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311 results for “function dataset”
Dataset for paper "Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity"
<p>Interpreting the shifts in forest structure, plant community composition, diversity, and functional identity by using remote sensing-derived wildfire severity . New collected data</p>
The functional significance of tree species diversity in European forests - the FunDivEUROPE dataset
<p><span>The FunDivEUROPE project, short for "Functional Significance of Forest Biodiversity in Europe," aimed at exploring the intricate relationships between forest biodiversity and ecosystem functionality, focusing specifically on European forests. The project was a collaborative effort involving scientists from multiple disciplines and institutions. It entailed a comprehensive, large-scale assessment of forest biodiversity and its impact on ecosystem functions in a network of observational plots spanning the European continent. This extensive network enabled us to systematically examine how variations in tree species diversity and functional traits influenced key ecosystem functions.</span></p> <p><span>In total, 209 mature forest plots measuring 30 x 30 meters were located</span> <span>in six European countries, ranging from boreal to Mediterranean zones, with each representing a major European forest type: Finland (boreal forest), Poland (hemiboreal forest), Germany (temperate deciduous forest), Romania (mountainous deciduous forest), Italy (thermophilous deciduous forest), and Spain Mediterranean mixed forest). Richness levels of one, two, three, four, and five target species were replicated within and across regions.</span></p> <p><span>A major strength of the FunDivEUROPE project was the general philosophy to measure all ecosystem functions in all plots, following the same protocol by the same observers across the six forest types. In each of the 209 plots, 27 ecosystem functions were measured.</span></p> <p><span>Here, we present data on a high number of basic data for each of the 209 plots, describing geographic and geomorphological, as well as soil and bedrock characteristics, climate variables, and several measures of tree diversity. We further show data of the 27 ecosystem functions, which were classified into six groups reflecting basic ecological processes, and which have established links to supporting, provisioning, regulating or cultural ecosystem services. Details about the measurement protocols are provided.</span></p> <p><span>Major results from the FunDivEUROPE project shed light on the fundamental importance of biodiversity in European forests. The project revealed that diverse forests tend to be more resilient to disturbances, sequester more carbon, and provide enhanced diversity of forest-associated taxa. Moreover, the study highlighted the crucial role of particular tree species and functional traits in shaping ecosystem services and functions. The findings of FunDivEUROPE thus offer insights for forest management and conservation practices, advocating for the preservation and restoration of diverse forest ecosystems.</span></p>
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Dataset: Thermal noise calibration of functionalized cantilevers for force microscopy: effects of the colloidal probe position.
<p>Dataset for article "Thermal noise calibration of functionalized cantilevers for force microscopy: effects of the colloidal probe position"</p><p>The raw data is in the 6 zip files (AIO*.zip), which contains thermal noise spectra measured on the raw cantilevers close to the free end (folders AIO#, where #=1, 2 or 3 for samples A, B or C), or on the loaded cantilever at various positions along its length (folders AIO#-ScanHF, where #=1, 2 or 3 for samples A, B or C). The file format is Matlab data file (.mat), it include the vectors f (for frequency axis, in Hz) and p (power spectrum density, in m^2/Hz). Other variables are erreur (some internal check that the calibration of the interferometer is pertinent) and PointW (mean intensity collected by the interferometer, and mean contrast on the 2 quadrature signals). For the loaded cantilever, we also record the laser spot position (XFaisceau and YFaisceau, in µm, origin close to the free end on the cantilever), some timing information to track for drifts, and ellipse (a calibration step of the quadrature phase interferometer).