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

description: A dataset containing 3967188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 {
 "or" : [
 "Issue is Geodetic datum assumed WGS84",
 "Issue is Coordinate rounded",
 "Issue is Country derived from coordinates"
 ]
 },
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset includes 3967188 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0065258-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-59354
title: Redemption tidings, vol. 39, nos. 1-52, 4 Jan. - 27 Dec. 1963

description: [description english/roman)] Issued weekly. "A full gospel magazine" -- subtitle.
DOI: 10.15468/dl.q5sacb
title: Occurrence Download

description: A dataset containing 118278 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Specimen"
 ]
 },
 "CoordinateUncertaintyInMeters 0.0-10000.0",
 "Country is United States of America",
 "Geometry POLYGON((-124.535 32.531,-114.131 32.531,-114.131 42.01,-124.535 42.01,-124.535 32.531))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Fungi",
 "Year 1900-2022"
 ]
}

 The dataset includes 118278 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0392493-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qr6b96
title: Occurrence Download

description: A dataset containing 372352 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Batumi Raptor Count (BRC) - Autumn migration data"
 ]
}

 The dataset includes 372352 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019334-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qybydp
title: Occurrence Download

description: A dataset containing 1451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bubo virginianus (J.F.Gmelin, 1788)",
 "Country is Mexico"
 ]
}

 The dataset includes 1451 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004517-160623103540712/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2ym4kh
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Neomensularia F.Wu, L.W.Zhou & Y.C.Dai, 2016"
 ]
}

 The dataset includes 51 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031877-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dku9x7
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Clusia cuneifolia Cuatrec."
 ]
}

 The dataset includes 87 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004517-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrubjb
title: Occurrence Download

description: A dataset containing 629327 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((2.479608666666667 32.097476, 2.479608666666667 49.184106666666665, -31.565747 49.184106666666665, -31.565747 32.097476, 2.479608666666667 32.097476))",
 "EventDate is 2019-09-01,2019-09-30"
 ]
}

 The dataset includes 629327 records from 715 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031873-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4fhy7m
title: Occurrence Download

description: A dataset containing 55 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Spain",
 "Country is Portugal"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Caloplaca pulchrevirens (Anzi) Jatta"
 ]
}

 The dataset includes 55 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008476-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.prqbbm
title: Occurrence Download

description: A dataset containing 1237201 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cygnus olor (J.F.Gmelin, 1789)"
 ]
}

 The dataset includes 1237201 records from 543 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004517-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ndd0qk
title: Occurrence Download

description: A dataset containing 1003 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Stenocercus guentheri (Boulenger, 1885)"
 ]
}

 The dataset includes 1003 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0031682-191105090559680/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bm2fqs
title: Occurrence Download

description: A dataset containing 17151 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Drynaria (Bory) J.Sm."
 ]
}

 The dataset includes 17151 records from 209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039097-231002084531237/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uv3ee2
title: Occurrence Download

description: A dataset containing 433 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Myrmotherula assimilis Pelzeln, 1868"
 ]
}

 The dataset includes 433 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004517-170826194755519/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5yt32n
title: Occurrence Download

description: A dataset containing 74378 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Acer L."
 ]
}

 The dataset includes 74378 records from 412 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008719-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kpuz5s
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is China",
 "Country is Chinese Taipei"
 ]
 },
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oreolalax liangbeiensis Liu & Fei, 1979"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0140464-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yk4tdc
title: Occurrence Download

description: A dataset containing 21078194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 21078194 records from 3212 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0182639-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48597/32fh-d74u
title: Measurement of OC/EC at Niembro

description: Measurement of OC/EC at Niembro
DOI: 10.15468/dl.yb7z42
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Maxillaria miniata (Lindl.) L.O.Williams"
 ]
}

 The dataset includes 74 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109915-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u4n3gq
title: Occurrence Download

description: A dataset containing 4715 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.41977 6.52475,-74.45817 6.52376,-74.44777 6.41438,-74.33854 6.41805,-74.34992 6.52781,-74.41977 6.52475))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 4715 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109917-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9z7z9c
title: Occurrence Download

description: A dataset containing 1031506 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cettia cetti (Temminck, 1820)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 1031506 records from 1505 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109914-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11152388
title: Dataset related to "Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution"

description: Three .zip files contain the PDB files, mature protein sequences (without predicted signal peptides), and corresponding JSON files from AlphaFold2 containing pLDDT scores.

Two .output files contain the all-vs-all sequence and structural similarity scores.
DOI: 10.5281/zenodo.11152389
title: Dataset related to "Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution"

description: Three .zip files contain the PDB files, mature protein sequences (without predicted signal peptides), and corresponding JSON files from AlphaFold2 containing pLDDT scores.

