cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14802916
title: Replication Data for: A comparison of simplified modeling approaches and simulation quality of an industrial R717-HTHP

description: Replication Data for



Wernhart, M., Verdnik, M., Pertiller, G., & Rieberer, R. (2024). A comparison of simplified modeling approaches and simulation quality of an industrial R717-HTHP. 16th IIR Gustav Lorentzen Conference on Natural Refrigerants, College Park, USA. https://doi.org/10.18462/iir.gl2024.1277 (https://zenodo.org/records/14216859)

(Copyright © 2024, IIF/IIR)
DOI: 10.5281/zenodo.14802917
title: Replication Data for: A comparison of simplified modeling approaches and simulation quality of an industrial R717-HTHP

description: Replication Data for



Wernhart, M., Verdnik, M., Pertiller, G., & Rieberer, R. (2024). A comparison of simplified modeling approaches and simulation quality of an industrial R717-HTHP. 16th IIR Gustav Lorentzen Conference on Natural Refrigerants, College Park, USA. https://doi.org/10.18462/iir.gl2024.1277 (https://zenodo.org/records/14216859)

(Copyright © 2024, IIF/IIR)
DOI: 10.5281/zenodo.14526988
title: Absolute units for proteins in Arabidopsis clock models up to U2020.5

description: The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025, doi 10.1038/s44320-025-00086-5. The files are organised using the standard Investigation-Study-Assay ISA hierarchy, and formatted as a Research Object, which is a .ZIP archive file with annotations. The live, updatable resource is also available at https://fairdomhub.org/investigations/570 - this is recommended as the easiest to navigate and we'll correct any errors that we find after publication.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet WP1a RNA dataset of Flis et al. 2015, without global reoptimisation. New data are acquired to test these protein levels using Nano-Luciferase (NanoLUC) reporter fusion proteins in transgenic plants.

Therefore these models retain the distinction, where U2019 retains the regulation of later PRRs by activation by earlier-expressed genes from the P2011 model, and U2020 replaces this regulation with repression of earlier-expressed PRRs by later-expressed PRRs. The model development is described in more detail in the 'Model Evolution' document attached. Models are in SBML and Antimony formats.

Some early versions of the files with internal nomenclature might remain private and not included in the static Snapshot shared with the publication. The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza et al. The biorXiv preprint version (https://doi.org/10.1101/2024.09.03.609973) and the final publication will also be linked here: the models and analysis are identical in both.

A Snapshot of this investigation is also available on FAIRDOMHub.org, DOI: 10.15490/fairdomhub.1.investigation.570.1. Note we often have to make the Snapshot before we have the publication DOI, so that link is not within the Snapshot.
DOI: 10.5281/zenodo.14526989
title: Absolute units for proteins in Arabidopsis clock models up to U2020.5

description: The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025, doi 10.1038/s44320-025-00086-5. The files are organised using the standard Investigation-Study-Assay ISA hierarchy, and formatted as a Research Object, which is a .ZIP archive file with annotations. The live, updatable resource is also available at https://fairdomhub.org/investigations/570 - this is recommended as the easiest to navigate and we'll correct any errors that we find after publication.

Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet WP1a RNA dataset of Flis et al. 2015, without global reoptimisation. New data are acquired to test these protein levels using Nano-Luciferase (NanoLUC) reporter fusion proteins in transgenic plants.

Therefore these models retain the distinction, where U2019 retains the regulation of later PRRs by activation by earlier-expressed genes from the P2011 model, and U2020 replaces this regulation with repression of earlier-expressed PRRs by later-expressed PRRs. The model development is described in more detail in the 'Model Evolution' document attached. Models are in SBML and Antimony formats.

Some early versions of the files with internal nomenclature might remain private and not included in the static Snapshot shared with the publication. The input data files, the computational environment for model development (a Docker image in the 'Reproducibility Toolset' assay) and the relevant model files are included here, as published in Urquiza et al. The biorXiv preprint version (https://doi.org/10.1101/2024.09.03.609973) and the final publication will also be linked here: the models and analysis are identical in both.

