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

description: A dataset containing 1063 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Henicorhina leucoptera Fitzpatrick, Terborgh & Willard, 1977"
 ]
}

 The dataset includes 1063 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0255549-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ymfpee
title: Occurrence Download

description: A dataset containing 248 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platycorypha Tuthill, 1945"
 ]
}

 The dataset includes 248 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0125292-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrcsxm
title: Occurrence Download

description: A dataset containing 2521 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bradypterus sylvaticus Sundevall, 1860"
 ]
}

 The dataset includes 2521 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0281268-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3spfn
title: Occurrence Download

description: A dataset containing 62729 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "Country is Netherlands",
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "Country is Norway",
 "Country is Sweden",
 "Country is Denmark",
 "Country is Belgium",
 "Country is France",
 "Country is Spain"
 ]
 },
 "OccurrenceStatus is Present",
 "TaxonKey is Phylloscopus inornatus (Blyth, 1842)",
 "Year 1970-2022"
 ]
}

 The dataset includes 62729 records from 83 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0120517-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3qqtw5
title: Occurrence Download

description: A dataset containing 49326 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Psorophora Robineau-Desvoidy, 1827"
 ]
}

 The dataset includes 49326 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0125291-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.esjzs6
title: Occurrence Download

description: A dataset containing 904 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Erythronium sibiricum (Fisch. & C.A.Mey.) Krylov"
 ]
}

 The dataset includes 904 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0431478-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2udpnq
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xenoperdix udzungwensis Dinesen, Lehmberg, Svendsen, Hansen & Fjeldså, 1994"
 ]
}

 The dataset includes 43 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029079-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kcsk98
title: Occurrence Download

description: A dataset containing 285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sousa chinensis (Osbeck, 1765)"
 ]
}

 The dataset includes 285 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0175174-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zw635j
title: Occurrence Download

description: A dataset containing 84 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Poikilospermum cordifolium (Barg.-Petr.) Merr."
 ]
}

 The dataset includes 84 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231855-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zxspba
title: Occurrence Download

description: A dataset containing 7813 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aucuba japonica Thunb.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7813 records from 168 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257174-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.punkjq
title: Occurrence Download

description: A dataset containing 341 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hydnophytum formicarum Jack"
 ]
}

 The dataset includes 341 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0231820-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ev49vn
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pandanus labyrinthicus Kurz ex Miq."
 ]
}

 The dataset includes 6 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0139510-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mp5s7d
title: Occurrence Download

description: A dataset containing 309274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salmo salar Linnaeus, 1758",
 "Year 2000-2021"
 ]
}

 The dataset includes 309274 records from 135 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0280728-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2wdysu
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Begonia howii Merr. & Chun"
 ]
}

 The dataset includes 15 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084214-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2hegh5
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Schizodon corti Schultz, 1944"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0220239-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z5bxen
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Genista sericea Wulfen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 151 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0298214-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wb94zn
title: Occurrence Download

description: A dataset containing 570 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erythrina lanata Rose"
 ]
}

 The dataset includes 570 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064092-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y7f8fs
title: Occurrence Download

description: A dataset containing 15439 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trifolium stellatum L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 15439 records from 178 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0257853-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11995739
title: 1p_BLA_sync_permutation_social_valence

description: Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interaction


Highlights:



Classification of molecularly-defined glutamatergic neuron types in mouse BLA with distinct spatial expression patterns.

BLALypd1 neurons are positive-valence neurons innately responding to food and promoting normal feeding.

BLAEtv1 neurons innately respond to aversive and social stimuli.

BLAEtv1 neurons promote fear learning and social interactions.


 



"Step by step" for codes for BLA neuron calcium imaging analysis




Either using our demo files or your calcium imaging and behavior CSV files need to be used: Demo lists: 1. Figure4_food, 2. Figure5_social, 3. Figure5_fear_conditioning, 4. suppl.fig10_longitudinal_footshock_social.