Two .output files contain the all-vs-all sequence and structural similarity scores.
DOI: 10.15468/dl.w6cmt5
title: Occurrence Download

description: A dataset containing 428819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-74.33663 6.91561,-74.85761 6.58372,-74.9144 5.89188,-74.32419 5.85441,-73.99142 6.26649,-73.95374 6.74061,-74.33663 6.91561))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chordata"
 ]
}

 The dataset includes 428819 records from 104 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0109916-240626123714530/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.15102576
title: Additional file 4 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 4 Table S4. Identification of novel miRNAs in sedr pollen. Nine novel miRNAs were predicted in sedr pollen using Mirnovo software. miRNAs sequences and theirs coverage features are presented in this table.
DOI: 10.6084/m9.figshare.15102567
title: Additional file 1 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 1 Table S1. Identification of known miRNAs in sunflower pollen. The clean sRNA reads were aligned against the miRBase database which resulted in the identification of 495 shared miRNAs in two samples.
DOI: 10.6084/m9.figshare.8286839
title: Additional file 2: of Retrovirus insertion site analysis of LGL leukemia patient genomes

description: Table S1. Results of 10 simulated runs to determine how the proportion of infected cells and the length of the retrovirus affects detection by the insertion pipeline. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.15102570
title: Additional file 2 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 2 Table S2. Identification of known miRNAs in sedr pollen. The clean sRNA reads were aligned against the miRBase database which resulted in the identification of 423 shared miRNAs in two samples.
DOI: 10.6084/m9.figshare.8286839.v1
title: Additional file 2: of Retrovirus insertion site analysis of LGL leukemia patient genomes

description: Table S1. Results of 10 simulated runs to determine how the proportion of infected cells and the length of the retrovirus affects detection by the insertion pipeline. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.15102570.v1
title: Additional file 2 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 2 Table S2. Identification of known miRNAs in sedr pollen. The clean sRNA reads were aligned against the miRBase database which resulted in the identification of 423 shared miRNAs in two samples.
DOI: 10.6084/m9.figshare.15102582
title: Additional file 5 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 5 Table S5. Detection of sunflower and sedr miRNAs in honey bee midgut. The miRNAs that were detected in both biological replications of each treatment were kept for further analysis. Interestingly, all the identified miRNAs (11 miRNAs in each group) were detected in both biological replications in both plants. Of these miRNAs, nine miRNAs i.e. miR-148a-3p, miR-26a, miR-21-5p, miR-143, miR-27a, miR-203, let-7 g, miR-126, and miR-30d exist in both two groups (honey bee fed with sunflower and sedr pollen). The miR-101 and miR-103 were only detected in honey bees fed with sunflower, while miR-199b-3p and miR-206 were found in honey bees treated with sedr pollen.
DOI: 10.6084/m9.figshare.15102582.v1
title: Additional file 5 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 5 Table S5. Detection of sunflower and sedr miRNAs in honey bee midgut. The miRNAs that were detected in both biological replications of each treatment were kept for further analysis. Interestingly, all the identified miRNAs (11 miRNAs in each group) were detected in both biological replications in both plants. Of these miRNAs, nine miRNAs i.e. miR-148a-3p, miR-26a, miR-21-5p, miR-143, miR-27a, miR-203, let-7 g, miR-126, and miR-30d exist in both two groups (honey bee fed with sunflower and sedr pollen). The miR-101 and miR-103 were only detected in honey bees fed with sunflower, while miR-199b-3p and miR-206 were found in honey bees treated with sedr pollen.
DOI: 10.6084/m9.figshare.8286842
title: Additional file 3: of Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

description: Table S4. List of all P-value ranked genes in the gene-based association analysis of heading days/plant height/seed set rate/panicle length/grain length/100 grains weight/flag leaf length/flag leaf width/panicle number per plant. (XLSX 169 kb)
DOI: 10.6084/m9.figshare.8286842.v1
title: Additional file 3: of Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

description: Table S4. List of all P-value ranked genes in the gene-based association analysis of heading days/plant height/seed set rate/panicle length/grain length/100 grains weight/flag leaf length/flag leaf width/panicle number per plant. (XLSX 169 kb)
DOI: 10.6084/m9.figshare.15102585
title: Additional file 6 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 6 Table S6. Target prediction of 11 diet-derived miRNAs in honey bee via PITA, Miranda and RNAHybrid softwares. Those targets that were predicted by two out of the three tools were selected as potential targets of each gene. In total, 121 target genes were predicted for 11 diet derived miRNAs.
DOI: 10.6084/m9.figshare.8286845
title: Additional file 3: of Retrovirus insertion site analysis of LGL leukemia patient genomes

description: Table S2. The output of the pipeline to investigate HERV-K proviruses and prevalence of polymorphic HERV-K proviruses in 51 LGL leukemia patients. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.15102585.v1
title: Additional file 6 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 6 Table S6. Target prediction of 11 diet-derived miRNAs in honey bee via PITA, Miranda and RNAHybrid softwares. Those targets that were predicted by two out of the three tools were selected as potential targets of each gene. In total, 121 target genes were predicted for 11 diet derived miRNAs.
DOI: 10.6084/m9.figshare.8286845.v1
title: Additional file 3: of Retrovirus insertion site analysis of LGL leukemia patient genomes

