cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16743948
title: Hydrohemistry in the Romanian inner shelf waters - July-August 2022 (PN 19 20 01 02 - National Project)

description: Dataset contains hydrochemistry data from the Romanian inner shelf waters (bottom depths between 15 and 67 m), in July 2022. Data were collected on board R/V Mare Nigrum, during a cruise conducted within the national project "Multidisciplinary research to improve knowledge of the climate change and human pressure interaction and its effects on the Black Sea ecosystem" – PN 19 20 01 02. Twenty-one stations distributed along 4 main transects (Sf. Gheorghe-SE, Portita-SE, Constanta-SE, and Mangalia-E) were performed for water column investigations by the GeoEcoMar team. In situ measurements of physical-chemical seawater parameters were done at each sampling station using a YSI EXO2 multiparameter sonde. Seawater samples were collected with 5L Niskin bottles from different depths and further analyzed in the GeoEcoMar lab for nutrients and chlorophylls (both by spectrometry).
DOI: 10.5281/zenodo.16744397
title: Geochemistry in the Romanian inner shelf waters - July-August 2022 (PN 19 20 01 02 - National Project)

description: Dataset contains geochemistry data from the Romanian inner shelf waters (bottom depths between 15 m and 67 m), in July-August 2022. Data were collected on board R/V Mare Nigrum, during a cruise conducted within the national project "Multidisciplinary research to improve knowledge of the climate change and human pressure interaction and its effects on the Black Sea ecosystem" – PN 19 20 01 02. Twenty-one stations distributed along 4 main transects (Sf. Gheorghe-SE, Portita-SE, Constanta-SE, and Mangalia-E) were performed for sediment investigations by the GeoEcoMar team.  Sediment samples were collected using Van Veen grab sampler and Multicorer MARK II-400 and analyzed for major and minor components as well as trace elements (by X ray fluorescence) in the GeoEcoMar lab.
DOI: 10.5281/zenodo.16752245
title: Granulometry in the Romanian shelf waters - August 2021 (PN 19 20 01 02 - National Project)

description: Dataset contains granulometry data collected in the Romanian shelf during a cruise conducted in August 2021, on board R/V Mare Nigrum, within the national project "Multidisciplinary research to improve knowledge of the climate change and human pressure interaction and its effects on the Black Sea ecosystem" – PN 19 20 01 02. Thirty stations were performed for grain size investigations by the GeoEcoMar team. Sediment samples were collected using Van Veen grab sampler and Multicorer MARK II-400 and analyzed for grain size composition and textural parameters with Mastersizer 2000E Ver. 5.20 (MALVERN) equipment in the GeoEcoMar lab.
DOI: 10.5281/zenodo.13324732
title: ForestPaths: European canopy height map

description: This repository contains a 10 m resolution canopy height map of the year 2020 over Europe derived from Sentinel-1 and Sentinel-2 data. The canopy height model was trained using both GEDI and ICESat-2 data.

The map is available as COGs over a 100 km grid in the spatial reference system EPSG 3035 (ETRS89 / LAEA Europe).
DOI: 10.5281/zenodo.14968641
title: Genomic insights into the virulence repertoire and hemibiotrophic lifestyle of the grape black rot pathogen Phyllosticta ampelicida ampelicida

description: Phyllosticta ampelicida is the causal agent of black rot in grapevines, a disease that is widespread worldwide. This fungus infects leaves, stems, and fruits, causing circular lesions that are brown or tan with reddish margins and typically contain small black pycnidia. In this study, we assembled the genomes of 3 isolates of the species and compared their virulence factor repertoire with other phylogenetically related organisms and other grapevine pathogens.
DOI: 10.5281/zenodo.15380037
title: MD Simulation of Antimicrobial Peptide Molecule Ku04AMP01 and various ligands

description: An experimental Antimicrobial Peptide, KU04AMP01, may eliminate Gram negative pathogens by damaging cellular barrier and genomic DNA.

This repository contains codes and data of Molecular Dynamics of Ku04AMP01 molecule in water, as well as in complex with ligands Phosphatedylglycerol (PGL) and Phosphatedylethanolamine (PEA), individually.

