cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14469/hpc/15026
title: Raw data files for McArthur et al., "Antigen mobility regulates the dynamics and precision of antigen capture in the B cell immune synapse"

description: Supporting raw data files for McArthur et al "Antigen mobility regulates the dynamics and precision of antigen capture in the B cell immune synapse". The study investigated how antigen mobility affects B cells' ability to capture antigens from presenting membranes, using planar lipid bilayers as membrane substrates. Bilayer fluidity and antigen mobility were characterized using fluorescence recovery after photobleaching and single particle tracking (Fig. 1, S2). The research examined how antigen mobility impacts B cell spreading and phospho-signalling (Fig. 2), calcium flux (Fig. 3), NF-κB and NFAT transcription factor activation (Fig. 4), antigen extraction quantity (Fig. 5), spatiotemporal kinetics of extraction (Fig. 6), trafficking to MHCII+ compartments (Fig. 7), and B cells' ability to discriminate between low/high-affinity antigens on bilayers with varying mobility (Fig. 8). The data collectively demonstrate that reduced antigen mobility enhances both the speed and selectivity of antigen extraction in the B cell immune synapse.
DOI: 10.14469/hpc/2298
title: 3,3',4,4'-tetrahydro-1H,1'H-2,2'-spirobi[quinoline] - 14a

description: Crystallographic data in CIF format + original image data collected from difractometer.
DOI: 10.5281/zenodo.14648237
title: DATA_Single species in vitro assays with soil nitrifying bacteria and archaea as a first-tier tool for assessing the toxicity of pesticides on soil microorganisms
DOI: 10.5281/zenodo.14648238
title: DATA_Single species in vitro assays with soil nitrifying bacteria and archaea as a first-tier tool for assessing the toxicity of pesticides on soil microorganisms
DOI: 10.5281/zenodo.14965860
title: DATA_Single species in vitro assays with soil nitrifying bacteria and archaea as a first-tier tool for assessing the toxicity of pesticides on soil microorganisms
DOI: 10.5281/zenodo.15014056
title: DATA_Single species in vitro assays with soil nitrifying bacteria and archaea as a first-tier tool for assessing the toxicity of pesticides on soil microorganisms
DOI: 10.14469/hpc/2303
title: 6,6',8,8'-tetraphenyl-3,3',4,4'-tetrahydro-1H,1'H-2,2'-spirobi[quinoline] - 27

description: Crystallographic data in CIF format + original image data collected from difractometer.
DOI: 10.14469/hpc/2301
title: 6,6',8,8'-tetrabromo-3,3',4,4'-tetrahydro-1H,1'H-2,2'-spirobi[quinoline] - 26

description: Crystallographic data in CIF format + original image data collected from difractometer.
DOI: 10.14469/hpc/2300
title: 6,6'-dibromo-3,3',4,4'-tetrahydro-1H,1'H-2,2'-spirobi[quinoline] - 25

description: Crystallographic data in CIF format + original image data collected from diffractometer.
DOI: 10.14469/hpc/2339
title: 1,3,10,12-tetrabromo-5,5a,6,7,7a,8,13,14-octahydrocyclopentadiquinoline - 18b

description: Crystallographic data in CIF format + original image data collected from diffractometer.
DOI: 10.14469/hpc/2340
title: 1,3,11,13-tetrabromo-5a,6,7,8,8a,9,14,15-octahydro-5H-quinolinoacridine - 19b

description: Crystallographic data in CIF format + original image data collected from difractometer.
DOI: 10.5883/ds-lpepa22
title: Marius Hannes Eisele, Brendan Furneaux, Tomas Roslin, Otso Ovaskainen, Brent C. Emerson and Carmelo Andujar

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.6084/m9.figshare.28582964
title: Nutritional status, symptoms, and inflammation among older adults with different functional levels with cancer in palliative care.

