cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.42jb2n
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neoechinorhynchus cribbi",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019007-251120083545085/datasets/export for details.
DOI: 10.5281/zenodo.15176059
title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein - Cytotoxic CD4 T cell staining experiment 2 FCS files

description: FCS files for Cytotoxic CD4 T cell staining, and an excel key indicating disease status for each donor. See README file for more instructions.
DOI: 10.5281/zenodo.15310800
title: Invasive non-native riparian vegetation indirectly destabilises riverbanks: code and dataset

description: Code and data to support the study: 'Invasive non-native riparianvegetation indirectly destablishes riverbanks'



Code is is in the form of R markdown written in R
DOI: 10.5281/zenodo.13899887
title: raw crater counts for layered ejecta craters

description: JMARS .jlf shape files that contain the measurement area polygon and crater measurements (diameters, center lat/lon, and a degradation classification). And .csv files of crater measurements. Names of files indicate the region for the counts. See associated publication for descriptions of those regions.
DOI: 10.5281/zenodo.13899942
title: raw crater counts for radial ejecta craters

description: JMARS .jlf shape files that contain the measurement area polygon and crater measurements (diameters, center lat/lon, and a degradation classification). And .csv files of crater measurements. Names of files indicate the region for the counts. See associated publication for descriptions of those regions.
DOI: 10.5281/zenodo.17034610
title: Nature's Contributions to People provided by terrestrial vertebrates in Europe

description: This dataset contains information on the terrestrial vertebrate species that provide nature's contributions to people in Europe, and how they are spatially distributed across Europe. A total of 12 NCP are considered: 8 regulating NCP (agricultural pest control, mosquito control, tick host control, pine moth control, invasive Asian hornet control, carrion elimination, seed dispersal, pollination) and 4 cultural NCP (community interest, evolutionary heritage, nature tourism and wildlife watching, and game). We provide the information on NCP provided by species in a binary table in CSV format, and provide raster files for the individual species-based NCP maps, including with and without filtering for societal demand.
DOI: 10.5281/zenodo.17079942
title: Reentrant topology and reverse pumping in a quasiperiodic flux ladder

description: This upload includes raw data, processed data, and plots used in the article titled "Reentrant topology and reverse pumping in a quasiperiodic flux ladder". By following the instructions provided in the accompanying README files, readers can reproduce the results shown in the accompanying plots and in the linked article "https://arxiv.org/pdf/2508.04452".
DOI: 10.5281/zenodo.14289070
title: Dataset - Report on the fertilizer value and contribution to greenhouse gas emissions of waste streams and their composts
DOI: 10.5281/zenodo.15880591
title: Survey data for Cross-cultural analysis of smile perception and satisfaction with smile appearance among Latvian and Uzbek young adults

description: This dataset contains anonymized responses from 100 participants (50 from Latvia and 50 from Uzbekistan) who completed cross-cultural survey on smile perception and satisfaction with smile appearance. The research focuses on self-reported satisfaction with smile appearance, previous orthodontic treatment experience, and esthetic preferences based on smile images.

Each dataset file includes following variables:

-       Orthodontic treatment history (Yes/No)

-       Duration of treatment (if applicable)

-       Satisfaction with orthodontic treatment results (scale 1–5)

-       Self-satisfaction with smile appearance (scale 1–5)

-       Desired changes in smile (options: nothing, color of teeth, shape of teeth, other)

-       Preferred smile type (options: 1– high smile line, 2– average smile line, or 3– low smile line)

-       Preferred smile arc (options: 1– parallel smile arc, 2– straight smile arc, or 3– reverse smile arc)

-       Participant’s gender (Female, Male, Other)

The data are provided in two separate files:

-       survey lv.xlsx  

-       survey uz.xlsx  

The dataset is fully anonymized and does not contain any personally identifying information.

The questionnaire was provided in four languages (English, Latvian, Uzbek, and Russian) to ensure clarity and accessibility for both groups. The full survey is attached as a .docx file:

-       Questionnaire.docx 

Participants were informed about the purpose of the study at the beginning of the questionnaire. Completion of the survey was considered as providing informed consent. The study was approved by the Ethics Commission of the University of Latvia.