Note

Demo files are already preprocessed H5 files, so you can skip 2-3steps.




you need to download "core_codes" (logger.py, preprocessing.py, util.py) to synchronize the extracted behavior statistics with calcium traces (The TTL emission-reception delay is negligible (less than 30ms), therefore the behavioral statistics time series can be synchronized with calcium traces by the emission/receival time on both devices) and it would generate combined one H5 file (behavior+calcium data)

Run Synchrnoize_h5generation.py code to apply core-codes (preprocessing) to your data:




import core.preprocessing as prep


 




You can run each code (5 codes) described in the paper to generate the results: 1. Fear Conditioning, 2.social, 3. food, 4. permutation, 5, suppl.10 social_footshock.py code number 4 is the percentage comparison with shuffling of data in Figure4-5 as bar graph you can reproduce using the code: Figure4_5_permutation_bargraph.




required




Note

-System requirements Python (3.10.8): we used a Python IDE for professional developers by JetBrains, Pycharm. Packages: suite2p : https://github.com/MouseLand/suite2p




pip install git+https://github.com/MouseLand/suite2p.git


 




matplotlib




pip install matplotlib
pip install PyQt5


 




numpy




Warning

our code included : matplotlib Qt5Agg An Error is happening because Google Colab and Jupyter run on virtual environments which do not support GUI outputs as you cannot open new windows through a browser. Running it locally on a code editor(Spyder, or even IDLE) ensures that it can open a new window for the GUI to initialize.




Tip



"our analysis pipeline is based on basic python packages:"





>  import numpy as np
>import h5py as h5
>import pandas as pd


 


Installation guide above



Demo -Demo_data.zip




Acknowledgement


Yue Zhang

 

https://github.com/limserenahansol/1p_BLA_sync_permutation_social_valence



Github link for this
DOI: 10.5281/zenodo.11995740
title: 1p_BLA_sync_permutation_social_valence

description: Genetically- and spatially-defined basolateral amygdala neurons control food consumption and social interaction


Highlights:



Classification of molecularly-defined glutamatergic neuron types in mouse BLA with distinct spatial expression patterns.

BLALypd1 neurons are positive-valence neurons innately responding to food and promoting normal feeding.

BLAEtv1 neurons innately respond to aversive and social stimuli.

BLAEtv1 neurons promote fear learning and social interactions.


 



"Step by step" for codes for BLA neuron calcium imaging analysis




Either using our demo files or your calcium imaging and behavior CSV files need to be used: Demo lists: 1. Figure4_food, 2. Figure5_social, 3. Figure5_fear_conditioning, 4. suppl.fig10_longitudinal_footshock_social.




Note

Demo files are already preprocessed H5 files, so you can skip 2-3steps.




you need to download "core_codes" (logger.py, preprocessing.py, util.py) to synchronize the extracted behavior statistics with calcium traces (The TTL emission-reception delay is negligible (less than 30ms), therefore the behavioral statistics time series can be synchronized with calcium traces by the emission/receival time on both devices) and it would generate combined one H5 file (behavior+calcium data)

Run Synchrnoize_h5generation.py code to apply core-codes (preprocessing) to your data:




import core.preprocessing as prep


 




You can run each code (5 codes) described in the paper to generate the results: 1. Fear Conditioning, 2.social, 3. food, 4. permutation, 5, suppl.10 social_footshock.py code number 4 is the percentage comparison with shuffling of data in Figure4-5 as bar graph you can reproduce using the code: Figure4_5_permutation_bargraph.




required




Note

-System requirements Python (3.10.8): we used a Python IDE for professional developers by JetBrains, Pycharm. Packages: suite2p : https://github.com/MouseLand/suite2p




pip install git+https://github.com/MouseLand/suite2p.git


 




matplotlib




pip install matplotlib
pip install PyQt5


 




numpy




Warning

our code included : matplotlib Qt5Agg An Error is happening because Google Colab and Jupyter run on virtual environments which do not support GUI outputs as you cannot open new windows through a browser. Running it locally on a code editor(Spyder, or even IDLE) ensures that it can open a new window for the GUI to initialize.




