cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24818709.v1
title: Dataset for Intelligent Searching System on Resumes and Legal documents

description: This dataset includes codes and dataset about intelligent searching system on resume and legal documents.
DOI: 10.6084/m9.figshare.29128235.v1
title: figures and data

description: figures and data
DOI: 10.6084/m9.figshare.3558645.v1
title: Appendix C. Density and isotopic values of sampled invertebrate taxa.

description: Density and isotopic values of sampled invertebrate taxa.
DOI: 10.6084/m9.figshare.3811299.v1
title: numeric trait data

description: All numeric trait data, both raw data values and normalised.<br>File: Schizosaccharomyces-pombe-numeric-trait-data.tar.gz
DOI: 10.17632/2z3ydnwpzk
title: Experimental investigations of mineral-organic chondritic analogs under hydrothermal conditions: implications for carbonaceous asteroids

description: Data set for paper Serra et al. Experimental investigations of mineral-organic chondritic analogs under hydrothermal conditions: implications for carbonaceous asteroids
DOI: 10.6084/m9.figshare.13663859.v1
title: Source data supporting "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions"

description: Source data supporting "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".
DOI: 10.6084/m9.figshare.20280060.v1
title: data.xlsx

description: This is excel data of paper.
DOI: 10.6084/m9.figshare.26509864.v1
title: date set

description: This dataset contains the minimum required data to reproduce the results of the following paper:　”Utility of neuromelanin-sensitive MRI in the diagnosis of dementia with Lewy bodies<b>”</b>
DOI: 10.6084/m9.figshare.26757286.v1
title: Additional file 2 of AI-driven convolutional neural networks for accurate identification of yellow fever vectors

description: Additional file 2: Database S1.
DOI: 10.21227/x5c0-yg36
title: "Microstrip Antenna Dataset for S-Parameters and 2-D Radiation Patterns"

description: "The dataset contains approximately 190,000 microstrip-antenna samples. Each sample includes S-parameters evaluated at 101 frequency points, together with a 17-dimensional encoded-domain representation of the S-parameters based on a Lorentzian-resonance formulation, as well as 2-D far-field radiation patterns sampled at 11 frequency points. The dataset covers diverse operating conditions spanning 0.5\u201310 GHz and substrate permittivities \u03b5r\u200b\u2208[2,10], and includes S-parameter responses with widely varying resonance amplitudes and quality factors. It is well suited for training antenna performance evaluators and inverse-design networks."
DOI: 10.5281/zenodo.18410125
title: Species lists and trait data in support of the manuscript "Temporal insights into afforestation: a 25-year study of woodland expansion"

description: Fungal species presence/absence matrices (EMF_species_list.csv and sapro_list.csv);

EMF species traits (EMF_spore_size.csv and EMF_sporocarp_size.csv);

Saprotroph species traits (sapro_traits.csv);

Plant species cover matrix (plant_list.csv);

Plant species traits (plant_traits.csv).
DOI: 10.5281/zenodo.18410124
title: Species lists and trait data in support of the manuscript "Temporal insights into afforestation: a 25-year study of woodland expansion"

description: Fungal species presence/absence matrices (EMF_species_list.csv and sapro_list.csv);

EMF species traits (EMF_spore_size.csv and EMF_sporocarp_size.csv);

Saprotroph species traits (sapro_traits.csv);

Plant species cover matrix (plant_list.csv);

Plant species traits (plant_traits.csv).
DOI: 10.5281/zenodo.18410135
title: Classic Graph Datasets for Node Classification
DOI: 10.5281/zenodo.18410134
title: Classic Graph Datasets for Node Classification
DOI: 10.57967/hf/7668
title: kompsat_image_text_dataset
DOI: 10.15468/dl.22mcn5
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monstrilla filogranarum",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005163-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g83vuk
title: Occurrence Download

description: A dataset containing 215 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prainea limpato",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 215 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005164-260126135527185/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.31177786.v1
title: <b>The pan-genome of 1,107 spotted sea bass accessions reveals </b><b>gene evolution patterns</b><b> during domestication selection</b>