</p><p>The SEM images of the samples are included in the zip file SEMimages.zip</p><p>All analysis scripts (Matlab .m files) are included:</p><ul><li>AnalyseAll.m reads the raw data files and extract all the pertinent information, saving it to file AnalyseAll.mat</li><li>Analysis_cp analyses the pre-processed data with the single contact point model</li><li>Analysis_endload analyses the pre-processed data with the rigid end load model</li><li>figspectrum.m creates Fig. 4 of the article</li><li>plot_cp_endload.m creates Fig. 5 and 6 of the article</li></ul><p>All other scripts (.m) are dependencies that are necessary for the 3 former scripts to run. All scripts are commented and should be self explanatory. Of interest are the scripts mode_shape_cp.m and mode_shape_endload.m, which compute the resonant mode shape of a loaded cantilever for the two models, when given the parameters on the load size and position.</p>
Divergent evolution of sleep functions - Joyce et al 2024 Dataset - Part 2 of 4
<p>This is the full experimental dataset associated to "Divergent evolution of sleep functions" by Joyce et al 2024, Nature Communications. See https://lab.gilest.ro/papers/divergent-evolution-of-sleep-functions/ for more information.</p> <p>The dataset contains 86 zip files for a total of about 170GB. Once uncompressed, they will explode 622 ethoscope db files for a total of 330Gb, covering behavioural analysis of more than 11.000 animals. These are the RAW data as collected from the ethoscopes. A separate zip archive with all the R/Python scripts and the metadata is also provided. This also contains confocal images for BRP analysis.</p> <ul> <li>Part 1 of 4: <a href="https://doi.org/10.5281/zenodo.10554851" target="_blank" rel="noopener">10.5281/zenodo.10554851 </a></li> <li>Part 2 of 4: <a href="https://doi.org/10.5281/zenodo.10557238" target="_blank" rel="noopener">10.5281/zenodo.10557238 (this page)</a></li> <li>Part 3 of 4: <a href="https://doi.org/10.5281/zenodo.10557310" target="_blank" rel="noopener">10.5281/zenodo.10557310</a></li> <li>Part 4 of 4: <a href="https://doi.org/10.5281/zenodo.10966461" target="_blank" rel="noopener">10.5281/zenodo.10966461</a></li> </ul> <p> </p>
Datasets for "Peatland evaporation across hemispheres: contrasting controls and sensitivity to climate warming driven by plant functional types" - Version 2
<p>Version 2 of datasets used for analyses in the paper titled "Peatland evaporation across hemispheres: contrasting controls and sensitivity to climate warming driven by plant functional types" submitted to Biogeosciences. There are two datasets - one from Kopuatai bog, Aotearoa New Zealand, and one from Mer Bleue bog, Canada - which contain gap-filled and filtered data that were used to produce the results of our study.</p> <p>Due to improvements made to our methodology following the paper peer review process, the data in this version slightly differs from that of the previous version. Information on these revisions can be found in the README file below or the Discussion/Peer Review tab of our paper.</p> <p> </p> <p> </p>
Dataset for publication "Decoding Niobium Carbide MXene Dual Functional Photoactive Cathode in Photoenhanced Hybrid Zinc-Ion Capacitor"
<p>This is a dataset for publication "Decoding Niobium Carbide MXene Dual-Functional Photoactive Cathode in Photoenhanced Hybrid Zinc-Ion Capacitor". It contains all relevant data from the aforementioned publication. The details about how to read these data is contained within the readme file.</p>
SFC-A68: A dataset for benchmarking space function and space access element classification methods in entire floors of multi-unit apartment buildings
<p> </p> <p><strong>SFC-A68</strong>: "A dataset for benchmarking space function and space access element classification methods in entire floors of multi-unit apartment buildings"</p> <p><strong>Authors:</strong> "Amir Ziaee, Georg Suter, Laura Keiblinger"</p> <p><strong>Copyright:</strong> "Design Computing Group TU Wien, 2024"</p> <p><strong>Credits:</strong> "Design Computing Group TU Wien"</p> <p><strong>License:</strong> "GNU GENERAL PUBLIC LICENSE Version 3"</p> <p><strong>Version:</strong> "1.0.2"</p> <p><strong>Maintainer:</strong> "Amir Ziaee"</p> <p><strong>Email:</strong> "amir.ziaee@tuwien.ac.at"</p> <p><strong>Acknowledgments:</strong> "The authors gratefully