 

Initial docking was performed by AMDock, followed by Molecular Dynamics Simulations using GROMACS.
DOI: 10.5281/zenodo.10776381
title: Consumers-Generated Textual Data on Emotional Intelligence and Perceived Value from Online Second-Hand Retail Platforms
DOI: 10.5281/zenodo.16530750
title: TIMCI Senegal pre-post dataset

description: This dataset contains data from the TIMCI (Tools for Integrated Management of Childhood Illness) quasi-experimental pre-post study in Senegal (NCT05065320), which was conducted by the Cheikh Anta Diop University of Dakar (UCAD) in collaboration with the Swiss Tropical & Public Health Institute (Swiss TPH). Data were collected with ODK between August 16, 2021 and March 31, 2023 (19,5 months) in 20 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.16934349
title: The authigenic and detrital neodymium isotopic composition in the modern Mediterranean Sea: implication for paleocirculation proxy

description: The authigenic and detrital neodymium isotopic composition in the modern Mediterranean Sea: implication for paleocirculation proxy — numerical data

 

This data file contains the numerical data of the study ‘The authigenic and detrital neodymium isotopic composition in the modern Mediterranean Sea: implications for paleocirculation proxy’. It contains five sheets:

1.         New data on authigenic (foraminiferal tests or leachates) and residual Nd isotopic composition in the Mediterranean Sea

2.         Compilation of authigenic, detrital and seawater eNd values in the Mediterranean Sea.

3.         Elemental composition of leachates from the new samples

4.         Compilation of the Nd isotopic composition of Mediterranean seawater and the detrital Nd isotopic composition at the closest sites to the seawater stations in order to evaluate the influence of the local Nd source on the seawater Nd isotopic composition

5.         Parameters used for a 6-box model to assess the Nd cycle in the Mediterranean Sea
DOI: 10.5281/zenodo.17037338
title: CTD data from Southern Black Sea, June 2023

description: The dataset contains hydrophysical data collected in Southern Black Sea withing the Turkish EEZ in June 2023 in framework of the R/V Bilim-2 cruise supported by EU-funded BRIDGE-BS project. Automated in-situ measurements of physical, chemical and optical parameters were performed with SBE 9-11 plus CTD profiler equipped with the following sensors: SBE-43 dissolved oxygen sensor, SBE 27 pH and O.R.P. sensor, WetLabs ECO FLNTU chlorophyll fluorescence and turbidity sensor, and LI-COR Biospherical PAR sensor. The raw data from total 152 casts were processed with SBE Seasoft V2 package, imported to ODV collection and, upon performing quality control, exported to output file. The output file contains following parameters: Pressure, Temperature, Salinity, Oxygen (SBE 43), PAR, Fluorescence, Turbidity, pH, ORP.
DOI: 10.5281/zenodo.17074005
title: Establishing a Novel Echocardiographic Protocol in Sheep: Achieving Apical Views for Advanced Cardiac Assessment and Validation in a Heart Failure Model
DOI: 10.5281/zenodo.10705560
title: Data on LT and UK Consumers' Emotional Intelligence and Perceived Value and Future Intentions Related to Renting Clothing / Buying Second-Hand Clothing Online

description: This project has received funding from the Research Council of Lithuania (LMTLT), agreement No [S-MIP-22-27].
DOI: 10.5281/zenodo.10932193
title: Breakthrough curves under variable saturation conditions to explore the effects of particle size and charge density on the transport of nanoplastic particles through sand
DOI: 10.5281/zenodo.15962824
title: Aligned DNA sequence matrix for phylogenetic analyses in the article "A new Epicrionops (Amphibia: Gymnophiona: Rhinatrematidae) species from Ecuador with preliminary taxonomic revision of the genera Epicrionops (Boulenger) and Amazops (Wilkinson)"

description: Aligned DNA sequence matrix for phylogenetic analyses of the article "A new species of Epicrionops (Amphibia: Gymnophiona: Rhinatrematidae) from Ecuador with preliminary taxonomic revision of the genera Epicrionops (Boulenger) and Amazops (Wilkinson)"

The matrix is in NEXUS format. Genes are arranged as follows:



tRNA =  1- 259 1223- 1321 ;

charset ND1codonPos1 =  260-1220\3;

charset ND1codonPos2 =  261-1221\3;

charset ND1codonPos3 =  262-1222\3;

charset 16S = 1322-3068;

charset 12S = 3069-3604;

charset CO1codonPos1 =  3606-4995\3;

charset CO1codonPos2 =  3607-4993\3;

charset CO1codonPos3 =  3605-4994\3;
DOI: 10.5281/zenodo.16752352
title: Granulometry in the Romanian shelf waters - July-August 2022 (PN 19 20 01 02 - National Project)

