cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17211279
title: Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base

description: The Iterative Bleaching Extends Multiplexity (IBEX) imaging method is an iterative immunolabeling and chemical bleaching method that enables highly multiplexed imaging of diverse tissues. Development of the IBEX method and related software was led by Dr. Andrea Radtke and Dr. Ziv Yaniv. IBEX and related methods, Ce3D, Ce3D-IBEX, Opal-plex, were originally developed in the laboratory of Dr. Ronald N. Germain, US National Institutes of Health.
The IBEX Imaging Community is an international group of scientists committed to sharing knowledge related to multiplexed imaging in a transparent and collaborative manner. This open, global repository is a central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). This dataset contains the current state of knowledge with respect to the IBEX microscopy imaging protocol.
How to use the Knowledge-Base:

Save a copy to your computer.
To find a reagent: Open the reagent_resources.csv file found in the data directory. Use a spreadsheet application to filter the columns based on target name, target species, vendor, etc.
To view a complete list of fluorescent probes tested by the IBEX imaging community: Open the fluorescent_probes.csv file. This file reports the spectral properties and inactivation conditions of each fluorescent probe.
To import publications cited in the Knowledge-Base, import the publications.bib file found in the data directory to your reference manager.
To view a local copy of the website: Open the index.md file found in the docs directory using a markdown editor such as the free Visual Studio Code.
To view supporting information for a reagent (images, publications, notes): Open a specific target-conjugate-orcid combination under the docs-supporting_material directory structure using a markdown editor. This can also be visualized from the Reagent Resources page and filtered using a catalog number or other unique identifier in your web browser.

Join the online IBEX Imaging community and contribute your knowledge. For more details on how to contribute, see these instructions.
This research was supported by:

The Intramural Research Program of the NIH, National Institute of Allergy and Infectious Diseases and National Cancer Institute, under grants 1ZIAAI001290-02, 1ZIAAI000545-33, 1ZIAAI000758-24, 1ZIAAI000974-16, 1ZIAAI001034-14.
 The Wellcome Trust, under grant 224586/Z/21/Z.
 The National Institute of Allergy and Infectious Diseases, NIH, under grant 1ZIAAI001343-01.
DOI: 10.5281/zenodo.7693278
title: Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base

description: The Iterative Bleaching Extends Multiplexity (IBEX) imaging method is an iterative immunolabeling and chemical bleaching method that enables highly multiplexed imaging of diverse tissues. Development of the IBEX method and related software was led by Dr. Andrea Radtke and Dr. Ziv Yaniv. IBEX and related methods, Ce3D, Ce3D-IBEX, Opal-plex, were originally developed in the laboratory of Dr. Ronald N. Germain, US National Institutes of Health.
The IBEX Imaging Community is an international group of scientists committed to sharing knowledge related to multiplexed imaging in a transparent and collaborative manner. This open, global repository is a central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). This dataset contains the current state of knowledge with respect to the IBEX microscopy imaging protocol.
How to use the Knowledge-Base:

Save a copy to your computer.
To find a reagent: Open the reagent_resources.csv file found in the data directory. Use a spreadsheet application to filter the columns based on target name, target species, vendor, etc.
To view a complete list of fluorescent probes tested by the IBEX imaging community: Open the fluorescent_probes.csv file. This file reports the spectral properties and inactivation conditions of each fluorescent probe.
To import publications cited in the Knowledge-Base, import the publications.bib file found in the data directory to your reference manager.
To view a local copy of the website: Open the index.md file found in the docs directory using a markdown editor such as the free Visual Studio Code.
To view supporting information for a reagent (images, publications, notes): Open a specific target-conjugate-orcid combination under the docs-supporting_material directory structure using a markdown editor. This can also be visualized from the Reagent Resources page and filtered using a catalog number or other unique identifier in your web browser.

Join the online IBEX Imaging community and contribute your knowledge. For more details on how to contribute, see these instructions.
This research was supported by:

The Intramural Research Program of the NIH, National Institute of Allergy and Infectious Diseases and National Cancer Institute, under grants 1ZIAAI001290-02, 1ZIAAI000545-33, 1ZIAAI000758-24, 1ZIAAI000974-16, 1ZIAAI001034-14.
 The Wellcome Trust, under grant 224586/Z/21/Z.
 The National Institute of Allergy and Infectious Diseases, NIH, under grant 1ZIAAI001343-01.
DOI: 10.15468/dl.mt4nyg
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-91.47318 -63.34538, -78.20984 -63.34538, -78.20984 -48.34505, -91.47318 -48.34505, -91.47318 -63.34538))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2024",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020970-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.85ebfb
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monomorium pharaonis",
 "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 9 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020971-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6n5vg8
title: Occurrence Download

description: A dataset containing 5673 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Propuesta para rescatar y conservar la paleobiota de la Cantera Tlayúa, en Tepexí de Rodríguez, Puebla: Fase II"
 ]
}