description: This study aimed to assess the nutritional status, symptoms, food intake, and inflammatory activity of older adults with cancer with Karnofsky Performance Status scale (KPS) ≥ 50% receiving palliative care. Cross-sectional study with outpatients divided into two groups by the Karnofsky Performance Status scale: 80 to 100% (Group 1) and 50 to 70% (Group 2). Nutritional status was assessed using the Mini Nutritional Assessment (MAN), food intake using the 24-hour food recall, symptoms using the Edmonton Symptom Assessment System and serum interleukin-6 (IL-6) levels were measured. Age was 69.6±5.9 years (p=0.80 comparing groups[A1] ). MNA was higher for Group 1 (23.4±2.7 vs 19.4±3.1, p&lt;0.001). Group 2 ingested lower amounts of total energy (p=0.003), carbohydrates (p=0.017), protein (p=0.007), total fat (p=0.004), saturated fat (p=0.006), fiber (p=0.012), and dietary cholesterol (p=0.009). Group 2 had a greater intensity of symptoms such as pain (p=0.02), nausea (p=0.01), shortness of breath (p=0.04) and lack of sensation of wellbeing. There was no difference in IL-6 between groups (p=0.13), however, higher IL-6 was associated with a higher prevalence of dyspnea and a lower calorie, carbohydrate, and dietary cholesterol intake. The lower the functional capacity of older people with cancer, the worse their nutritional status, with lower nutrient intake and greater number of symptoms. This study brings an important scientific contribution to older people with cancer in palliative care, supporting nutritional and symptom assessment in health care. [A1]Sugerimos remover para não confundir o leitor.
DOI: 10.15468/dl.wskkpd
title: Occurrence Download

description: A dataset containing 2106 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Urochloa deflexa (Schumach.) H.Scholz)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 2106 records from 75 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005320-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2lmlhb
title: CCDC 2402112: Experimental Crystal Structure Determination

description: Related Article: Yu-Si Liu, Zhe-Kun Xu, Jia-Mei Zhang, Xiao-Gang Chen, Yan Qin, Zhong-Xia Wang|2025|Dalton Trans.|54|4706|doi:10.1039/D4DT03416C
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.cc2lml94
title: CCDC 2402106: Experimental Crystal Structure Determination

description: Related Article: Yu-Si Liu, Zhe-Kun Xu, Jia-Mei Zhang, Xiao-Gang Chen, Yan Qin, Zhong-Xia Wang|2025|Dalton Trans.|54|4706|doi:10.1039/D4DT03416C
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.st53tc
title: Occurrence Download

description: A dataset containing 42 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Sceptrothelys grandiclava (Walker, 1835)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 42 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005321-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2hjtpk
title: CCDC 2310079: Experimental Crystal Structure Determination

description: Related Article: Letian Chen, Peng Zou, Jinke Chen, Letian Xu, Ben Zhong Tang, Zujin Zhao|2025|Nat.Commun.|16|1656|doi:10.1038/s41467-025-56923-6
description: Related Article: Letian Chen|2025|CSD Communication|||
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.cc2hjtvq
title: CCDC 2310084: Experimental Crystal Structure Determination

description: Related Article: Letian Chen, Peng Zou, Jinke Chen, Letian Xu, Ben Zhong Tang, Zujin Zhao|2025|Nat.Commun.|16|1656|doi:10.1038/s41467-025-56923-6
description: Related Article: Letian Chen|2025|CSD Communication|||
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.29vq3z
title: Occurrence Download

description: A dataset containing 1157 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Urochloa dictyoneura (Fig. & De Not.) Veldkamp)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 1157 records from 109 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005323-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qydkrv
title: Occurrence Download

description: A dataset containing 15817021 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Butterfly distribution records for the UK from Butterfly Conservation, up to 2019"
 ]
}

 The dataset includes 15817021 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005310-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.byz4nf
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Calendula suffruticosa subsp. cinerea (Ohle) P.Silveira & A.C.Gonç.",
 "Year 1975-2025"
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005324-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.phv88s
title: Occurrence Download

description: A dataset containing 688 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhopalosiphum rufiabdominale (Sasaki, 1899)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 688 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005325-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dh23j2
title: Occurrence Download

description: A dataset containing 756 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Urochloa distachyos (L.) T.Q.Nguyen)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 756 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005326-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c46y5e
title: Occurrence Download

