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3,655 results for “Structural data”
Data from: Top-down control of carbon sequestration: grazing affects microbial structure and function in salt marsh soils
Tidal wetlands have been increasingly recognized as long-term carbon sinks in recent years. Work on carbon sequestration and decomposition processes in tidal wetlands focused so far mainly on effects of global-change factors such as sea-level rise and increasing temperatures. However, little is known about effects of land use, such as livestock grazing, on organic matter decomposition and ultimately carbon sequestration. The present work aims at understanding the mechanisms by which large herbivores can affect organic matter decomposition in tidal wetlands. This was achieved by studying both direct animal-microbe interactions and indirect animal-plant-microbe interactions in grazed and ungrazed areas of two long-term experimental field sites at the German North Sea coast. We assessed bacterial and fungal gene abundance using quantitative PCR, as well as the activity of microbial exo-enzymes by conducting fluorometric assays. We demonstrate that grazing can have a profound impact on the microbial community structure of tidal wetland soils, by consistently increasing the fungi-to-bacteria ratio by 38-42%, and therefore potentially exerts important control over carbon turnover and sequestration. The observed shift in the microbial community was primarily driven by organic matter source, with higher contributions of recalcitrant autochthonous (terrestrial) vs. easily degradable allochthonous (marine) sources in grazed areas favoring relative fungal abundance. We propose a novel and indirect form of animal-plant-microbe interaction: top-down control of aboveground vegetation structure determines the capacity of allochthonous organic matter trapping during flooding and thus the structure of the microbial community. Furthermore, our data provide the first evidence that grazing slows down microbial exo-enzyme activity and thus decomposition through changes in soil redox chemistry. Activities of enzymes involved in C cycling were reduced by 28-40%, while activities of enzymes involved in N cycling were not consistently affected by grazing. It remains unclear if this is a trampling-driven direct grazing effect, as hypothesized in earlier studies, or if the effect on redox chemistry is plant mediated and thus indirect. This study improves our process-level understanding of how grazing can affect the microbial ecology and biogeochemistry of semi-terrestrial ecosystems that may help explain and predict differences in C turnover and sequestration rates between grazed and ungrazed systems.
Data from: Riverine barriers have little influence on genetic structure of Rattus tanezumi
Rivers may hinder population migration and promote genetic differentiation of terrestrial animals. Most studies testing the riverine barrier hypothesis have yielded positive results, while very few studies do not support this hypothesis. In this study, 384 Asian house rats (Rattus tanezumi) were collected fromYunnan,China. By combined use of the sequence markers of mitochondrial (mtDNA) and nuclear (IRBP), we tested the influence of five local rivers on the population genetics of R. tanezumi. A total of 81 mtDNA haplotypes and 135 IRBP haplotypes were determined, and many of which were shared by two or more of the six geographic regions. AMOVA analyses showed that most variations happened either within populations or among populations, while very few variations (<15%) happened among the six geographic regions formed by the five rivers. SAMOVA analysis classified the mtDNA sequences into three groups, while no genetic differentiation was detected on IRBP. Our results concluded that riverine barriers in the study area have little influence on the genetic structure of R. tanezumi.
Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA (mtDNA) indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.
Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
Data from: Functional diversity and structural disorder in the human ubiquitination pathway
The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred – E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions.
Data from: First-principles calculations of structural, electronic, magnetic and elastic properties of Mo2FeB2 under high pressure
The structural and electronic density of states, magnetic, and elastic properties of Mo2FeB2 under high pressure have been investigated with first principles calculations. Furthermore, the thermal dynamic properties of Mo2FeB2 were also studied with the quasiharmonic Debye model. The volume of Mo2FeB2 decreases with the increasing pressure. Using the analysis of the density of the states, atom population and Mulliken overlap population, it is observed that as the pressure increases, the B-B bonds are strengthened, and the B-Mo covalency decreases. Moreover, for all pressures, Mo2FeB2 is detected in the antiferromagnetic phase and the magnetic moments decrease with the increasing pressure. The calculated bulk modulus, shear modulus, Young's modulus, Poisson's ratio and universal anisotropy index all increase with the increasing pressure. From thermal expansion coefficient analysis, it is found that Mo2FeB2 shows good volume invariance under high pressure and temperature. The examination of the dependence of heat capacity on the temperature and pressure shows that heat capacity is more sensitive to temperature than to pressure
Characterising Pythonic Data Structure Usage Scenarios in Textbooks
Open the record for dataset details and reuse information.