 The dataset includes 5673 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020973-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17211252
title: MARS-Net v2.0: Multilayer Adaptive Resilience Supply Chain Dataset and Simulation Scripts

description: MARS-Net v2.0: Multilayer Adaptive Resilience Supply Chain Dataset and Simulation Scripts.
DOI: 10.5281/zenodo.17211253
title: MARS-Net v2.0: Multilayer Adaptive Resilience Supply Chain Dataset and Simulation Scripts

description: MARS-Net v2.0: Multilayer Adaptive Resilience Supply Chain Dataset and Simulation Scripts.
DOI: 10.15468/dl.cdpwbs
title: Occurrence Download

description: A dataset containing 5482 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversidad asociada a la modificación del PMA de la línea a 110 kV entre Chorodó y Apartadó (variante Uramita)"
 ]
}

 The dataset includes 5482 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020974-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tuj82k
title: Occurrence Download

description: A dataset containing 251 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquarius elongatus",
 "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 251 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020975-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17211254
title: Characterization of porous nanoparticles using the lattice Boltzmann   method for fluid flow

description: Data to generate graphs
DOI: 10.5281/zenodo.17211255
title: Characterization of porous nanoparticles using the lattice Boltzmann   method for fluid flow

description: Data to generate graphs
DOI: 10.15468/dl.4czmwd
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amanita silvatica"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020976-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e2sh92
title: Occurrence Download

description: A dataset containing 130804 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carcinus maenas)",
 "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 130804 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020957-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.syddmu
title: Occurrence Download

description: A dataset containing 130804 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carcinus maenas)",
 "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 130804 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020956-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xgnf4s
title: Occurrence Download

description: A dataset containing 130804 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Carcinus maenas)",
 "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 130804 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020959-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hy85ff
title: Occurrence Download

description: A dataset containing 357 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aquarius paludum",
 "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 357 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020977-250920141307145/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.30223450
title: Source data for main figures and supplementary figures of the manuscript entitled "<i>mop1</i> affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin."

description: Meiotic recombination generates new genetic combinations and ensures proper chromosome segregation, yet its regulation remains unclear in many species. Here we show that <i>Mediator of paramutation1</i> (<i>Mop1</i>), a regulator of DNA methylation, reshapes the recombination landscape in maize. High-resolution crossover mapping reveals that loss of MOP1 reduces crossover numbers during male meiosis, while the total number in female meiosis remains largely unchanged despite local shifts in crossover distribution. We find that new crossovers occur on miniature inverted-repeat transposable elements (MITEs), particularly in regions with greater genetic diversity. Analysis of DNA and chromatin modifications, together with gene expression, shows that loss of MOP1 reduces methylation at MITEs near genes enriched with histone marks linked to open and active chromatin, and downregulates a gene required for chromosome organization. Together, these findings suggest that both chromosome structure and transposon methylation contribute to recombination control, providing new insights into epigenetic control of genetic variation.
DOI: 10.6084/m9.figshare.30223450.v2
title: Source data for main figures and supplementary figures of the manuscript entitled "<i>mop1</i> affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin."

description: Meiotic recombination generates new genetic combinations and ensures proper chromosome segregation, yet its regulation remains unclear in many species. Here we show that <i>Mediator of paramutation1</i> (<i>Mop1</i>), a regulator of DNA methylation, reshapes the recombination landscape in maize. High-resolution crossover mapping reveals that loss of MOP1 reduces crossover numbers during male meiosis, while the total number in female meiosis remains largely unchanged despite local shifts in crossover distribution. We find that new crossovers occur on miniature inverted-repeat transposable elements (MITEs), particularly in regions with greater genetic diversity. Analysis of DNA and chromatin modifications, together with gene expression, shows that loss of MOP1 reduces methylation at MITEs near genes enriched with histone marks linked to open and active chromatin, and downregulates a gene required for chromosome organization. Together, these findings suggest that both chromosome structure and transposon methylation contribute to recombination control, providing new insights into epigenetic control of genetic variation.
DOI: 10.6084/m9.figshare.30223450.v1
title: Source data for main figures and supplementary figures of the manuscript entitled "<i>mop1</i> affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin."

