cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14726686
title: 3.1. Human adipose-derived Mesenchymal Stem/Stromal cells' stemness markers when cultured in bioinks 2 and 3 for 12 days

description: Human adipose-derived Mesenchymal Stem/Stromal cells' stemness markers when cultured in bioinks 2 and 3 for 12 days. MSC kit was used to analyze the stemness markers from MSCs isolated from the hydrogels made with bioinks 2 and 3 after 2 and 12 days to investigate if their culture in 3D inside the hydrogels altered their stemness marker expression.

Markers:



Positive:



CD90

CD105

CD73

CD44



Negative:



CD34, CD45, CD11b or CD14, CD19 or CD79α, and HLA-DR.




Sample codes:



FAG 242: bioink 2

FAG 251: bioink 3

HAG 242: bioink 2 with a hyaluronic acid/dermatan sulfate/collagen cocktail instead of fibrinogen.

HAG 251:  bioink 3 with a hyaluronic acid/dermatan sulfate/collagen cocktail instead of fibrinogen.


File codes:



Mix: positive markers.

viab: annexin and propidium iodide viability sample.

Neg: negative markers cocktail.

Iso: isotype control to test inespecific signals.

Monomarcage (french): samples marked with a single fluorochrome to do internal compensations.

NM: non-marquées = non-tagged or non-stained cells; used to do FSC/SSC cytometry calibrations.
DOI: 10.5281/zenodo.14850946
title: 14.1. Ink-jet bioprinting nozzle aperture time impact on cell viability of human adipose-derived mesenchymal stem cells.

description: AD-MSCs were bioprinted with the ink-jet device at different nozzle aperture times (milliseconds) to investigate the impact of the aperture time variable on cell mortality. Three different experiments were made: MK1, MK2 and MK3. Files provided:



Excel file: compilation of all the results; sample codes describing the sample registered in the flow citometry files. Analysis and plotting of the results.

ZIP folders: raw data from the three experiments (MK1, MK2 and MK3).


Controls were taken:



Cells after trypsination, before inclusion in the bioink.

Cells in the bioink prior to bioprinting.

Cells that were subjected to the pressure in the cartridge during the whole process of bioprinting, but were not bioprinted, then being a control of the cells being in the bioink for the whole duration of the jetting process.
DOI: 10.5281/zenodo.14531731
title: Reversible Intercalation in Non-covalent Semiconducting Two-dimensional Crystals via Molecular Tetris

description: This repository contains the source data for the manuscript "Reversible Intercalation in Non-covalent Semiconducting Two-dimensional Crystals via Molecular Tetris"
DOI: 10.5281/zenodo.15703419
title: Plant diversity and functional traits in semi-natural grassland habitats

description: This dataset includes functional trait data, CSR functional strategies, indices for species and functional diversity, and NDVI data for three Irish semi-natural grassland habitats: GS1 - dry calcareous and neutral grassland; GS2 - dry-humid acid grassland; GS4 - wet grassland.
DOI: 10.5281/zenodo.17089353
title: Supplementary data for: Potential trade-off between temperature and tissue loss resistance in corals associating with algal symbionts in the genus Durusdinium

description: Supplementary data for: Potential trade-off between temperature and tissue loss resistance in corals associating with algal symbionts in the genus Durusdinium. All raw data and R codes for statistical analysis are available here and the details of each file are provided on Readme, or Table S8 of the publication.
DOI: 10.5281/zenodo.15776691
title: Impact of Thoracic Aortic disease endovascular treatment on Cardiac function (ITACA study)
DOI: 10.5281/zenodo.16261076
title: Bidirectional editing unveils gene interactions in human brain evolution