Simulation data archive: The influence of rotational discontinuities on the formation of reconnected structures at collisionless shocks - hybrid simulations
<p>Code and data used in preparation for submission to JGR: Space physics.</p>
Dataset and code for the publication "From Unstructured Product Descriptions to Structured Data for Industry 4.0 with ChatGPT"
<p>This is the code as well as the dataset for our publication "From Unstructured Product Descriptions to Structured Data for Industry 4.0 with ChatGPT".</p><p>Please see the README.md for more information.</p>
Data for: On the adsorption mechanism of humic substances on kaolinite and their microscopic structure
<p>Soil organic matter (SOM) and various inorganic minerals represent key components of soils. During pedogenesis and due to biological activity these species interact, having a crucial impact on the formation of an aggregated soil structure with a hierarchical arrangement from nano to macro scale. In this process, the formation of organo–mineral microaggregates represents a dominant factor affecting soil functions and properties. This study focuses on the interactions between humic substances (HSs) and the mineral kaolinite as typical representatives of SOM and soil minerals. By performing classical molecular dynamics (MD) simulations on models of HSs and kaolinite, we demonstrate how two dominant but chemically different kaolinite surfaces affect the stability of HSs microaggregates. By analyzing volumetric, structural, and energetic properties of SOM–kaolinite models, we explain possible mechanisms of the formation of stable SOM–clay aggregates and show how a polarized environment affects the electrostatic interactions, stabilizing the microscopic structure of SOM–mineral aggregates. Our results showed that when stable aggregates of HSs are confined in kaolinite nanopores, their interactions with kaolinite surfaces disintegrate them into smaller subaggregates. These subaggregates are adsorbed more strongly on the polar aluminol surface of kaolinite compared to less the active hydrophobic siloxane surface.</p> <p>E. Galicia-Andrés, C. Oostenbrink, M.H. Gerzabek and D. Tunega<br>On the adsorption mechanism of humic substances on kaolinite and their microscopic structure<br>Minerals 11 (2021), 1138<br>doi: <a href="https://doi.org/10.3390/min11101138">10.3390/min11101138</a></p>
Selected data sets for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'
<p>Data sets used in the for the manuscript <strong>Marsh<em> </em>et<em> </em>al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'</strong>. The DOIs that link to all other data sets used in the publication are available in Tables S2-5 of the supplementary information. The z-score standardised data, and outputs of RMarkdown documents outline all the steps in the processing and analysis of the data are available at https://zenodo.org/uploads/13161799.</p> <p> </p> <p>This repository contains data used for:</p> <h3><strong><em>Mean canopy height</em></strong></h3> <p>Canopy height and vertical profiles of forest structure were compiled using airborne remote sensing with LiDAR collected by NERC’s Airborne Research Facility (ARF) in November 2014, using a Leica ALS50-II LiDAR. A Beer-Lambert approximation was used to convert point clouds to plant area density (PAD) distributions, a similar measure to leaf-area index, but where methods do not distinguish between leaves and branches or trunks. LiDAR measurements for the carbon plots were converted to rasters with 0.5 × 0.5 m cell size. Plots were rotated to a North-South axis if necessary</p> <h3><br><em><strong>Spectral diversity</strong></em></h3> <p>Spectral measurements were made on five leaves attached to tree branches used to measure leaf chemical traits. Leaves were randomly selected but we avoided damaged and young plant material to avoid potential confounding factors. Reflectance spectra (350–2500 nm) were acquired using a FieldSpec 4, produced by Analytical Spectral Devices (ASD, Boulder, Colorado, USA). The spectroradiometer's contact probe was mounted on a clamp and firmly pushed down onto the sample against a black background so that no extraneous light was included in the measurement. Spectral measurements were taken halfway between the petiole and leaf tip, and between the main vein and the leaf edge, with the abaxial surface pointing towards the probe. The readings were calibrated against a Spectralon white reference panel every five samples. Leaf reflectance measured at 430 nm, 660 nm, 1450, 1980 nm and 2350 nm align closely with absorption features for pigments, water content, proteins and cellulose. Spectral diversity calculated from these absorption features can provide an integrated measure of the functional trait variability within plant communities and may be used as a proxy for functional diversity.</p> <p> </p> <h3><em><strong>Liana abundance</strong></em></h3> <p>Percentage liana cover for large canopy and emergent trees. The four quadrants of the canopy were scored as 0 (no lianas), 1 (1-20%), 2 (20-40%), 3 (40-60%), 4 (60-80%) and 5 (80-100%).</p> <p> </p> <h3><em><strong>Leaf-area index<br></strong></em></h3> <p>Leaf area index (LAI) for carbon plots was derived from hemispherical photos (Sigma 8mm SRL fish eye lens and Canon EOS 600D digital camera, mounted on a tripod at 1 m height). Between 5-27 photos were taken over time in each subplot. Images were processed with Hemisfer® software (www.wsl.ch/dienstleistungen/produkte/software/hemisfer/index_EN). LAI was calculated with the method by Thimonier et <em>al</em>. (2010) <em>European Journal of Forest Research</em> 129, 543–562 (2010), with a canopy clumping correction applied from Chen & Cihlar (1995) <em>IEEE Transactions on Geoscience and Remote Sensing</em> 33, 777–787.</p> <p> </p> <h2>Funding</h2> <p>Analyses were carried out, and data were collected, as part of the BALI (Biodiversity And Land-use Impacts on tropical ecosystem function) using the following funding:</p> <ul> <li>NERC's Human Modified Tropical Forests research programme (grant number NE/K016377/1 awarded to the BALI consortium)</li> <li>MHN was supported by a PhD scholarship from the Conselho Nacional de Pesquisa e Desenvolvimento (CNPq, grant No. 201516/2014-4) from Brazil</li> </ul>
Data for: "The influence of urban and agricultural landscape context on forest diversity and structure across ecoregions "
<p>This is the data associated with "The influence of urban and agricultural landscape context on forest diversity and structure across ecoregions" by JP Schmit, LR Johnson, M Baker, L Darling, R Fahey, DH Locke, AT Morzillo, NF Sonti, TLE Trammell, MFJ Aronson, and ML Johnson, published in Ecosphere in 2025.</p>
DeepStruc: Towards structure solution from pair distribution function data using deep generative models
<p>XYZ files, PDF dataset and XGB model to use MetalFinder which is one of the baseline models in the paper.</p>
Data from: Does a coexisting congener affect the genetic structure and selfing rate via reproductive interference?