A Snapshot of this investigation is also available on FAIRDOMHub.org, DOI: 10.15490/fairdomhub.1.investigation.570.1. Note we often have to make the Snapshot before we have the publication DOI, so that link is not within the Snapshot.
DOI: 10.15468/dl.8h3d77
title: Occurrence Download

description: A dataset containing 5451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Machine Observation, Human Observation, Material sample, Material citation, Specimen, Living Specimen, Occurrence evidence)",
 "Country is China",
 "GadmGid is CHN.6.15_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "Month is one of (January, February, March, April, May, June, July, August, September, October, November, December)",
 "TaxonKey is Lepidoptera",
 "Year 2009-2023"
 ]
}

 The dataset includes 5451 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000182-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z9dn42
title: Occurrence Download

description: A dataset listing the 11 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is one of (United Kingdom of Great Britain and Northern Ireland, Norway, Sweden, Denmark)",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Virgularia, Virgularia Lamarck, 1816)"
 ]
}

 The dataset's 11 records were derived from 59 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000176-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/e74tcv
title: Colección de Antozoos del Atlántico Sur

description: La Colección de Anthozoos del Atlántico Sur (CAAS) es un set de datos creado y mantenido por el Laboratorio de Biología de Cnidarios (LABIC), dependiente de la Facultad de Ciencias Exactas y Naturales de la Universidad Nacional de Mar del Plata (FCEyN-UNMdP) y del Instituto de Investigaciones Marinas y Costeras (IIMyC, UNMdP-CONICET). La constitución de la CAAS, representa la apertura de la colección del LABIC a otros investigadores y colegas del país y del mundo. Así mismo, su digitalización, curación y el desarrollo de una detallada base de datos, la revalorizarán y la harán más visible. En ese sentido, tiene por objetivo asegurar el cuidado de la colección de cnidarios anthozoos, la determinación de ejemplares como soporte de líneas de investigación institucionales y regionales y actualización de la base de datos de la colección para su disponibilidad a la comunidad bajo el portal GBIF y el Portal de datos Biodiversidad.AR Es esperable que la CAAS se establezca como la colección de referencia de cnidarios antozoos de Argentina debido a la representatividad del material colectado, con muestras desde hace más de 30 años, y siendo el LABIC el único laboratorio del país dedicado íntegramente al estudio de anémonas de mar de Argentina y otras regiones de Latinoamérica. La CAAS consta principalmente de anémonas de mar (Actiniaria y Corallimorpharia) de la costa y plataforma continental argentina y zonas adyacentes; y en menor medida de otras regiones de Latinoamérica gracias a las colaboraciones realizadas por el grupo responsable con colegas de Costa Rica, Panamá, México, Brasil y Uruguay.
DOI: 10.5281/zenodo.14870430
title: Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma

description: This repository contains the Seurat objects used to produce the results in: Rade, M., Grieb, N., Weiss, R. et al. Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma. Nat Cancer 5, 1318–1333 (2024). https://doi.org/10.1038/s43018-024-00763-8

“seurat_harmony_tcell_pub..Rds” is a subset (only T cells) of “seurat_harmony_pub.Rds”. For the T-cell object, we have added added the VDJ sequences and genes from TCR-Seq to the meta.data slot. This was done with the R package scRepertoire.
DOI: 10.5281/zenodo.14870431
title: Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma

description: This repository contains the Seurat objects used to produce the results in: Rade, M., Grieb, N., Weiss, R. et al. Single-cell multiomic dissection of response and resistance to chimeric antigen receptor T cells against BCMA in relapsed multiple myeloma. Nat Cancer 5, 1318–1333 (2024). https://doi.org/10.1038/s43018-024-00763-8

“seurat_harmony_tcell_pub..Rds” is a subset (only T cells) of “seurat_harmony_pub.Rds”. For the T-cell object, we have added added the VDJ sequences and genes from TCR-Seq to the meta.data slot. This was done with the R package scRepertoire.
DOI: 10.15468/dl.6ttvnq
title: Occurrence Download

description: A dataset containing 7114 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Symphyotrichum pilosum (Willd.) G.L.Nesom, Aster pilosus var. pilosus, Aster pilosus f. pilosus, Aster pilosus Willd., Aster ericoides var. villosus (Michx.) Torr. & A.Gray, Aster juniperinus E.S.Burgess, Aster pilosus subsp. pilosus, Aster pilosus var. demotus S.F.Blake, Aster villosus Michx., Aster ericoides var. platyphyllus Torr. & A.Gray, Aster pilosus f. pulchellus Benke, Aster chrysogonii Sennen, Aster ericoides var. pilosus (Willd.) Porter, Aster ericoides f. villosus (Torr. & A.Gray) Voss, Aster pilosus var. platyphyllus (Torr. & A.Gray) S.F.Blake)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 7114 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000183-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14871333
title: THE USE OF DIGITAL PLATFORMS AND SIMULATORS FOR TEACHING PROFESSIONAL COMMUNICATION IN RUSSIAN IN TECHNICAL UNIVERSITIES

