cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15471232
title: Tumour-infiltrating regulatory T cells engage Nrf2 signalling to support their metabolic adaptation in hepatocellular carcinoma

description: Scanpy AnnData H5AD files containing clustered and annotated single-cell CITE-seq data using in the manuscript analyses. The data is separated in several files organised by datasets (Liver/Blood, Tumour/Background and Integrated Liver/Tumour/Background), types of data (RNA or Protein) and subset (All cells or Treg-like subset).
DOI: 10.5281/zenodo.17305001
title: Tumour-infiltrating regulatory T cells engage Nrf2 signalling to support their metabolic adaptation in hepatocellular carcinoma

description: Repository of aggregated samples with Cellranger and Scanpy AnnData H5AD files and TCR mudata files containing clustered and annotated single-cell multi-seq data. The Cellranger outputs have been aggregated by compartments (Liver/Blood or Tumour/Background). The annotated Scanpy data is separated in several files organised by compartments (Liver/Blood, Tumour/Background and Integrated Liver/Tumour/Background), types of data (RNA, Protein or TCR) and subset (All cells or Treg-like subset).
DOI: 10.5281/zenodo.17241756
title: Cross-Boundary Communication and Governance Network Dataset: Brazilian Coastal-Marine Extractive Reserves (RESEXs), Bragança Region, Pará

description: This dataset contains social network analysis (SNA) data examining communication and collaboration networks between key stakeholders involved in the co-management of four neighboring Brazilian coastal-marine extractive reserves (RESEXs) in the Bragança region, Pará, North Brazil. Data were collected through semi-structured interviews and SNA surveys conducted between November and December 2022.

 

The dataset includes:

- Node data (23 organizations/actors) with network centrality metrics calculated using Gephi 0.10.1

- Edge data (directed, weighted links) representing communication and collaboration relationships

- Network weights based on interaction type (communication/collaboration) and duration (recent/long-lasting), ranging from 0-4

 

The dataset is suitable for research on multi-level governance, protected area co-management, stakeholder network analysis, and cross-boundary conservation coordination.

 

Study area: Araí-Peroba (Augusto Corrêa), Caeté-Taperaçu (Bragança), Tracuateua, and Gurupi-Piriá (Viseu) extractive reserves.

 

Files included:

1. CrossBoundaryCommGovMismatches_nodes.csv - Actor attributes and centrality metrics

2. CrossBoundaryCommGovMismatches_links.csv - Network edges with weights

3. README.md - Complete documentation and methodology
DOI: 10.5281/zenodo.15591050
title: METZE 3 –Phytoplankton abundance and biomass, Varna Lake, 2024

description: This dataset contains Phytoplankton abundance and biomass data collected  in Varna Lake (24-25.09.2024), , in the framework of H2020 DOORS Project. Taxonomic identification of phytoplankton cell counts were done under inverted microscope (Nikon Eclipse Ti, equipped with video-interactive image analysis system (Nis Elements) at 400 x magnification, according to the Black Sea region procedures described in Moncheva and Parr, 2010. Cell density was recalculated in cells/L and the biomass in mg/m3.
DOI: 10.5281/zenodo.16681767
title: 3D DIC surface elevation measurements - Series S

description: This dataset contains the results of an experimental campaign aimed at retrieving the instantaneous free-surface elevation of the dynamic air-water interface of an open-channel flow-like in a laboratory flume using remote sensing technology.The acquisition was made possible by employing the Digital Image Correlation (DIC) technique.

The data acquisition campain was possible thanks to the fundings provided by the Department of Civil and Structural Engineering of the University of Sheffield (United Kingdom) and by the Engineering and Physical Sciences Research Council under grant agreement EP/R022275/1.

The experiments were conducted as part of the requirements for the fullfilment of the criteria prescribed to award a PhD title.

See the Readme file for further information.
DOI: 10.5281/zenodo.17081396
title: DataSetTest
DOI: 10.5281/zenodo.3242302
title: PERCEIVE_WP4_T4-5_Citizens vs Practitioners views of the EU Cohesion Policy_20191006_v01

description: The data set include data generated by PERCEIVE project Task 4.5. based on the results of the Section III of the focus group performed in WP1 at the level of each PERCEIVE case-study region. The data set referring to the local stakeholders' perception on hierarchy of regional needs and CP's contribution in addressing them. The data set contains individual report for each PERCEIVE case-study region regarding the above mentioned information.
DOI: 10.5281/zenodo.13076686
title: 3D DIC surface elevation measurements - Series Q

description: This dataset contains the results of an experimental campaign aimed at retrieving the instantaneous free-surface elevation of the dynamic air-water interface of an open-channel flow-like in a laboratory flume using remote sensing technology.The acquisition was made possible by employing the Digital Image Correlation (DIC) technique.