description: A dataset containing 267792 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation)",
 "Geometry POLYGON((113.61608 -34.07331,116.14855 -36.60579,130.42251 -34.30354,144.23601 -44.89389,149.53119 -44.66367,154.63465 -38.66079,154.59614 -24.17363,149.30096 -19.79936,142.16399 -9.66945,141.09555 -9.77702,139.86174 -16.34598,136.63859 -10.36013,130.27747 -10.92531,123.97621 -12.66238,119.3717 -18.41801,113.38585 -20.72026,112.0045 -23.48296,113.61608 -34.07331))",
 "TaxonKey is one of (Macropus rufus (Desmarest, 1822), Phascolarctos cinereus (Goldfuss, 1817), Wyulda squamicaudata Alexander, 1918, Gowidon longirostris (Boulenger, 1883), Bryobatrachus nimbus Rounsevell, Ziegeler, Brown, Davies & Littlejohn, 1994, Wollemia nobilis W.G.Jones et al., Brachychiton rupestris (Lindl.) A.Terracc., Banksia baueri R.Br., Caleana major R.Br., Angiopteris evecta (G.Forst.) Hoffm.)"
 ]
}

 The dataset includes 267792 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005298-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15009187
title: Base de Datos Fragmentación Metropolitana en México

description: Comprende el conjunto de datos con los cuales se elaboró el índice de fragmentación metropolitana en México.

Acopio de datos. Se procesaron y vincularon datos de cuatro fuentes:



Sistema Nacional de Información Municipal (INAFED) 

Finanzas Públicas Estatales y Municipales (EFIPEM) 

Delimitación de Zonas Metropolitanas de México (SEDATU, CONAPO, INEGI)

Censo de Población y Vivienda 2020 (INEGI)


Instrumentos usados. Mediante programación Python se procesaron y vincularon las fuentes para integrar una base de datos segmentada por conjuntos de municipios pertenecientes a zonas metropolitanas, reportando datos de ingresos propios, ingresos externos y población. Los datos aquí reportados corresponden a la Etapa de estudio sobre la fragmentación financiera, en etapas en proceso se incorporan variables económicas y geográficas a escala rural-urbana.

Ámbito territorial y geográfico. Municipios que conforman zonas metropolitanas en México.

Hardware y Software.



Intel(R) Core(TM) ¡7-7700HQ CPU @ 2.80GHz 2.81 GHz 32.0 GB  Intel(R) HD Graphics 63 NVIDIA GeForce GTX 1050

IBM SPSS Statistics 27 

Visual Studio Code

Excel 365



QGIS 3.32.0-Lima
DOI: 10.5281/zenodo.15009188
title: Base de Datos Fragmentación Metropolitana en México

description: Comprende el conjunto de datos con los cuales se elaboró el índice de fragmentación metropolitana en México.

Acopio de datos. Se procesaron y vincularon datos de cuatro fuentes:



Sistema Nacional de Información Municipal (INAFED) 

Finanzas Públicas Estatales y Municipales (EFIPEM) 

Delimitación de Zonas Metropolitanas de México (SEDATU, CONAPO, INEGI)

Censo de Población y Vivienda 2020 (INEGI)


Instrumentos usados. Mediante programación Python se procesaron y vincularon las fuentes para integrar una base de datos segmentada por conjuntos de municipios pertenecientes a zonas metropolitanas, reportando datos de ingresos propios, ingresos externos y población. Los datos aquí reportados corresponden a la Etapa de estudio sobre la fragmentación financiera, en etapas en proceso se incorporan variables económicas y geográficas a escala rural-urbana.

Ámbito territorial y geográfico. Municipios que conforman zonas metropolitanas en México.

Hardware y Software.



Intel(R) Core(TM) ¡7-7700HQ CPU @ 2.80GHz 2.81 GHz 32.0 GB  Intel(R) HD Graphics 63 NVIDIA GeForce GTX 1050

IBM SPSS Statistics 27 

Visual Studio Code

Excel 365



QGIS 3.32.0-Lima
DOI: 10.15468/dl.a9cqse
title: Occurrence Download

description: A dataset containing 112 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Halicampus brocki (Herald, 1953)"
 ]
}

 The dataset includes 112 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005327-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sypvut
title: Occurrence Download

description: A dataset containing 101940 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gymnorhinus cyanocephalus Wied-Neuwied, 1841",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 101940 records from 71 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005289-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13023/2024.alum.200
title: Chamomile Infusion

description: Includes data on the aluminum content of chamomile infusion
DOI: 10.5281/zenodo.15013633
title: RMD files, associated RDS files and datasets,  FISH metadata and Biorender license related to NMED-A140141

description: Dear Editor and Reviewer,

First of all, thank you for taking the time to review this work. To make your exploration of the code as smooth and efficient as possible, we have prepared a detailed mapping between the Supplementary Tables and the corresponding analysis scripts. You will find this information in the attached Excel file ("Tables_assigned_codes").