description: The article discusses the use of digital platforms and simulators for teaching professional communication in Russian in non-linguistic universities. Modern educational technologies, such as Moodle, Zoom platforms and specialized simulators, provide ample opportunities for the formation of professional and communicative competence of students in technical, medical and other fields. The authors focus on the integration of digital resources into the educational process, which helps to increase the motivation of students, develop their independence, self-control and skills of effective business communication. A special place is occupied by the description of the methodology for the development of professional courses, including audio and video materials, interactive tasks and simulators of real professional situations. The results of the study confirm that the use of digital technologies allows you to structure the learning process, automate the control of learning, improve listening, writing and speaking skills, as well as increase student engagement. Simulators of professional situations provide simulation of the real communication environment, which makes training practice-oriented and more effective. The article emphasizes the importance of a well-planned training program that combines digital technologies and methodological guidance from a teacher. This approach ensures the comprehensive development of language and professional skills necessary for a successful student career. The conclusion is made about the need for further development and implementation of digital platforms in the educational environment to improve the quality of teaching Russian as a foreign language.
DOI: 10.5281/zenodo.14871334
title: THE USE OF DIGITAL PLATFORMS AND SIMULATORS FOR TEACHING PROFESSIONAL COMMUNICATION IN RUSSIAN IN TECHNICAL UNIVERSITIES

description: The article discusses the use of digital platforms and simulators for teaching professional communication in Russian in non-linguistic universities. Modern educational technologies, such as Moodle, Zoom platforms and specialized simulators, provide ample opportunities for the formation of professional and communicative competence of students in technical, medical and other fields. The authors focus on the integration of digital resources into the educational process, which helps to increase the motivation of students, develop their independence, self-control and skills of effective business communication. A special place is occupied by the description of the methodology for the development of professional courses, including audio and video materials, interactive tasks and simulators of real professional situations. The results of the study confirm that the use of digital technologies allows you to structure the learning process, automate the control of learning, improve listening, writing and speaking skills, as well as increase student engagement. Simulators of professional situations provide simulation of the real communication environment, which makes training practice-oriented and more effective. The article emphasizes the importance of a well-planned training program that combines digital technologies and methodological guidance from a teacher. This approach ensures the comprehensive development of language and professional skills necessary for a successful student career. The conclusion is made about the need for further development and implementation of digital platforms in the educational environment to improve the quality of teaching Russian as a foreign language.
DOI: 10.15468/dl.p97mqr
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Peucetia viridana (Stoliczka, 1869)"
 ]
}

 The dataset includes 210 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000184-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14870820
title: Structural and functional significance of two conserved lysine residues in acylated sites of Kingella kingae RtxA cytotoxin

description: Data underlying the figures in the publication “Structural and functional significance of two conserved lysine residues in acylated sites of Kingella kingae RtxA cytotoxin”, published in Biochimie, 2024 Dec 31:S0300-9084(24)00320-1.

https://doi.org/10.1016/j.biochi.2024.12.016

 

Description of Files:

THS_2A: Functional complementation of four different fusion pairs, quantified by measuring β-galactosidase activity in bacterial extracts of E. coli strain BTH101.

THS_2B: Functional complementation of T25-RtxC with T18-proRtxA529–718 fusion variants.

THS_2C: Functional complementation of T25-RtxC with T18-proRtxA529–623, T18-proRtxA624–718, or T18-proRtxA529–718.

THS_2D: Functional complementation of T25-RtxC with T18-proRtxA529–623 fusion variants containing substitutions K558R and K558Q.

THS_2E: Functional complementation of T25-RtxC with the T18-proRtxA624–718 fusion variants containing substitutions K689R and K689Q.

Binding_3BL: Cell binding of RtxA variants to sheep erythrocytes.

Binding_3BR: Cell binding of RtxA variants to sheep erythrocytes after washing with alkaline carbonate.

Far-UV_3CL: Far-UV spectra of RtxA variants.

Near-UV_3CR: Near-UV spectra of RtxA variants.

Lysis_4A: Erythrocyte lysis in the presence of RtxA variants.
DOI: 10.5281/zenodo.14870821
title: Structural and functional significance of two conserved lysine residues in acylated sites of Kingella kingae RtxA cytotoxin

description: Data underlying the figures in the publication “Structural and functional significance of two conserved lysine residues in acylated sites of Kingella kingae RtxA cytotoxin”, published in Biochimie, 2024 Dec 31:S0300-9084(24)00320-1.

https://doi.org/10.1016/j.biochi.2024.12.016

 

Description of Files:

THS_2A: Functional complementation of four different fusion pairs, quantified by measuring β-galactosidase activity in bacterial extracts of E. coli strain BTH101.

THS_2B: Functional complementation of T25-RtxC with T18-proRtxA529–718 fusion variants.

