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opencc-by-4.0Oct 2024View details →

Dominant contribution of Asgard archaea to eukaryogenesis (2024) Tobiasson, V., Koonin, E. PROCESSED DATA AND METADATA

<h1>Main data deposit for "Dominant contribution of Asgard archaea to eukaryogenesis". </h1> <p>Victor Tobiasson, Jacob Luo, Yuri I Wolf, Eugene V Koonin</p> <p>Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA</p> <p><strong>The Origin of eukaryotes is one of the key problems in evolutionary biology. The demonstration that the Last Eukaryotic Common Ancestor (LECA) already contained the mitochondrion, an endosymbiotic organelle derived from an alphaproteobacterium, and the discovery of Asgard archaea, the closest archaeal relatives of eukaryotes inform and constrain evolutionary scenarios of eukaryogenesis. We undertook a comprehensive analysis of the origins of the core eukaryotic genes tracing to the LECA within a rigorous statistical framework centered around evolutionary hypotheses testing using constrained phylogenetic trees. The results reveal dominant contributions of Asgard archaea to the origin of most of the conserved eukaryotic functional systems and pathways. A limited contribution from Alphaproteobacteria was identified, primarily relating to the energy transformation systems and Fe-S cluster biogenesis, whereas ancestry from other bacterial phyla was scattered across the eukaryotic functional landscape, without consistent trends. These findings suggest a model of eukaryogenesis in which key features of eukaryotic cell organization evolved in the Asgard ancestor, followed by the capture of the Alphaproteobacterial endosymbiont, and augmented by numerous but sporadic horizontal acquisition of genes from other bacteria both before and after endosymbiosis. </strong></p> <div> <div> <div>Version 0.3, updated 180325</div> <div> </div> <div> </div> <div>Main data repository for:</div> <div>Dominant contribution of Asgard archaea to eukaryogenesis (2024) </div> <div>Tobiasson, V., Koonin, E.</div> <div> </div> <div>Contains all final parsed data from the main Eukaryogenesis project </div> <div>investigating the evolutionary ancetries of eukaryotic protein families. </div> <div> </div> <div>Currently (non-static) available at: </div> <div>https://www.biorxiv.org/content/10.1101/2024.10.14.618318v2</div> <div>https://assets-eu.researchsquare.com/files/rs-5352492/v1/2f9c68ae-cf3e-420a-8d29-867b6fb1a878.pdf</div> <div> </div> <div>All code used to generate the data present within this repository available at: </div> <div>https://github.com/VictorTobiasson/eukgen </div> <div> </div> <div> </div> <div>### General information</div> <div> </div> <div>To identify associations between prokaryotic and eukaryotic protein families, separate</div> <div>hidden Markov model (HMM) databases for prokaryotes and eukaryotes were constructed </div> <div>using a custom, cascaded, sequence-to-profile clustering pipeline, implemented using </div> <div>mmseqs2, followed by a multistep data-reduction and multiple sequence alignment (MSA) </div> <div>procedure to generate HMM profiles using hhsuite. </div> <div> </div> <div>A prokaryotic database of 37 million protein sequences was curated from prokaryotic </div> <div>genomes obtained from the NCBI GenBank in November 2023 and supplemented with proteins </div> <div>extracted from 146 Asgard genome assemblies. To avoid inclusion of genes present only </div> <div>within a narrow subset of species, possibly resulting from horizontal transfer from </div> <div>eukaryotes post LECA, we reconstructed the “soft-core” pangenome for each of the 26 </div> <div>curated prokaryotic taxonomic classes. These pangenomes include only those genes that </div> <div>are present in at least 67% of the families within each class of Bacteria and Archaea. </div> <div>The initial eukaryotic database consisted of 30 million protein sequences from 993 </div> <div>species taken from EukprotV3 and cleaned using mmseqs2 to remove likely prokaryotic </div> <div>contaminants. </div> <div> </div> <div>Both databases were clustered and MSAs constructed for all non, singleton clusters </div> <div>and HMM profiles created. The resulting eukaryotic HMM dataset was queried against </div> <div>the prokaryotic dataset using hhblits to identify sets of homologous protein sequences. </div> <div>Each eukaryotic cluster and all its significant prokaryotic hits constituted an individual</div> <div> sequence set, hereinafter referred to as an Eukaryotic/Prokaryotic Orthologous Cluster </div> <div>(EPOC). The EPOCs constitute groups of homologous proteins from eukaryotes and prokaryotes </div> <div>(each EPOC contains a unique set of eukaryotic proteins, but