Overview of the code and its purpose : 

Below is a brief description of each script and what it covers:

1/ Cohort_description_MTB : Provides an overview of sample and cohort counts before and after filtering.

2/ Decontamination_pipeline : Contains all the steps related to data filtration, from the raw data to the final phyloseq object.

3/ Alluvial_plot_tables : Includes all details and data related to each step of the decontamination pipeline. It contains counts at both the phylum and genus levels, before and after filtering, as well as the alluvial plots illustrating these changes.

4/ Prevalence_occurrence_predominance : Describes the distribution of taxa across different sample types and cohorts. It also includes the predominance score attribution, species and ASV-level assignments, and the Fusobacterium nucleatum animalis Clade 2 classification.

5/ Tumor_versus_NAT : Performs volcano plot comparisons of taxa significantly abundant between tumor and NAT in CRC primary tumors (PT) and metastases (MT), adjusted per patient.

6/ taxa_sharing : Identifies shared taxa at the genus and ASV levels between CRC PT and MT within individual patients.

7/ figures_METBIOME : Provides direct access to the final improved figures presented in the paper, without needing to go through the full scripts. All previous figure versions are still accessible in the corresponding scripts, along with the Supplementary Tables and Figures.

Additional Files Provided : 

To facilitate the reproducibility of the results, we have included:

- All necessary files to run the code, including RDS files and datasets.

- Biorender license information for the custom-made figures included in the paper.

- FISH data : Including the files, metadata, and images for each image presented in the main article.

Additionally, if you feel that the clarity or flow of the code could be improved in any way, please do not hesitate to ask. We are more than happy to refine or adjust it upon request to ensure smooth readability and usability.

If you have any questions or need further clarifications, please don’t hesitate to reach out. We truly appreciate your time and efforts in reviewing this work!

Best regards,Philippe Stevens, on behalf of the co-authors
DOI: 10.15468/dl.eqhr8v
title: Occurrence Download

description: A dataset containing 2097 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Urochloa eminii (Mez) Davidse)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1945"
 ]
}

 The dataset includes 2097 records from 186 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005329-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.srfxby
title: Occurrence Download

description: A dataset containing 201 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Dalbergia tabascana Pittier"
 ]
}

 The dataset includes 201 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005330-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4q5h6q
title: Occurrence Download

description: A dataset containing 78 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tinocallis platani (Kaltenbach, 1843)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 78 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005328-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4vxj9w
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Portugal",
 "TaxonKey is Herniaria algarvica Chaudhri",
 "Year 1975-2025"
 ]
}

 The dataset includes 14 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005331-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6073/pasta/3e290f60357f34b88c42135aabeefdf7
title: Interagency Ecological Program and US Fish and Wildlife Service: San Francisco Estuary Enhanced Delta Smelt Monitoring Program data, 2016-2023

description: The Enhanced Delta Smelt Monitoring Program (EDSM) was initiated by the U.S. Fish and Wildlife Service in 2016. EDSM focuses on providing real-time data to help managers respond to population patterns of Delta Smelt within the upper San Francisco Estuary, primarily by providing estimates of Delta Smelt distribution and abundance. The dataset can also be useful in evaluating habitat use and behavior patterns of this species and other fish species of interest. Sampling is done year round via Kodiak trawls and larval (“20-mm”) gear to sample Delta Smelt across most life stages. Sites are chosen via stratified random sampling. Over the course of a week, field crews sample between 18 and 41 random sites. A minimum of two tows are conducted at each site. All fish collected are identified (in the field when possible, in the lab for early life stages), measured, enumerated, and recorded. In addition to fish information, environmental data are collected for each sampling event.
 For more information: https://https://www.fws.gov/office/lodi-fish-and-wildlife