description: Comparative genomic studies between contemporary humans and extinct hominins have revealed key evolutionary modifications, but their roles in scaffolding our species’ distinctive traits remain poorly understood. The sheer number of sapiens-specific genetic variants uncovered so far makes it challenging to investigate the mechanisms underlying these recent evolutionary changes at scale. To address this, we developed a scalable gene-editing framework implemented in cortical brain organoids. We prioritized 15 candidate genes among the few carrying nearly fixed protein-coding mutations that distinguish us from other hominins, and developed a CRISPR-Cas9 dual-screen strategy to systematically interrogate the genes’ roles and, above all, their interactions. Combining overexpression and downregulation effects within the same cell, for all possible gene pairs, we mapped the genes’ impacts on single-cell transcriptomic profiles and differentiation potential in cortical brain organoids. We reconstructed the regulatory architecture among genes predicted to have a significant impact on corticogenesis. Pooling all perturbation pairs, we observe marked cell type-specific effects, alternative cell fates favoring neurons or glia, as well as the timing of emergence of interneuron populations. A core subnetwork made up of KIF15, NOVA1, RB1CC1 and SPAG5 was found to be a central regulator across cortex cell types.
DOI: 10.5281/zenodo.14145821
title: TIMCI Hospital Cost Data Senegal

description: Referral Institution cost data for 3 Centres de Sante in the Thies region of Senegal
DOI: 10.5281/zenodo.10978774
title: The boreal soil microbiome of different urban green spaces

description: This study describes the soil microbiome in relation to the aboveground plant diversity of three types of urban green spaces: built green spaces with sown lawns, planted trees and ornamental flowerbeds, open green spaces such as meadows and pastures, and urban forests. 

Data includes information on study sites, soil physio-chemical properties, vegetation, and soil microbiome: Plot information, Soil properties, Vegetation, Meta includes column information in sheets plot and soil. In vegetation sheet column names are species. Explanations for species name abbreviations can be found in sheet meta2. Micoboal commnity composition and taxonomy in Bacteria_nmds and Fungi_nmds.
DOI: 10.5281/zenodo.14177682
title: Field data of soil greenhouse gas fluxes from SOMMIT long-term experiments

description: This is a database of field data of soil greenhouse gas fluxes and ancillary data from long-term experiments (LTEs) that participated in the task 1 of the work package 3 from SOMMIT. As of November 2024 (V 1.0) six LTEs have contributed with data: "ACBB Estrées-Mons, France", "Rutzendorf_17, Austria", "Maintainance of organic orchards, Italy", "Fagna, Italy", "ULBF-Ljubljana, Slovenia" and "Grabow 2, Poland". All LTEs are referenced according to the LTE Index from https://doi.org/10.5281/zenodo.7598122. The data includes soil greenhouse gas fluxes (N2O, CO2 and CH4) under different management practices, as well as ancillary data that might be useful to explain the observed fluxes. The database includes metadata on how soil greenhouse flux data and ancillary data were collected. Individual soil gas flux estimates are also expressed in CO2 equivalents [mg CO2-eq m-2 h-1], thereby providing a dataset on the contribution of soil CO2, N2O and CH4 fluxes to the soil global warming potential. This product is part of the EJP SOIL internal project SOMMIT, and serves as deliverables WP3.2 and WP3.3.
DOI: 10.5281/zenodo.11542875
title: The boreal soil microbiome of different urban green spaces

description: This study describes the soil microbiome in relation to the aboveground plant diversity of three types of urban green spaces: built green spaces with sown lawns, planted trees and ornamental flowerbeds, open green spaces such as meadows and pastures, and urban forests. 

Data includes information on study sites, soil physio-chemical properties, vegetation, and soil microbiome: Plot information, Soil properties, Vegetation, Meta includes column information in sheets plot and soil. In vegetation sheet column names are species. Explanations for species name abbreviations can be found in sheet meta2. Micoboal commnity composition and taxonomy in Bacteria_nmds and Fungi_nmds.
DOI: 10.5281/zenodo.14042458
title: TIMCI Hospital Cost Codes Tanzania

description: Codes for Hospital Cost Data for Tanzania, in English and Swahili
DOI: 10.5281/zenodo.17159840
title: Data and R scripts related to the article "Patterns and drivers of fish-mediated nutrient cycling on the world's tropical reefs"

description: See details of files in the "description.pdf"
DOI: 10.5281/zenodo.14079502
title: Landscape structure of bacterial and fungal community composition in Culex tarsalis mosquitoes, the West Nile Virus vectors, in the United States

description: Raw sequence data for fungi (ITS1 region)
DOI: 10.5281/zenodo.14080098
title: Landscape structure of bacterial and fungal community composition in the West Nile Virus vector, Culex tarsalis

description: Raw sequence data for fungi (ITS1 region)
DOI: 10.5281/zenodo.15824641
title: Amazonian Podzols - a carbon time bomb? - dataset

description: Cumulative respiration data from Amazonian Podzol samples which were subjected to different treatments.
DOI: 10.5281/zenodo.16163866
title: Data and code for paper "Freihardt (under submission) Micro-Mobilities"

description: This is the replication code and dataset underlying the paper: 

