cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10090595
title: Temporal dynamics of invertebrate community assembly in Lake Victoria since the Late Pleistocene based on chitinous remains

description: Preserved assemblages of invertebrate remains in lacustrine sediment reveal temporal variations of community composition and environmental conditions. However, records for large tropical lakes are scarce. Lake Victoria, the largest tropical lake, has a dynamic history of changes in water level, biogeochemistry, and fish community composition over the past ~17,000 cal yr BP. In order to quantify changes in the invertebrate assemblage of Lake Victoria from the Late Pleistocene throughout the Holocene, we examined chitinous remains of Cladocera and larval dipterans (Chironomidae and Chaoboridae) from a sediment core (37 m water depth) dated from ~13,700 cal yr BP to present. We identified four major phases in the invertebrate assemblage throughout this period of lake history. First, Chironomidae and Chaoboridae appeared at low abundances during the earliest stages of the lake inundation in the late Pleistocene, at a time when Cladocera were notably absent. Second, chaoborids and chironomids increased in abundance during the Mid Holocene, which coincided with high diatom production towards the end of the Holocene African Humid Period. Third, starting ~4,700 cal yr BP, Alona, a predominantly littoral cladoceran genus, consistently appeared in the invertebrate assemblage alongside changes in mixing regimes and persisted throughout the Late Holocene to present. Fourth, the arrival of both Chydorus and Bosmina longirostris marked the establishment of an abundant cladoceran assemblage at ~1,350 cal yr BP. The assemblage then gradually shifted toward the increasing dominance of B. longirostris, a planktonic cladoceran. This study provides the first multi-millennial record of sedimentary invertebrate assemblages in Lake Victoria, and elucidates some of the temporal development of these communities throughout most of the modern ecosystem's dynamic history. Overall, we provide novel insights into the temporal dynamics of invertebrate community assembly in relation to climatic and environmental variability in tropical lakes.
DOI: 10.5281/zenodo.11109986
title: DMM fits for SI figure 2

description: Input file to replicate construction of supplemental figure 2. Results of a DMM fit to a 16S microbiome collection derived from pulmonary sputum samples collected by pwCF.
DOI: 10.5281/zenodo.5121553
title: Dataset of sampled and/or logged Chlorophyll, Total Suspended Matter, Turbidity and Water temperature in Dutch Case study areas

description: Dataset of sampled and/or logged Chlorophyll, Total Suspended Matter, Turbidity and Water temperature in Dutch Case study areas at multiple stations in 2018, 2019 and 2020.
description: CoastObs_insitu_Data_2018_2019_HZv1.xlxs: Dataset of analysed chlorophyll-a and total suspended matter from in-situ sampling in 2018 and 2019 in the Wadden Sea and Eastern Scheldt. Dataloggers: Aggregated daily values of Chlorophyll (ug/l), Turbidity (FTU) and Water Temperature (degC) of logged data with JFE Ocean INFINITY-CLW devices. Daily values of Chlorophyll and Turbidity through mode and median aggregation of approx. 14000 records a day.
DOI: 10.5281/zenodo.5121554
title: Dataset of sampled and/or logged Chlorophyll, Total Suspended Matter, Turbidity and Water temperature in Dutch Case study areas

description: Dataset of sampled and/or logged Chlorophyll, Total Suspended Matter, Turbidity and Water temperature in Dutch Case study areas at multiple stations in 2018, 2019 and 2020.
description: CoastObs_insitu_Data_2018_2019_HZv1.xlxs: Dataset of analysed chlorophyll-a and total suspended matter from in-situ sampling in 2018 and 2019 in the Wadden Sea and Eastern Scheldt.

Dataloggers: Aggregated daily values of Chlorophyll (ug/l), Turbidity (FTU) and Water Temperature (degC) of logged data with JFE Ocean INFINITY-CLW devices. Daily values of Chlorophyll and Turbidity through mode and median aggregation of approx. 14000 records a day.
DOI: 10.5281/zenodo.7729336
title: Flemish Political Ambition Survey

description: Dataset based on a survey about political ambition among a random sample of the youth population ( aged 18-35) in Flanders (Belgium), N = 1,000
DOI: 10.5281/zenodo.7729337
title: Flemish Political Ambition Survey

description: Dataset based on a survey about political ambition among a random sample of the youth population ( aged 18-35) in Flanders (Belgium), N = 1,000
DOI: 10.5281/zenodo.10992465
title: Cellular-resolution X-ray microtomography of an entire mouse brain: supporting data, scripts and parameters

description: Abstract 

Purpose: Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge.

