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.

352

datasets available to search

ShareScore release 0.9.0

Dataset results

352 results for “Data Enrichment”

Learn how ShareScore rates datasets ↗

zenodo36/100

Post-revision data and R Script for Murtagh et al. 'The scent of enrichment: Exploring the effect of odour and biological salience on behaviour during enrichment of kennelled dogs.'

Data and analysis file (written in R studio) for the paper Murtagh et al. 'The scent of enrichment: Exploring the effect of odour and biological salience on behaviour during enrichment of kennelled dogs.' Updated based on reviewer comments and additional analyses requested (master data and analysis filed labelled with 'rev' suffix).

opencc-by-4.0Apr 2019View details →

dryad36/100

A new pipeline for removing paralogs in target enrichment data

Target enrichment (such as Hyb-Seq) is a well-established high throughput sequencing method that has been increasingly used for phylogenomic studies. Unfortunately, current widely used pipelines for analysis of target enrichment data do not have a vigorous procedure to remove paralogs in target enrichment data. In this study, we develop a pipeline we call Putative Paralogs Detection (PPD) to better address putative paralogs from enrichment data. The new pipeline is an add-on to the existing HybPiper pipeline, and the entire pipeline applies criteria in both sequence similarity and heterozygous sites at each locus in the identification of paralogs. Users may adjust the thresholds of sequence identity and heterozygous sites to identify and remove paralogs according to the level of phylogenetic divergence of their group of interest. The new pipeline also removes highly polymorphic sites attributed to errors in sequence assembly and gappy regions in the alignment. We demonstrated the value of the new pipeline using empirical data generated from Hyb-Seq and the Angiosperm 353 kit for two woody genera Castanea (Fagaceae, Fagales) and Hamamelis (Hamamelidaceae, Saxifragales). Comparisons of datasets showed that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed evident differences between data from HybPiper and data from our new PPD pipeline. We further evaluated the accuracy and error rates of PPD by BLAST mapping of putative paralogous and orthologous sequences to a reference genome sequence of Castanea mollissima. Compared to HybPiper alone, PPD identified substantially more paralogous gene sequences that mapped to multiple regions of the reference genome (31 genes for PPD compared with 4 genes for HybPiper alone). In conjunction with HybPiper, paralogous genes identified by both pipelines can be removed resulting in the construction of more robust orthologous gene datasets for phylogenomic and divergence time analyses. Our study demonstrates the value of Hyb-Seq with data derived from the Angiosperm 353 probe set for elucidating species relationships within a genus, and argues for the importance of additional steps to filter paralogous genes and poorly aligned regions (e.g., as occur through assembly errors), such as our new PPD pipeline described in this study.

opencc-zeroJun 2021View details →

dryad36/100

Data from: Nutrient enrichment increases invertebrate herbivory and pathogen damage in grasslands

This dataset contains data on leaf damage by invertebrates and pathogens derived in a globally-distributed experiment manipulating nutrient addition (Nutrient Network). In total we estimated leaf damage on 153 plant taxa from twenty-seven grasslands worldwide, under ambient conditions and with experimentally elevated nitrogen and phosphorus. Additionally, we give MAT and MAP from WorldClim 1 for each site and percent cover for each plant species in the respective plot.

opencc-zeroOct 2021View details →

dryad36/100

Data from: Triggered Golgi membrane enrichment promotes PtdIns(4,5)P2 generation for plasma membrane repair

The maintenance of plasma membrane integrity and a capacity for efficiently repairing damaged membranes are essential for cell survival. Large-scale wounding depletes various membrane components at the wound sites, including phosphatidylinositols, yet little is known about how phosphatidylinositols are generated after depletion. Here, working with our in vivo C. elegans epidermal cell wounding model, we discovered phosphatidylinositol 4-phosphate (PtdIns4P) accumulation and local phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] generation at the wound site. We found that PtdIns(4,5)P2 generation depends on the delivery of PtdIns4P, PI4K, and PI4P 5-kinase PPK-1. In addition, we show that wounding triggers enrichment of the Golgi membrane to the wound site, and that is required for membrane repair. Moreover, genetic and pharmacological inhibitor experiments support that the Golgi membrane provides the PtdIns4P for PtdIns(4,5)P2 generation at the wounds. Our findings demonstrate how the Golgi apparatus facilitates membrane repair in response to wounding and offers a valuable perspective on cellular survival mechanisms upon mechanical stress in a physiological context.