description: Dataset contains granulometry data collected in the Romanian shelf during a cruise conducted in July-August 2022, onboard R/V Mare Nigrum, within the national project "Multidisciplinary research to improve knowledge of the climate change and human pressure interaction and its effects on the Black Sea ecosystem" – PN 19 20 01 02. Thirty-one stations were performed for grain size investigations by the GeoEcoMar team. Sediment samples were collected using Van Veen grab sampler and Multicorer MARK II-400 and analyzed for grain size composition and textural parameters with Mastersizer 2000E Ver. 5.20 (MALVERN) equipment in the GeoEcoMar lab.
DOI: 10.5281/zenodo.13169401
title: Subglacial particle tracking dataset from the Otemma Glacier, southwestern Switzerland

description: Subglacial radio-tagged particle tracking dataset from the snout marginal zone of the Otemma Glacier, southwestern Switzerland. 325 RFID-tagged particles injected into a snout-marginal subglacial channel were tracked from the glacier surface using roving and stationary RFID antennas as they were transported downstream in the mid to late 2021 melt season. Field data collection was performed following the particle tracking methodology detailed in Jenkin et al. (2023). Downstream transport distance modelling was performed as detailed in the Supporting Information to the article "Low bedload mobility in an Alpine subglacial channel".  

The data provided herein comprise:

tags.csv - tagged particle metadata with columns:ID: particle ID codeseed_time: time of particle seeding in subglacial channel [fractional day of year]weight: particle weight [g]density: particle density [g/cm3]a: particle longest axis [mm]b: particle intermediate axis [mm]c: particle shortest axis [mm]

roving_antenna.csv - distribution of recieved radio signals from tagged particles with columns:time: fractional day of yearID: tagged particle ID codeRSSI: received signal strength indication X: easting of antenna point location when signal received [EPSG:2056]Y: northing of antenna point location when signal received [EPSG:2056]Z: altitude of antenna point location when signal received [m a.s.l.]

stationary_antennas.csv - duration tagged particles in-range of stationary antennas with columns:time: time of particle detection [fractional day of year]antenna: antenna ID codeID: tagged particle ID codeduration: time particle in range of antenna [fraction of day]X: easting of stationary antenna location [EPSG:2056]Y: northing of stationary antenna location [EPSG:2056]

point_localisations.csv - daily particle point localisations and along-channel transport distances based on roving antenna data with columns:ID: tagged particle ID codeday: day of yearX: easting of tagged particle point location [EPSG:2056]Y: northing of tagged particle point location [EPSG:2056]CI: 95% spatial confidence interval from 2D probability density estimate [WKT geometry] ** provided where number of RFID points used for localisation is >3

models.csv - downstream particle transport distance based on unification of roving and stationary antenna data with columns:time: fractional day of yearID: tagged particle ID codedistance: downstream particle transport distance [m]

model_params.csv - model metadata with columns:ID: tagged particle ID codeantenna_range: maximum detection radius around antenna point location [m]time_threshold: minimum time tagged particle must be detected for consideration [s]RMSE: root mean squared error of distance model for tagged particle [m]
DOI: 10.5281/zenodo.13341584
title: ForestPaths: European canopy cover map

description: This repository contains a 10 m resolution canopy cover (at 5m height) map of the year 2020 over Europe derived from Sentinel-1 and Sentinel-2 data. The map is available as COGs over a 100 km grid in the spatial reference system EPSG 3035 (ETRS89 / LAEA Europe).  

Known issues

-        Due to the lack of GEDI data over the north of Europe, the accuracy of the model is expected to be lower above 52 degrees latitude.
DOI: 10.5281/zenodo.15486332
title: Datasets for Manuscript "Corticonigral projections recruit substantia nigra pars lateralis dopaminergic neurons for auditory threat memories"
DOI: 10.5281/zenodo.15511964
title: MD Simulation of DNA gyrase subunit A (gyrA) protein of P. aeruginosa, with mutations recorded in 1996 and 2018, each in complex with Nalidixic Acid (NDX) ligand molecule

description: Mutated sequences of DNA gyrase (subunit A) protein (recorded in in 1996 and 2018) associated with P. aeruginosa are modeled and individually docked with a molecule of Nalidixic Acid. The data from subsequent Molecular Dynamics simulation is presented.