Approach: Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 × 8 offset acquisitions were stitched to reconstruct a 15,000^3 voxel volume. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs.

Results: We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 μm voxel size. The data were block-wise transformed to a common coordinate system then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer.

Conclusions: This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers.

Data

File b32_atlas_registration.zip contains the input data, parameter files and output data of affine and non-rigid registration of the 32 x 32 x 32 voxels downsampled microtomography image to the Allen Mouse Brain Common Coordinate Framework v3.

File create_sharded_Neuroglacer_format.pdf will provide instructions how to create gZip-compressed, sharded, pre-computed Neuroglancer format via the open source software igneous. This is currently still missing.

Processing

Reconstruction of extended field microtomography images mit projection stitching in horizontal and vertical direction was achieved with our software pipeline mosaicreconstruction.

The 32 x  32 x 32 voxels downsampled microtomography image was registered with the open source software elastix (and transformix). The elastix.log file states the used command line options. Directory names require adapting for reproducing the results. 

As terabyte large images and the non-rigid transformation parmeters do not fit into memory, we developed a distributed hierarchical approach with sub-volume transformations for the high resolution level, see LargeVolumeTransformix. The high resolution tomography volume (moving volume) was warped to the atlas (fixed volume) by dividing the fixed space into 12 × 12 × 12 target subregions, such that the axes-aligned extended moving image subregion, the moving image transformed subregion, and the transformation parameters all fit in memory for an isotropic target voxel resolution of 0.65 μm.
DOI: 10.5281/zenodo.11077782
title: Survey of Citizen Scientists

description: This dataset reports on a survey on the overall experiences of a citizen scientist population, mainly in Europe. Dimensions investigated include activities undertaken, knowledge of open science concepts, and data practices.

The corresponding publication for this dataset is:

O’Grady, M., Mangina, E. Citizen scientists—practices, observations, and experience. Humanit Soc Sci Commun 11, 469 (2024). https://doi.org/10.1057/s41599-024-02966-x
DOI: 10.5281/zenodo.10853582
title: Focal mechanisms of the Southeastern Alps and surroundings

description: We report the focal mechanisms (FPS) of earthquakes that occurred in the southeastern Alps and surrounding areas (latitude ~ 45°N-47.5°N and longitude ~ 10°E-15°E) from 1928 to 2023.

The FPS have been collected and revised from literature or, depending on data availability, newly computed both by first polarities inversion or by means of seismic moment tensor.

For more details about the catalogue (V 1.0, V 1.1) refer to the paper:

Saraò, A., Sugan, M., Bressan, G., Renner, G., and Restivo, A.: A focal mechanism catalogue of earthquakes that occurred in the southeastern Alps and surrounding areas from 1928–2019, Earth Syst. Sci. Data, 13, 2245–2258, https://doi.org/10.5194/essd-13-2245-2021, 2021

Cite as:

Sugan, M., Saraò, A., Magrin, A., Snidarcig, A., Bressan, G., Renner, G., Romano, M. A., Guidarelli, M., Santulin, M., Di Bartolomeo, P., & Restivo, A. (2024). Focal mechanisms of the Southeastern Alps and surroundings (2.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10853582

 

V 2.0, March - doi: 10.5281/zenodo.10853582



corrected some typos;

added new FPS solutions for the period 2014-2023


V 1.1, April 2021 - doi: 10.5281/zenodo.4660412



corrected some typos;  

added priority criteria code

added code to describe the changes applied with respect to the original solutions 


V 1.0, November 2020 - doi: 10.5281/zenodo.4284971
DOI: 10.5281/zenodo.11073212
title: Survey of Citizen Scientists

description: This dataset reports on a survey on the overall experiences of a citizen scientist population, mainly in Europe. Dimensions investigated include activities undertaken, knowledge of open science concepts, and data practices.

