cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17901552
title: Quantifying polydopamine shell hydration in core–shell colloids by analytical ultracentrifugation: Implications for self-assembly and structural color of photonic crystals (Data)

description: This is the raw and processed data for the main manuscript and supporting information:

Quantifying polydopamine shell hydration in core–shell colloids by analytical ultracentrifugation: Implications for self-assembly and structural color of photonic crystals

A readme file containing all descriptions can be found in the main folder. All data are sorted according to their appearance in the figures of the main manuscript and supporting information.

Abstract:

Polystyrene–polydopamine (PS@PDA) core–shell particles are widely used as building blocks to form colloidal photonic crystals with tunable light absorption. Increasing the PDA shell thickness typically leads to more saturated colors but also diminishes the structural order of the resulting assemblies. To understand this phenomenon, we correlate particle properties in solution with the structural properties of the formed colloidal crystals. In particular, we focus on correlating the water swellability of the PDA shell with the agglomeration behavior upon drying. To this end, we combine density variation sedimentation velocity (SV) and buoyant density gradient equilibrium (DGE) experiments in analytical ultracentrifugation (AUC) to quantify the hydration of the PDA shell. Density variation SV-AUC in H2O–D2O mixtures yields the particle’s anhydrous density, while DGE-AUC, using an in situ formed sucrose gradient, reveals the buoyant density at the isopycnic position in the measurement cell. Mass balance analysis then enables quantification of the water mass incorporated within the PDA shell. These combined experiments show that PDA shell hydration generally increases with shell thickness and depends on the reaction parameters chosen for the shell formation process. The structural order and photonic properties of colloidal crystals formed from the different PS@PDA particles decrease with increasing shell thickness, indicating that more swollen shells promote aggregation during self-assembly and thus disturb structural order. Advanced AUC experiments therefore provide access to key physicochemical characteristics of functional colloids and establish valuable process–structure–property relations for the design of colloidal photonic crystals.
DOI: 10.15468/dl.veebby
title: Occurrence Download

description: A dataset containing 507 records in GBIF matching the query:
SELECT
 '560' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 56.135291543055025
 AND decimalLatitude &lt;= 61.2993700571118
 AND decimalLongitude &gt;= 129.519183390344
 AND decimalLongitude &lt;= 150.2980624689629
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 507 records were derived from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005212-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18410596
title: Wavelet-Transformer-GHG-Prediction
DOI: 10.5281/zenodo.18410597
title: Wavelet-Transformer-GHG-Prediction
DOI: 10.5281/zenodo.15554220
title: NMR FID for Design and In Vitro Evaluation of Novel GC373-Like SARS-CoV-2 Main Protease Inhibitors

description: NMR FID data for synthetic compounds described in the manuscript "Design and In Vitro Evaluation of Novel GC373-Like SARS-CoV-2 Main Protease Inhibitors"
DOI: 10.5281/zenodo.15554221
title: NMR FID for Design and In Vitro Evaluation of Novel GC373-Like SARS-CoV-2 Main Protease Inhibitors

description: NMR FID data for synthetic compounds described in the manuscript "Design and In Vitro Evaluation of Novel GC373-Like SARS-CoV-2 Main Protease Inhibitors"
DOI: 10.15468/dl.gt4jwq
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coenobita rubescens",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 51 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005227-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g8bkgq
title: Occurrence Download

description: A dataset containing 164 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.occurrencestatus = 'PRESENT'
 AND (GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '2765942', TRUE) OR GBIF_STRINGARRAYCONTAINS(occurrence.classifications['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c'], '2765940', TRUE))
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 164 records were derived from 637 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005180-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.thsmze
title: Occurrence Download

description: A dataset containing 564 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Asia",
 "Country is Indonesia",
 "Geometry POLYGON((43.34078 -15.04163,163.65922 -15.04163,163.65922 33.04163,43.34078 33.04163,43.34078 -15.04163))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Hipposideros larvatus",
 "Year 2000-2026"
 ]
}

 The dataset includes 564 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005228-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/hgds-0m93
title: "Transformed Image Examples used in \"Reducing Domain Shift in Road Sign Detection with Image-Conditioned Diffusion Models\""

description: "This dataset provides sample images transformed by an image-conditional diffusion model."
DOI: 10.15468/dl.fjaj87
title: Occurrence Download

description: A dataset containing 986882 species occurrences available in GBIF matching the query:
{
 "and" : [
 "KingdomKey is Plantae",
 "Country is India",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Human Observation, Machine Observation)"
 ]
}

 The dataset includes 986882 records from 239 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005205-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.31179313
title: S&P 500 stock price data

description: Daily closing prices of all constituent companies in the S&P 500 index as of October 5, 2025, collected from January 2022 to September 2025. The data was obtained using the yahoo finance api.
DOI: 10.6084/m9.figshare.31179313.v1
title: S&P 500 stock price data

description: Daily closing prices of all constituent companies in the S&P 500 index as of October 5, 2025, collected from January 2022 to September 2025. The data was obtained using the yahoo finance api.
DOI: 10.15468/dl.dpngr5
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Bassia hyssopifolia",
 "Year 2000-2026"
 ]
}