acknowledge support by Grant Austrian Science Fund (FWF): I 5171-N, Laura Keiblinger, and participants in course '259.428-2021S Architectural Morphology' at TU Wien for data collection. "</p> <p><strong>Description:</strong> "The analysis of building models for usable area, building safety, and energy efficiency requires accurate classification data of spaces and related space elements such as doors. To reduce input model preparation effort and errors, automated classification of spaces and related space elements is desirable. We introduce the SFC-A68 dataset, which models entire floors of 275 multi-unit apartment buildings in 13 countries. The SFC-A68 consists of three data representation formats: tabular, graph, and multi-view image datasets that are derived from the same source data. It covere 22 space function and six space access element classes."</p> <p> </p> <p> </p> <p> </p>
Zeiss Lattice Light Sheet 7 Point Spread Functions and example dataset
<p>This repository contains some point spread functions (PSFs) distilled from imaging fluorescent beads, 200nm, <a href="https://www.thermofisher.com/order/catalog/product/F8811?SID=srch-srp-F8811" target="_blank" rel="noopener noreferrer">F8811</a> in an agarose gel, on a Zeiss Lattice Light sheet 7 microscope. The bead images from which the PSF were distilled are contained in this repo.</p> <p>Several images were acquired with varying settings of the light sheet (light sheet was always set as the 30 um x1000 nm).</p> <p>These three parameters were varied:</p> <p>FS: focus sheet (-100, -75, -25, 0)</p> <p>FW: focus waist (40, 45, 50, 55, 60, 65, 70, 75, 80, 85)</p> <p>AC: aberration control (150, 155, 160, 165, 170, 175, 180, 185, 190)</p> <p>The file psf-200nm correspond to the best settings taken between the different settings. The two other files (psf-300nm, psf-400nm) correspond to resampled versions of the psf-200nm file.</p> <p>The all-psfs.tif contains the deskewed psf ordered similarly as the poster uploaded in this version of the repository (ELMI-2024-poster.pdf).</p> <p>A sample czi file (Hela Kyoto, raw data) is provided to test deconvolution algorithms.</p> <p>Note that none of these data is deskewed.</p> <p>--------------------</p> <p>Here's a protocol to prepare a gel containing beads at a good enough density:</p> <ul> <li> <p>Material:</p> <ul> <li>Agarose 2%</li> <li>Fluorescent beads, 200nm, <a href="https://www.thermofisher.com/order/catalog/product/F8811?SID=srch-srp-F8811">F8811</a>. Stock is 1000x</li> </ul> </li> <li> <p>Protocol:</p> <ul> <li>Put the agarose to warm up at 90C.</li> <li>Vortex the beads stock.</li> <li>Dilute a 100 times the bead dilution in PBS (10 uL in 1mL), vortex.</li> <li>Prepare a clean slide, and a clean coverglass (22x22mm).</li> <li>Take 90uL of agarose, put in a 1.5mL tube, add 10uL of the diluted beads, vortex.</li> <li>Take 50uL of this agarose solution, put it on the slide, add the coverglass on top.</li> <li>Put this slide in the fridge and wait a few minutes.</li> <li>Use nailpolish to seal the coverglass. Wait long enoughfor the nailpolish to dry.</li> </ul> </li> </ul> <p>You should a gel of about 100um thickness.</p> <p>It should be possible to add a bit of free dye in the gel in order to help focusing the light sheet. Ideally a bit of far-red free dye, like Alexa 647.</p>
Catalog and moment rate function dataset of shallow VLFE southeast off the Kii Peninsula, in the Nankai subduction zone
<h2>Catalog</h2> <p>"VLFE_catalog_latestUTC" is the catalog file. Estimated origin time (JST), longitude, latitude, seismic moment, duration, seismic moment (half-value width), half-value width, Variance reduction, and estimated origin time (UTC) of each shallow VLFE are listed. </p> <p>"VLFE_catalog_SP_latestUTC" is the catalog file for shallow VLFEs evaluated via a single Küpper wavelet with various durations. </p> <h2>Inversion results</h2> <p>YYYYDDMMHHMM is the directory name of a shallow VLFE that occurred in HH:MM DD MM YYYY (JST). </p> <ul> <li>YYYYDDMMHHMM_VR.dat: spatiotemporal variation of variance reduction in inversion procedure. </li> <li>YYYYDDMMHHMM_param.stfvlf: parameter file for inversion. Station names and their weight in inversion are listed.