The corresponding publication for this dataset is:

O’Grady, M., Mangina, E. Citizen scientists—practices, observations, and experience. Humanit Soc Sci Commun 11, 469 (2024). https://doi.org/10.1057/s41599-024-02966-x
DOI: 10.5281/zenodo.10691732
title: The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages

description: This is the datasets and R script for our  manuscript titled "The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages."


Study area and sampling of Mecsek_species_Szivaketal.xlsx data


The study area is situated in the Mecsek Mountains in Hungary. Stream insects were collected using the kick and sweep sampling technique. A hand net with a frame width of 25 cm and a mesh size of 1000 µm was employed. The collection involved disturbing an area of 0.25 × 0.25 m. We employed a stratified random multihabitat sampling procedure. We collected 20 sample units from the major microhabitats in proportion to their occurrence within the reaches. Each sample unit was individually processed and sorted in the laboratory to ensure thorough and accurate analysis.


Disperse_trait_Szivaketal.xlsx data is based on DISPERSE database (Sarremejane et al., 2020)


Methods for microhabitat_coverage_reach_transect.xlsx: Prior to sampling, we divided each 100 m long reach into 20 transects of comparable length and created microhabitat coverage maps. Using these maps, we assessed the proportionate coverage of different microhabitat types within each reach


References:


Sarremejane, R., Cid, N., Stubbington, R., Datry, T., Alp, M., Cañedo-Argüelles, M., Cordero-Rivera, A., Csabai, Z., Gutiérrez-Cánovas, C., Heino, J., Forcellini, M., Millán, A., Paillex, A., Pařil, P., Polášek, M., Tierno de Figueroa, J. M., Usseglio-Polatera, P., Zamora-Muñoz, C., & Bonada, N. (2020). DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Scientific Data, 7(1), 386. https://doi.org/10.1038/s41597-020-00732-7
DOI: 10.5281/zenodo.11394181
title: The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages

description: This is the datasets and R script for our  manuscript titled "The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages."


Study area and sampling of Mecsek_species_Szivaketal.xlsx data


The study area is situated in the Mecsek Mountains in Hungary. Stream insects were collected using the kick and sweep sampling technique. A hand net with a frame width of 25 cm and a mesh size of 1000 µm was employed. The collection involved disturbing an area of 0.25 × 0.25 m. We employed a stratified random multihabitat sampling procedure. We collected 20 sample units from the major microhabitats in proportion to their occurrence within the reaches. Each sample unit was individually processed and sorted in the laboratory to ensure thorough and accurate analysis.


Disperse_trait_Szivaketal.xlsx data is based on DISPERSE database (Sarremejane et al., 2020)


Methods for microhabitat_coverage_reach_transect.xlsx: Prior to sampling, we divided each 100 m long reach into 20 transects of comparable length and created microhabitat coverage maps. Using these maps, we assessed the proportionate coverage of different microhabitat types within each reach


References:


Sarremejane, R., Cid, N., Stubbington, R., Datry, T., Alp, M., Cañedo-Argüelles, M., Cordero-Rivera, A., Csabai, Z., Gutiérrez-Cánovas, C., Heino, J., Forcellini, M., Millán, A., Paillex, A., Pařil, P., Polášek, M., Tierno de Figueroa, J. M., Usseglio-Polatera, P., Zamora-Muñoz, C., & Bonada, N. (2020). DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Scientific Data, 7(1), 386. https://doi.org/10.1038/s41597-020-00732-7
DOI: 10.5281/zenodo.8125636
title: The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages

description: This is the datasets and R script for our  manuscript titled "The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages."


Study area and sampling of Mecsek_species_Szivaketal.xlsx data


The study area is situated in the Mecsek Mountains in Hungary. Stream insects were collected using the kick and sweep sampling technique. A hand net with a frame width of 25 cm and a mesh size of 1000 µm was employed. The collection involved disturbing an area of 0.25 × 0.25 m. We employed a stratified random multihabitat sampling procedure. We collected 20 sample units from the major microhabitats in proportion to their occurrence within the reaches. Each sample unit was individually processed and sorted in the laboratory to ensure thorough and accurate analysis.