The data acquisition campain was possible thanks to the fundings provided by the Department of Civil and Structural Engineering of the University of Sheffield (United Kingdom) and by the Engineering and Physical Sciences Research Council under grant agreement EP/R022275/1.

The experiments were conducted as part of the requirements for the fullfilment of the criteria prescribed to award a PhD title.

See the Readme file for further information.
DOI: 10.5281/zenodo.14522716
title: 2024WR037763R
DOI: 10.5281/zenodo.17130717
title: Gene therapy supports long-term reconstitution of patient hematopoietic stem cells in deficiency of adenosine deaminase 2

description: The raw data pertain to the publication by Rigamonti C. et al., entitled “Gene therapy supports long-term reconstitution of patient hematopoietic stem cells in deficiency of adenosine deaminase 2”, and will be made publicly available at the time of article publication.
DOI: 10.5281/zenodo.14780093
title: 7.1. Stemness markers evaluated by flow citometry after dissociation of Hydrogel Microbeads Seeded with 1 Million/mL Human Adipose-Derived Mesenchymal Stem/Stromal Cells, produced with Bioinks 2 and 3 with a hyaluronic acid/dermatan sulfate/collagen cocktail instead of fibrinogen via Inkjet Bioprinting Using a 50 µm Nozzle and Cultured for 21 Days.

description: Stemness markers evaluated by flow citometry after dissociation of Hydrogel Microbeads Seeded with 1 Million/mL Human Adipose-Derived Mesenchymal Stem/Stromal Cells, produced with Bioinks 2 and 3 with a hyaluronic acid/dermatan sulfate/collagen cocktail instead of fibrinogen via Inkjet Bioprinting Using a 50 µm Nozzle and Cultured for 21 Days.

Data from the dissociation and quantification of the cells issued from the microbeads is supplied in excel format.

Inkjet bioprinting parameters:



Nozzle diameter: 50 µm.

Aperture time: 10 ms.

Jetting pressure: 5 bar.

Inkjet device temperature: 37°C.


Sample codes:



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

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

NM: non-marquées (cells without labelling, used to calibrate the citometer).

Mix: mix of positive markers.

iso: isotype internal control to calibrate unespecific signals.

viab: viability sample labelled with annexin (labels apoptotic cells) and propidium iodide (labels necrotic cells).

Monomarquage: samples labelled with only one marker to compensate internal citometer signals.
DOI: 10.5281/zenodo.15595426
title: Tracking the reorganisations of MVPA opportunities during the transition to adulthood: a longitudinal study
DOI: 10.5281/zenodo.16961710
title: Data for the analysis of Anthropocene temperature slopes

description: This repository contains:

(1) univariate input data (67 files):

(1.1) GISTEMP,

(1.2) ERSSTv5,

(1.3) CoralHydro2k d18O subset,

(1.4) CoralHydro2k SrCa subset,

(1.5) for RUS-95-d18O and RUS-95-SrCa the series with removed annual cycle;

 

(2) bivariate input data (19 files):

(2.1) CoralHydro2k subset;

 

(3) data on a 10-yr raster (2 files):

(3.1) f_slope_data.txt (input file name, time, proxy slope, error),

(3.2) slope_data.txt (time, input file name, SST slope, error, warming percentages, weighted means, relative spreads).

 

For details see the corresponding publication (Mudelsee & Felis, 2025, submitted manuscript).

This work has been funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), project number 468589022 (M.M.), within the SPP 2299, project number 441832482.
DOI: 10.5281/zenodo.16963574
title: Onboarding survey at University of Chemistry and Technology, Prague, 2023

description: The shift from pre-graduate to postgraduate level of studies, together with a potential change of institution/employer can be a challenging time for many PhD candidates. In private sector, onboarding procedures are a common practicer.

To asses the need for onboarding procedure development at University of Chemistry and Technology, Prague (UCT Prague), an 11-question survey was conducted among UCT Prague's PhD candidates (131 response, 49%) and employees (134 responses, 51%). Their responses overwhelmingly showed, that while most did not even hear about the term Onboarding (65%) and even less had experienced it in private sector (15%) or in academia (18%), most would appreciate such practice at UCT Prague both for PhD candidates (87%) and for employees (85%) alike.

