Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
161
datasets available to search
ShareScore release 0.9.0
Dataset results
161 results for “Production function”
Collected explanations on features and functionalities of four SSI management system products.
<p>Collected textual explanations from the white papers of EverID, uPort, LifeID, and IBM Verify Credentials.</p>
Data from: Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks
<p><span>This data was collected in the species × genetic diversity experiment of the Biodiversity–Ecosystem Functioning Experiment China Platform (BEF-China, <a href="http://www.bef-china.com/">www.bef-china.com</a>). This data set includes four species (<em>Alniphyllum fortunei</em>, <em>Cinnamanum camphora</em>, <em>Daphniphyllum oldhamii</em>, and <em>Idesia polycarpa</em>) with the mother trees of all tree individuals known, and </span><span>the offspring from the same mother tree was defined as a seed family. In total, 92 subplots with 4 tree diversity levels were included: species diversity (1 or 4 species) and genetic diversity (1 or 4 seed families per species) which resulted in four tree diversity levels: one species with one seed family (1.1), one species with four seed families (1.4), four species with one seed family per species (4.1) and four species with four seed families per species (4.4). For tree functional traits, five leaf functional traits were measured in 2017 and 2018, including leaf area (LA), specific leaf area (SLA), chlorophyll content (CHL), leaf nitrogen content (LN), and leaf carbon content (LC). Herbivory was visually recorded as leaf damage in 2017. Soil fungal diversity was used as proxies for unspecified trophic interactions. Soil samples were taken on subplot level for the 1.1 and 1.4 diversity treatments, but on plot level for the 4.1 and 4.4 diversity treatments in 2017. Tree community productivity was summed by the biomass of individual trees in each subplot and individual tree biomass (kg) was calculated using the biomass equation (H × BA × CV) of the BEF-China experiment, where CV is a correction factor for stem shape and wood density.</span></p>
Both diversity and functional composition affect productivity and water use efficiency in experimental temperate grasslands
Open the record for dataset details and reuse information.
Data from: Multiple facets of diversity effects on plant productivity: species richness, functional diversity, species identity and intraspecific competition
Open the record for dataset details and reuse information.
Data from: The functional diversity–productivity relationship of woody plants is climatically sensitive
Open the record for dataset details and reuse information.
Data from: Functional and phylogenetic diversity explain different components of diversity effects on biomass production
Open the record for dataset details and reuse information.
Data from: Phytoplankton functional composition determines limitation by nutrients and grazers across a lake productivity gradient
Open the record for dataset details and reuse information.
Data from: Functional traits, not productivity, predict openness to seedling recruitment in alpine plant communities under climatic warming
Open the record for dataset details and reuse information.
Data from: Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks
Open the record for dataset details and reuse information.
Data from: High environmental stress and productivity increase functional diversity along a deep-sea hydrothermal vent gradient
Open the record for dataset details and reuse information.
Data from: Resilience of seed production to a severe El Niño‐induced drought across functional groups and dispersal types
Open the record for dataset details and reuse information.
SGS-LTER Effects of grazing on ecosystem structure and function (GZTX): Net Primary Production on the Central Plains Experimental Range, Nunn, Colorado, USA 1992-2011, ARS Study Number 32
This data package was produced by researchers working on the Shortgrass Steppe Long Term Ecological Research (SGS-LTER) Project, administered at Colorado State University. Long-term datasets and background information (proposals, reports, photographs, etc.) on the SGS-LTER project are contained in a comprehensive project collection within the Digital Collections of Colorado (http://digitool.library.colostate.edu/R/?func=collections&collection_id=3429). The data table and associated metadata document, which is generated in Ecological Metadata Language, may be available through other repositories serving the ecological research community and represent components of the larger SGS-LTER project collection. When the CPER was established in 1939, researchers constructed a .5-1 ha grazing exclosure in each of the pastures. These areas have remained protected from grazing for the past 70 years. The remaining areas have been grazed for the past 20+ years. This collection of pastures and exclosures provided an extraordinary opportunity to reinitiate grazing and protection, and evaluate the balance between degradation and aggradation. We proposed to rearrange fences and expose areas to grazing that have been protected for 50 years, and protect areas from grazing that had been grazed for 50 years. The combinations of grazing conditions were: 1. Long-term protection 2. Long-term grazing (moderate) 3. 50 years of protection followed by grazing 4. 50 years of grazing followed by protection Net primary production, nitrogen dynamics, cattle utilization, and community dynamics of vegetation were measured. Additional information and referenced materials can be found: http://hdl.handle.net/10217/85596.