description: Spotted sea bass (<i>Lateolabrax maculatus</i>) is an ecologically and economically important species that supports a large-scale aquaculture industry in China. However, most farmed populations have not undergone systematic breeding programs and are characterized by undocumented empirical selection and poorly defined target traits. Understanding genetic diversity and gene evolutionary patterns for farmed populations is critical for designing appropriate breeding management for the future. In this study, we assembled a chromosome-level reference genome (636.65 Mb) and performed population genetics analyses using 1,107 representative wild and farmed accessions. Significant genetic differentiation and reduced genetic diversity was observed for farmed populations. Pan-genome of 1,107 accessions further identified 86.48 Mb of non-reference novel sequences (NRNS) and 206 novel genes absent from the reference genome. Gene presence/absence variation (PAV) analysis revealed farmed populations encode fewer genes than wild counterparts, implying gene loss and negative selection during domestication process. Lost genes were enriched for immune response and nervous system development, indicating the urgent need introducing wild accessions as essential genetic resources for future breeding programs. Notably, selection signatures and comparative PAV analyses across independent farmed populations revealed parallel domestication effects at both loci and gene levels, suggesting similar selective pressures despite different aquaculture practices and domestication histories. Our study provides the first pan-genome of spotted sea bass that deciphers gene evolution in domestication selection and delivers critical insights for sustainable breeding programs for farmed aquatic species.
DOI: 10.6084/m9.figshare.31177786
title: <b>The pan-genome of 1,107 spotted sea bass accessions reveals </b><b>gene evolution patterns</b><b> during domestication selection</b>

description: Spotted sea bass (<i>Lateolabrax maculatus</i>) is an ecologically and economically important species that supports a large-scale aquaculture industry in China. However, most farmed populations have not undergone systematic breeding programs and are characterized by undocumented empirical selection and poorly defined target traits. Understanding genetic diversity and gene evolutionary patterns for farmed populations is critical for designing appropriate breeding management for the future. In this study, we assembled a chromosome-level reference genome (636.65 Mb) and performed population genetics analyses using 1,107 representative wild and farmed accessions. Significant genetic differentiation and reduced genetic diversity was observed for farmed populations. Pan-genome of 1,107 accessions further identified 86.48 Mb of non-reference novel sequences (NRNS) and 206 novel genes absent from the reference genome. Gene presence/absence variation (PAV) analysis revealed farmed populations encode fewer genes than wild counterparts, implying gene loss and negative selection during domestication process. Lost genes were enriched for immune response and nervous system development, indicating the urgent need introducing wild accessions as essential genetic resources for future breeding programs. Notably, selection signatures and comparative PAV analyses across independent farmed populations revealed parallel domestication effects at both loci and gene levels, suggesting similar selective pressures despite different aquaculture practices and domestication histories. Our study provides the first pan-genome of spotted sea bass that deciphers gene evolution in domestication selection and delivers critical insights for sustainable breeding programs for farmed aquatic species.
DOI: 10.5281/zenodo.18409212
title: SuperDARN data in netCDF format (2007-May)

description: 2007-May SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6592028
title: SuperDARN data in netCDF format (2007-May)

description: 2007-May SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.15468/dl.sp9756
title: Occurrence Download

description: A dataset containing 900 records in GBIF matching the query:
SELECT
 '556' 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;= 100.73714263693424
 AND decimalLongitude &lt;= 118.65636510707594
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 900 records were derived from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005156-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c2yrsx
title: Occurrence Download

description: A dataset containing 125 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Coenobita carnescens",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 125 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005165-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18409596
title: Codes for "Marine Heatwaves Shift Ocean Net Primary Productivity from the Tropics to the Poles"

description: Codes, detailed descriptions, and examples supporting the manuscript “Marine Heatwaves Shift Ocean Net Primary Productivity from the Tropics to the Poles” are provided. In addition, MATLAB (.mat) files containing the fitted results for the CBPM and CAFE datasets under marine heatwave and positive sea surface temperature anomaly (SSTA) conditions are included.
DOI: 10.15468/dl.hs6qan
title: Occurrence Download

description: A dataset containing 441 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pseudolmedia spuria",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 441 records from 45 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005166-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gtyg44
title: Occurrence Download

description: A dataset containing 62294 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tubificoides",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 62294 records from 150 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005141-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9p5p2r
title: Occurrence Download

description: A dataset containing 30198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Tenodera sinensis"
 ]
}