 

The data from the Molecular Modelling and Docking Simulations can be found here:

Roy, A. (2025). Docking of several proteins associated with strains of Pseudomonas aeruginosa with various antibiotic molecules [Data set]. Zenodo. https://doi.org/10.5281/zenodo.15383904
DOI: 10.5281/zenodo.17568967
title: Warming fluctuations strengthen the photo-phagotrophic coupling in mixoplanktonic protists
DOI: 10.5281/zenodo.16530971
title: TIMCI Kenya pre-post dataset

description: This dataset contains data from the TIMCI (Tools for Integrated Management of Childhood Illness) quasi-experimental pre-post study in Kenya (NCT05065320), which was conducted by the University of Nairobi (UoN) in collaboration with the Swiss Tropical & Public Health Institute (Swiss TPH). Data were collected with ODK between September 13, 2021 and February 8, 2023 in 19 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.6573159
title: A population in perpetual motion: highly dynamic roosting behaviour of a tropical island endemic bat

description: Dataset and R script for the manuscript "A population in perpetual motion: highly dynamic roosting behaviour of a tropical island endemic bat". During the embargo period, data is available upon request from the authors (muriel.dietrich@ird.fr).
DOI: 10.5281/zenodo.17342623
title: Global surge-type glacier and surge hazards inventory_Lovell et al._2025v2

description: This is a global inventory of surge-type glaciers and surge-related hazards in .xlsx and .shp format. This has been updated since Version v1 following peer review. A further update will be added once the publication this data accompanies has been published.
DOI: 10.5281/zenodo.18013223
title: ForestPaths: European canopy cover map

description: This repository contains a 10 m resolution canopy cover (at 5m height) map of the year 2020 over Europe derived from Sentinel-1 and Sentinel-2 data. The map is available as COGs over a 100 km grid in the spatial reference system EPSG 3035 (ETRS89 / LAEA Europe).  

Known issues

-        Due to the lack of GEDI data over the north of Europe, the accuracy of the model is expected to be lower above 52 degrees latitude.
DOI: 10.5281/zenodo.18066139
title: ForestPaths: European FHD map

description: This repository contains a 10 m resolution FHD map of the year 2020 over Europe derived from Sentinel-1 and Sentinel-2 data. The map is available as COGs over a 100 km grid in the spatial reference system EPSG 3035 (ETRS89 / LAEA Europe). 

Known issues

-        Due to the lack of GEDI data in the north of Europe, the accuracy of the model is expected to be lower above 52 degrees latitude.
DOI: 10.5281/zenodo.15166797
title: Test
DOI: 10.5281/zenodo.17277038
title: OriginLab files for figures with complete dataset
DOI: 10.60888/epos-gnss-vblo00esp
title: GNSS data of VBLO00ESP, Villablino, Spain

description: Permanent GNSS station dataset as RINEX files
DOI: 10.5281/zenodo.17488750
title: Harappan final 1

description: Mihael Koprivnikar
DOI: 10.5281/zenodo.15380258
title: Molecular Dynamics Simulations of Antimicrobial Peptide KU04AMP01 in complex with some conserved DNA-segments of Multi-Drug Resistant Pathogens

description: An experimental Antimicrobial Peptide, KU04AMP01, may eliminate Gram negative pathogens by damaging cellular barrier and genomic DNA.

This repository contains codes and data of Molecular Dynamics of KU04AMP01 in complex with various segments of DNA taken that are common to the genomes of two pathogens, Acinetobacter baumannii and Pseudomonas aeruginosa. 

The conserved sequences were revealed computationally by analyzing the fastas of both bacterial genomes. This was followed by batch-docking of the DNA segments built from those sequences with a KU04AMP01 molecule using HDOCK, and subsequent molecular dynamics of the best-docked and worst-docked poses using GROMACS.
DOI: 10.5281/zenodo.15263728
title: Tricky logic riddles for LLM reasoning evaluation

description: This dataset consists of a small collection of logic-based riddles, including tricky questions and some math problems that require lateral thinking, and interpretation of nuanced language.

The purpose of this dataset is to evaluate the reasoning capabilities of large language models (LLMs) when faced with cognitively challenging prompts that simulate real-world ambiguity and trick-based logic. Each riddle has a clearly defined answer, allowing the dataset to be used for qualitative or automated benchmarking of model responses. This problems are commonly known online but do not have a clear source.

Additionally, the dataset includes of a short historical passage ( spurce: Wikipedia) followed by a series of factual comprehension questions. The purpose of this resource is to assess the ability of language models to extract and recall explicit information from structured textual input.
DOI: 10.5281/zenodo.17037092
title: CTD data from Southern Black Sea, December 2022

description: The dataset contains hydrophysical data collected in Southern Black Sea withing the Turkish EEZ in December 2022 in framework of the R/V Bilim-2 cruise supported by EU-funded BRIDGE-BS project. Automated in-situ measurements of physical, chemical and optical parameters were performed with SBE 9-11 plus CTD profiler equipped with the following sensors: SBE-43 dissolved oxygen sensor, SBE 27 pH and O.R.P. sensor, WetLabs ECO FLNTU chlorophyll fluorescence and turbidity sensor, and LI-COR Biospherical PAR sensor. The raw data from total 74 casts were processed with SBE Seasoft V2 package, imported to ODV collection and, upon performing quality control, exported to output file. The output file contains following parameters: Pressure, Temperature, Salinity, Oxygen (SBE 43), PAR, Fluorescence, Turbidity, pH, ORP.
DOI: 10.5281/zenodo.17429046
title: BatchQC: Negative Binomial Simulation Data