Intended use:

This data supports research in cross-cultural psychology, dental esthetics, orthodontic outcomes, smile perception, and self-perception of the smile. It is suitable for academic research, educational projects, and meta-analyses on esthetic preferences.
DOI: 10.5281/zenodo.13628031
title: Nature's Contributions to People provided by terrestrial vertebrates in Europe

description: This dataset contains information on the terrestrial vertebrate species that provide nature's contributions to people in Europe, and how they are spatially distributed across Europe. A total of 12 NCP are considered: 8 regulating NCP (agricultural pest control, mosquito control, tick host control, pine moth control, invasive Asian hornet control, carrion elimination, seed dispersal, pollination) and 4 cultural NCP (community interest, evolutionary heritage, nature tourism and wildlife watching, and game). We provide the information on NCP provided by species in a binary table in CSV format, and provide raster files for the individual species-based NCP maps, including with and without filtering for societal demand.
DOI: 10.5281/zenodo.17529345
title: Data supporting 'Flow morphology and patterns in porous media convection: A persistent homology analysis'

description: Temperature fields are stored.

SIMULATIONS A -The results are relative to 10 simulations labelled as "A" in the corresponding manuscript. Matlab and python scripts to access and visualize the data are also provided. The fields are taken at 1 horizontal plane located near the boundary. Several snapshots are available in the early and late stages of the flow.

SIMULATIONS C -The results are relative to 18 simulations labelled as "C" in the corresponding manuscript. Matlab and python scripts to access and visualize the data are also provided. The fields are taken at 2 horizontal planes located near the boundary and at the centerline. For each plane, 10 snapshots are available.
DOI: 10.5281/zenodo.15740206
title: Genome-wide SNPs data and past distribution models reveal genetic admixture and isolation in the range-restricted Psittacanthus auriculatus mistletoe species

description: This is a raw dataset for 80 samples conducted through Genotyping-by-sequencing method. Library preparation was performed with DNA digestion using the apkI restriction enzyme, and the samples were sequenced using the Illumina NovaSeq 2 ´ 150 platform (Illumina, Inc., San Diego, CA, USA).
DOI: 10.5281/zenodo.13899958
title: raw crater counts for background regions

description: JMARS .jlf shape files that contain the measurement area polygon and crater measurements (diameters, center lat/lon, and a degradation classification). And .csv files of crater measurements. Names of files indicate the region for the counts. See associated publication for descriptions of those regions.
DOI: 10.5281/zenodo.14834171
title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein - CELSR2 FCS files

description: FCS files for CELSR2 staining, and an excel key indicating disease status for each donor.
DOI: 10.5281/zenodo.15577591
title: Multiplex antigen screening of Cerebrospinal Fluid detects microbial and autoantigenic epitopes associated with Multiple Sclerosis
DOI: 10.5281/zenodo.15791901
title: Datasets for "Community of arbuscular mycorrhizal fungi shifts its foraging functional traits in response to grassland fertilisation" paper

description: This study combines results from our two experiments to demonstrate how the functional foraging traits of a symbiotic fungal community (AMF) shift with nutrient addition (grassland fertilisation) and how they differ between two major functional groups of host plants.
DOI: 10.5281/zenodo.14236442
title: Phenotypic and genotypic data of genomic selection study of spring frost tolerance of Norway spruce
DOI: 10.5281/zenodo.14505715
title: Datasets and scripts used in Gonzalo/Jacquiod et al. for rhizosphere microbiota network analysis

description: This submission contains all the datasets and intermediate files generated in the study by Gonzalo/Jacquiod et al. on the rhizosphere microbiota network analysis.