 The dataset includes 30198 records from 80 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005167-260126135527185/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.31177963
title: Supplementary Material for: Prognostic Role of Circular RNAs in Mantle Cell Lymphoma: A Competing Endogenous RNA Network Analysis

description: Objective: This study evaluated the prognostic role of circular RNAs (circRNAs) in individuals diagnosed with mantle cell lymphoma (MCL), using the framework of the competing endogenous RNA (ceRNA) network model.
Methods: Differentially expressed circRNAs were identified from the GSE159808 dataset, and differentially expressed messenger RNAs (mRNAs) were extracted from GSE32018. Corresponding microRNAs (miRNAs) were retrieved to construct a ceRNA regulatory network relevant to MCL. Functional enrichment analysis and survival analysis were performed on 35 mRNAs incorporated in the ceRNA network to identify transcripts associated with survival outcomes in MCL. A prognostically relevant ceRNA subnetwork was then constructed based on these results.
Results: Thirteen circRNAs (9 upregulated, 4 downregulated) and 457 differentially expressed mRNAs were identified. The initial ceRNA network included 11 circRNAs, 40 miRNAs, and 35 mRNAs. Gene Ontology analysis indicated enrichment in pathways related to dentin-containing tooth development, the plasma membrane signaling receptor complex, and growth factor receptor binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant involvement in the B-cell receptor signaling pathway, Fc gamma receptor-mediated phagocytosis, and the Wnt signaling pathway. Survival analysis identified six mRNAs significantly associated with overall survival in individuals with MCL. These results were used to derive a refined prognostic ceRNA network consisting of 6 mRNAs, 7 miRNAs, and 6 circRNAs.
Conclusion: CircRNAs may regulate MCL prognosis by modulating miRNA–mRNA interactions within the ceRNA network. These findings suggest a regulatory mechanism by which circRNAs contribute to molecular pathways influencing disease progression and survival in MCL.
DOI: 10.6084/m9.figshare.31177963.v1
title: Supplementary Material for: Prognostic Role of Circular RNAs in Mantle Cell Lymphoma: A Competing Endogenous RNA Network Analysis

description: Objective: This study evaluated the prognostic role of circular RNAs (circRNAs) in individuals diagnosed with mantle cell lymphoma (MCL), using the framework of the competing endogenous RNA (ceRNA) network model.
Methods: Differentially expressed circRNAs were identified from the GSE159808 dataset, and differentially expressed messenger RNAs (mRNAs) were extracted from GSE32018. Corresponding microRNAs (miRNAs) were retrieved to construct a ceRNA regulatory network relevant to MCL. Functional enrichment analysis and survival analysis were performed on 35 mRNAs incorporated in the ceRNA network to identify transcripts associated with survival outcomes in MCL. A prognostically relevant ceRNA subnetwork was then constructed based on these results.
Results: Thirteen circRNAs (9 upregulated, 4 downregulated) and 457 differentially expressed mRNAs were identified. The initial ceRNA network included 11 circRNAs, 40 miRNAs, and 35 mRNAs. Gene Ontology analysis indicated enrichment in pathways related to dentin-containing tooth development, the plasma membrane signaling receptor complex, and growth factor receptor binding. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated significant involvement in the B-cell receptor signaling pathway, Fc gamma receptor-mediated phagocytosis, and the Wnt signaling pathway. Survival analysis identified six mRNAs significantly associated with overall survival in individuals with MCL. These results were used to derive a refined prognostic ceRNA network consisting of 6 mRNAs, 7 miRNAs, and 6 circRNAs.
Conclusion: CircRNAs may regulate MCL prognosis by modulating miRNA–mRNA interactions within the ceRNA network. These findings suggest a regulatory mechanism by which circRNAs contribute to molecular pathways influencing disease progression and survival in MCL.
DOI: 10.6084/m9.figshare.31177966
title: Supplementary Material for: Pharmacological STING Activation Enhances Autophagy-Mediated Clearance of Mycobacterium tuberculosis in Human Macrophages