description: This .zip file contains all the data needed to create the simulated data used in the creation of the negative binomial model check for BatchQC. Instructions and code on how to use this data to recreate our results is available on the manuscript GitHub repository.
DOI: 10.5281/zenodo.16615177
title: KCNQ1 intermediate simulation files
DOI: 10.5281/zenodo.14963716
title: Linking Historical Types with the Current Taxonomy: DNA Sequence Generation and Molecular Phylogenetic Inferences for Thirteen Macrofungal Species
DOI: 10.5281/zenodo.17482979
title: Above- and Belowground Impacts of Spartina patens Invasion in Mediterranean Salt Marshes: Ecological Insights and Management Priorities
DOI: 10.5281/zenodo.17138179
title: Data behind figures for "Thermodynamical Relaxation in the Kinetic Range of Strong Turbulence associated with Magnetotail Reconnection"
DOI: 10.5281/zenodo.15238051
title: Coarse-Grained Molecular Dynamics Simulations of SARS-CoV-2 E Protein embedded in homogeneous mono-unsaturated model membranes

description: Coarse-grained MD simulations of the SARS-CoV-2 E protein (PDB ID: 5X29) embedded in homogeneous mono-unsaturated model membranes of varying equilibrium thickness. Lipids with 3, 4, 5, or 6 beads per acyl chain were used (Martini lipids DYPC, DOPC, DGPC, and a custom lipid).

All simulations were performed using GROMACS 2016 and the Martini 2.2 force field. The Berendsen thermostat was set to 313 K and a semi-isotropic Berendsen barostat was set to 1 bar in both directions. The compressibility modulus in both dimensions was 3 × 10−5 bar−1 with time constant 3 ps. Electrostatics and van der Waals (vdW) were shifted with a cutoff r-value of 1.2 nm. All systems underwent 100,000 steps of steepest-descent energy minimization prior to MD simulation with a timestep of 0.025 ps.

Protein backbone beads were restrained with an elastic network which bonded all backbone bead pairs within 1.4 nm of one another with force constants of 5,000 kJ mol−1 nm−1. Five replicas of each system were simulated in the NPT ensemble for 10 μs. We discarded the first half of each trajectory prior to analysis. To determine the bulk leaflet thickness t0, we performed separate 2 μs NPT simulations of membranes composed of each lipid species listed above, but without a protein embedded. We discarded the first half of each trajectory prior to analysis.

Analysis performed using nougat. Figures and figure generation script included.
DOI: 10.5281/zenodo.16744460
title: Hydrochemistry in the Romanian shelf waters - August 2021 (PN 19 20 01 02 - National Project)

description: Dataset contains hydrochemistry data from the Romanian shelf waters (bottom depths between 15 and 224 m), in August 2021. Data were collected onboard R/V Mare Nigrum, during a cruise conducted within the national project "Multidisciplinary research to improve knowledge of the climate change and human pressure interaction and its effects on the Black Sea ecosystem" – PN 19 20 01 02. Thirty stations distributed along 4 main transects (Sf. Gheorghe-SE, Portita-SE, Constanta-SE, and Mangalia-E) were performed for water column investigations by the GeoEcoMar team. In situ measurements of physical-chemical seawater parameters were done at each sampling station using a CTD SBE 25, with SBE 32 Rosette. Seawater samples were collected with 5L Niskin bottles from different depths and further analyzed in the GeoEcoMar lab for nutrients, chlorophylls and phaeophytin, TOC, and total mercury.
DOI: 10.5281/zenodo.17418093
title: Mean-Opacity Tables for Probing the Interior and Atmosphere of Giant Planets

description: Mean-Opacity Tables for Probing the Interior and Atmosphere of Giant Planets. The tables apply to nine elemental compo-sitions relevant to giant planets, and span pressures from 1e-6 − 1e5 bar and temperatures from 100 − 6000 K. There are cloud-free and cloudy tables.
DOI: 10.5281/zenodo.15422501
title: Raw data for the manuscript: Vertical transport of polystyrene nanoplastics in natural soils under unsaturated conditions : Influence of particle size and texture

description: Breakthrough curves and recovered mass to evaluate the effect of particle size and texture on the transport of polystyrene nanoplastics in natural soils under unsaturated conditions