cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10805412
title: Supplementary data to article "From single trees to country-wide maps: Modeling mortality rates in Germany based on the Crown Condition Survey"

description: This repository provides regression models and annual prediction rasters for tree mortality in Germany.  

Regression models:Logistic regression models which predict tree mortality for the species (beech = Fagus sylvatica, oak = Quercus petraea and robur, pine = Pinus sylvestris, spruce = Picea abies) and species groups (OB = other broadleaves, OC = other conifers) based on observations of dead trees in theGerman Crown Condition Survey (Waldzustandserhebung) and a set of environmental predictor variables. The predictors come from the domains of climate (clim), site conditions (site, i.e. topography, soil, land cover, deposition), tree age (age) and some models contain pairwise interaction terms between predictors (inter). All models were fit in R and are represented as objects of the class glm and stored in files of the type rds.

Prediction rasters:Spatial predictions of the mortality rate across Germany for each tree species and species group and for each year from 1998 to 2022. The rasters have a spatial resolution of 100 m. Missing valuesmark areas where the species/group does not occur. The mortality values are given as integers between 0 (no mortality) and 10000 (100% mortality). The coordinate reference system is Lambert Azimuthal Equal Area (LAEA; EPSG:3035). The rasters are provided in the file format GeoTIFF (tif).

A detailed description of the data sources and analyses can be found in the following article.

Citation:Knapp, N., Wellbrock, N., Bielefeldt, J., Dühnelt, P., Hentschel, R., Bolte, A., 2024. From single trees to country-wide maps: Modeling mortality rates in Germany based on the Crown Condition Survey.

Contact:nikolai.knapp@thuenen.de
DOI: 10.5281/zenodo.12635894
title: Raw datasets for paper "River Surface Velocimetry Reconstruction via Graph-enhanced Neural Operator"
DOI: 10.5281/zenodo.12635895
title: Raw datasets for paper "River Surface Velocimetry Reconstruction via Graph-enhanced Neural Operator"
DOI: 10.5281/zenodo.12206226
title: DIAMOND_Methyl_Haplo_table

description: methylationLevels.csv

Metadata by Klaus Von GRAFENSTEIN, Engineer

24/06/2024

Data from Michel, et al. « Non-Invasive Multi-Cancer Diagnosis Using DNA Hypomethylation of LINE-1 Retrotransposons ». Preprint. Oncology, 23 janvier 2024. doi:10.1101/2024.01.20.23288905

Generated with code : https://github.com/ProudhonLab/DIAMOND

Columns:



    Sample_ID = Sample identifier composed of  : the sequencing dataset code, followed by "S" and the sample number inside the sequencing batch*

    Cohorte = Cohort of the sample (Discovery or Validation)

    Disease_status = Biological class of the sample

   Metastasis_status = Factor of if the sample is from a metastatic patient or not (M+ or M0). NA when the sample is healthy plasma or Metastasis_status is unknown

    Stage = Cancer stage of the sample ( 1 to 4 ). NA when the sample is healthy plasma or Stage is unknown

    Age.range = Age between a 5-year range of the patient or donor

    Sex = Sex of the patient or donor (F or M). NA when the sex is unknown

    Haplotype proportions = columns with the name of the amplicon (1,2,4,5,6 or 7) and haplotype code (0 unmethylated, 1 methylated, for each CpG site of the amplicon). Value between 0 and 1

    Methylation rate = columns with the name of the amplicon (1,2,4,5,6 or 7) and CpG site number. Value between 0 and 1
DOI: 10.5281/zenodo.12206227
title: DIAMOND_Methyl_Haplo_table

description: methylationLevels.csv

Metadata by Klaus Von GRAFENSTEIN, Engineer

24/06/2024

Data from Michel, et al. « Non-Invasive Multi-Cancer Diagnosis Using DNA Hypomethylation of LINE-1 Retrotransposons ». Preprint. Oncology, 23 janvier 2024. doi:10.1101/2024.01.20.23288905

Generated with code : https://github.com/ProudhonLab/DIAMOND

Columns:



    Sample_ID = Sample identifier composed of  : the sequencing dataset code, followed by "S" and the sample number inside the sequencing batch*

    Cohorte = Cohort of the sample (Discovery or Validation)

    Disease_status = Biological class of the sample

   Metastasis_status = Factor of if the sample is from a metastatic patient or not (M+ or M0). NA when the sample is healthy plasma or Metastasis_status is unknown

    Stage = Cancer stage of the sample ( 1 to 4 ). NA when the sample is healthy plasma or Stage is unknown

    Age.range = Age between a 5-year range of the patient or donor

    Sex = Sex of the patient or donor (F or M). NA when the sex is unknown

    Haplotype proportions = columns with the name of the amplicon (1,2,4,5,6 or 7) and haplotype code (0 unmethylated, 1 methylated, for each CpG site of the amplicon). Value between 0 and 1

    Methylation rate = columns with the name of the amplicon (1,2,4,5,6 or 7) and CpG site number. Value between 0 and 1
DOI: 10.5281/zenodo.12629029
title: A systematic meta-analysis of the role of perceptual and conceptual novelty in guiding infant looking behaviour

description: These are the data, codebooks, and scripts required to reproduce the results of the paper Kunin, L., Piccolo, S., Saxe, R., & Liu, S. (under revision). A systematic meta-analysis of the role of perceptual and conceptual novelty in guiding infant looking behaviour.

A previous version of the data and code can be found at https://zenodo.org/records/11084599.
DOI: 10.5281/zenodo.12635801
title: Initial model and Molecular Dynamics trajectory of WGR domain of PARP2 with ZN  ions

description: Files:

1. Initial model of PARP2 WGR domain (based on PDB entry: 6F5B) with two sites potentially capable of binding zinc ions: one formed by residues E97, C98, H160 and another - by residues H106, C109, E138

2. PARP2 WGR domain with Zn ions bound after energy minimization.

3. 400 ns MD trajectory of PARP2 WGR domain with Zn ions.
DOI: 10.5281/zenodo.12635802
title: Initial model and Molecular Dynamics trajectory of WGR domain of PARP2 with ZN  ions

description: Files:

1. Initial model of PARP2 WGR domain (based on PDB entry: 6F5B) with two sites potentially capable of binding zinc ions: one formed by residues E97, C98, H160 and another - by residues H106, C109, E138

2. PARP2 WGR domain with Zn ions bound after energy minimization.

3. 400 ns MD trajectory of PARP2 WGR domain with Zn ions.
DOI: 10.5519/qd.rpfdtf1d
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5066/p13mhcb8
title: Estimated crop irrigation water use withdrawals in Ranegras Plain Groundwater Basin, Arizona for 2023

description: Observations of irrigated agricultural land within the Ranegras Plain Groundwater Basin in Arizona. Crops were verified in situ twice in 2023, first on May 10th and again on Sep 28th; based on digitized field boundaries. Field boundaries were digitized from U.S. Department of Agriculture, National Agriculture Imagery Program County Mosaic 2023 imagery for Arizona and supplemented with the Sentinel2 imagery collection accessed via the European Space Agency, Copernicus Browser (https://browser.dataspace.copernicus.eu/). Satellite images were also used to identify the length of the growing season and crop condition. Water withdrawals were calculated using the modified Blaney-Criddle model of calculating consumptive use (U.S. Bureau of Reclamation, 1992 appendix A) using crop coefficients from Doorenbos and Pruitt (1975), the number of acres with active crops, crop condition, and irrigation system efficiency. The withdrawal equation was modified from "Water withdrawals for irrigation, municipal, mining, thermoelectric-power, and drainage uses in Arizona outside of active management areas, 1991-2000" (Tadayon, 2005) to account for variations in water application.


Data are available as a shapefile for visualization or as a stand-alone csv table for attributes only.

Bureau of Reclamation, 1992, Plan of study and methods manual for Colorado River system consumptive uses and losses report 1985–1990: Bureau of Reclamation, Appendix A, 23 p.