some clusters of prokaryotic </div> <div>proteins can be present in multiple EPOCs) that were used for phylogenetic tree </div> <div>construction, annotation, and evolutionary hypothesis testing. </div> <div> </div> <div>To infer the most likely prokaryotic ancestry of the eukaryotic proteins in each EPOC, </div> <div>rather than relying on the tree topology directly, we employed a probabilistic approach </div> <div>for evolutionary hypothesis testing using constraint trees. We exhaustively sampled all </div> <div>arrangements of likely sister clades and obtained Expected Likelihood Weights (ELW) for </div> <div>the set of possible sister clade models. As the ELW metric is analogous to model selection </div> <div>confidence, here we take it to be proportional to the probability of a sampled prokaryotic </div> <div>clade to be the true sister group of the given eukaryotic clade among a set of competing </div> <div>sister clades. For each EPOC, our analysis dynamically accounts for long branch outliers </div> <div>and is robust to phylogenetically non-homogenous clades. This analysis is further capable </div> <div>of resolving eukaryotic paraphyly, treating each eukaryotic clade within a EPOC as a </div> <div>single datapoint for downstream analysis. Our resulting data contains EPOCs annotated </div> <div>using profiles generated from KEGG Orthology Groups (KOGs), each with an MSA generated </div> <div>using muscle5, a maximum likelihood tree inferred using IQtree2 and associated ELW values </div> <div>for all candidate prokaryotic sister phyla. The analysis of prokaryotic ancestry was </div> <div>performed only for those eukaryotic clades that included more than 5 distinct taxonomic </div> <div>labels, with at least one coming from Amorphea and one from Diaphoretickes, the two </div> <div>expansive eukaryotic clades considered to represent either the first or the second </div> <div>bifurcation in the evolution of eukaryotes. Thus, these clades likely represent genes </div> <div>mapping back to the LECA.</div> <div> </div> <div>For further details please see main publication or contact</div> <div>victor.tobiasson@nih.gov</div> <div>eugene.koonin@nih.gov</div> <div> </div> <div> </div> <div>### Included files</div> <div> </div> <div>Unless otherwise stated all files contained are tab separated and utf-8 encoded </div> <div>with the first row containing header information. </div> <div>All data entries encoding lists are “|” (pipe) separated. </div> <div>Fields without data values are filled with string entries of “none”.</div> <div> </div> <div>--- Databases ---</div> <div>euk72_ep.tar.gz</div> <div>prok2311_as.tar.gz</div> <div>Prok2311As_final_clusters.tsv</div> <div>Euk72Ep_final_clusters.tsv</div> <div>prok2311_as.hmmDB.tar.gz</div> <div>euk72_ep.hmmDB.tar.gz</div> <div> </div> <div>--- Annotation and Curation ---</div> <div>NCBI_taxonomy_species_addendum.tsv</div> <div>NCBI_taxonomy_class_addendum.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>KEGG_category_mapping.tsv</div> <div>KEGG_metadata.tsv</div> <div> </div> <div>--- EPOC data ---</div> <div>EPOC_data.tar.gz</div> <div>EPOC_annotation_KEGG.tsv</div> <div>EPOC_data.tsv</div> <div>EPOC_data.pangenomes_s10.tsv</div> <div>EPOC_data.pangenomes_s25.tsv</div> <div>EPOC_data.pangenomes_s67.tsv</div> <div>EPOC_data.GTDB.tsv</div> <div> </div> <div># euk72_ep.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files </div> <div>constituting the initial eukaryotic mmseqs2 database with taxonomy annotation. </div> <div>Constructed from a pre-selected list of 72 eukaryotic proteomes downloaded from </div> <div>NCBI as well as a “clean” version of Eukprot, lacking highly prokaryotic-like </div> <div>contaminant sequences. </div> <div> </div> <div># prok2311_as.tar.gz</div> <div>Gunzip-ed .tar archive containing a single directory with 10 files constituting the </div> <div>initial prokaryotic mmseqs2 database with taxonomy annotation. Constructed from </div> <div>47545 complete genomes retrieved from NCBI in November 2023. </div> <div> </div> <div># prok2311_as.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from prok2311_as non--singleton clusters, contains 26286 profiles.</div> <div> </div> <div># euk72_ep.hmmDB.tar.gz</div> <div>Gunzip-ed .tar archive containing 6 files. Comprises an HHSuite Databse formatted </div> <div>from euk72_ep non-singleton clusters, contains 1631704 profiles.