 The dataset includes 101 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005230-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wu7ax
title: Occurrence Download

description: A dataset containing 208 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coenobita spinosus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 208 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005231-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18410637
title: Attenuation data from the paper "Unveiling the seismic attenuation characteristics in the mantle beneath Southeast Asia: Insights into mantle dynamics and tectonic processes"

description: The results of the seismic attenuation measurement from the paper  "Unveiling the seismic attenuation characteristics in the mantle beneath Southeast Asia: Insights into mantle dynamics and tectonic processes".
DOI: 10.5281/zenodo.18410636
title: Attenuation data from the paper "Unveiling the seismic attenuation characteristics in the mantle beneath Southeast Asia: Insights into mantle dynamics and tectonic processes"

description: The results of the seismic attenuation measurement from the paper  "Unveiling the seismic attenuation characteristics in the mantle beneath Southeast Asia: Insights into mantle dynamics and tectonic processes".
DOI: 10.5281/zenodo.18410143
title: The Role of Digitalization in Improving the Performance of the Batik Brand to Enhance SDGs 12

description:
DOI: 10.5281/zenodo.18410142
title: The Role of Digitalization in Improving the Performance of the Batik Brand to Enhance SDGs 12

description:
DOI: 10.15468/dl.2vhpxj
title: Occurrence Download

description: A dataset containing 433 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coenobita variabilis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 433 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005233-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8arcs8
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanolagus Kobyliansky, 1986",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-16.6672 18.7728,-16.5468 17.7486,-16.9133 16.7746,-17.0265 15.925,-17.4754 15.299,-17.9607 15.0106,-18.0159 14.6088,-17.2825 13.9103,-17.2971 12.4437,-17.1163 12.0176,-16.8424 11.8396,-16.9887 11.3363,-16.91 11.0108,-16.709 10.8496,-9.0352 10.8496,-9.0352 19.8496,-16.8896 19.8496,-17.0371 19.3335,-16.6672 18.7728))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014112-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f28j2c
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanolagus Kobyliansky, 1986",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((-10.6036 29.6447,-11.635 28.8496,-9.0352 28.8496,-9.0352 33.4562,-9.6631 32.8696,-9.7766 32.3158,-10.3241 31.5424,-10.3942 30.6542,-10.1716 30.2225,-10.6036 29.6447))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014114-250525065834625/datasets/export for details.
DOI: 10.25625/4laipc
title: Precipitation_stable_water_isotopes_2021-2022

description: Time series of stable water isotope data from precipitation/throughfall samples, taken from custom-built rain collectors on the RTG2300 IMP plots (quintets 3, 4, 6, 8) and the nearby open-sky climate-stations. One collector per plot. The obtained water samples were analyzed for the isotopic compositions of hydrogen and oxygen at the Center for Stable Isotope Research and Analysis (KOSI, Georg-August-University Göttingen, Germany), using a high temperature conversion analyzer (TC/EA, Thermo Electron Corporation, Bremen, Germany) coupled via a Con-Flo III interface to a Delta V Plus isotope ratio mass spectrometer (Thermo Electron Corporation, Bremen, Germany).
DOI: 10.25625/4laipc/c8eng6
title: precipitation_stable_water_isotopes_metadata.tab

description: metadata
DOI: 10.25625/4laipc/ekn7y2
title: precipitation_stable_water_isotopes_2021-2022.tab

description: stable water isotope data
DOI: 10.25625/y0ux4i
title: Stable_water_isotopes_2021

description: Soil and xylem samples were taken once in summer 2021 from all plots of quintets 3, 4, 6, 8 of the RTG2300 sites. We took stem cores at breast height from n=8 trees (1 core per tree) and 4 soil cores, each in the middle between a pair of trees. Soil cores were separated in 7 depth intervals. Water was extracted from all samples using cryogenic vacuum distillation and subsequently analyzed for the isotopic compositions of hydrogen and oxygen at the Center for Stable Isotope Research and Analysis (KOSI, Georg-August-University Göttingen, Germany), using a high temperature conversion analyzer (TC/EA, Thermo Electron Corporation, Bremen, Germany) coupled via a Con-Flo III interface to a Delta V Plus isotope ratio mass spectrometer (Thermo Electron Corporation, Bremen, Germany). Gravimetric water content was calculated from fresh and oven-dried (105°C) sample weight.
DOI: 10.25625/y0ux4i/9scbki
title: stable_water_isotopes-soil_xylem-2021.tab

description: Data
DOI: 10.25625/y0ux4i/xhixvp
title: Metadata_stable_water_isotopes_2021.tab

description: Metadata for the file "stable_water_isotopes-soil_xylem-2021.csv"
DOI: 10.15468/dl.mwuvm5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanolagus Kobyliansky, 1986",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((17.9648 19.8496,8.9648 19.8496,8.9648 10.8496,17.9648 10.8496,17.9648 19.8496))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014116-250525065834625/datasets/export for details.
DOI: 10.15468/dl.ztt83n
title: Occurrence Download

description: A dataset containing 1649 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis Daudin, 1802",
 "Year 2020-2025"
 ]
}

