cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.0tlqsd
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-65.53440 -35.84607,-40.99094 -35.84607,-40.99094 -26.02429,-65.53440 -26.02429,-65.53440 -35.84607))",
 "HasCoordinate is true",
 "TaxonKey is Regnellidium diphyllum Lindm.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 56 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000720-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bzsjy
title: Occurrence Download

description: A dataset containing 13814 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cistus crispus L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13814 records from 99 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079197-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.labrsy
title: Occurrence Download

description: A dataset containing 505257 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dryocopus martius (Linnaeus, 1758)"
 ]
}

 The dataset includes 505257 records from 497 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000715-190813142620410/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bufw99
title: Occurrence Download

description: A dataset containing 171460 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Torilis japonica (Houtt.) DC.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 171460 records from 1020 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0079201-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymzf9z
title: Occurrence Download

description: A dataset containing 123559 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Insecta collection of Museum of Natural and Environmental History, Shizuoka"
 ]
}

 The dataset includes 123559 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003364-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.76udm2
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Macaca leucogenys Li, Zhao & Fan, 2015, Macaca arctoides (I.Geoffroy Saint-Hilaire, 1831), Hylobates lar (Linnaeus, 1771), Rhinopithecus roxellana (A.Milne-Edwards, 1870), Nomascus concolor (Harlan, 1826), Trachypithecus crepusculus (Elliot, 1909), Nycticebus bengalensis (Lacépède, 1800), Macaca assamensis (McClelland, 1840), Hoolock tianxing Peng-Fei Fan, Kai He, Xing Chen et al., 2017, Macaca mulatta (Zimmermann, 1780), Hoolock hoolock (Harlan, 1834), Macaca cyclopis (Swinhoe, 1863), Nomascus leucogenys (Ogilby, 1840), Nomascus hainanus (Thomas, 1892), Trachypithecus francoisi (de Pousargues, 1898), Nycticebus pygmaeus Bonhote, 1907, Semnopithecus schistaceus Hodgson, 1840, Trachypithecus shortridgei (Wroughton, 1915), Macaca leonina (Blyth, 1863), Rhinopithecus bieti A.Milne-Edwards, 1897, Macaca munzala Sinha, Datta, Madhusudan & Mishra, 2005, Trachypithecus leucocephalus Tan, 1957, Rhinopithecus brelichi Thomas, 1903, Trachypithecus pileatus (Blyth, 1843), Trachypithecus phayrei (Blyth, 1847), Nomascus nasutus (Kunkel d'Herculais, 1884), Macaca thibetana (A.Milne-Edwards, 1870))",
 "Country is China",
 "HasCoordinate is true",
 "Year is greater than or equal to 1960",
 "Year is less than or equal to 1980"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0053757-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fnsqa6
title: Occurrence Download

description: A dataset containing 372969 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lotus corniculatus L."
 ]
}

 The dataset includes 372969 records from 829 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007078-170714134226665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3c8ije
title: Occurrence Download

description: A dataset containing 5857 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pohlia annotina (Hedw.) Lindb."
 ]
}

 The dataset includes 5857 records from 94 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007078-171002173027117/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xjfmhf
title: Occurrence Download

description: A dataset containing 24833 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pontederia cordata L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 24833 records from 288 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003370-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25cm4h
title: Occurrence Download

description: A dataset containing 66734 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polystichum setiferum (Forssk.) T.Moore ex Woyn.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 66734 records from 586 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003373-240130105604617/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/n16di6
title: Experimental data on faujasites for sustained antibiotic release

description: Files include experimental data on faujasites for sustained antibiotic release:Data (.tif) includes:TEM_CeY.tifTEM_CeY-TMP.tifTEM_LaY.tifTEM_LaY-TMP.tifSEM_CeY.tifSEM_LaY.tifSEM_LaY-TMP.tifSEM-CeY-TMP.tifData (.jpg) includes:FTIR_map_CeY.jpgFTIR_map_CeY-TMP.jpgFTIR_map_LaY.jpgFTIR_map_LaY-TMP.jpgData (.csv) includes:FTIR_spectra.csvList of abbreviations:SEM – scanning electron microscopy;FTIR - Fourier Transform Infrared Spectroscopy;TEM - Transmission Electron Microscopy
DOI: 10.15468/dl.rdsv55
title: Occurrence Download

description: A dataset containing 780 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is Indonesia",
 "GadmGid is IDN.32_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Primates"
 ]
}