</div> <div> </div> <div># NCBI_taxonomy_species_addendum.tsv</div> <div>Taxonomy mapping file with manually curated ‘class’ level annotation for poorly </div> <div>annotated species. </div> <div> </div> <div>taxid: NCBI taxid</div> <div>proposed_class_id: Manually assigned NCBI taxid</div> <div>proposed_class_label: NCBI class name</div> <div>org_name: NCBI organism name</div> <div> </div> <div># NCBI_taxonomy_class_addendum.tsv</div> <div>Class revision file mapping poorly populated class level entries to higher order </div> <div>manually curated labels. Also includes information for small classes with shallow </div> <div>taxonomy which are deleted from the EPOC analysis at the level of tree construction.</div> <div> </div> <div>taxid: NCBI taxid</div> <div>ncbi_class: NCBI taxid of rank corresponding to ‘class’ following manual </div> <div>amendment as per NCBI_taxonomy_species_addendum.tsv</div> <div>revised_class_id: Manually assigned NCBI taxid of rank corresponding to ‘class’</div> <div>revised_class_label: Proposed cleartext name of manually revised revised_class_id </div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.tsv</div> <div>Final taxonomy at NCBI rank ‘class’ following revisions for all sequences in Euk72Ep or </div> <div>Prok2311As. These taxonomic labels are used for EPOC tree annotation. </div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of manually revised NCBI rank ‘class’ identifier for annotation</div> <div> </div> <div># Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Final taxonomy at GTDB rank ‘phylum’ transferred using marker genes from GTDB release 220</div> <div> </div> <div>acc: mmseqs database header in either prok2311_as or euk72_ep databases</div> <div>taxid: NCBI taxid for organism</div> <div>superkingdom: Top level NCBI taxonomy classification Bacteria, Archaea or Eukarya, </div> <div>used to define Eukaryotic outgroups in EPOC analysis</div> <div>class: Cleartext name of assigne GTDB phylum</div> <div> </div> <div># Prok2311As_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation  </div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># Euk72Ep_final_clusters.tsv</div> <div>Cluster mapping file for accessions within the initial Prok2311A database to the </div> <div>final clusters used for HMM creation</div> <div> </div> <div>cluster_acc: cluster representative</div> <div>acc: cluster member</div> <div> </div> <div># EPOC_data.tar.gz</div> <div>Gunzip-ed directory containing 16035 EPOC folders. Each folder is named corresponding </div> <div>to the eukaryotic cluster representative which generated its profile as an ID </div> <div>Matches the tree_name field in EPOC_data_prok2311As.tsv</div> <div>contains the following files:</div> <div> </div> <div><EPOC_ID>.merged.fasta: sequences for all members of the EPOC</div> <div><EPOC_ID>.merged.fasta.leaf_mapping: tsv separated file containing taxonomy and tree reduction data</div> <div><EPOC_ID>.merged.fasta.muscle: main cropped MSA for tree generation </div> <div><EPOC_ID>.merged.fasta.muscle.iqtree: IQtree2 output from tree generation</div> <div><EPOC_ID>.merged.fasta.muscle.treefile.annot: annotated newick tree file with final tree</div> <div><EPOC_ID>.merged.tree_data.tsv: final parsed tree data with columns matching  EPOC_data_prok2311As.tsv</div> <div> </div> <div>EPOCs with more than one possible eukaryotic sister phyla also contains </div> <div>a folder "constraint_analysis" with constraint tree information used for </div> <div>ELW value calculation. </div> <div> </div> <div># EPOC_data.tsv</div> <div>Main resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) </div> <div>based on pangenomes defined as including 10% of species per class. This is the main</div> <div>data to be used for genereting the core dataset and for data visualistation</div> <div>Contains information regarding tree breakdown, LCA membership and phylogenetic </div> <div>distances between all detected LCAs. Equivalent to the stacked dataframes from all </div> <div>EPOC directories in EPOC_data </div> <div> </div> <div>tree_name: unique index for each EPOC </div> <div>euk_clade_rep: unique index for each annotated eukaryotic clade within each tree_name</div> <div>euk_clade_size: number of original sequences represented by euk_clade_rep</div> <div>euk_clade_weight: metric for taxonomic purity for each euk_clade_rep</div> <div>euk_leaf_clade: boolean indicating whether euk_clade_rep contains a single leaf</div> <div>euk_LCA: lowest taxa spanning all members in euk_clade_rep</div> <div>euk_scope: list of all taxonomic classes in euk_clade_rep</div> <div>euk_scope_len: length of euk_scope list</div> <div>prok_clade_rep: unique index for each annotated prokaryotic clade for each euk_clade_rep</div> <div>prok_clade_size: number of original sequences represented by prok_clade_rep</div> <div>prok_clade_weight: metric for taxonomic purity for each prok_clade_rep</div> <div>prok_leaf_clade: boolean indicating whether prok_clade_rep contains a single leaf</div> <div>prok_taxa: lowest taxa spanning all members in prok_clade_rep</div> <div>dist: tree-distance from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>top_dist: graph-distance (node-distance) from lowest tree node containing all members of prok_clade_rep to lowest tree node containing all members of euk_clade_rep</div> <div>raw_stem_length: tree-distance from lowest tree node containing the union of all members of prok_clade_rep and euk_clade_rep to the tree node containing all members of euk_clade_rep</div> <div>median_euk_leaf_dist: median value for all tree distances from the tree node containing all members of euk_clade_rep to the individual leaves</div> <div>stem_length: raw_stem_length/median_euk_leaf_dist</div> <div>logL: log likelihood of best constraint tree constructed</div> <div>deltaL: log likelihood difference between constraint tree for prok_clade_rep and best constraint tree constructed</div> <div>bp-RELL: validation metric from IQtree -trees, see iqtree.org</div> <div>bp-RELL_accept: as above</div> <div>p-KH: as above</div> <div>p-KH_accept: as above</div> <div>p-SH: as above</div> <div>p-SH_accept: as above</div> <div>c-ELW: as above</div> <div>c-ELW_accept: as above</div> <div>p-AU: as above</div> <div>p-AU_accept: as above</div> <div> </div> <div># EPOC_data.pangenomes_s10.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 10% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s25.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 25% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.pangenomes_s67.tsv</div> <div>Resulting data from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>based on pangenomes defined as including 67% of species per class.</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.GTDB.tsv</div> <div>Resulting data  from all Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>under revised taxonomy from GTDB based on data from Euk72Ep_Prok2311As_final_classes.GTDB.tsv</div> <div>Identical file structure to EPOC_data.tsv</div> <div> </div> <div># EPOC_data.alpha_replicates.tsv</div> <div>Resulting data from 20 repetitions of Eukaryotic/Prokaryotic Orthologous Clusters (EPOCs) calculated </div> <div>from a subset of Alphaproteobacterial-derived EPOCs. </div> <div>Identical file structure to EPOC_data.tsv with the addition of:</div> <div> </div> <div>rep: indicating technical replicate number, 0-19</div> <div> </div> <div># EPOC_annotation_KEGG.tsv</div> <div>Parsed HHblits output of HMM profiles generated from KEGG KOGs (KEGG Orthologous Groups) </div> <div>against eukaryotic profiles constituting each EPOC</div> <div> </div> <div>Query: query name equal to tree_name from EPOC_data</div> <div>Target: target name equal to kogid in KEGG_category_mapping and KEGG_metadata</div> <div>Prob: data from HHblits, see https://github.com/soedinglab/hh-suite/wiki</div> <div>E-value : as above</div> <div>P-value : as above</div> <div>Score: as above</div> <div>SS: as above</div> <div>Cols: as above</div> <div>Identities: as above</div> <div>Similarity: as above</div> <div>Sum_probs: as above</div> <div>Query-HMM-start: as above</div> <div>Query-HMM-end: as above</div> <div>Template-HMM-start: as above</div> <div>Template-HMM-end: as above</div> <div>Template_columns: as above</div> <div>Template_Neff : as above</div> <div>Pairwise_cov: calculated pairwise coverage from Query and Target start and end</div> <div>Description: category_name from KEGG_category_mapping</div> <div> </div> <div># KEGG_category_mapping.tsv</div> <div>Mapping of relevant KOG identifiers to their higher order categories as </div> <div>"Maps" "Modules" or "Reactions" as per KEGG see https://www.kegg.jp/kegg/pathway.html</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>category_id: KEGG map, module, or reaction number</div> <div>category_name: cleartext name for KOG identifier</div> <div> </div> <div># KEGG_metadata.tsv</div> <div>File mapping KOGs to BRITE classification and to additional databases of chemical properties.</div> <div> </div> <div>kogid: unique KOG identifier</div> <div>name: cleartext name for KOG identifier</div> <div>brite_A: list of BRITE-A sets including KOG</div> <div>brite_B: list of BRITE-A sets including KOG</div> <div>brite_C: list of BRITE-A sets including KOG</div> <div>EC: list of Enzyme commission numbers associated with KOG, see https://enzyme.expasy.org/</div> <div>TC: list of transporter classification numbers associated with KOG, see https://www.tcdb.org/</div> <div>RN: list of KEGG reaction numbers associated with KOG</div> <div>CA: list of CAZY numbers associated with KOG, see http://www.cazy.org/</div> <div>GO: list of GO terms associated with KOG, see https://geneontology.org/</div> </div> <div> </div> </div>