The zip file contains the following items:



The OTU tables (16S and ITS)

The design file

The plant data file

The R script used for network buidling using Poisson Log Normal method with the StARS approach (STStability Approach to Regularization Selection)

The Python script used ofr searching for cycle basis in the networks

The nine networks generated at 97% stability 

All intermediates files that were generated
DOI: 10.5281/zenodo.15103874
title: Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein - Compiled flow cytomtetry data for all donors

description: Compiled results from all flow cytometry experiments performed in the "Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to ⍺-synuclein" study.

Not all donors were inlcuded for each experiment. Donors not inlcuded for a particular experiment has been indicated by "Not screened".
DOI: 10.5281/zenodo.15470768
title: Genetically engineered extracellular vesicles-based collagen-targeting bioinspired scaffold for tendon regenerative repair

description: Tendon injuries, particularly massive tendon defects, pose significant clinical challenges due to the limited regenerative capacity of tendons and suboptimal outcomes of current therapies. This study presents a bioinspired scaffold that integrates genetically engineered extracellular vesicles (EVs) with collagen-targeting capabilities into a decellularized bovine tendon sheet (DBTS) for tendon regenerative repair. Tendon-derived stem cells (TDSCs) were genetically modified to overexpress biglycan (Bgn) and fibromodulin (Fmod), producing bioactive EVs that drive tenogenic differentiation via the miR-145-5p/TGFβ2 signaling pathway. The incorporation of a collagen-targeting peptide (CTP) on EVs surfaces ensured efficient attachment and sustained release at the injury site. The resulting bioinspired scaffold (TDSCsBgn/Fmod/CTP EVs-DBTS) provided a supportive microenvironment for tendon regeneration, demonstrated in vitro by improved stem cell proliferation, migration and tenogenic differentiation, and in vivo by enhanced collagen alignment, extracellular matrix remodeling, and biomechanical performance. This scaffold represents a paradigm shift in cell-free regenerative strategies, offering targeted modulation of the tendon niche with translational potential for treating massive tendon injuries.
DOI: 10.5281/zenodo.14356912
title: Dataset to the article 'The beach bioreactor: unraveling the anomaly of intensive carbon remineralization above a deep oxycline'

description: This repository contains model output files for the research article:

Felix Auer, Janek Greskowiak, Rena Meyer, Anja Reckhardt, Moritz Holappels (2025), The beach bioreactor: unraveling the anomaly of intensive carbon remineralization above a deep oxycline

Model description: 

A two-dimensional numerical reactive transport model was created, simulating tidal and wave-driven groundwater flow and oxygen (O2) dynamics in the saltwater recirculation cell of the beach aquifer at Spiekeroog Beach, Germany. The model was developed using COMSOL Multiphysics™ v.6.1 and couples variably saturated flow (Richards Equation) with reactive O2 transport. Boundary conditions and parameters were informed by field data, as described in the corresponding manuscript. Two seasonal scenarios (summer and winter) were simulated to capture differences in biogeochemical activity and inputs, and beach morphology. Atmospheric O2 input in the periodic tide-induced desaturated surface beach layer (re-aeration) and its effect on O2 distribution was explored via separate model runs. The simulations were performed in two stages: first resolving transient groundwater flow during a tidal cycle, then coupling with reactive transport to reach quasi-steady-state O2 profiles.

Model Output:

Model output files in this repisitory are available both for the "Summer" and the "Winter" simulation. Files with the ending "_flow_tidal_cycle" contain the 2D-values for hydraulic heads (m), as well as x- and y-component of the porewater flow velocity (m/s), resolved every 2 minutes for an entire tidal cycle (720 min). Files with the ending "_cO2_tidal_cycle" contain the 2D-values for oxygen concentration (µmol/l), resolved every 20 minutes for a quasi steady-state tidal cycle (720 min). Files with the ending "_cO2_tidal_cycle_NoReAir" contain the same, but with the re-aeration process switched off.
DOI: 10.5281/zenodo.17511447
title: Tunable Exciton Transport in Fully Hybridized van der Waals Trilayers

description: This repository contains the data associated with the publication "Tunable Exciton Transport in Fully Hybridized van der Waals Trilayers" by Huan Liu et al.Phys. Rev. Lett. 2025 - DOI: https://doi.org/10.1103/vd6b-8js6

All data files are provided as plain-text .txt files. Each file includes a header describing the data type and units. Filenames are self-explanatory and correspond to the quantities discussed in the paper and supplementary information.