Freihardt, Jan (under submission): Micro-Mobilities.
DOI: 10.5281/zenodo.14168335
title: Dataset of the microbial communities in chronosequences samples from the MINOTAUR Project

description: The MINOTAUR chronosequences microbiological dataset includes five sheets detailing soil biodiversity dynamics across Europe. It features metadata, DNA extraction metrics, bacterial ASV abundances from 16S NGS sequencing, and taxonomic affiliations, alongside contact and funding details.
DOI: 10.5281/zenodo.14958868
title: TIMCI India RCT dataset

description: This dataset contains data from the TIMCI (Tools for Integrated Management of Childhood Illness) cluster Randomized Controlled Trial (RCT) in India (NCT04910750), which was conducted by King George's Medical University (KGMU) in collaboration with the Swiss Tropical & Public Health Institute (Swiss TPH). Data were collected using ODK between June 20, 2022 to April 21, 2023 (10 months) in 106 facilities.

To request access to this dataset:



Contact the TIMCI consortium directly

Clearly state your intended purpose for data analysis


When using the data, please ensure proper attribution.
DOI: 10.5281/zenodo.15765791
title: Data from "Deep-sea mining risks for sharks, rays, and chimaeras"

description: Datasets, extended data, and code for the manuscript "Deep-Sea Mining Risks for Sharks, Rays, and Chimaeras" by Judah AB, Mull CG, Dulvy NK, Finucci B, Assad VE, and Drazen JC.
DOI: 10.5281/zenodo.17207510
title: Sediment grain size dataset of intertidal shellfish sandbanks within Ría de Arousa, Spain

description: The GEOMA Research group from the University of Vigo implements a solution to improve the knowledge of the sediment dynamics, the stability of the ecosystem substratum, and its response to the predicted Climate Change outcome (INTERM). The INTERM solution is based on sedimentological monitoring of sandbanks at specific locations of clam exploitation in the Ría de Arousa (Pontevedra, Spain).

Since 2022, we collected sediments in seven locations with current (Camaxe, Xastelas, O Sarrido, Fefiñans, O Bohido, and Lavanqueira) or stopped (Lombos de Ulla) shellfish activity. The sediment grain size distribution was determined by dry and wet sieving using meshes of 2, 1, 0.5, 0.25, 0.125, and 0.063 mm. We separate the sediment grain size fraction larger and smaller than 0.063mm by wet sieving. The grain size distribution of the grains larger than 0.063 was determined by dry sieving whereas for the grains smaller than 0.063 by the pipette method (see Folk, R. L. (1980). Petrology of sedimentary rocks. Hemphill publishing company).

This study is part of the “Accelerating and upscaling transformational adaptation in Europe: demonstration of water-related innovation packages (TRANSFORMAR)" coordinated by the Universiteit Antwerpen and funded by the European Union’s Horizon program (H2020_101036683).

This version:



  Includes new grain size measurements performed on samples collected in February 2025

  Corrects bugs detected in the weight of the fine fraction. Additionally, 12 sample distributions (Table 1) have been replaced with new measurements due to processing errors

  Corrects minor errors


Table 1. Sample distributions replaced with new measurements






Bank



Sample



Date (yy/mm/dd)





Camaxe



CX7



2022/10/25





Camaxe



CXPlaya



2022/10/25





Camaxe



CX8



2022/10/25





Xastelas



XLT2



2022/10/25





Xastelas



XLT3



2022/10/25





Xastelas



X10



2022/10/25





Lavanqueira



L3



2022/10/25





Lavanqueira



L4



2022/10/25





Sarrido



SAR4



2023/09/30





Lombos 



M5



2024/02/26





Lombos



M6



2024/02/26





Xastelas



X10



2024/02/12
DOI: 10.5281/zenodo.16754429
title: GENPOL project. Survey about equality policies at local level in Spain