opencc-by-4.0Jul 2022View details →

AMOC reconstruction between 1981 and 2016 from hydrographic data using an empirical linear regression model from Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, https://doi.org/10.5194/os-17-285-2021, 2021.

<p>Dataset used to create Figure 8 in Worthington et al., 2021 (https://doi.org/10.5194/os-17-285-2021). Details of the data and methods can be found in the journal article.<br> <br> Worthington, E. L., Moat, B. I., Smeed, D. A., Mecking, J. V., Marsh, R., and McCarthy, G. D.: A 30-year reconstruction of the Atlantic meridional overturning circulation shows no decline, Ocean Sci., 17, 285–299, <a href="https://doi.org/10.5194/os-17-285-2021">https://doi.org/10.5194/os-17-285-2021</a>, 2021.</p>

Data and code for: Rachel A Reeb, J Mason Heberling, & Sara E Kuebbing (2024). Cross-continental comparison of plant reproductive phenology shows high intraspecific variation in temperature sensitivity. AoB PLANTS, plae058

<p>Data and Analysis Code for: </p> <p>Rachel A Reeb, J Mason Heberling, Sara E Kuebbing (2024). Cross-continental comparison of plant reproductive phenology shows high intraspecific variation in temperature sensitivity. <em>AoB PLANTS</em>, plae058. <a href="https://doi.org/10.1093/aobpla/plae058">https://doi.org/10.1093/aobpla/plae058</a></p> <p>Includes two R markdown files ("climate_data_extraction_code.rmd" is the script for data extraction and cleaning and "Data_Analysis_V2.rmd" is the analysis script), the associated datasets (in .csv format), and the metadata file ("readme.txt").</p>

opencc-by-4.0Sep 2024View details →

Image data of co-localization of IgG and HEV ORF2 protein in a case of hepatitis E-associated kidney disease

<p><span>Image data for a co-localization study of IgG with HEV ORF2 protein in a </span><span>de novo immune complex-mediated glomerulonephritis (GN) case in</span><span> a kidney transplant recipient </span><span>with chronic hepatitis E (Leblond and Helmchen, et al. 2024).<span>  </span>Immunofluorescence images are provided for 25 glomeruli at low magnification (20x, 0.227 micron/pixel) and for 16 glomeruli at high magnification (100x, 0.0454 micron/pixel). For each example glomeruli the green channel represents IgG antibody staining with FITC, and the magenta channel represent anti-HEV ORF2 staining using Alexa Fluor 546.</span></p> <p><span>Methods: </span></p> <p><span>Mouse monoclonal antibody clone 1E6 against the HEV ORF2 protein was incubated for 1h at a dilution of 1:125 followed by a mix of Alexa Fluor 546-conjugated goat anti-mouse antibody (Invitrogen BV, A11018) and FITC-conjugated Rabbit anti-Human IgG (Gamma chain, Diagnostic Biosystem, F008) for 1hat a dilution of 1:50. Following automated staining, the slides were hand -washed in distilled H<sub>2</sub>O. Tissue was covered with Vectashield® Antifade Mounting Medium with DAPI (VectorLaboratories, H-1200), covered with a coverslip and stored at 4°C until evaluation.</span></p> <p><span>Immunofluorescence images were acquired with an upright fluorescence microscope (AxioImager.Z2 controlled by ZEN Blue software; 89 North Photofluor LM-75 light source, and Axiocam 503 mono camera; Zeiss, Jena, Germany), equipped with the following objectives: 20x (NA 0.5, Plan-NEOFLUAR), 40x (NA 1.4 oil, Plan-APOCHROMAT), and 100x (NA 1.45 oil, Plan-APOCHROMAT) objectives. This setup provides an excellent spatial resolution (nominally about 200 nm lateral resolution in our study; pixel size was 45.4 nm for 100x objective). High resolution images were taken with the 100x objective using the ApoTome.2 module with deconvolution (grid 5 lp/mm; section thickness 0.7 µm). We used Vysis Abbott Chroma filter sets (Blue: excitation (ex) 335-383 nm, emission (em) 420-470; green: ex 481-507 nm; em 521-551 nm; red: ex 534-556 nm, em 574- 606 nm). Co-localization of IgG and HEV ORF2 staining was quantified using Fiji software (Schindelin et al., 2012) and the JACoP ImageJ plug-in. </span></p>