If you use these data, please cite the original publication.

For any additional information or questions, please contact: liuhuansklt@163.com
DOI: 10.5281/zenodo.14013671
title: GBIF records of Isopoda: Oniscidea in Canada from 18 Jan 2024 - 20 Oct 2024

description: GBIF records of Isopoda: Oniscidea in Canada from 18 Jan 2024 - 20 Oct 2024

Obtained with occ_search() in the rgbif R package.

These records only include entries where basisOfRecord = "MATERIAL_SAMPLE" or "PRESERVED_SPECIMEN"
DOI: 10.5281/zenodo.16755072
title: Diverse prokaryotic strategies associated with soil organic matter priming

description: “Data_Figure_1.csv”

This file contains flux data of respiration rates, delta 13C signature, and derived calculations of SOM mineralisation and labile C mineralisation rate. This data was used in Figure 1, Figure A.1, and Table A.6.

 

“Data_Table_2.csv”

This file contains soil pool change data such as total C balance, MBC, ammonium, nitrate, pH, and quantitative PCR. This data was used in Table 2, Table A.7, and Figure A.2.

 

“OTU_Sample.csv”

This file contains the OTU count table at DNA level for both samples per sample. No reads were removed (n0). This file was used in DNA alpha and beta diversity analysis shown in the appendix.

 

“OTU_sample_P1_Grange_n2.csv”

This file contains the OTU count table per sample. Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“OTU_sample_P1_Moorepark_n2.csv”

This file contains the OTU count table per sample. Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“OTU_sequence_Grange.csv”

This file contains the OTU’s representative 16S V4 sequence (>97% clustering). Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“OTU_sequence_Moorepark .csv”

This file contains the OTU’s representative 16S V4 sequence (>97% clustering). Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“OTU_taxonomy_P1_Grange_n2.csv”

This file contains the OTU’s taxonomic assignment against SILVA. Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“OTU_taxonomy_P1_Moorepark_n2.csv”

This file contains the OTU’s taxonomic assignment against SILVA. Doubletons from the sequencing process were removed (n2). This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“sample_info.csv”

This file contains the experimental information to sample relation for both samples per sample. This file was used in DNA alpha and beta diversity analysis shown in the appendix.

 

“Sample_info_P1_Grange.csv”

This file contains the experimental information to sample relation. This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.

 

“Sample_info_P1_Moorepark .csv”

This file contains the experimental information to sample relation. This file was used in Figure 2, Table 3 and further DNA and RNA community composition analysis per soil shown in the appendix.
DOI: 10.5281/zenodo.15412158
title: Alternatively activated monocyte derived myeloid cells promote extracellular pathogen persistence within pulmonary fungal granulomas

description: Inhaled fungal pathogens often generate granuloma-contained latent infections that can reactivate to cause invasive disease. However, the mechanisms underlying the inability to generate sterilizing immunity against latent infection remains poorly understood.  Here, we leveraged spatial transcriptomics and flow cytometry to characterize the immune dynamics and cellular architecture of cryptococcal granulomas. Using fate mapping and murine genetic tools, we demonstrate that alternative activation of monocyte-derived myeloid cells by CD4+ T helper 2 cells antagonizes pulmonary fungal clearance during latent infection. In contrast to the prevailing view in the field, we find that alternatively activated myeloid cells are not an intrinsic replication niche for the fungus and more broadly, Cryptococcus predominantly resides in the extracellular environment. We propose a T helper 2 cell-myeloid circuit establishes a local immunosuppressive environment to drive extracellular fungal persistence, which could be leveraged as a new target for host-directed therapy to treat latent fungal infections.
description: Spatial transcriptomics