</li> <li>YYYYDDMMHHMM_solution.png: Image file illustrating inversion result. </li> <li>YYYYDDMMHHMM_stf_optimal.sac: SAC format file for the estimated optimal moment rate function of a shallow VLFE. </li> <li>YYYYDDMMHHMM_stf_optimal.dat: ASCII format file for the estimated optimal moment rate function of a shallow VLFE. Estimation errors were evaluated from five-time simulated annealing procedures for different random seeds. </li> <li>YYYYDDMMHHMM_solution_SP.png: Image file illustrating inversion result based on the single-pulse assumption.</li> <li>YYYYDDMMHHMM_stf_optimal_SP.sac: SAC format file for the estimated optimal moment rate function of a shallow VLFE based on the single-pulse assumption.</li> <li>YYYYDDMMHHMM_stf_optimal_SP.dat: ASCII format file for the estimated optimal moment rate function of a shallow VLFE based on the single-pulse assumption.</li> </ul> <p><strong>Details for methods and results</strong></p> <p><span>Takemura, S.</span>, <span>Yabe, S.</span>, <span>Emoto, K.</span>, & <span>Baba, S.</span> (<span>2025</span>). <span>Along-dip variations in source characteristics of shallow slow earthquakes controlled by topography of subducted oceanic plate</span>. <em>Journal of Geophysical Research: Solid Earth</em>, <span>130</span>, e2024JB030751. <a href="https://doi.org/10.1029/2024JB030751">https://doi.org/10.1029/2024JB030751</a></p>
Supplementary datasets for eRNA community and Functional annotations
<p>Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics, to understand the responses of active bacterial, archaeal, and eukaryotic communities, to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel eDNA study which revealed the homogenization of biodiversity across KH conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced in eukaryotes than in bacteria. In contrast, gene expression patterns did not differ between months or across land-use type, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results show that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.</p>
Dataset for a Function Identification Problem
<p>This dataset contains experimental corpus (i.e., executable binaries) for <br> the paper, <em>A Look Back on a Function Identification Problem</em>,<br> which has been presented in the 37th Annual Computer Security Applications Conference (ACSAC '21).</p>
Human ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects"
<p>Human axial and sagittal ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects".</p> <p>Code to process and reconstruct the data is available here: <a href="https://github.com/usc-mrel/lowfield_maxgirf">https://github.com/usc-mrel/lowfield_maxgirf</a></p>
Phantom ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects"
<p>Phantom ISMRMRD datasets for "MaxGIRF: Image Reconstruction Incorporating Concomitant Field and Gradient Impulse Response Function Effects".</p> <p>Code to process and reconstruct the data is available here: <a href="https://github.com/usc-mrel/lowfield_maxgirf">https://github.com/usc-mrel/lowfield_maxgirf</a></p>
Dataset related to article "Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses "
<p>This record contains raw datarelated to article "Functional characterization and immunomodulatory properties of Lactobacillus helveticus strains isolated from Italian hard cheeses "</p> <p>Lactobacillus helveticus carries many properties such as the ability to survive gastrointestinal transit, modulate the host immune response, accumulate biopeptides in milk, and adhere to the epithelial cells that could contribute to improving host health. In this study, the applicability as functional cultures of four L. helveticus strains isolated from Italian hard cheeses was investigated. A preliminary strain characterization showed that the ability to produce folate was generally low while antioxidant, proteolytic, peptidase, and β-galactosidase activities resulted high, although very variable, between strains. When stimulated moDCs were incubated in the presence of live cells, a dose-dependent release of both the pro-inflammatory cytokine IL-12p70 and the anti-inflammatory cytokine IL-10, was shown for all the four strains. In the presence of cell-free culture supernatants (postbiotics), a dose-dependent, decrease of IL-12p70 and an increase of IL-10 was generally observed. The immunomodulatory effect took place also in Caciotta-like cheese made with strains SIM12 and SIS16 as bifunctional (i.e., immunomodulant and acidifying) starter cultures, thus confirming tests in culture media. Given that the growth of bacteria in the cheese was not necessary (they were killed by pasteurization), the results indicated that some constituents of non-viable bacteria had immunomodulatory properties. This study adds additional evidence for the positive role of L. helveticus on human health and suggests cheese as a suitable food for delivering candidate strains and modulating their anti-inflammatory properties.</p> <p> </p>