Phenotype data (composition, functionality, end-product quality) of wheat grown in Flanders, Belgium
<p>Data for the Ph.D. dissertation entitled: Outline of four degrees of diversification for understanding bread wheat (<em>Triticum aestivum</em> L.) quality. For further details on the content of the files, the meaning of abbreviations and used techniques, it is referred to the Ph.D. manuscript. </p> <p>For further details, please contact the author. </p>
Functional structure mediates the responses of productivity to addition of three nitrogen compounds in a meadow steppe
<p><span>Atmospheric nitrogen (N) deposition is altering grassland productivity and community structure worldwide. Deposited N comes in different forms, which can have different consequences for productivity due to differences in their fertilization and acidification effects. We hypothesize that these effects may be mediated by changes in plant functional traits. We investigated the responses of </span><span>aboveground primary productivity</span><span> and community functional composition to addition of three nitrogen compounds (NH4NO3, [NH4]2SO4, and CO[NH2]2) at the rates of 0, 5, 10, 20 g N m-2 yr-1. We used structural equation modeling (SEM) to evaluate how functional structure influences the responses of productivity to the three N compounds. Nitrogen addition increased community-level leaf chlorophyll content but decreased leaf dry matter content and phosphorus concentration. These changes were mainly due to intra-specific variation. Functional dispersion of traits was reduced by N addition through changes in species composition. SEM revealed that fertilization effects were more important than soil acidification for the responses of productivity to CO(NH2)2 addition, which enhanced productivity by decreasing functional trait dispersion. In contrast, the effects of (NH4)2SO4 and NH4NO3 were primarily due to soil acidification, influencing productivity via community-weighted means of functional traits. Our results suggest that N forms with different fertilizing and acidifying effects influence productivity via different functional traits pathways. Our study also emphasizes the need for in situ experiments with the relevant N compounds to accurately understand and predict the ecological effects of atmospheric N deposition on ecosystems.</span></p>
Data from: Plant functional diversity modulates global environmental change effects on grassland productivity
1. Although much research has explored changes in ecosystem functions associated with global environmental changes, the mechanistic pathways behind the observed changes remain poorly understood. 2. Using an 11-year experiment that increased growing season precipitation and nitrogen deposition in a temperate steppe, we explored the relative importance of direct and indirect environmental change effects on plant primary productivity. 3. We show that increases in water and nitrogen availability influenced plant productivity via both direct and indirect pathways. While both treatments stimulated plant productivity, changes in plant productivity cannot be explained by observed changes in species or phylogenetic diversity. Instead, the indirect effects of water and nitrogen addition were through their positive effects on plant functional diversity. Importantly, while the increase in one component of functional diversity (community-level weighted mean of plant stature) resulted in increased productivity, the increase in another component of functional diversity (functional dispersion) resulted in decreased productivity. 4. Synthesis. Our study provides the first evidence for the opposite effects of community weighted means and functional dispersion of plant functional traits on grassland productivity, and highlights the importance of both traits of dominant species and trait distribution among species in modulating the effects of global changes on ecosystem functions.
Data from: Functional traits of marine macrophytes predict primary production
The relationship between community structure and the functioning of ecosystems is the subject of ongoing debate. Biological or functional trait-based approaches that capture life strategy, morphology and behavioural characteristics have received far less attention than taxonomic diversity in this context, despite their more intuitive link to ecosystem functioning. Macrophyte primary production underpins aquatic food webs, regulates benthic and pelagic ecosystems and is a key aspect of the global carbon cycle. This study spans a range of aquatic biomes across Europe and aims to examine potential for predicting primary production of macrophyte communities based on the functional traits of species and identify the traits that are the most informative indicators of macrophyte production. Macrophyte primary production was assessed based on the oxygen production of the whole community, linked to biomasses of selected biological traits derived of its component species and analysed using the novel boosted regression trees modelling technique. Results showed that functional traits derived from macrophyte community data explained most of the variation in primary production of macrophyte communities without the need to incorporate environmental data on the habitats. Macrophyte primary production was influenced by a combination of tolerance, morphology and life habit traits; however tolerance traits contributed most of variability in macrophyte primary production when all traits were analysed jointly. This study also showed the existence of trait clustering as the studied trait categories were not fully independent; strong interlinkages between and within trait categories emerged. Our study suggests that functional trait analysis captures different aspects of ecosystem functioning and thereby enables assessing primary production of macrophyte communities over geographically distinct areas without extensive taxonomic and environmental data. This could result in a novel framework through which a simplification of the general procedure of production estimations and comparisons across environmental gradients can be achieved.