On top of the current state of affairs, respondents were asked to list informations, that they wished to have received during their start at UCT Prague. These responses were subsequently used to adapt a compilation of adaptation plans from private sector, so the newly created adaptation plan for UCT Prague would reflect needs of PhD candidates at this institution.
DOI: 10.5281/zenodo.15129753
title: Floating marine macro litter DOORS cruise 3, 01-20 June 2024

description: The  datasest contains floating marine macro litter (> 2.5 cm)  data obesrved during  R/V Mare Nigrum cruise #3, in  33 transects located in the Bulgarian, Turkish and Georgian  Black Sea waters, 1-20 June, 2024 in the framework H2020 DOORS Project. The file contains information for the densities of floating marine macro litter (expressed in number of items. km-2) along survey transects, locations of transects (middle of transect) and date of the observation. The FML densities were determined in compliance with MSFD protocol for visual observations based on fixed-width strip transect method.
DOI: 10.5281/zenodo.14753208
title: 4.4. Stemness markers evaluated by flow citometry after dissociation of Hydrogel Microbeads Seeded with 1 Million/mL Human Adipose-Derived Mesenchymal Stem/Stromal Cells, produced with Bioinks 2 and 3 via Inkjet Bioprinting Using a 50 µm Nozzle and Cultured for 21 Days.

description: Stemness markers evaluated by flow citometry after dissociation of Hydrogel Microbeads Seeded with 1 Million/mL Human Adipose-Derived Mesenchymal Stem/Stromal Cells, produced with Bioinks 2 and 3 via Inkjet Bioprinting Using a 50 µm Nozzle and Cultured for 21 Days.

Inkjet bioprinting parameters:



Nozzle diameter: 50 µm.

Aperture time: 10 ms.

Jetting pressure: 4 bar.

Inkjet device temperature: 37°C.


Sample codes:



FAG 242: bioink 2

FAG 251: bioink 3

NM: non-marquées (cells without labelling, used to calibrate the citometer).

Mix: mix of positive markers.

iso: isotype internal control to calibrate unespecific signals.

viab: viability sample labelled with annexin (labels apoptotic cells) and propidium iodide (labels necrotic cells).

Monomarquage: samples labelled with only one marker to compensate internal citometer signals.
DOI: 10.5281/zenodo.15205599
title: Bone retouchers MSA Bushman Rock Shelter

description: Database comprising measurements and descriptions of bone surface modifications (taphonomy, used areas) for a set of bone retouchers retrieved from the Middle Stone Age deposits of Bushman Rock Shelter (Limpopo Province, South Africa).
DOI: 10.5281/zenodo.18102026
title: Daily Z500 reanalyses ERA
DOI: 10.5281/zenodo.18102027
title: Daily Z500 reanalyses ERA
DOI: 10.15468/dl.qxc8ax
title: Occurrence Download

description: A dataset containing 9192 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Agriotes obscurus"
 ]
}

 The dataset includes 9192 records from 296 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069477-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12725940
title: Laser welding of copper and aluminum alloys.

description: Preliminary database on dissimilar laser welding with bobbling technique.
DOI: 10.5281/zenodo.15015662
title: CN-LandMap: the First China National Land Function and Use Map

description: Based on low-cost and open source big dataset and automated program systems, we produce the land blocks dataset, including blocks(>1,200,000) and samples(>800,000) and the First China National Land Function and Use Map(CN-LandMap) covering 361 cities in 34 provinces in entire China land of about 9,600,000km2. Compared with the existing methods, the boundary division efficiency of functional zones is improved by more than 90%, the mixing degree of functional zones is decreased by 30%. The results showed that CN-LandMap had achieved an accuracy of 75.54% and a Kappa coefficient of 0.6457 at the national scale. 