 The dataset includes 780 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004073-250415084134356/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3jfdx
title: Occurrence Download

description: A dataset containing 282 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Euleptes europaea (Gené, 1839)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 282 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002663-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14755530
title: Communication of perceptual predictions from the hippocampus to the deep layers of the parahippocampal cortex

description: Current evidence suggests that the hippocampus is essential for exploiting predictive relationships during perception. However, it remains unclear whether the hippocampus drives the communication of predictions to sensory cortex, or receives prediction signals from elsewhere. Here, we collected 7T fMRI data in the medial temporal lobe (MTL) during a task in which auditory cues predicted abstract shapes. Strikingly, neural patterns evoked by predicted shapes in CA2/3, pre/parasubiculum and the parahippocampal cortex (PHC) were negatively correlated to patterns evoked by the same shapes when actually presented. Using layer-specific analyses, we ask: In which direction are predictions communicated between the hippocampus and neocortex? Specifically, superficial layers of the MTL cortex project to the hippocampus, while the deep layers receive feedback projections. Informational connectivity analyses revealed that communication between CA2/3 and PHC was specific to the deep layers of PHC. These findings are in line with the hippocampus generating predictions through pattern completion in CA2/3 and feeding these predictions back to the neocortex.
description: System requirements

Running these analysis scripts requires Matlab (version R2021b or later), and the SPM12 toolbox (freely available at https://www.fil.ion.ucl.ac.uk/spm/). These scripts have been tested using Matlab versions R2021b and R2024b. No non-standard hardware is required.

Installation guide

The Matlab scripts and data files can simply be copied to a folder of your choice. The relevant scripts are:



Behavioural_analysis.m

Decode_predictions.m

Decode_predictions_layers.m

InformationalConnectivity_subfields_whole.m

InformationalConnectivity_subfields_post.m

InformationalConnectivity_subfields_post_LOC.m


Please change the path to the SPM 12 folder at the top of these scripts to the path to SPM 12 on your machine. When running one of the scripts, please make sure the folder containing the script is the current Matlab folder (e.g. by selecting 'Change Folder' when prompted).

Instructions for use

Simple run the scripts listed above to reproduce all the graphs and statistical analyses described in the manuscript. The scripts will automatically load the fMRI time courses for the regions of interest for all participants, and run the analyses described in the Methods section of the manuscript. Note that the Informational Connectivity scripts take longer to run, since they create a permuted baseline consisting of 100 iterations per participant.
DOI: 10.5281/zenodo.14755531
title: Communication of perceptual predictions from the hippocampus to the deep layers of the parahippocampal cortex

description: Current evidence suggests that the hippocampus is essential for exploiting predictive relationships during perception. However, it remains unclear whether the hippocampus drives the communication of predictions to sensory cortex, or receives prediction signals from elsewhere. Here, we collected 7T fMRI data in the medial temporal lobe (MTL) during a task in which auditory cues predicted abstract shapes. Strikingly, neural patterns evoked by predicted shapes in CA2/3, pre/parasubiculum and the parahippocampal cortex (PHC) were negatively correlated to patterns evoked by the same shapes when actually presented. Using layer-specific analyses, we ask: In which direction are predictions communicated between the hippocampus and neocortex? Specifically, superficial layers of the MTL cortex project to the hippocampus, while the deep layers receive feedback projections. Informational connectivity analyses revealed that communication between CA2/3 and PHC was specific to the deep layers of PHC. These findings are in line with the hippocampus generating predictions through pattern completion in CA2/3 and feeding these predictions back to the neocortex.
description: System requirements

Running these analysis scripts requires Matlab (version R2021b or later), and the SPM12 toolbox (freely available at https://www.fil.ion.ucl.ac.uk/spm/). These scripts have been tested using Matlab versions R2021b and R2024b. No non-standard hardware is required.

Installation guide

The Matlab scripts and data files can simply be copied to a folder of your choice. The relevant scripts are:



Behavioural_analysis.m

Decode_predictions.m

Decode_predictions_layers.m

InformationalConnectivity_subfields_whole.m

InformationalConnectivity_subfields_post.m

InformationalConnectivity_subfields_post_LOC.m


Please change the path to the SPM 12 folder at the top of these scripts to the path to SPM 12 on your machine. When running one of the scripts, please make sure the folder containing the script is the current Matlab folder (e.g. by selecting 'Change Folder' when prompted).