opencc-by-sa-4.0Aug 2021View details →

LTER-Italy site Delta del Po e Costa Romagnola figure

<p>Geographical representation of the LTER-Italy site Delta del Po e Costa Romagnola (LTER_EU_IT_058) - DEIMS-ID <a href="https://deims.org/6869436a-80f4-4c6d-954b-a730b348d7ce">https://deims.org/6869436a-80f4-4c6d-954b-a730b348d7ce</a></p>

opencc-by-4.0Jun 2023View details →

Dataset for: Mudrik, N., & Charles, A. S. (2022). Multi-Lingual DALL-E Storytime. arXiv preprint arXiv:2212.11985.

<p>This dataset represents the comprehensive collection of data generated during the study presented in the paper available at https://arxiv.org/abs/2212.11985.</p> <p>If your research incorporates this data and results in a publication - Please cite both the dataset and the paper.</p>

edi52/100

Regional E-Atlas of the Greater Phoenix Region: Areas of significant agricultural and residential groundwater use, 1996-2000

Spatial distribution of well water usage (groundwater) for the period 1996 - 2000. These data present significant areas of agricultural and residential groundwater use during this period. This is a spatial data object with a Coordinate Reference System (CRS) of EPSG:3479 NAD83(NSRS2007) / Arizona Central (ft); https://www.spatialreference.org/ref/epsg/3479/). The coordinate reference system (CRS) associated with these data when they were constructed initially was misrepresented in early versions (<= knb-lter-cap.101.8) of this dataset. The CAP LTER has attempted to assign a CRS based on reasonable values but the accuracy of the identified CRS cannot be certain.

openCC0Dec 2022View details →

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PFAS, Coliform, and E. coli Data from Freshwater Canals, Brackish Water in Biscayne Bay, and Ocean Salt Water from Miami Beaches, Florida, USA, July 2023

This package contains data on levels of Per- and polyfluoroalkyl substances (PFAS), Coliform, and E. coli from samples collected at 15 water sampling sites in and around Biscayne Bay, Florida on 2023-07-27 as part of the Coastal Ecosystem-Research Experience for Teachers (CE-BIORETS) program. The sites included waterways leading to Biscayne Bay (freshwater canals), Biscayne Bay directly (marine brackish water), and ocean water from Miami beaches (marine salt water). A total of 500 mL of surface water was collected (at approximately 30 cm depth) from each site. Samples were run through a Solid Phase Extraction process (SPE) and then dried using a Nitrogen Evaporator. Extracts were then analyzed by Liquid Chromatography-Triple quadrupole Mass Spectrometry (LC-MS/MS) to determine the quantity of each of the different PFAS (ng/L) present in the sample. The same sites were selected for Coliform and E. coli colony forming units’ detection, and samples were collected at the same time as the PFAS samples. Samples were analyzed by pouring 100 mL of collected water into the wells on a ColiPlate. The 15 plates were incubated for 1 day at 37°C to determine if Coliforms and E. coli were detected. Data collection for this project is complete.

openCC (other)Jun 2025View details →

opencc-by-4.0Nov 2020View details →

Magnetic hyperthermia with e-Fe2O3 nanoparticles

<p>These data correspond to the figures in the paper: Gu Y. et al. RSC Adv., 2020, 10, 28786–28797. doi:10.1039/d0ra04361c.</p>

opencc-by-4.0Nov 2023View details →

Dataset de Terremotos en la Península Ibérica e Islas Canarias (Últimos 15 Días)

<p>El "Dataset de Terremotos en la Península Ibérica e Islas Canarias (Últimos 15 Días)" es un conjunto de datos que recopila información detallada sobre terremotos registrados en la Península Ibérica e Islas Canarias durante un período de tiempo específico que abarca los últimos 15 días desde que se ejecutó la recolección de los datos. Este conjunto de datos se enfoca en eventos sísmicos con una magnitud igual o superior a 1.5 en la escala sismológica de Richter o que han sido percibidos por la población local.</p><p>Cada entrada en el dataset proporciona datos esenciales, incluyendo la descripción del evento, la fecha y hora en la que ocurrió en Coordinación Universal (UTC), la hora local ajustada según la ubicación geográfica precisa, las coordenadas de latitud y longitud donde se originó el terremoto, la profundidad del foco, la magnitud en la escala de Richter, el tipo de magnitud utilizada, la intensidad máxima registrada y detalles sobre la localización geográfica exacta del evento.</p><p>Este conjunto de datos se actualiza periódicamente para garantizar que los datos sean relevantes y actuales, lo que lo convierte en una valiosa fuente de información para el estudio de la actividad sísmica en la región. Los datos recopilados son esenciales para comprender la sismicidad en la Península Ibérica e Islas Canarias, así como para abordar temas relacionados con la seguridad, la mitigación de riesgos y la investigación en el campo de la sismología.</p>