THS_2C: Functional complementation of T25-RtxC with T18-proRtxA529–623, T18-proRtxA624–718, or T18-proRtxA529–718.

THS_2D: Functional complementation of T25-RtxC with T18-proRtxA529–623 fusion variants containing substitutions K558R and K558Q.

THS_2E: Functional complementation of T25-RtxC with the T18-proRtxA624–718 fusion variants containing substitutions K689R and K689Q.

Binding_3BL: Cell binding of RtxA variants to sheep erythrocytes.

Binding_3BR: Cell binding of RtxA variants to sheep erythrocytes after washing with alkaline carbonate.

Far-UV_3CL: Far-UV spectra of RtxA variants.

Near-UV_3CR: Near-UV spectra of RtxA variants.

Lysis_4A: Erythrocyte lysis in the presence of RtxA variants.
DOI: 10.5281/zenodo.13952131
title: Assessing the feasibility and acceptability of a pre-clinic vital signs assessment in primary care: a pilot study.
DOI: 10.5281/zenodo.13952132
title: Assessing the feasibility and acceptability of a pre-clinic vital signs assessment in primary care: a pilot study.
DOI: 10.15468/dl.bpt64q
title: Occurrence Download

description: A dataset containing 46801 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is SA Flora",
 "IucnRedListCategory is VU"
 ]
}

 The dataset includes 46801 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000185-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z5xpek
title: Occurrence Download

description: A dataset containing 940 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriovixia laglaizei (Simon, 1877)"
 ]
}

 The dataset includes 940 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000186-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9je54m
title: Occurrence Download

description: A dataset containing 1452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Plethodon shenandoah Highton & Worthington, 1967"
 ]
}

 The dataset includes 1452 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000187-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q9qg2x
title: Occurrence Download

description: A dataset containing 42967 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is SA Flora",
 "IucnRedListCategory is NT"
 ]
}

 The dataset includes 42967 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000188-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ks4jex
title: Occurrence Download

description: A dataset containing 15303 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Symphyotrichum squamatum (Spreng.) G.L.Nesom, Aster linifolius Griseb., Conyza berteroana Phil., Aster bangii Rusby, Erigeron semiamplexicaulis var. semiamplexicaulis, Aster divaricatus var. sandwicensis A.Gray ex H.Mann, Erigeron semiamplexicaule Meyen, 1843, Conyza squamata Spreng., Aster pseudobarcinonensis Sennen, 1929, Erigeron semiamplexicaule var. semiamplexicaule, Aster subtropicus Morong, Erigeron tripolioides Phil., Carphephorus junceus Durand, Aster divaricatus Baker, Erigeron semiamplexicaulis Meyen, Tripolium subulatum var. brasilianum DC., Aster pseudobarcincnensis Sennen, Aster divaricatus var. sandwicensis A.Gray, Tripolium moelleri Phil., Tripolium conspicuum Lindl. ex DC., Aster barcinonensis Sennen, Aster squamatus var. squamatus, Tripolium oliganthum Phil., Baccharis asteroides Colla, Tripolium imbricatum Nutt., Tripolium conspicuum Gay, Tripolium conspicuum J.Rémy, 1849, Aster sandwicensis (A.Gray ex H.Mann) Hieron., Aster subulatus var. sandwicensis (A.Gray ex H.Mann) A.G.Jones, Conyzanthus squamatus (Spreng.) Tamamsch., Aster squamatus (Spreng.) Hieron., Aster squamatus (Spreng.) Hieron. ex Sodiro, Symphyotrichum subulatum var. squamatum (Spreng.) S.D.Sundb., Aster squamatus var. tripolioides (Phil.) Hieron., Aster moelleri (Phil.) Reiche, Aster asteroides (Colla) Rusby)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 15303 records from 392 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000190-250214102907787/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14870960
title: Spatial profiling of human pancreas during type 1 diabetes progression

description: Spatial transcriptomic profiling on the CosMx platform (NanoString, Seattle, WA). Pancreatic tissue from six nPOD organ donors - three with T1D (6228, 6247, 6456) and three without diabetes (6431, 6339, 6229), matched by age and sex. For each donor, five consecutive FFPE tissue sections from the pancreatic body region were cut at a thickness of 4 microns.
DOI: 10.5281/zenodo.14870961
title: Spatial profiling of human pancreas during type 1 diabetes progression

description: Spatial transcriptomic profiling on the CosMx platform (NanoString, Seattle, WA). Pancreatic tissue from six nPOD organ donors - three with T1D (6228, 6247, 6456) and three without diabetes (6431, 6339, 6229), matched by age and sex. For each donor, five consecutive FFPE tissue sections from the pancreatic body region were cut at a thickness of 4 microns.