cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16739877
title: Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

description: Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally record grid cells with two-photon calcium imaging over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting a slow plasticity mechanism that results in an increasingly fragmented and stable map. The backward shifts partially reset daily, reflecting a slower consolidation timescale. We show that though individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics keep them on the same two-dimensional torus during this plastic period. Next, we build a simple entorhinal-hippocampal model that explains the diverse phenomena - grid field shifts, fragmentation, and increasing fidelity of the spatial map - and predicts slow Hebbian plasticity in the return hippocampus-to-entorhinal pathway. Finally, using ex vivo slice electrophysiology, we show that plasticity in an indirect hippocampus-to-MEC pathway correlates with spatial learning performance and could account for the hypothesized slow plasticity of the model. Together, our study provides multifaceted evidence of slow plasticity in synapses from the hippocampus to the MEC, elucidating the formation of stable and fragmented maps that combine internal and cue-driven positional estimates in rich environments, elucidating cognitive map formation during spatial learning.
description: Code README:

All code need MATLAB R2020a or beyond to run. All dependent codes should be included. No non-standard software needed. 

No specific installation needed to run the code. Set path to the entire code folder in MATLAB should permit it to run

The codes are arranged by figures and should reproduce figure panels. Please email lujia.chen@nih.gov pr lujiachen1994@gmail.com if there are missing data or code that stop the code from running
DOI: 10.5281/zenodo.16739878
title: Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

description: Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally record grid cells with two-photon calcium imaging over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting a slow plasticity mechanism that results in an increasingly fragmented and stable map. The backward shifts partially reset daily, reflecting a slower consolidation timescale. We show that though individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics keep them on the same two-dimensional torus during this plastic period. Next, we build a simple entorhinal-hippocampal model that explains the diverse phenomena - grid field shifts, fragmentation, and increasing fidelity of the spatial map - and predicts slow Hebbian plasticity in the return hippocampus-to-entorhinal pathway. Finally, using ex vivo slice electrophysiology, we show that plasticity in an indirect hippocampus-to-MEC pathway correlates with spatial learning performance and could account for the hypothesized slow plasticity of the model. Together, our study provides multifaceted evidence of slow plasticity in synapses from the hippocampus to the MEC, elucidating the formation of stable and fragmented maps that combine internal and cue-driven positional estimates in rich environments, elucidating cognitive map formation during spatial learning.
description: Code README:

All code need MATLAB R2020a or beyond to run. All dependent codes should be included. No non-standard software needed. 

No specific installation needed to run the code. Set path to the entire code folder in MATLAB should permit it to run

The codes are arranged by figures and should reproduce figure panels. Please email lujia.chen@nih.gov pr lujiachen1994@gmail.com if there are missing data or code that stop the code from running
DOI: 10.15468/dl.yvc5tv
title: Occurrence Download

description: A dataset containing 20853 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caragana arborescens",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 20853 records from 320 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012777-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3955a
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Lamium orvala",
 "Country is Netherlands",
 "HasCoordinate is true"
 ]
}

 The dataset includes 168 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012781-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wgp6kx
title: Occurrence Download

description: A dataset containing 21019 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calidris acuminata",
 "Geometry POLYGON((119.300000 20.500000, 122.100000 20.500000, 122.100000 25.400000, 119.300000 25.400000, 119.300000 20.500000))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 21019 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012778-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j6d8ey
title: Occurrence Download

description: A dataset containing 30070 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bucanetes githagineus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 30070 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012784-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ehg6wz
title: Occurrence Download

description: A dataset containing 3408 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is one of (Astilbe thunbergii)"
 ]
}

 The dataset includes 3408 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012786-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17194941
title: The all-sky aurora, GNSS TEC and scintillation, geomagnetic and VLF receiver data on 1 December 2023
DOI: 10.5281/zenodo.17194942
title: The all-sky aurora, GNSS TEC and scintillation, geomagnetic and VLF receiver data on 1 December 2023
DOI: 10.15468/dl.x3fcrj
title: Occurrence Download

description: A dataset listing the 492989 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Country is United States of America",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 492989 records were derived from 2632 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012768-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bv24un
title: Occurrence Download

description: A dataset containing 89 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia oblonga (Nees) Lindau"
 ]
}

 The dataset includes 89 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260475-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fhq232
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Argostemma pumilum Benn."
 ]
}

 The dataset includes 51 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0046883-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nqjdh7
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "InstitutionCode is one of (snsd, cas, fmnh)",
 "TaxonKey is Apistogramma cinilabra Römer, Duponchelle, Diaz, Davilla, Sirvas, Catchay & Renno, 2011"
 ]
}