Now, you can download a TIFF file for a specific province with "*_v01_2023_14.tif" or CN-LandMap with "China_v01_2023.tif". The guidance document (00_CN-LandMap_User Guides_v1.0.pdf) provides more information.
DOI: 10.5281/zenodo.14933605
title: Seasonal productivity and water use in herbaceous salt marsh plants on the South Texas Gulf Coast

description: This dataset contains seasonal and diurnal ecophysiological and environmental measurements for five species of herbaceous salt marsh plants: Borrichia frutescens, Salicornia virginica, Batis maritima, Monanthochloe littoralis, and Limonium nashii. Data was collected repeatedly across multiple seasons from 2024-2025 at a single coastal salt marsh site (Coyote Island, Port Aransas, Texas). Individual plants and environmental data were sampled at multiple time points throughout sampling days (approx. 05:00 am-05:00 pm) to capture finer-scale diurnal patterns. The following measurements are included in this dataset:



Net CO2 assimilation (A), transpiration (E), stomatal conductance (gs), intercellular CO2 concentration (Ci), external air temperature (Tair), external relative humidity (RH), leaf-to-air vapor pressure deficit (VPD), maximum quantum efficiency of PSII (Fv/Fm), quantum yield of PSII (ΦPSII): obtained via LI-6800 Portable Photosynthesis and Fluorescence System (LiCor)

Leaf/stem water potential (Ψ): obtained via Model 1505D Pressure Chamber (PMS Instruments, Inc.)

Soil moisture (SM): obtained gravimetrically from 10 cm soil cores

Soil porewater salinity (PW sal): obtained via centrifugation of 10 cm soil cores and measured using a refractometer

Tidal creek salinity (sal): obtained in the field using a refractometer


All data is in raw, unsummarized form, with the exception of raw data ouputs obtained using the LI-6800 Portable Photosynthesis System which were reformatted for analysis purposes.
DOI: 10.5281/zenodo.16994814
title: Dementia pathways in Lewy body disease

description: This is an upload for the manuscript with running title "Dementia pathways in Lewy body disease" by Nelvagal et al., that has raw regional quantitative pathology data generated for the manuscript (Tabular pathology data used to produce all figures and supplementary data), Python Scripts to run SuStaIn used for disease subtyping and progression modelling (SuStaIn analyses) based on https://github.com/ucl-pond/pySuStaIn , R Code Scripts using existing libraries to perform statistical analyses and create visualisations and Qupath .groovy Scripts and .json object classifier used on all image quantification pathology data. In addition, there is also a Knowledge Resource Table (KRT) detailing all resources used in this manuscript.
DOI: 10.5281/zenodo.15606285
title: Dataset from Merone CSO-CW (Italy)

description: This dataset was collected as part of the monitoring activities carried out during the MULTISOURCE project on a full-scale aerated hybrid treatment wetland located in Merone, Italy. The system, designed by IRIDRA Srl in collaboration with Como Acqua Srl, aims to mitigate frequent and prolonged combined sewer overflows (CSOs), which can persist for days and result in untreated discharges into receiving waters, intensifying environmental pollution.

The hybrid system integrates four aerated wetland beds with a surface flow wetland to improve pollutant removal efficiency while keeping operational costs significantly lower than those of conventional infrastructure. Its high hydraulic flexibility allows it to adapt to intense weather events, making it a resilient and sustainable solution for urban water management. In addition to its technical performance, the system offers key co-benefits, including cost savings, biodiversity support, and educational value.
DOI: 10.5281/zenodo.15743469
title: Dataset of "Enhanced vibrational optical activity by near-zero index chiral effective media"

description: Fig. 2a (alpha_ee.csv) . Dependence of the real (third column) and imaginary (second column ) parts of the dimensionless electric polarisability alpha_ee over the impinging wavelength (in micron, first column).

Fig. 2b (alpha_em.csv). Dependence of the real (third column) and imaginary (second column ) parts of the dimensionless electric-magneto polarisability alpha_em over the impinging wavelength (in micron, first column).

Fig. 2c (alpha_me.csv). Dependence of the real (third column) and imaginary (second column ) parts of the dimensionless magneto-electric polarisability alpha_me over the impinging wavelength (in micron, first column).

Fig. 2d (alpha_mm.csv). Dependence of the real (third column) and imaginary (second column ) parts of the dimensionless magnetic polarisability alpha_mm over the impinging wavelength (in micron, first column).

Fig. 2e (ReEpsEff.csv) . Dependence of the real part of the effective permittivity (third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 2f (ReKappasumEff.csv). Dependence of the real part of the sum of effective chirality parameter kappa (third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 2g (ImKappasumEff.csv). Dependence of the imaginary part of the sum of effective chirality parameter kappa (third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 2h (MuEff.csv). Dependence of the real part of the sum of effective permeability mu_eff-1 (third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 3a (ORD.csv). Dependence of ORD (in degree, third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 3b (ASF.csv). Dependence of ASF (third column) over impinging wavelength (in micron, first column), and NS filling fraction (second column).