description: Meiotic recombination generates new genetic combinations and ensures proper chromosome segregation, yet its regulation remains unclear in many species. Here we show that <i>Mediator of paramutation1</i> (<i>Mop1</i>), a regulator of DNA methylation, reshapes the recombination landscape in maize. High-resolution crossover mapping reveals that loss of MOP1 reduces crossover numbers during male meiosis, while the total number in female meiosis remains largely unchanged despite local shifts in crossover distribution. We find that new crossovers occur on miniature inverted-repeat transposable elements (MITEs), particularly in regions with greater genetic diversity. Analysis of DNA and chromatin modifications, together with gene expression, shows that loss of MOP1 reduces methylation at MITEs near genes enriched with histone marks linked to open and active chromatin, and downregulates a gene required for chromosome organization. Together, these findings suggest that both chromosome structure and transposon methylation contribute to recombination control, providing new insights into epigenetic control of genetic variation.
DOI: 10.15468/dl.j9ddwa
title: Occurrence Download

description: A dataset containing 4629 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cardiospermum grandiflorum)",
 "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 4629 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020978-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25573/serc.29873261
title: Dataset: Estimation of blue carbon for the mangrove community of La Playa, Gulf of Montijo, Panama

description: Presentamos datos del suelo, biomasa aérea total y necromasa para 4 transectos de manglares. Dos tipos franja y dos tipos estuario. Que son identificados como las zonas de uso de una comunidad de recolectores de concha negra (<i>Anadara tuberculosa</i>) en el Golfo de Montijo, Veraguas. Los datos fueron colectados entre septiembre y diciembre de 2019. El estudio brindo información del estado de salud de los manglares a las comunidades y del valor del servicio de reservas de carbono en el sitio.We present data for the soil, total aboveground biomass, and necromass of four mangrove transects. Two transects surveyed fringe ecotypes and two surveyed estuarine ecotypes. These areas were identified as land-use zones for the communities who harvest mangrove cockle (<i>Anadara tuberculosa</i>) in the Gulf of Montijo, Veraguas. Data were collected between September and December 2019. The study provided information on the health of mangroves to the communities and the value of carbon stock services at the site.
DOI: 10.25573/serc.29873261.v1
title: Dataset: Estimation of blue carbon for the mangrove community of La Playa, Gulf of Montijo, Panama

description: Presentamos datos del suelo, biomasa aérea total y necromasa para 4 transectos de manglares. Dos tipos franja y dos tipos estuario. Que son identificados como las zonas de uso de una comunidad de recolectores de concha negra (<i>Anadara tuberculosa</i>) en el Golfo de Montijo, Veraguas. Los datos fueron colectados entre septiembre y diciembre de 2019. El estudio brindo información del estado de salud de los manglares a las comunidades y del valor del servicio de reservas de carbono en el sitio.We present data for the soil, total aboveground biomass, and necromass of four mangrove transects. Two transects surveyed fringe ecotypes and two surveyed estuarine ecotypes. These areas were identified as land-use zones for the communities who harvest mangrove cockle (<i>Anadara tuberculosa</i>) in the Gulf of Montijo, Veraguas. Data were collected between September and December 2019. The study provided information on the health of mangroves to the communities and the value of carbon stock services at the site.
DOI: 10.5517/ccdc.csd.cc1ytsr9
title: CCDC 1812252: Experimental Crystal Structure Determination

description: Related Article: P. Kuś, J. Kusz, M. Książek|2025|Acta Crystallogr.,Sect.C:Cryst.Struct.Chem.|81|548|doi:10.1107/S2053229625007314
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2myqjv
title: CCDC 2441638: Experimental Crystal Structure Determination

description: Related Article: Mukaila A. Ibrahim, René T. Boeré, Kathryn E. Preuss|2025|RSC Advances|15|32299|doi:10.1039/d5ra03587b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2myqkw
title: CCDC 2441639: Experimental Crystal Structure Determination

description: Related Article: Mukaila A. Ibrahim, René T. Boeré, Kathryn E. Preuss|2025|RSC Advances|15|32299|doi:10.1039/d5ra03587b
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2jcwsl
title: CCDC 2335130: Experimental Crystal Structure Determination

description: Related Article: S.S. Khan, M.B.H. Howlader, E. Zangrando, M.C. Sheikh, R. Miyatake|2025|IUCrData|10|x250789|doi:10.1107/S2414314625007898
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.dhqd5f
title: Occurrence Download

description: A dataset containing 473108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is one of (UKR.4_1, UKR.20_1)",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 473108 records from 430 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020864-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qms4ce
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limnogonus fossarum",
 "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 23 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0020980-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.