Study of Calabrian Sounding Objects. Field Notes - E. Ruperto

<p>This dataset contains the ethnomusicological data concerning the study of traditional sounding objects in Calabria generated for the EU-funded research LoMus - Local Sound for a New Musicality. </p><p> </p><p>LoMus - Local Sound for a New Musicality. Enhancing Musical Participation through a Local Sonic Practice is a research project funded under the Marie Skłodowska Curie Action. LoMus investigates ways of expanding musical participation through the use of sounding objects and contemporary music techniques.</p>

Study of Calabrian Sounding Objects. Interview and Field Notes - E. Curcio

opencc-by-4.0Dec 2022View details →

Schedatura dei notai dell'Italia meridionale e insulare dei secc. XIII-XV di cui si conservano i rispettivi registri

<p>L’obiettivo della schedatura dei notai nell'ambito del progetto NotMed (EL NOTARIAT PÚBLIC EN LA MEDITERRÀNIA OCCIDENTAL: ESCRIPTURA, INSTITUCIONS, SOCIETAT I ECONOMIA (SEGLES XIII-XV) - Ministerio de Ciencia e Innovación. PID2019-105072GB-I00 - <a href="https://www.ub.edu/notmed/">https://www.ub.edu/notmed/</a>) era quello di conoscere il numero di volumi in legatura (protocolli notarili, bastardelli, etc.) esistenti nell’Italia meridionale e insulare per i secoli medievali e di creare una base per ulteriori ricerche.</p> <p>Hanno contribuito:</p> <p>Giuliano Capriolo, Andrea Casalboni, Gemma Teresa Colesanti, Martina Del Popolo, Corinna Drago, Alessandro Gaudiero, Antonio Macchione, Eleni Sakellariou, Daniela Santoro, Vera Isabell Schwarz-Ricci, Chiara Sciarroni, Alessandro Soddu, Maria Elisabetta Vendemia, Elisa Turrisi e Maurizio Vesco.</p> <p>NB.</p> <ul> <li>       Nella dicitura “volumi in legatura” rientrano sia veri e proprio protocolli notarili sia bastardelli sia fascicoli rilegati.</li> <li>       Il limite cronologico è l’anno 1500, tuttavia nei casi di notai che iniziano a rogare nella seconda metà del ‘400 sono confluiti nel censimento anche i registri dei primi decenni del ‘500.</li> <li>       Per ogni notaio è stata compilata una singola scheda, tranne in due casi nei quali i protocolli si conservano in due istituzioni diverse.</li> <li>       I volumi miscellanei sono stati conteggiati e schedati con una nota specifica inserita nel campo commento.</li> <li>       È da tener presente che la base di rilevamento è eterogenea: alcune indicazioni si basano sull’esame autoptico del materiale, altre sulle indicazioni dell’inventario on line dell’archivio o su lavori pubblicati in precedenza. Per questo motivo si consiglia di consultare sempre le osservazioni del compilatore nel campo commento e le indicazioni sulla fonte dell’informazione.</li> </ul>

A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models

<p>Dataset corresponding to the associated publication, "A Missing Piece of the E-Region Puzzle: High-Resolution Photoionization Cross Sections and Solar Irradiances in Models."  The dataset includes high-resolution photoionization and photoabsorption cross section for O and N<sub>2</sub> as well as high-resolution solar spectrum.  Photoionization rates from model runs obtained from AURIC and the Meier photoionization code are also included.  Please refer to the readme for information on the data structure.</p> <p><strong>***Please note that the paper is under review and has not been accepted yet.***</strong></p>

opencc-by-4.0Sep 2022View details →

Concatenated Data from the Chang'E-1 and -2 Microwave Radiometers

<p>This dataset includes a binary table collecting all data released by NAOC from the Chang'E 1 and 2 Microwave Radiometers, as well as gridded, map-projected versions of those data. Please see readme.md for a detailed description of contents.</p>

opencc-by-4.0Jan 2024View details →

Dataset - Terminology of e-Oral Health: Consensus Report of the IADR's e-Oral Health Network Terminology Task Force.