Euthanized mice were perfused with 20 ml PBS followed by 20 ml 4% PFA and then inflated with OCT from trachea. Lung tissues were collected and immediately fast frozen for storage at -80 °C. Sections were made with CrypStat by 10 mm directly on slides provided by 10X Genomics. Xenium Prime 5K kit was utilized for spatial transcriptomics according to commercial instructions. Briefly, sections were hybridized with priming oligos and then washed by RNase to release the RNA strand, followed by polishing to allow probe hybridization for the target RNA. We did not add customized probes on pre-designed mouse pan tissue & pathways panel containing 5006 probes. Unbound probes were washed away, and ligation was performed to ensure probe specificity by generating a circular DNA from hybridized probe, which was enzymatically amplified subsequently. Cell segmentation staining and autofluorescence quenching were performed before loading slides into Xenium Analyzer at NIAMS.
DOI: 10.5281/zenodo.14901927
title: Artificial Intelligence in Psychotherapy Scale
DOI: 10.5281/zenodo.17675153
title: Data from 'Individually redundant effectors are collectively required for bacterial pathogen virulence'
DOI: 10.5281/zenodo.15882121
title: Dataset for cross-cultural analysis of smile characteristics among Latvian and Uzbek young adults

description: This dataset includes measurements of smile characteristics collected from standardized frontal photographs of 100 participants aged 20-35-years (50 Latvian and 50 Uzbek). The study aimed to assess cultural differences in smile esthetics by analyzing key morphological features of the smile.

Variables capture anatomical and esthetic features commonly evaluated in smile design and treatment planning.

The dataset includes following variables:

-       Smile type (high, average, low), 

-       Smile symmetry (symmetrical, asymmetrical),

-       Number of teeth displayed in a smile (only fully visible teeth counted), 

-       Position of the maxillary incisor edge relative to the lower lip (touching, not touching, slightly covered, fully covered),

-       Smile arc (parallel, straight, reverse, not visible),

-       Dental midline (coincident or non-coincident with facial midline.

The data are provided in two files:

-       smile characteristics lv.xlsx – Smile assessments of Latvian participants

-       smile characteristics uz.xlsx – Smile assessments of Uzbek participants

All data are fully anonymized and do not include any photographic images or personal identifiers.

Smile photographs used for measurement were obtained with written informed consent for research purposes. Photographs are not shared publicly due to ethical concerns and potential identifiability of participants. Participants did not provide consent for public sharing of their images. Data were anonymized. The study was approved by the Ethics Commission of the University of Latvia.

Intended Use: 

This raw dataset supports research in dental esthetics, orthodontics, restorative dentistry, cross-cultural variation in facial esthetics, and smile classification. It is suitable for academic research, educational projects, and comparative esthetic analysis.
DOI: 10.5281/zenodo.15620807
title: LuwianSiteAtlas: A Spatial and Semantic Dataset of Bronze Age Settlements in Western Anatolia

description: This dataset presents a comprehensive digital catalog of 483 archaeological settlement sites in western Anatolia dated to the Middle and Late Bronze Age (c. 2000–1200 BCE). Compiled over a decade, the dataset integrates data from excavation reports, systematic surface surveys, historical sources, and remote sensing. Each site is georeferenced and documented with metadata including chronological attribution, site function, archaeological features, bibliographic references, and proximity to ancient mineral resources. Originally maintained as spreadsheets, the data have been migrated to a structured MySQL relational database and are accessible via an open-access web platform. Designed for semantic interoperability, the dataset enables comparative, geospatial, and interdisciplinary research across archaeology, digital humanities, and historical geography. Standardized metadata and semantic linking promote reuse and integration within broader digital infrastructures. This resource supports both expert and public users in analyzing regional settlement systems and fosters more inclusive approaches to the study of Bronze Age Anatolia.
DOI: 10.5281/zenodo.17525758
title: Raw data for ATG2 is a triglyceride transfer protein

description: Data and images used to generate graphs in Korfhage et. al.; ATG2 is a triglyceride transfer protein. Files are labeled according to their corresponding figure in the PNAS article. Data include excel sheets used for generating graphs, raw images used to for densitometry of flotation assays, and targeted lipidomics datasets.