Doorenbos, J. and Pruitt, W.O.,1975, Guidelines for predicting crop water requirements: Irrigation and drainage paper FAO No. 24, p195, https://www.nrc.gov/docs/ML1821/ML18215A282.pdf.

Tadayon, Saeid, 2005, Water withdrawals for irrigation, municipal, mining, thermoelectric-power, and drainage uses in Arizona outside of Active Management Areas, 1991–2000: U.S. Geological Survey Scientific Investigations Report 2004-5293, 28 p, https://doi.org/10.3133/sir20045293.
DOI: 10.5519/qd.oko8crs4
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.15468/dl.mmxamg
title: Occurrence Download

description: A dataset containing 35 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Melanophryniscus admirabilis Di-Bernardo, Maneyro & Grillo, 2006",
 "Year 1974-2024"
 ]
}

 The dataset includes 35 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010199-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10023518
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_00
DOI: 10.5281/zenodo.10023519
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_00
DOI: 10.15468/dl.j5hf8j
title: Occurrence Download

description: A dataset containing 188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Exilisciurus whiteheadi (Thomas, 1887), Exilisciurus exilis (Müller, 1838))"
 ]
}

 The dataset includes 188 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010200-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10023522
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_02
DOI: 10.5281/zenodo.10023523
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_02
DOI: 10.15468/dl.7tzghb
title: Occurrence Download

description: A dataset containing 115 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Witheringia stellata (Greenm.) Hunz."
 ]
}

 The dataset includes 115 records from 51 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010201-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.men9ye
title: Occurrence Download

description: A dataset containing 414 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Yucca periculosa Baker"
 ]
}

 The dataset includes 414 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010202-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.6504123
title: REPIN population analysis in 49 Stenotrophomonas maltophilia genomes

description: This dataset contains the genome sequences of 49 S. maltophilia strains (input.zip) and the processed data from four individual RAREFAN runs. RAREFAN identifies RAYTs REPINS for each supplied genome and a reference genome. Four different strains where used as a reference genome: AA1, AB550 FDARGOOS_649, ISMMS3, and Sm53. The data were processed with default RAREFAN job parameters. Links to the original RAREFAN jobs are given below.
DOI: 10.5281/zenodo.10023520
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_01
DOI: 10.5281/zenodo.10023521
title: welborn_24_streaming_large_scale_electron_microscopy_data_counted_data_part_01
DOI: 10.26030/gmec-d793
title: Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival

description: Saccharomyces cerevisiae flocculation occurs when fermentable sugars are limiting and is therefore considered as a way to enhance the survival chance of Flo-expressing yeast cells. In this paper, the role of Flo1p in mating was demonstrated by showing that the mating efficiency, which contributes to the increased survival rate as well by generating genetic variability, is increased when cells flocculate. This was revealed by liquid growth experiments in a low shear environment and differential transcriptome analysis of FLO1 expressing cells compared to the non-flocculent wild-type cells. The results show that a floc provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation. S. cerevisiae strains BY4742 WT, BY4742::FLO8 and BY4742 [FLO1] were grown in microgravity and 1-g. A transcriptomic analysis was performed and the transcriptome data were integrated with the high quality protein-protein interaction networks. The identified high score sub-networks (qvalue < 0.001) were considered and further evaluated concerning their GO enrichment using a hypogeometric test. The data were from the Ying B-1 experiment.
DOI: 10.15468/dl.p3mmxg
title: Occurrence Download

description: A dataset containing 1429408 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plantago lanceolata L."
 ]
}

 The dataset includes 1429408 records from 5061 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010198-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8mxrsv
title: Occurrence Download

description: A dataset containing 18571 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (Australia)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1907",
 "Year is less than or equal to 1907"
 ]
}

 The dataset includes 18571 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049600-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/frebh5
title: Range table from planktonic foraminifers in ODP Hole 151-912C
DOI: 10.15468/dl.x34es4
title: Occurrence Download

description: A dataset containing 1763 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Buddleja davidii Franch."
 ]
}