Data from: Quantifying the importance of functional traits for primary production in aquatic plant communities
1. Aquatic plant meadows are important coastal habitats that sustain many ecosystem functions such as primary production and carbon sequestration. Currently, there is a knowledge gap in understanding which plant functional traits e.g. leaf size or plant height underlie primary production in aquatic plant communities. 2. To study how plant traits are related to primary production, we conducted a field survey in the Baltic Sea, Finland, which is characterized by high plant species and functional diversity. 30 sites along an exposure gradient were sampled (150 plots) and nine plant morphological and chemical traits measured. The aim was to discern how community-weighted mean traits affect community production and whether this relationship changes along an environmental gradient using structural equation modelling (SEM). 3. Plant height had a direct positive effect on production along the exposure gradient (r = 0.33) and indirect effects through two leaf chemical traits, Leaf δ15N and Leaf δ13C (r = 0.24 and 0.18 respectively) resulting in a total effect of 0.28. In plant communities experiencing varying exposure, traits such as root N concentration and leaf δ15N had positive and negative effects on production, respectively. 4. Synthesis: Our results demonstrate that the relationship between plant functional traits and community production is variable and changes over environmental gradients. Plant height generally has a positive effect on community production along an exposure gradient, while the link between other traits and production changes in plant communities experiencing varying degrees of exposure. Thus, the underlying biological mechanisms influencing production differ in plant communities, emphasizing the need to resolve variability and its drivers in real-world communities. Importantly, functionally diverse plant communities sustain ecosystem functioning differently and highlight the importance of benthic diversity for coastal ecosystem stability.
Data repository for "Scalable Quantum Monte Carlo with Direct-Product Trial Wave Functions"
<p>This Zenodo deposit provides a comprehensive collection of raw data, processed data, and scripts associated with the research paper available at <a href="https://arxiv.org/abs/2306.15186" target="_new">https://arxiv.org/abs/2306.15186</a>.</p> <p>Contents:</p> <p>- data.zip includes all the QMCpack inputs and outputs, which can be used in the blocking analysis to obtain the AFQMC energy. Processed Data "SI for DP-MSD-AFQMC.xlsx" contains the AFQMC results after the blocking analysis in XLSX format. "SI for DP-MSD-AFQMC.xlsx" also includes the energies from all other methods presented in the paper.</p> <p>- scripts.zip contains all the Python scripts used in running calculations for the paper. This includes scripts to generate LAS-AFQMC and CAS-AFQMC trials (under scripts/utils) in QMCpack format, as well as inputs for each compound.</p>
Transposable element products, functions, and regulatory networks in Arabidopsis thaliana
<h1>README</h1> <p>This dataset includes the main outputs from the work titled <strong>Transposable element products, functions, and regulatory networks in <em>Arabidopsis thaliana</em>.</strong></p> <h2><strong>Summary</strong></h2> <p>Transposable elements (TEs) are DNA sequences with the ability to propagate themselves within and across genomes. Their mobilization is catalyzed by self-encoded factors, yet these factors have been poorly investigated due to difficulties in defining TE genes in genomes. Here, we leveraged extensive long- and short-read transcriptome data, together with structural predictions, transcription factor binding site identification, and transcriptional network analyses, to construct a comprehensive atlas of TE transcripts and TE-encoded products in the model organism <em>Arabidopsis thaliana</em>. We uncovered hundreds of transcriptionally competent TEs, each potentially encoding multiple proteins either through distinct genes, alternative splicing, or post-translational processing. Structural-based protein analyses revealed dozens of hitherto unidentified domains of unknown function, enabling us to predict proteins with multimerization and DNA binding domains forming macromolecular complexes involved in transposition. Furthermore, we demonstrate that TE expression is highly intertwined with the transcriptional network of cellular genes, and identified transcription factors and cis-regulatory elements associated with their coordinated expression during development or in response to environmental cues. This comprehensive atlas of TE-genes and TE-proteins provides a valuable resource for studying the mechanisms involved in transposition and their consequences for genome and organismal function.