<p>README<br>====================<br>This repository contains the data and documentation for a research project. It includes the dataset,<br>which is provided in CSV format and the original PDF with the survey answers.</p> <p>Research Information<br>====================<br>Terminology of e-Oral Health: Consensus Report of the IADR’s e-Oral Health Network Terminology<br>Task Force. Authors reported multiple definitions of e-oral health and related terms, and used several definitions<br>interchangeably, like mhealth, teledentistry, teleoral medicine and telehealth. The International<br>Association of Dental Research e-Oral Health Network (e-OHN) aimed to establish a consensus on<br>terminology related to digital technologies used in oral healthcare.</p> <p>This dataset contains data from a survey about digital oral health. The survey asked participants to provide their definition of various terms related to digital oral health, as well as their agreement with the provided definitions. The dataset also includes three figures that the participants were asked to review.</p> <p>The purpose of this dataset is to collect data on the public's understanding of digital oral health terms and to identify areas where there may be confusion or misinterpretation. The data from this dataset could be used to develop educational materials or to improve the way that digital oral health information is communicated to the public.</p> <p>Additional notes<br>====================<br>The data is not currently cleaned or preprocessed.</p> <p>Dataset<br>====================<br>The dataset file, named "dataset.csv," is in this repository. It contains the raw anonymized data<br>collected from the participants in a structured format. Each row represents a respondent, and the<br>columns correspond to different variables.</p> <p>Codebook<br>====================<br>The codebook file, named "codebook.pdf," is also included in this repository. It provides a<br>comprehensive description of the variables present in the dataset. The codebook outlines each<br>variable's meaning, type, and possible values, allowing users to understand and analyze the data<br>effectively.</p> <p>Metadata<br>====================<br>No metadata is provided</p> <p>Files<br>====================<br>01_readme.txt this readme file<br>02_codebook.pdf The codebook of the dataset<br>03_dataset.csv The dataset in csv format<br>04_e-OHN Delphi (2023-02-03).pdf The output from the survey</p> <p>Usage<br>====================<br>To work with the dataset, you can download the "dataset.csv" file and import it into your preferred<br>software or programming language for analysis. The codebook provides valuable information about<br>the variables, allowing you to understand the data structure and make informed decisions during your<br>analysis.<br>Please note that while every effort has been made to ensure the accuracy and quality of the data, it is<br>important to review the codebook and understand the context of the research before concluding the<br>dataset.</p> <p>License<br>====================<br>The data and documentation in this repository are provided under the CC BY-SA.<br>This license enables reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. If you remix, adapt, or build upon the material, you must license the modified material under identical terms. CC BY-SA includes the following elements:</p> <p> BY: credit must be given to the creator.<br> SA: Adaptations must be shared under the same terms.<br> <br>Please refer to the license file for further details on how the data can be used and shared.</p> <p>Contact Information<br>====================<br>For any questions, clarifications, or inquiries related to the dataset or research project, please contact<br>Assoc Prof Dr Sergio Uribe, sergio.uribe@rsu.lv</p>

opencc-by-4.0Aug 2023View details →

CSBCSet: Um conjunto de dados para uma década de CSBC, seus eventos e publicações

<p>In this paper, we present a dataset about a decade of publications in the Brazilian Computing Society Congress (CSBC), between 2013 and 2022. We specify the extraction, processing and adjusments, storage and opening of data, with its limitations, challenges and lessons learned . We analyzed the data and metadata scenario, perceiving positive and negative aspects of the scope. Finally, we forward proposals for potential applications of this dataset, and related threats to validity.</p>

opencc-by-sa-4.0Nov 2024View details →

PM_051486_E_Senterada

<u>File Name</u>: PM_051486_E_Senterada.jpg <br><u>Sublocation</u>: Casa Leonardo <br><u>Location</u>: Senterada <br><u>Province</u>: Catalunya, Lleida <br><u>Country</u>: Spain <br><u>Header</u>: Casa rural Casa Leonardo Hotel Eco Boutique, interior <br><u>Description</u>: Casa rural Casa Leonardo Hotel Eco Boutique Interior <br><u>Keywords</u>: 20th C, Catalunya, Cultural heritage, Europe, Folklore, Furniture/accessory furnishing, Lleida, Museum/private collection, Period, Senterada, Spain, Thematic <br><br><u>Author</u>: Photo: Paul M.R. Maeyaert <br><u>Copyright</u>: Paul M.R. Maeyaert <br>