 The dataset includes 1763 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097983-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6gtvrx
title: Occurrence Download

description: A dataset containing 2476 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Viburnum odoratissimum Ker Gawl."
 ]
}

 The dataset includes 2476 records from 182 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0313193-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4evgst
title: Occurrence Download

description: A dataset containing 14030 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Parentucellia viscosa (L.) Caruel"
 ]
}

 The dataset includes 14030 records from 341 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0391955-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uupdnx
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bomarea bredemeyeriana Herb."
 ]
}

 The dataset includes 71 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097988-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w64u77
title: Occurrence Download

description: A dataset containing 48 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Ipomoea gigantea (Silva Manso) Choisy"
 ]
}

 The dataset includes 48 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098016-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2qv24f
title: Occurrence Download

description: A dataset containing 2492 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Dianthus giganteus d'Urv., Dianthus gratianopolitanus Vill.)",
 "Geometry POLYGON((-9.36035 44.71551,-10.59082 42.81152,-11.82129 36.80928,-7.69043 36.17336,-3.38379 35.88905,3.12012 38.13456,9.18457 38.20366,11.7334 37.16032,12.78809 34.74161,17.09473 33.79741, 23.15918 34.23451,30.10254 32.62087,33.2666 32.99024,35.72754 35.03,33.00293 35.53223,28.69629 35.17381,28.34473 36.31513,25.7959 37.50973,24.91699 39.90974,28.78418 40.6473,30.71777 41.17865,36.87012 45.213,38.18848 46.98025,38.71582 47.7541,39.94629 47.93107,40.20996 49.61071,37.0459 50.34546,35.72754 50.40152,33.79395 52.26816,31.68457 51.94426,31.4209 53.27835,32.56348 53.43572,30.98145 54.77535,30.89355 55.52863,28.43262 56.02295,27.20215 57.65716,27.37793 58.30949,27.90527 59.17593,29.66309 59.88894,27.6416 60.58697,31.50879 62.75473,28.78418 69.83962,30.89355 70.28912,29.22363 71.55274,21.75293 71.30079,14.28223 70.14036,11.38184 67.47492,4.87793 63.66576,-5.53711 71.52491,-10.63477 71.69129,-21.5332 67.74276,-28.56445 65.36684,-24.3457 61.35461,-9.36035 44.71551))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1980",
 "Year is less than or equal to 2021"
 ]
}

 The dataset includes 2492 records from 48 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239134-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5rdynk
title: Occurrence Download

description: A dataset containing 1714213 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Pl@ntNet observations"
 ]
}

 The dataset includes 1714213 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098000-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.35hg52
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bathytoshia centroura (Mitchill, 1815)",
 "Year 1000-1899"
 ]
}

 The dataset includes 5 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0272910-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nwhscg
title: Occurrence Download

description: A dataset containing 1308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "CoordinateUncertaintyInMeters 0.0-100.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Geranium richardsonii Fisch. & Trautv.",
 "Year 1990-2023"
 ]
}

 The dataset includes 1308 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097981-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.arzfnz
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is North America",
 "CoordinateUncertaintyInMeters 0.0-100.0",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Delphinium barbeyi (Huth) Huth",
 "Year 1990-2023"
 ]
}

 The dataset includes 211 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097970-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nbgh3d
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cophixalus amabilis Kraus, 2012"
 ]
}

 The dataset includes 8 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0295948-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9f4ewb
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Acantharia",
 "HasCoordinate is true",
 "Country is one of (United Kingdom of Great Britain and Northern Ireland)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239153-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rg7hvy
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bomarea angustissima Killip"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0097975-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ax8a7
title: Occurrence Download

description: A dataset containing 245 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Filosia",
 "HasCoordinate is true",
 "Country is one of (United Kingdom of Great Britain and Northern Ireland)",
 "HasGeospatialIssue is false",
 "Year is greater than 2009"
 ]
}

 The dataset includes 245 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0239154-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ff7vge
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bomarea caucana Alzate"
 ]
}

 The dataset includes 12 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0098007-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.