Fig. 3c (ORD_dnmol.csv). Dependence of ORD (in degree, third column) over enantiomeric imbalance (first column), and NS filling fraction (second column).

Fig. 3d (ASF_dnmol.csv). Dependence of ASF (third column) over enantiomeric imbalance (first column), and NS filling fraction (second column).

Fig. 4a (ORD_enhance_Compare.csv). Dependence of ORD enhancement factor for Ag (second column), and for AZO (third column) over impinging wavelength (in micron, first column).

Fig. 4b (ASF_enhance_Compare.csv). Dependence of ASF enhancement factor for Ag (second column), and for AZO (third column) over impinging wavelength (in micron, first column).
DOI: 10.5281/zenodo.14081783
title: Landscape structure of bacterial and fungal community composition in the West Nile Virus vector, Culex tarsalis

description: Raw data sequence for bacteria (16S v3v4 region)
DOI: 10.5281/zenodo.14948584
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.14951555
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.17554013
title: BRD2 bridging TFIID and histone acetylation in transcriptional initiation.

description: Members of the bromodomain and extraterminal domain (BET) transcription factor family play a central role in the regulation of gene expression. BET domain factors have also been proposed as major targets for multiple diseases, with inhibitors designed to block the binding of BET bromodomains to acetylated histones. However, recent studies demonstrated that the BET-domain of BRD4 is not involved in its transcriptional function and the specific mechanisms by which other individual BET-domain containing proteins distinctly regulate transcription remain poorly understood. Here, we demonstrate that BRD2 promotes transcriptional initiation by RNA Polymerase II (Pol II) at gene promoters and enhancers, predominantly in a bromodomain-dependent manner. Our biochemical studies demonstrated that histone H4K16 acetylated histone-bound BET domain of BRD2 facilitates the recruitment of the transcription preinitiation complex TBP/TFIID to chromatin. Loss or inhibition of BRD2 bromodomains prompts the formation of BRD2-specific nuclear foci that sequester TFIID away from chromatin, leading to a genome-wide defect in transcriptional initiation. Our molecular studies demonstrated that the BET domains of BRD2 and BRD4 are not functionally exchangeable, highlighting distinct but cooperative roles for BET-domain family members in transcriptional initiation and elongation control to promote proper regulation of gene expression.
description: Sample
library strategy
molecule
organism
cell line
construct
treatment


TT-seq_01_BRD2-AID_28hDox_GFP_3hH2O
TT-seq
total RNA
human
DLD1 BRD2AID
GFP
28hDox


TT-seq_02_BRD2-AID_28hDox_GFP_3hAux
TT-seq
total RNA
human
DLD1 BRD2AID
GFP
28hDox+3hAux


TT-seq_03_BRD2-AID_28hDox_GFP-BRD2_3hAux
TT-seq
total RNA
human
DLD1 BRD2AID
GFP-BRD2
28hDox+3hAux


TT-seq_04_BRD2-AID_28hDox_GFP-BRD2deltaBD_3hAux
TT-seq
total RNA
human
DLD1 BRD2AID
GFP-BRD2∆BD
28hDox+3hAux




 




Data processing
FastQC v 0.11.2, trimming using Trimmomatic (TRAILING:30 MINLEN:20). Reads aligned to the GRCh38 genome using STAR v.2.5.2 and only uniquely mapped reads with a two-mismatch threshold were considered and quantified to the gene level using FeatureCounts 2.0.1 with: -p -B -C -s 2 . Bam files were converted into bigwig (.bw) track files (RPKM normalized).


Assembly/genome
hg38


Platform/design
Illumina NextSeq 2000 (PE x50)
DOI: 10.5281/zenodo.15574840
title: Regional hotspots of environmental pressures identified in the European Union 27 Member States, United Kingdom and Switzerland at NUTS 2 level.

description: Cell size: 100 m. Spatial reference: ETRS 1989 LAEA.
DOI: 10.5281/zenodo.14288425
title: Olivine's high radiative conductivity increases slab temperature by up to 200 K - Tables

description: This repository contains the tables of the manuscript entitled: 'Olivine's high radiative conductivity  increases slab temperature by up to 200 K', and submitted by Enrico Marzotto, Alexander Koptev, Sergio Speziale, Monica Koch Müller, Nada Abdel-Hak, Sarah B. Cichy, Sergey Lobanov.