<p>Data archived here were used for analyses in Katsuhara et al. "Does a coexisting congener affect the genetic structure and selfing rate via reproductive interference?" Data is in two worksheets.</p>
Massive Compression for High Data Rate Macromolecular Crystallography: Impact on Diffraction Data and Subsequent Structural Analysis
<p>This is a dataset containing raw "uncompressed" diffraction data from test sample.</p> <p>Data are collected on a lysozyme sample at 7.5 keV for a S-SAD experiment at the AMX beamline using an EIGEr 9M detector.</p> <p>The compression used, to generate the cbf files can be derived from the filenames: </p> <p>BINx: pixel binning by a factor x</p> <p>SUMx: frame summing by a factor x </p> <p>J2Kx: JPEG2000 compression used with a factor of x</p> <p>HCOMPx: Hcompress used with a scale factor x </p> <p>For example: lyso_BIN2_SUM2_HCOMP4 was compressed using 2x pixel binning + 2x frame summing + Hcompress with scale of 4. </p> <p>More information will be included after publication, in the meantime, please contact author if details about processing are required.</p> <p>All zstd tar directories contain the cbf files, ready to be processed. </p> <p>All data were collected at the AMX beamline at the NSLS-II using a DECTRIS EIGER X 9 M detector. </p> <p> </p> <p>See more details from the related work (xds.inpo files included) </p>
Experimental-data-driven deep learning strategy for Structural Health Monitoring of a plate in acoustic fields
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MODES DATA - vertical structure functions v2
Open the record for dataset details and reuse information.
Data for Tuning Higher Order Structure in Colloidal Fluids
<p> </p> <p>Representative confocal image data and LAMMPS script for Tuning Higher Order Structure in Colloidal Fluids</p>
Supplementary Data for article: Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists
<p>This is a collection of scripts and research data to assess the robustness of forest structure characterization from airborne laser scanning (ALS). It replicates the main analysis in the article <em>Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists</em> and accompanies the main research data set (<a href="https://doi.org/10.5281/zenodo.10878070" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10878070</a>).</p> <p>In this replication study, we assess the derivation of canopy height models (CHMs) from point cloud data, how sensitive CHM algorithms are to pulse density variation and how uncertainties and biases propagate to commonly used forest structure metrics.</p> <p>The main data source for this study are ALS point clouds from nine U.S. sites, acquired by the National Ecological Observatory Network (NEON, 6 sites, 3 km x 3 km) and by the United States Geological Survey's 3DEP program (3 sites, also 3 km x 3 km). The underlying data can be found here: https://data.neonscience.org/data-products/DP3.30024.001 (NEON) and here: https://apps.nationalmap.gov/lidar-explorer (3DEP)</p> <p>The different data layers are:</p> <p><strong>replicate.US.R</strong> </p> <p> is a single R script that contains all the code necessary to reproduce the analyses, including point cloud manipulations and derivation of CHMs from the raw data as well as the overall robustness analysis. To replicate the processing of the raw point clouds step by step, this script should be located in a folder called "rscripts".</p> <p><strong>pointclouds_original.zip</strong></p> <p> is the set of original point clouds (3 km x 3 km in extent) used for the replication test, separated into 9 subfolders/sites. Can be used to reproduce the original workflow by placing them in a folder called "data/original". The script will then automatically produce derived point clouds at pulse densities of 2 and 16 per squaremetre and process them into digital terrain models (DTMs), digital surface models (DSMs) and CHMs. Note that, for convienence, these derived products are also included in a separate .zip file (cf. below).</p> <p><strong>processed_foranalysis.zip</strong></p> <p> is the set of derived products (DTMs, DSMs, CHMs), separated into 9 subfolders/sites, i.e. the result of processing the original point clouds. To use these layers directly with the provided script, they should be put into a folder called "processed_foranalysis".</p> <p><strong>summaries.zip</strong></p> <p><strong> </strong>is a set of summary statistics (as .csv files) that were used to generate the main analysis tables in the replication study. To use these summary statistics directly with the provided script, they should be put into a folder called "summaries".</p> <p><strong>figures.zip</strong></p> <p> is a set of figures displayed in the Supplementary Material of the paper <em>Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists</em>.</p>
Functional characterization of 3D-protein structures informed by human genetic diversity - data
<p>Supplementary data for https://www.biorxiv.org/content/early/2017/08/29/182287</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.