Disperse_trait_Szivaketal.xlsx data is based on DISPERSE database (Sarremejane et al., 2020)


Methods for microhabitat_coverage_reach_transect.xlsx: Prior to sampling, we divided each 100 m long reach into 20 transects of comparable length and created microhabitat coverage maps. Using these maps, we assessed the proportionate coverage of different microhabitat types within each reach


References:


Sarremejane, R., Cid, N., Stubbington, R., Datry, T., Alp, M., Cañedo-Argüelles, M., Cordero-Rivera, A., Csabai, Z., Gutiérrez-Cánovas, C., Heino, J., Forcellini, M., Millán, A., Paillex, A., Pařil, P., Polášek, M., Tierno de Figueroa, J. M., Usseglio-Polatera, P., Zamora-Muñoz, C., & Bonada, N. (2020). DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Scientific Data, 7(1), 386. https://doi.org/10.1038/s41597-020-00732-7
DOI: 10.5281/zenodo.8125637
title: The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages

description: This is the datasets and R script for our  manuscript titled "The spatial extent and the dispersal strategy of species shape the occupancy frequency distribution of stream insect assemblages."


Study area and sampling of Mecsek_species_Szivaketal.xlsx data


The study area is situated in the Mecsek Mountains in Hungary. Stream insects were collected using the kick and sweep sampling technique. A hand net with a frame width of 25 cm and a mesh size of 1000 µm was employed. The collection involved disturbing an area of 0.25 × 0.25 m. We employed a stratified random multihabitat sampling procedure. We collected 20 sample units from the major microhabitats in proportion to their occurrence within the reaches. Each sample unit was individually processed and sorted in the laboratory to ensure thorough and accurate analysis.


Disperse_trait_Szivaketal.xlsx data is based on DISPERSE database (Sarremejane et al., 2020)


Methods for microhabitat_coverage_reach_transect.xlsx: Prior to sampling, we divided each 100 m long reach into 20 transects of comparable length and created microhabitat coverage maps. Using these maps, we assessed the proportionate coverage of different microhabitat types within each reach


References:


Sarremejane, R., Cid, N., Stubbington, R., Datry, T., Alp, M., Cañedo-Argüelles, M., Cordero-Rivera, A., Csabai, Z., Gutiérrez-Cánovas, C., Heino, J., Forcellini, M., Millán, A., Paillex, A., Pařil, P., Polášek, M., Tierno de Figueroa, J. M., Usseglio-Polatera, P., Zamora-Muñoz, C., & Bonada, N. (2020). DISPERSE, a trait database to assess the dispersal potential of European aquatic macroinvertebrates. Scientific Data, 7(1), 386. https://doi.org/10.1038/s41597-020-00732-7
DOI: 10.5281/zenodo.8346668
title: Arceuthobium M.Bieb. (Viscaceae) parasitizing an angiosperm: the unique case of Arceuthobium azoricum Hawksw. & Wiens in the Azores islands

description: Dataset for manuscript "Arceuthobium M.Bieb. (Viscaceae) parasitizing an angiosperm: the unique case of Arceuthobium azoricum Hawksw. & Wiens in the Azores islands".
DOI: 10.5281/zenodo.10593978
title: Data for "Rotational phase transitions in antifluorite-type osmate and iridate compounds"

description: Publication available at https://doi.org/10.1088/1361-648X/ad2fef
DOI: 10.5281/zenodo.10593979
title: Rotational phase transitions in antifluorite-type osmate and iridate compounds

description: -In the folder "SC_XRD" are gathered the average integrated intensities (m90 file) and the cif file resulting from refinements with anharmonic ADPs for all compounds at all temperatures. The two refinements for K2OsBr6 in the low symmetry phases are performed with harmonic ADPs.

-In the folder "Fig2_maps" are the precession maps shown in Fig2: original binary .sfrm raw data file and .png images are included.