description: Objective: The cGAS-STING pathway is a critical sensor in the innate immune response to intracellular pathogens, yet its therapeutic potential for augmenting macrophage-mediated control of Mycobacterium tuberculosis (Mtb) remains incompletely understood. This study investigated whether pharmacological activation of the STING pathway could enhance autophagy to promote Mtb clearance in human macrophages.
Methods: Human THP-1 monocytes were differentiated into macrophages and infected with Mtb. The effects of the STING agonist MIW815 (ADU-S100) on Mtb phagocytosis, intracellular bacterial survival, and autophagic flux were assessed using a combination of molecular and cellular techniques, including qRT-PCR, western blotting, colony-forming unit (CFU) assays, and confocal immunofluorescence microscopy. The dependency on the cGAS-STING pathway was confirmed using siRNA-mediated gene silencing.
Results: Pharmacological activation of STING with ADU-S100 significantly enhanced Mtb phagocytosis and subsequent intracellular clearance. This enhanced bactericidal activity was mechanistically linked to an increase in autophagic flux, as evidenced by elevated LC3-II protein levels and significantly increased colocalization of Mtb with lysosomal compartments. Importantly, treatment with the autophagy inhibitor hydroxychloroquine or silencing of cGAS significantly reversed these phenotypes, confirming the pivotal role of the STING-autophagy axis.
Conclusion: Activating the STING pathway with ADU-S100 is a potent host-directed strategy to bolster macrophage autophagy and enhance the elimination of intracellular Mtb. This provides a strong rationale for exploring STING agonists as a novel therapeutic intervention for tuberculosis, addressing a significant and clinically relevant challenge in infectious disease.
DOI: 10.6084/m9.figshare.31177966.v1
title: Supplementary Material for: Pharmacological STING Activation Enhances Autophagy-Mediated Clearance of Mycobacterium tuberculosis in Human Macrophages

description: Objective: The cGAS-STING pathway is a critical sensor in the innate immune response to intracellular pathogens, yet its therapeutic potential for augmenting macrophage-mediated control of Mycobacterium tuberculosis (Mtb) remains incompletely understood. This study investigated whether pharmacological activation of the STING pathway could enhance autophagy to promote Mtb clearance in human macrophages.
Methods: Human THP-1 monocytes were differentiated into macrophages and infected with Mtb. The effects of the STING agonist MIW815 (ADU-S100) on Mtb phagocytosis, intracellular bacterial survival, and autophagic flux were assessed using a combination of molecular and cellular techniques, including qRT-PCR, western blotting, colony-forming unit (CFU) assays, and confocal immunofluorescence microscopy. The dependency on the cGAS-STING pathway was confirmed using siRNA-mediated gene silencing.
Results: Pharmacological activation of STING with ADU-S100 significantly enhanced Mtb phagocytosis and subsequent intracellular clearance. This enhanced bactericidal activity was mechanistically linked to an increase in autophagic flux, as evidenced by elevated LC3-II protein levels and significantly increased colocalization of Mtb with lysosomal compartments. Importantly, treatment with the autophagy inhibitor hydroxychloroquine or silencing of cGAS significantly reversed these phenotypes, confirming the pivotal role of the STING-autophagy axis.
Conclusion: Activating the STING pathway with ADU-S100 is a potent host-directed strategy to bolster macrophage autophagy and enhance the elimination of intracellular Mtb. This provides a strong rationale for exploring STING agonists as a novel therapeutic intervention for tuberculosis, addressing a significant and clinically relevant challenge in infectious disease.