description: One of the main objectives of GENPOL III (PID2020-115568RB-I00) is to map the equality policies implemented by Spanish municipalities with more than 2,000 inhabitants. To achieve this, an online survey was conducted, inviting 2,251 Spanish municipalities to participate across three different waves. A total of 1,443 responses were obtained in several waves from 740 municipalities between 2023 and 2025.
description: The file includes the codebook with variables and values
DOI: 10.5281/zenodo.17535314
title: Dynamics and environmental drivers of methane and nitrous oxide fluxes at the soil and ecosystem levels in a wet tropical forest

description: Databases of environmental and greenhouse gas fluxes (methane (CH₄) and nitrous oxide (N₂O)) at the soil and ecosystem levels, recorded at the Guyaflux tropical forest site in French Guiana between 17 May 2016 and 2 August 2018. These data are presented in the scientific article entitled "Dynamics and environmental drivers of methane and nitrous oxide fluxes at the soil and ecosystem levels in a wet tropical forest" (EGUsphere [preprint]; https://doi.org/10.5194/egusphere-2025-3501; 2025). The data are daily averages for both the raw data and the 1st - 99th percentile range.
DOI: 10.5281/zenodo.14525072
title: D1.2.1_AGROECOseqC overall dataset_10.5281zenodo.14525072_Embargued_251031
DOI: 10.5281/zenodo.17011609
title: Experiemental data for: Predictions of wheat phenotypic variability by integrating high-throughput phenotyping observations into a crop growth model

description: This dataset is based on the ICASA data standard (http://dx.doi.org/10.1016/j.compag.2013.04.003). The Excel file is compatible with the AgMIP data translator to create crop model input files that can be dowloaded at https://github.com/agmip/translator-excel-python. Data are also provided as csv file.
DOI: 10.5281/zenodo.14006183
title: SERENA EJP SOIL: Erosion control map of Hungary

description: The internal EJP SOIL project SERENA contributed to the evaluation of soil multifunctionality aiming at providing assessment tools for land planning and soil policies at different scales. By co-working with relevant stakeholders, the project provided co-developed indicators and associated cookbooks to assess and map them, to report both on soil degradation, soil-based ecosystem services and their bundles, under actual conditions and for climate and land-use changes, at the regional, national, and European scales.

Present data was prepared according to the methodology of SERENA Soil erosion and soil erosion control cookbook for the territory of Hungary. The map of soil loss by water erosion (soil threat) was based on the RUSLE model. To create the soil loss map we used data on yearly precipitation of CARPATCLIM database, and AGRI4CAST MARS (R-factor); sand-, silt-, and clay content of DOSoReMI.hu database, and SOC map compiled in the framework of SERENA (K-factor); ESDAC LS-factor for the EU; ESDAC Cover Management factor for the EU (C-factor); ESDAC Support Practices factor for the EU (P-factor). For the soil erosion control, the difference between the erosion map without vegetation (C-factor = 1) and the erosion map with vegetation was calculated. The erosion maps with-, and without vegetation were categorized according to the cookbook, and the result map shows how many categories the pixel has changed when vegetation is taken into account (0: the pixel is in the same category in both maps, 1: minor role of vegetation, 2: moderate role of vegetation, 3: significant role of vegetation). 
description: The data are derived from the calculation of indicators based on a standard methodology established as part of the EJP Soil SERENA programme. Please keep in mind that:



It is the result of a modelling exercise and does not necessarily reflect reality.

Despite the efforts made to provide reliable data, the results may contain inconsistencies, depending in particular on the raw data available and level of accuracy of the techniques chosen and their prior knowledge.

It is necessary to consider how the results have been obtained in order to decide on their relevance in relation to the intended purpose of reuse.

These results are interesting from a scientific point of view, but their use for environmental management and policy issues should be done keeping the previous aspects in mind and complementing when necessary the provided results with the best available data.


Finally, it is the responsibility of the users of this information to decide whether it is appropriate to use these data and whether the data meet their needs. The authors of this resource can in no way be held responsible for the results obtained from the use of this data.
DOI: 10.5281/zenodo.16423399
title: Electron-phonon-dominated charge-density-wave fluctuations in TiSe2 accessed by ultrafast nonequilibrium dynamics

description: The files include figures, data, and source code related to the article titled "Electron-phonon-dominated charge-density-wave fluctuations in TiSe₂ accessed by ultrafast nonequilibrium dynamics."