</p> <h2><strong>File description</strong></h2> <p>It includes the following data:</p> <ol> <li><code>annots/TE_Functional_Annotation.Borreda2024.gtf</code> - Annotation file including Arabidopsis TEs and TE-genes. TE-genes defined in our work are indicated in the 'Source' column of the gtf. TAIR10-defined TEs for whom we did not annotate new transcripts are also included.</li> <li><code>seqs</code> - This folders includes all the transcript sequences (cDNAs.tsv) and the first and longest ORFs found in each of them (prot.csv), which were used for further analyses. The specific copy, gene, isoform and, in the case of proteins, ORF, is indicated for each sequence.</li> <li><code>structures</code> - The zipped folder <code>full_length_prots_pdbs.zip</code> includes all the 3D structures from full-length TE proteins. Note that identical proteins, which would result in identical structures, have been collapsed to reduce the total dataset size; equivalences can be found in <code>identical_proteins</code>.</li> <li><code>structures/SD_Cluster_Functions.tsv</code> - We clustered all Structural Domains (SD) based on 3D similarity and assigned a function to each cluster based on the database hits. This table indicated, for each of these SDs, to which cluster it belongs, the superfamily, family and element containing it, the number of Conserved Domains included within it and the number of hits with resolved (retrieved from the RCSB-PDB database) or predicted (AlphaFold2) protein structures. The last column includes the putative function assigned to each cluster.</li> <li><code>coexpression</code> - Coexpressed genes were classiffied into modules using WGCNA. In the table <code>Gene_Modules.tsv</code> we include, for each gene and TE-gene (provided it has expression in at least one sample, see methods on the publication for details), the TE family and superfamily when applicable and the module to which it belongs. The modules were named based on the results of the GO enrichment analysis of the genes contained. The results of this GO enrichment are included in <code>GO_Enrichment.tsv</code>, where we include the main funciton of the associated GOs, the number of entries and TE-genes within the module, a list of GO terms enriched in that specific module and finally a list of TE families enriched in each module.</li> <li><code>dapseq</code> - We reanalized the DAP-seq dataset from O'Malley 2016, selecting only TFBS with a binding site within a DAP-seq peak. The list of filtered peaks we found is reported in <code>DAPseq_TFBS_Motifs.tsv</code>. The columns include the coordinates of the TFBS (which have been filtered to fall within a DAP-seq peak and include the TFBS motif), the strand of the motif, the score of the motif reported by FIMO, the motif sequence, the Sequence Read identified for the original DAP-seq data, and the family, name and gene of the TF associated with that specific peak.</li> </ol>
Data from: Functionally diverse tree stands reduce herbaceous diversity and productivity via canopy packing
<p><b>1. </b>There is extensive experimental evidence for the importance of biodiversity in sustaining ecosystem functioning. However, such experiments typically prevent immigration by continuously removing non-target species, thereby questioning the generality of these findings to real-world ecosystems. This is particularly true in forest ecosystems where understorey herbaceous species are key biodiversity components but are usually weeded in tree diversity experiments. Consequently, little is known about how tree diversity influences the natural dynamics of understorey herbaceous layers.</p> <p><b>2.</b> We conducted a three-year non-weeded tree diversity experiment composed of eight woody species differing widely in plant economic strategies. We examined how the functional diversity and identity of tree species mixtures drive the temporal dynamics of understorey productivity, functional diversity, and composition through canopy packing.</p> <p><b>3.</b> Tree mixtures with high functional diversity experienced increased canopy packing over time, thereby decreasing understorey productivity and diversity. Furthermore, herbaceous communities were dominated by species with functional traits typical of low-light conditions (lower community-weighted mean (CWM) of maximum plant height, but larger CWM of specific leaf area) in response to increased canopy packing.</p> <p><b>4.</b> Our results provide mechanistic insights into the role of tree functional diversity in shaping the dynamics of biomass, functional diversity, and composition of the understorey herbaceous layer during the early successional period. It is expected that the effects of tree functional diversity would also be relevant over time due to the increasing usage of canopy space. This study highlights the significance of natural community processes in determining the effects of tree diversity on the temporal dynamics of previously neglected ecosystem structures and functioning.</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.