description: Table S2. The output of the pipeline to investigate HERV-K proviruses and prevalence of polymorphic HERV-K proviruses in 51 LGL leukemia patients. (XLSX 68 kb)
DOI: 10.6084/m9.figshare.15102589
title: Additional file 4 of Identification of proteins associated with development of psoriatic arthritis in peripheral blood mononuclear cells: a quantitative iTRAQ-based proteomics study

description: Additional file 4. The list of significantly changed proteins in the comparison of all psoriatic patients versus healthy controls, PsO group versus healthy controls, PsA group versus healthy controls, and PsA group versus PsO group, respectively.
DOI: 10.6084/m9.figshare.15102589.v1
title: Additional file 4 of Identification of proteins associated with development of psoriatic arthritis in peripheral blood mononuclear cells: a quantitative iTRAQ-based proteomics study

description: Additional file 4. The list of significantly changed proteins in the comparison of all psoriatic patients versus healthy controls, PsO group versus healthy controls, PsA group versus healthy controls, and PsA group versus PsO group, respectively.
DOI: 10.6084/m9.figshare.8286848
title: Additional file 4: of Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

description: Table S5. List of new loci in association analysis of heading days/plant height/seed set rate/panicle length/grain length/grain width/100 grains weight/ flag leaf length/panicle number per plant. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.8286848.v1
title: Additional file 4: of Genome-wide association study of important agronomic traits within a core collection of rice (Oryza sativa L.)

description: Table S5. List of new loci in association analysis of heading days/plant height/seed set rate/panicle length/grain length/grain width/100 grains weight/ flag leaf length/panicle number per plant. (XLSX 51 kb)
DOI: 10.6084/m9.figshare.15102591
title: Additional file 7 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 7 Table S7. KEGG pathway analysis of miR-206 target genes. This miRNA had the highest number of targets with 53 predicted genes. Enrichment analyses of miR-206 target genes indicated target genes participated in 21 different pathways while none of the identified pathways was significant.
DOI: 10.6084/m9.figshare.15102591.v1
title: Additional file 7 of Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut

description: Additional file 7 Table S7. KEGG pathway analysis of miR-206 target genes. This miRNA had the highest number of targets with 53 predicted genes. Enrichment analyses of miR-206 target genes indicated target genes participated in 21 different pathways while none of the identified pathways was significant.
DOI: 10.5281/zenodo.10697836
title: Benzodiazepines docked into human GABAAR and schistosome TRP channel binding pockets

description: Modeling benzodiazepine binding to TRP and GABAARs

Targets were obtained from public structure repositories. GABAAR coordinates were taken from RSCB, PDB accession 6HUP for a cryo-EM derived structure in its diazepam-bound state. The AlphaFold model AF-A0A5K4FCC0-F1-model provided starting coordinates for the S. mansoni TRP channel Smp_333650. Structure models were prepared for docking using the DockPrep utility of ChimeraX v1.7 (Meng et al. 2023) to fill in missing atoms, add hydrogens, assign partial charges (AMBER ff14SB), and exported in mol2 formats. SMILES for the benzodiazepine chemical series were generated using ChemDraw. Library preparation utilities fixpka (QUACPAC v2.1.2.1), OMEGA2 v4.1.1.1, and molcharge (QUACPAC v2.1.2.1) were used to assign protonation states, build energetically reasonable starting 3D conformers for docking, and assign partial charges (MMFF), respectively (OpenEye Scientific, Cadence Molecular Sciences, Inc.). Single conformations were exported in mol2 format for docking. Docking was performed using the program Gnina v1.0 (McNutt et al. 2021). To localize the search space in docking GABAAR, the binding pocket was specified based on the position of diazepam using the autobox option with a bounding box of 10 Angstroms. No sidechain flexibility was allowed for docking into the GABAAR. For the schistosome TRP channel, the site center was determined using the most probable site in the VSLD domain using the prediction tool p2rank (Krivák and Hoksza 2018). Due to steric restrictions within the putative binding pocket of the TRP channel, sidechain flexibility was enabled for pocket residues H827, H831, Y864, E867, E868, D893, F940, R943, H946, I947, Y1117, R1120. For both targets, extensive sampling was achieved using an exhaustiveness parameter of 64. CNN scoring was used for re-scoring final poses by setting cnn_scoring option to “rescore.” For CNN-based pose scoring, the “crossdock_default2018” model was selected. Docking poses were inspected and images created using PyMOL v2.5.4 (Schrodinger, LLC).

Krivák, Radoslav, and David Hoksza. 2018. “P2Rank: Machine Learning Based Tool for Rapid and Accurate Prediction of Ligand Binding Sites from Protein Structure.” Journal of Cheminformatics 10 (1): 39.

McNutt, Andrew T., Paul Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, and David Ryan Koes. 2021. “GNINA 1.0: Molecular Docking with Deep Learning.” Journal of Cheminformatics 13 (1): 43.

Meng, Elaine C., Thomas D. Goddard, Eric F. Pettersen, Greg S. Couch, Zach J. Pearson, John H. Morris, and Thomas E. Ferrin. 2023. “UCSF ChimeraX: Tools for Structure Building and Analysis.” Protein Science: A Publication of the Protein Society 32 (11): e4792.