These materials support the analyses and visualizations presented in the publication. The dataset may include time-resolved spectroscopy results, code used for simulations or data fitting, and figure source files used for generating plots in the manuscript.
DOI: 10.5281/zenodo.14178193
title: EJP SensRes bi-directional reflectance of soils

description: Repository of the database of bi-directional soil spectral reflectance measurements and the corresponding physico-chemical variables for soil carbon estimation. 




Soil samples from the chemistry laboratory were prepared for the spectral measurements that were carried out using a full-range PSR-3500 spectrometer in the range 350-2500 nm. The spectral sensor was mounted on a robotic arm to perform a regular sampling strategy involving multiple viewing angles and different soil water contents.  




Three main datasets were compiled, and they are summarized in Table 1 in the related .doc document.
DOI: 10.5281/zenodo.15576646
title: Raw Near-Infrared (NIR) spectral data obtained from the analysis of pure olive oil samples and samples of olive oil adulterated with sunflower, sesame, flaxseed, and other seed oils

description: Database containing NIR spectra of different samples (pure and adulterated) of olive oils. Legend: Extra virgin olive oil (EVOO), virgin olive oil (VOO) and olive oil (OO) pure samples that were adulterated with flax (FO), sunflower (SO), seeds (SEO) and sesame (SESO) oils.
DOI: 10.5281/zenodo.14081214
title: Landscape population genetics structure in the West Nile virus vector, Culex tarsalis

description: RADseq raw data
DOI: 10.5281/zenodo.14856482
title: dB@risoux dataset: A full year of 1-min soundscapes recorded in a cold temperate forest in France

description: This dataset contains 35 023 1-min audio recordings (i.e. soundscapes) collected in a temperate cold climax forest locally named ‘Risoux’ during the year 2019 (1 min every 15 min, day and night). The forest is located in the East of France in the Jura Mountains at the Swiss border (46°31'60.0"N 6°05'03.8"E ). The forest soundscape was recorded using one automatic SongMeter 4 recorders (Wildlife Acoustics Inc, Concord, MA, USA). The recorder was installed in the Risoux Forest central zone.

The composition of the soundscapes is a mix of biophony (mostly birds, but also insects and bellowing deer), geophony (e.g. rain and wind) and technophony (e.g. planes, chainsaws and possibly some gun shots and sheep bells)

This dataset is part of a long term monitoring of the Risoux forest started in July 2018. Four SongMeter 4 recorders were installed across the Risoux Forest central zone, along a West–East axis. The distance between the recorders was 1.00 ± 0.10 km. The position of the recorders was chosen to (1) cover the forest area, (2) sample a single habitat defined by the dominance of the European spruce, (3) avoid pseudo-replication between neighboring recorders, and (4) avoid technophony noise due to car traffic and local activities. This dataset was recorded by the recorder number 3.

This work was supported by the Parc Naturel Régional du Haut-Jura who received funding from the Région Bourgogne-Franche-Comté
DOI: 10.5281/zenodo.14144632
title: TIMCI Hospital Cost Data Codes

description: Codes associated with Hospital Cost Data for each of Kenya, Senegal and Tanzania
DOI: 10.5281/zenodo.15282425
title: E. Faecalis monocolonization study; Raw numerical data, statistical data, supplementary material and ARRIVE checklist

description: This file set includes the raw numerical data (excel file), statistical analyses (Graphpad Prism file), the supplementary material (pdf) and the ARRIVE checklist (pdf) in relation to the data and figures presented in the paper "Modulation of dextran sodium sulfate-induced colitis in germ-free mice by Enterococcus faecalis-monocolonization".
DOI: 10.5281/zenodo.14051595
title: TIMCI Hospital Cost Data Codes

description: Codes associated with Hospital Cost Data for each of Kenya, Senegal and Tanzania
DOI: 10.5281/zenodo.14529311
title: ClimEmpower Collection of Existing Climate Resilience Indicators

description: Within the ClimEmpower project, publications and lists of indicators to assess climate resilience have been collected and analysed. An overview of the used literature and a list of the collected indicators are provided in the form of an Excel table.
DOI: 10.5281/zenodo.16763318
title: Allochthonous Chemical Cues & Predation