Instructions for use

Simple run the scripts listed above to reproduce all the graphs and statistical analyses described in the manuscript. The scripts will automatically load the fMRI time courses for the regions of interest for all participants, and run the analyses described in the Methods section of the manuscript. Note that the Informational Connectivity scripts take longer to run, since they create a permuted baseline consisting of 100 iterations per participant.
DOI: 10.15468/dl.3serjq
title: Occurrence Download

description: A dataset containing 4680 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is EOD – eBird Observation Dataset",
 "TaxonKey is Spheniscus mendiculus Sundevall, 1871",
 "Year 2015-2025"
 ]
}

 The dataset includes 4680 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002664-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vkqwut
title: Occurrence Download

description: A dataset containing 858 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sepiolidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 858 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002665-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8q7nt7
title: Occurrence Download

description: A dataset containing 257 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Podarcis erhardii (Bedriaga, 1882)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 257 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002666-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.339gdj
title: Occurrence Download

description: A dataset containing 1 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, familyKey, family, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND countrycode = 'BE' AND "year" &gt;= 1900 AND hasCoordinate = TRUE AND familyKey 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 (LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL)AND familyKey IN (5666)AND coordinateUncertaintyInMeters &lt;= 10000GROUP BY "year", eeaCellCode, classKey, class, familyKey, family ORDER BY "year" DESC, eeaCellCode ASC, familyKey ASC;

 The dataset's 1 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002622-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r3p27f
title: Occurrence Download

description: A dataset containing 259 records in GBIF matching the query:
SELECT "year", GBIF_EEARGCode( 1000, decimalLatitude, decimalLongitude, COALESCE(coordinateUncertaintyInMeters, 1000) ) AS eeaCellCode, classKey, class, genusKey, genus, COUNT(*) AS occurrences, MIN(COALESCE(coordinateUncertaintyInMeters, 1000)) AS minCoordinateUncertaintyInMeters, MIN(GBIF_TemporalUncertainty(eventDate)) AS minTemporalUncertainty FROM occurrence WHERE occurrenceStatus = 'PRESENT' AND genusKey IN (2284443, 2202786, 2162003, 2161911, 2161467, 7652364, 2176168, 2149911, 3092125, 2771094, 8782549, 2457378, 2453882, 2457825, 2454645, 2465626, 2466496, 2459675, 2444141, 2444221, 2447418, 2441658, 2442664, 3266899, 2473221, 2445496, 5221394, 2443339, 4553469) AND countrycode = 'BE' AND "year" &gt;= 1900 AND hasCoordinate = TRUE AND genusKey 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 (LOWER(identificationVerificationStatus) NOT IN ( 'unverified', 'unvalidated', 'not validated', 'under validation', 'not able to validate', 'control could not be conclusive due to insufficient knowledge', 'uncertain', 'unconfirmed', 'unconfirmed - not reviewed', 'validation requested' ) OR identificationVerificationStatus IS NULL) AND coordinateUncertaintyInMeters &lt;= 10000 GROUP BY "year", eeaCellCode, classKey, class, genusKey, genus ORDER BY "year" DESC, eeaCellCode ASC, genusKey ASC;

 The dataset's 259 records were derived from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002621-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qf7m7x
title: Occurrence Download

description: A dataset containing 238 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Leopardus wiedii (Schinz, 1821)"
 ]
}

 The dataset includes 238 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002667-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymwrge
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Podarcis milensis (Bedriaga, 1882)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002668-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rpp3q4
title: Occurrence Download

description: A dataset containing 261 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Onychoteuthidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 261 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002669-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3zfhzz
title: Occurrence Download

description: A dataset containing 412 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Morphnus guianensis (Daudin, 1800)"
 ]
}

 The dataset includes 412 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002670-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3peqfg
title: Occurrence Download

description: A dataset containing 299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Algyroides nigropunctatus (Duméril & Bibron, 1839)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2013",
 "Year is less than or equal to 2018",
 "CoordinateUncertaintyInMeters is less than or equal to 1000"
 ]
}

 The dataset includes 299 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002671-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gmhaj2
title: Occurrence Download

description: A dataset containing 742 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Human Observation)",
 "Continent is North America",
 "OccurrenceStatus is Present",
 "TaxonKey is Lophocereus marginatus (DC.) S.Arias & Terrazas"
 ]
}

 The dataset includes 742 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002672-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z4fz75
title: Occurrence Download

description: A dataset listing the 73 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is Costa Rica",
 "Geometry POLYGON((-87.81477 4.49658,-83.12214 5.67615,-82.63492 8.59942,-85.9172 11.47142,-86.53263 11.21499,-87.81477 4.49658))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Echinoidea"
 ]
}

 The dataset's 73 records were derived from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002647-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pcsjqt
title: Occurrence Download

description: A dataset containing 574 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gonatidae",
 "Geometry POLYGON((170 20, 170 50, 120 50, 120 20, 170 20))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 574 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002673-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.