opencc-zeroMay 2023View details →

zenodo36/100

ORCID for Wikidata – Data enrichment forscientometric applications

For the 19th International Semantic Web Conference (ISWC 2020) at 2020-11-02 I created a short video to introduce the OrcBot project. For the conference publication see: https://ceur-ws.org/Vol-2773/paper-09.pdf GitHub repositorium: https://github.com/EvaSeidlmayer/orcid-for-wikidata

opencc-by-4.0Nov 2020View details →

dryad36/100

Data from: Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish, Oryzias latipes

Sagittal otoliths, typically composed of aragonite, are frequently laid down rather as vaterite during growth in hatchery-reared fish populations. Sagittal vateritisation is believed to impair individual hearing/balancing abilities, but the causal mechanism remains unclear. Here we experimentally demonstrated that rearing in Sr-rich water induces sagittal vateritisation in the HdrR-II1 inbred strain of the Japanese rice fish, Oryzias latipes. Both sagittae were partly vateritised in 70% of individuals subjected to the Sr2+ treatment (n = 10), whereas fish reared in normal tap water showed no sagittal vateritisation (n = 8). Our result is consistent with the theoretical prediction that vaterite becomes thermodynamically more stable than aragonite as the Sr2+ concentration in solution increases. A vateritic layer develops surrounding the original aragonitic sagitta in vateritised otoliths, some of which take on a comma-like shape. Electron probe microanalysis demonstrates that the vateritised phase is characterised by lower Sr2+ and higher Mg2+ concentrations than the aragonitic phase. It is unlikely that increased environmental Sr2+ is responsible for the sagittal vateritisation in farmed fish. However, our findings likely help to establish an in vivo assay using O. latipes to understand the physiological process underlying the sagittal vateritisation in farmed fish.

opencc-zeroMay 2023View details →

zenodo36/100

data for K-feldspar enrichment in the Pacific pelagic sediments before Miocene

This is the data associated with the manuscript K-feldspar enrichment in the Pacific pelagic sediments before Miocene published in Progress in Earth and Planetary Sciences.   The data includes: Sample ID and depth. Magnetic susceptibility. Weight fraction after chemical digestions (CBD and Na-pyrosulfate fusion). Grain size. XRD spectra.

opencc-by-4.0Aug 2023View details →

dryad36/100

Data from: Host plant height explains the effect of nitrogen enrichment on arbuscular mycorrhizal fungal communities

Nitrogen (N) enrichment is widely known to affect the root-associated arbuscular mycorrhizal fungal (AMF) community in different ways, for example, via altering soil properties and/or shifting host plant functional traits. However, empirical knowledge of their relative importance is still lacking. Using a long-term N addition experiment, we measured the AMF community taxonomic and phylogenetic diversity at the single plant species (roots of 15 plant species) and plant community (mixed roots) levels. We also measured four functional traits of 35 common plant species along the N addition gradient. We found divergent responses of AMF diversity to N addition for host plants with different innate heights (i.e., plant natural height under unfertilized treatment). Furthermore, our data showed that species-specific responses of AMF diversity to N addition were negatively related to the change in maximum plant height. When scaling up to the community level, N addition affected AMF diversity mainly by increasing the maximum plant height, rather than altering soil properties. Our results highlight that plant height drives the AMF community dynamics under nitrogen enrichment at both species and community levels, thus providing important implications for understanding the response of AMF diversity to anthropogenic nitrogen deposition.

opencc-zeroAug 2023View details →

dryad36/100

Raw target enrichment of conserved element sequence data for 24 black coral species

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (~250–3,000 m) during the early Silurian (~437 Ma) and subsequently radiated into, and diversified within, both continental shelf (<250 m) and abyssal (>3,000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of "source" slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection.

opencc-zeroAug 2023View details →

dryad36/100