Tip



"our analysis pipeline is based on basic python packages:"





>  import numpy as np
>import h5py as h5
>import pandas as pd


 


Installation guide above



Demo -Demo_data.zip




Acknowledgement


Yue Zhang

 

https://github.com/limserenahansol/1p_BLA_sync_permutation_social_valence



Github link for this
DOI: 10.15468/dl.y8zd8k
title: Occurrence Download

description: A dataset containing 538 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Caryopteris incana (Thunb. ex Houtt.) Miq.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 538 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0180880-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3tdxcf
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hyliota usambara W.L.Sclater, 1932"
 ]
}

 The dataset includes 42 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0345255-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3bh5yy
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eliurus penicillatus Thomas, 1908"
 ]
}

 The dataset includes 8 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0343806-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.kh6rrc
title: Occurrence Download

description: A dataset containing 10885 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-125.51016 23.92364,-59.09447 23.92364,-59.09447 49.57521,-125.51016 49.57521,-125.51016 23.92364))",
 "OccurrenceStatus is Present",
 "TaxonKey is Dasypus novemcinctus Linnaeus, 1758"
 ]
}

 The dataset includes 10885 records from 56 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0434010-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.45h6ac
title: Occurrence Download

description: A dataset containing 1278 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cichlopsis leucogenys Cabanis, 1850"
 ]
}

 The dataset includes 1278 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0329680-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.u269sn
title: Occurrence Download

description: A dataset containing 423255 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tussilago farfara L.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 423255 records from 897 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0286367-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/anp-a7s-bcf
title: Alhagi pseudalhagi subsp. kirghisorum (Schrenk) Yakovl.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/bej-ll6-nbk
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4n8-n65-q53
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4dl-8cr-530
title: Alhagi pseudalhagi subsp. kirghisorum (Schrenk) Yakovl.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/l6e-424-s1p
title: Triadica Lour.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dsk-evy-hr3
title: Cyathea caracasana (Klotzsch) Domin

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/n3v-rrv-pfc
title: Sarea difformis (Fr.) Fr.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/jjd-8wk-hx5
title: Triticum turgidum subsp. durum (Desf.) Husn.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/dfe-670-mnd
title: Poacynum pictum (Schrenk) Baill.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/sxr-289-dek
title: Pteroxygonum giraldii Dammer & Diels

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/146-6y1-dr4
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/66k-c6d-68x
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/wtl-w91-6ve
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/wy4-ga2-bm0
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/6qs-n9b-2pm
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qlq-stl-mej
title: Triticum turgidum subsp. dicoccum (Schrank ex Schübl.) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/5k1-bel-dak
title: Triticum aestivum subsp. spelta (L.) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/qws-zpw-27q
title: Triticum aestivum subsp. spelta (L.) Thell.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/wrh-t5q-zyp
title: Koenigia hookeri (Meisn.) T. M. Schust. & Reveal

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/6lv-5pn-397
title: Stauntonia angustifolia (Wall.) R. Br. ex Wall.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/clr-ldj-xdg
title: Triticum aestivum subsp. aestivum

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/d6z-ccw-79s
title: Liliaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/98l-2v7-ahx
title: Liliaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/j3j-zx1-yhb
title: Liliaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/3df-da8-59b
title: Dianthus atlanticus Romo

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/vqc-0gx-xx0
title: Liliaceae

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/5rb-b7l-5n4
title: Hypericum przewalskii Maxim.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/bf6-l8r-ar8
title: Sinosidus albescens (DC.) G. L. Nesom

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/xxn-2tq-y2e
title: Lysimachia christinae Hance

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/5f8-8dv-7n6
title: Aquilegia L.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/z72-dak-bgb
title: Campylotropis polyantha (Franch.) Schindl.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4re-kmn-vas
title: Desmodium Desv.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/4c4-hky-8vz
title: Rosa manshurica Buzunova

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.
DOI: 10.3535/fe4-c0g-t8a
title: Ferula bungeana Kitag.

description: Digital Specimen for the physical specimen hosted at Botanic Garden and Botanical Museum Berlin.