artificial neural networks (ANNs), and convolutional neural networks (CNNs). Herein, the codes in Matlab and Python/Tensorflow necessary to investigate the prediction models and reproduce the results of the paper are supplied. Also, microstructures together with their computed geometrical descriptors and effective properties are included.</p>
Linking biotic homogenisation with large-scale changes of species' associations
<p><span><span>This is the dataset used for the manuscript</span></span><em> Linking biotic homogenisation with large-scalechanges of species' associations</em></p> <p><span><span><b>Aim: </b><span>The impact of global change on biodiversity is commonly assessed in terms of changes in species distributions, community richness and community composition. Whether and how much associations between species, </span><i><span>i.e.</span></i><span> the degree of correlation in their spatial co-occurrence, </span><span>are also </span><span>chang</span><span>ing</span><span> is much less documented and mostly limited to local studies of ecological networks. </span><span>Here, we propose to quantify the large-scale patterns and changes of species' associations in bird communities</span><span> in relation to modifications in species composition</span><span>.</span></span></span></p> <p><span><span><b>Location:</b><span> France.</span></span></span></p> <p><span><span><b>Time period:</b><span> 2001-2017.</span></span></span></p> <p><span><span><b>Major taxa studied:</b><span> Common breeding birds.</span></span></span></p> <p><span><span><b>Methods: </b><span>We use network approaches to build three community-aggregated indices reflecting complementary aspects of species' associations. We characterise the spatio-temporal heterogeneity and dynamics of these indices using a large</span><span>-</span><span>scale</span><span> and high-resolution dataset of bird co-abundances of more than 100 species</span><span> monitored</span><span> for 17 years (2001-2017) from 1,969 sites across France. We </span><span>finally</span><span> test whether spatial and temporal changes in species association networks are related to species homogenisation estimated as the spatio-temporal dynamics of β-diversity</span><span>.</span></span></span></p> <p><span><span><b>Results: </b><span>We document non-random spatial distribution of both structure and temporal changes in species association networks.</span><span> W</span><span>e </span><span>also </span><span>report a</span><span> directional change in </span><span>association-based</span><span> indices </span><span>with</span><span> β-diversity </span><span>modifications </span><span>in space and time, suggesting a hitherto overlooked aspect of biotic homogenisation affecting species' associations.</span></span></span></p> <p><span><span><b>Main Conclusions: </b><span>Although species association networks are only approximations of species</span><span>'</span><span> interactions, our study highlights that</span><span> the modifications of</span><span> species association networ</span><span>ks </span><span>have to be considered</span><span>,</span><span> in addition to species </span><span>turnover</span><span>,</span><span> as biodiversity</span><span> fac</span><span>es </span><span>global change.</span></span></span></p> <p><span><span><span><b>Keywords:</b> Avifauna, β-diversity, homogenisation, community, interaction network, species' association.</span></span></span></p>
Supplementary material 1 from: Adamov EO, Rachkov VI, Kashirsky AA, Orlov AI (2021) Global outlook on large-scale nuclear power development strategies. Nuclear Energy and Technology 7(4): 263-270. https://doi.org/10.3897/nucet.7.74217
Global outlook on large-scale nuclear power development strategies
Dataset for "First Observations of Large Scale Traveling Ionospheric Disturbances Using Automated Amateur Radio Receiving Networks"
<p># 20171103.rbn_pskreporter_wspr_data.csv<br> #<br> # This data file contains the amateur radio spot data used in the manuscript:<br> # "First Observations of Large Scale Traveling Ionospheric Disturbances Using Automated Amateur Radio Receiving Networks"<br> # by Nathaniel A. Frissell W2NAF, Stephen R. Kaeppler AD0AE, Diego F. Sanchez KD2RLM, Gareth W. Perry KD2SAK,<br> # William D. Engelke AB4EJ, Philip J. Erickson W1PJE, Anthea J. Coster, J. Michael Ruohoniemi, and Joseph B. H. Baker<br> #<br> # Observations are provided courtesy of:<br> # 1. The Weak Signal Propagation Reporting Network (WSPRNet, https://www.wsprnet.org/)<br> # Operated by Bruce Walker W1BW<br> #<br> # 2. The Reverse Beacon Network (RBN, http://www.reversebeacon.net/)<br> # Operated by Nick Sinanis F5VIH/SV3SJ, David Pascoe KM3T, Mark Glenn K7MJG, Peter Smith N4ZR, Felipe Ceglia PY1NB/CT7ANO, and Dick Williams W3OA<br> #<br> # 3. PSKReporter (https://pskreporter.info/)<br> # Operated by Philip Gladstone N1DQ<br> #<br> # Explanation of Data Columns:<br> # freq: Frequency [kHz]<br> # ut: Time of Observation in Universal Time (UT)<br> # source: Observation Network (WSPRNet, RBN, or PSKReporter)<br> # tx_grid: Transmitter Maidenhead Gridsquare<br> # rx_grid: Receiver Maindenhead Gridsquare<br> # tx_lat: Transmitter Latitude (deg)<br> # tx_long: Transmitter Longitude (deg)<br> # rx_lat: Receiver Latitude (deg)<br> # rx_long: Receiver Longitude (deg)<br> # dist_Km: Ground-Level Great Circle Distance between Transmitter and Receiver (km)<br> # md_lat: Midpoint between Transmitter and Receiver Latitude (deg)<br> # md_long: Midpoint between Transmitter and Receiver Longitude (deg)<br> # slt_mid: Solar Local Time of Midpoint (hr)<br> #<br> # This datafile is a subset of the full WSPRNet/RBN/PSKReporter data, filtered with the following parameters:<br> # ut min: 2017-11-03 00:00:00<br> # ut max: 2017-11-03 23:59:59<br> # freq min: 14000.382<br> # freq max: 14280.0<br> # md_lat min: 20.004737453151876<br> # md_lat max: 54.99977112001497<br> # md_long min: -129.99845895196913<br> # md_long max: -60.008771378901315<br> # dist_Km min: 0.0<br> # dist_Km max: 19861.14355003741</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.