 The dataset includes 16 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231170-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sc23fx
title: Occurrence Download

description: A dataset containing 12141 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Türkiye",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 12141 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231663-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9prsed
title: Occurrence Download

description: A dataset containing 25 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hymenocallis pimana Laferr."
 ]
}

 The dataset includes 25 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0250088-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m5j6v8
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Scottish river macro-invertebrate records from 2007 collected by SEPA",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207599-230224095556074/datasets/export for details.
DOI: 10.15468/dl.9gajhq
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Bringing Reedbeds to Life Invertebrate Survey of three key reedbed sites in England in 2009, 2010",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207601-230224095556074/datasets/export for details.
DOI: 10.15468/dl.c332k3
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is BRERC Notable Species records within the last 10 years",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207604-230224095556074/datasets/export for details.
DOI: 10.15468/dl.4tke2g
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Nepeta suavis Stapf"
 ]
}

 The dataset includes 16 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047044-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.usaw5c
title: Occurrence Download

description: A dataset containing 50 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Arnaldoa weberbaueri (Muschl.) Ferreyra"
 ]
}

 The dataset includes 50 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003897-240202131308920/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5tn9mp
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Invertebrate surveys of various ponds in Scotland between 2010 and 2015",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207603-230224095556074/datasets/export for details.
DOI: 10.15468/dl.d3qd6f
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is MVZ Herp Collection (Arctos)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Triturus cristatus (Laurenti, 1768)"
 ]
}

 The dataset includes 91 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0278030-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycfey8
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oreobates discoidalis (Peracca, 1895)"
 ]
}

 The dataset includes 150 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0273355-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ru87rn
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Habenaria pinzonii R.González & Cuevas-Figueroa"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0236414-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.53kwsa
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is PondNet data 2012-2014",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207616-230224095556074/datasets/export for details.
DOI: 10.15468/dl.mr2d8h
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Porifera",
 "DatasetKey is Woodmeadow Invertebrate Survey 2016",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-25.03991 31.75, 41.65954 31.75, 41.65954 71.53037, -25.03991 71.53037, -25.03991 31.75))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0207627-230224095556074/datasets/export for details.
DOI: 10.15468/dl.pnrkvm
title: Occurrence Download

description: A dataset containing 13247 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Opiliaceae"
 ]
}

 The dataset includes 13247 records from 402 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234862-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hmyrku
title: Occurrence Download

description: A dataset containing 1202 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is North America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Liriodendron tulipifera L.",
 "Year 1993-2023"
 ]
}

 The dataset includes 1202 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238411-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w7vdxy
title: Occurrence Download

description: A dataset containing 61 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hymenocallis sonorensis Standl."
 ]
}

 The dataset includes 61 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0250100-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dupwxq
title: Occurrence Download

description: A dataset containing 269 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Metapanax delavayi (Franch.) J.Wen & Frodin"
 ]
}

 The dataset includes 269 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0234873-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2epkga
title: Occurrence Download

description: A dataset containing 264 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Platynota stultana Walsingham, 1884"
 ]
}

 The dataset includes 264 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260476-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dmq73y
title: Occurrence Download

description: A dataset containing 5408 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Chrysolophus pictus (Linnaeus, 1758)"
 ]
}

 The dataset includes 5408 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231173-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wkuju8
title: Occurrence Download

description: A dataset containing 221 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "Geometry POLYGON((-36.81516 -4.91915,-42.14027 -9.32446,-44.65759 -20.11989,-39.91341 -18.66759,-38.82826 -13.26979,-37.86397 -12.76738,-32.32534 -6.03175,-36.81516 -4.91915))",
 "OccurrenceStatus is Present",
 "TaxonKey is Byrsonima microphylla A.Juss.",
 "Year 1970-2023"
 ]
}

 The dataset includes 221 records from 31 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0238740-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cs782g
title: Occurrence Download

description: A dataset containing 4112730 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((-78.77003 0.47593,-79.10129 0.78522,-79.29248 0.85656,-79.47512 0.8908,-79.68058 0.8537,-79.75192 0.70246,-79.74336 0.40854,-79.57214 0.15742,-79.50651 -0.01666,-79.42375 -0.22497,-79.29024 -0.39721,-79.11331 -0.50565,-78.89073 -0.57699,-78.42844 -0.48853,-78.13737 -0.37153,-78.19199 0.27253,-78.3575 0.45231,-78.77003 0.47593))"
 ]
}

 The dataset includes 4112730 records from 595 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007127-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7j5ntj
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Justicia obtusicapsula Hedrén"
 ]
}

 The dataset includes 8 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0260478-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3vtyda
title: Occurrence Download

description: A dataset containing 211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Brazil",
 "GadmGid is BRA",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Colinus cristatus (Linnaeus, 1766)"
 ]
}

 The dataset includes 211 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0247097-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.