Dataset for: Short flowers for long tongues: functional specialization in a nocturnal pollination network of an asclepiad in long-tongued hawkmoths (Biotropica)
<p><span>Since Darwin, very long and narrow floral tubes have been known to represent the main floral morphological feature for specialized long-tongued hawkmoth pollination. However, specialization may be driven by other contrivances instead of floral tube morphology. Asclepiads are plants with a complex floral morphology where primary hawkmoth pollination had never been described. We detailed here the intricate pollination mechanism of the South American asclepiad <em>Schubertia grandiflora</em>, where functional specialization on long-tongued hawkmoth pollinators occurs despite the short floral tube of this species. We studied two plant populations in the Brazilian Cerrado and recorded floral visitors using different approaches, such as light-trapped hawkmoths for pollen analysis, direct field observations, and IR motion-activated cameras. Finally, using a community-level approach we applied an ecological network analysis to identify the realized pollinator niche of <em>S. grandiflora</em> among the available niches in the pollinator community. Throughout a period of 17 years, long-tongued hawkmoths were consistently recorded as the main floral visitors and the only effective pollinators of <em>S. grandiflora</em>. Flowers rely on highly modified corona and gynostegium, and enlarged nectar chambers, to drive visitors and pollination mechanism. Despite relatively short-tube, network analysis placed <em>S. grandiflora</em> in the module including exclusively long-tongued hawkmoth pollinators and the most phenotypically specialized sphingophilous plants in the community. These results represent the first example of functional specialization in long-tongued hawkmoths in an asclepiad species. However, this specialization is uncoupled from the long floral tubes historically associated with the sphingophily syndrome.</span></p>
Dataset of the paper "An Empirical Study on the Fault-Inducing Effect of Functional Constructs in Python"
<p>This package contains the dataset of the manuscript "An Empirical Study on the Fault-Inducing Effect of Functional Constructs in Python"</p>
Patch clamp dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
<p><span>Many genes, including <em>KCNH2</em>, contain </span><span>'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of <em>KCNH2, </em>a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death<em>. </em>Forty-two percent of <em>KCNH2</em> exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT <em>KCNH2</em> allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.</span></p>
Trafficking dataset for: A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2
<p><span>Many genes, including <em>KCNH2</em>, contain </span><span>'hotspot' domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of <em>KCNH2, </em>a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death<em>. </em>Forty-two percent of <em>KCNH2</em> exon 2 variants caused at least 50 % reduction in protein trafficking and 65% of these trafficking defective variants exerted a dominant-negative effect when co-expressed with a WT <em>KCNH2</em> allele as assessed using a calibrated patch clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this 'hotspot' domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.</span></p>
Datasets and Code for "Hypothesis Tests with Functional Data for Surface Quality Change Detection in Surface Finishing Processes"
<p>This is the set of data and computer code used for reproducing the results in Jin, Tuo, Tiwari, Bukkapatnam, Aracne-Ruddle, Lighty, Hamza, and Ding, 2022, “Hypothesis tests with functional data for surface quality change detection in surface finishing processes,” <em>IISE Transactions</em>, in press.</p>
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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.