 The dataset includes 1649 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014117-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9qudze
title: Occurrence Download

description: A dataset containing 1649 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anolis Daudin, 1802",
 "Year 2020-2025"
 ]
}

 The dataset includes 1649 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014118-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25625/0addbm
title: Stable_water_isotopes_2022

description: The data set contains stable water isotope data measured on water extracted from (1) soil samples of different depths and (2) tree xylem of suberized twigs of 12 different trees. Samples were taken (1) with a Pürckhauer soil corer and (2) by tree climbers on RTG2300 plots 6.1, 6.2 and 6.3 during summer 2022 in weekly intervals and were extracted using cryogenic vacuum distillation. The obtained water samples were analyzed for the isotopic compositions of hydrogen and oxygen at the Center for Stable Isotope Research and Analysis (KOSI, Georg-August-University Göttingen, Germany), using a high temperature conversion analyzer (TC/EA, Thermo Electron Corporation, Bremen, Germany) coupled via a Con-Flo III interface to a Delta V Plus isotope ratio mass spectrometer (Thermo Electron Corporation, Bremen, Germany).
DOI: 10.25625/0addbm/k6o47i
title: tree_water_isotopes_22.tab

description: :unav
DOI: 10.25625/0addbm/thfv5n
title: stable_water_isotopes_metadata.tab

description: Explanations to soil and tree water isotope data files
DOI: 10.25625/0addbm/zq911o
title: soil_water_isotopes_22.tab

description: :unav
DOI: 10.15468/dl.z2hzqm
title: Occurrence Download

description: A dataset containing 1273119 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphenisciformes"
 ]
}

 The dataset includes 1273119 records from 224 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014078-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.27t7ac
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Melanolagus Kobyliansky, 1986",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((9.2698 2.0276,9.1702 1.8496,17.9648 1.8496,17.9648 10.8496,8.9648 10.8496,8.9648 2.8113,8.9984 2.8234,9.2654 3.2175,9.4253 3.0783,9.2698 2.0276))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014119-250525065834625/datasets/export for details.
DOI: 10.25625/spi2c4
title: dendrometer_and_climate_daily_2019-2022

description: Daily time series of stem diameter measurements, taken with high-resolution dendrometers (DC2 and DC3, Ecomatik, Munich, Germany). Measurements were taken on the 20 IMP plots of the RTG2300, i.e. quintets 3, 4, 6 and 8. Per plot, four trees per species were equipped with a dendrometer. The data set also contains variables derived from dendrometer data with the treenetproc R package, including growth, maximum daily shrinkage and daily minimum tree water deficit. Additionally, the data set includes environmental variables, which were gathered on the study plots and used for modeling of tree water deficit, such as precipitation, VPD, temperature and soil moisture. For detailed description of the data columns, see the metadata excel-file. Data is processed using the treenetproc R package, which includes exclusion of outliers, correction of jumps and calculation of variables, such as tree water deficit and irreversible growth. Then, it was summarized to daily values and merged with climate data. This data set covers years 2019-2022.
DOI: 10.6084/m9.figshare.29026406.v1
title: Data for manuscript "Integrated multi-dimensional approaches reveal adaptations of vascular plants to aquatic environments"

description: "bait_peps.zip", the protein sequences of bait genes. These sequences were used for SWIPE search."swipe_peps.7z", the sequence of homologs in all species generated from the SWIPE search."swipe_aln_cln_aligned_peps.zip", the aligned sequences of homologs. These files were used to construct maximum likelihood trees and count gene copy numbers."Taxon_file.xlsx", the species' full names and abbreviations used in analyses.These datasets correspond to the Supplementary Figs. 6-19, and the Supplementary Tables 14 and 15.If you have any questions, please contact Lingyun Chen: lychen83@qq.com
DOI: 10.5281/zenodo.11191739
title: Training data composition determines machine learning generalization and biological rule discovery

description: Github: https://github.com/csi-greifflab/negative-class-optimization

Preprint: https://www.biorxiv.org/content/10.1101/2024.06.17.599333v1
DOI: 10.5281/zenodo.11191740
title: Training data composition determines machine learning generalization and biological rule discovery

description: Github: https://github.com/csi-greifflab/negative-class-optimization

Preprint: https://www.biorxiv.org/content/10.1101/2024.06.17.599333v1