-In the folder "RSD_maps" are the residual scattering density maps in the original .eps format generated by JANA2020 (Fig.3 and Fig.4)

-Folder "Fig5_script" contains the matlab code to generate Fig.5

-In the folder "Appendix" A are gathered the ".dsn"  graphics source file shown in Appendix A. Raw data can be found after the header line: "1 3 xxx  102   0.15  0.02  900 1  0  0.001  900  0  0  0"
DOI: 10.5281/zenodo.11075285
title: Usability of Open Data Portals

description: This dataset reports on the usability of Open Data Portals as reported by the European public. Knowledge of open science and data concepts is also reported.
DOI: 10.5281/zenodo.11507289
title: DATASET Estimating the Use of ChatGPT in Dental Research Publications

description: These files contain the data and the research script for analyzing the use of ChatGPT in dental research writing from 2018 to 2024. The dataset includes various CSV files with publication details and analysis scripts to investigate trends and patterns in the usage of specific signaling words associated with ChatGPT.
DOI: 10.5281/zenodo.11073210
title: Public Understanding of Common Data Concepts

description: This dataset reports on a survey on awareness amongst the European public of common data concepts, terms and principles. 

Elements of this survey were utilised in the following publication - 

O’Grady, M., Mangina, E. Citizen scientists—practices, observations, and experience. Humanit Soc Sci Commun 11, 469 (2024). https://doi.org/10.1057/s41599-024-02966-x
DOI: 10.5281/zenodo.8344968
title: FoodGenVir database

description: The foodGenVir database contains those MAGs obtained from food and food-related environments samples that were collected in the MASTER project and that harbored antimicrobial resistance (AMR) genes. In total, 1828 samples from food and food-producing environments that were successfully sequenced in MASTER and included in the analyses, which lead to 14,815 high-quality MAGs. The high-quality MAGs were recovered from the metagenomic samples by following the assembly-based pipeline described in Pasolli et al. (2019). The taxonomic assignment of these MAGs was performed by using phylophlan_metagenomics against the MetaRefSGB. The resulting MAGs were screened for AMR genes using the TORMES pipeline (Quijada et al., 2019) against the ResFinder database (Zankari et al., 2012; downloaded at version from 24/10/2022). In total, 928 MAGs harbored AMR genes. The current release contains the assembled-genome FASTA files from the AMR-carrying MAGs and a MASTER_MAGs_FGV.tsv table, that contains the taxonomic information of each MAG as well as the different AMR genes found in its genome and the antimicrobial compounds that those genes confer resistance to according to the ResFinder database.
description: {"references": ["Pasolli, E. et al., (2019) Extensive unexplored human microbiome diversity reavealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell, 176, 649-662.e20.", "Quijada, N. M., et al. (2019) TORMES: an automated pipeline for whole bacterial genome analysis. Bioinformatics, 35(21), 4207-4212", "Zankari, E., et al. (2012) Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy, 67(11), 2640-2644."]}
DOI: 10.5281/zenodo.8344969
title: FoodGenVir database

description: The foodGenVir database contains those MAGs obtained from food and food-related environments samples that were collected in the MASTER project and that harbored antimicrobial resistance (AMR) genes. In total, 1828 samples from food and food-producing environments that were successfully sequenced in MASTER and included in the analyses, which lead to 14,815 high-quality MAGs. 


The high-quality MAGs were recovered from the metagenomic samples by following the assembly-based pipeline described in Pasolli et al. (2019). The taxonomic assignment of these MAGs was performed by using phylophlan_metagenomics against the MetaRefSGB. The resulting MAGs were screened for AMR genes using the TORMES pipeline (Quijada et al., 2019) against the ResFinder database (Zankari et al., 2012; downloaded at version from 24/10/2022).


In total, 928 MAGs harbored AMR genes.


The current release contains the assembled-genome FASTA files from the AMR-carrying MAGs and a MASTER_MAGs_FGV.tsv table, that contains the taxonomic information of each MAG as well as the different AMR genes found in its genome and the antimicrobial compounds that those genes confer resistance to according to the ResFinder database.
DOI: 10.5281/zenodo.10593994
title: Arceuthobium M.Bieb. (Viscaceae) parasitizing an angiosperm: the unique case of Arceuthobium azoricum Hawksw. & Wiens in the Azores islands

description: Dataset for manuscript "Arceuthobium M.Bieb. (Viscaceae) parasitizing an angiosperm: the unique case of Arceuthobium azoricum Hawksw. & Wiens in the Azores islands".