cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.16894392
title: Context-Specific Genotoxicity in Therapeutic Base Editing for Genetic Hyperinflammation - Part 1

description: Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform– and cell type–specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62–89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type–specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR–Cas9, particularly in HSCs. While off-target sequence edits persisted, CBE-induced chromosomal translocations largely resolved in vivo. These findings establish therapeutic base editing for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide clinical translation of genome editors.
description: Murine T cells, HSCs and MEF cells were edited using Cas9 nuclease or evoCDA1-BE4max at the Unc13D locus. CAST-Seq was performed to assess the formation of chromosomal translocations between the on-target site and potential off-target sites.
DOI: 10.5281/zenodo.18526783
title: CPL-Code & CPL-Article with Github

description: Data presentation 

This dataset contains articles and github Nextflow workflows :



 





Articles and Code annotated with bioinformatics tools names contains in CPL-Article (https://doi.org/10.5281/zenodo.18526700) and CPL-Code (https://doi.org/10.5281/zenodo.18526760)

Nextflow Code (github) at time of the publication for each article contained in CPL-Article


Instructions



The experiments associated with these datasets are documented in : https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments/-/tree/main/Intermodal_entity_linking/Decoder-based_approaches/with_context?ref_type=heads
DOI: 10.5281/zenodo.18526784
title: CPL-Code & CPL-Article with Github

description: Data presentation 

This dataset contains articles and github Nextflow workflows :



 





Articles and Code annotated with bioinformatics tools names contains in CPL-Article (https://doi.org/10.5281/zenodo.18526700) and CPL-Code (https://doi.org/10.5281/zenodo.18526760)

Nextflow Code (github) at time of the publication for each article contained in CPL-Article


Instructions



The experiments associated with these datasets are documented in : https://gitlab.liris.cnrs.fr/sharefair/copalink-experiments/-/tree/main/Intermodal_entity_linking/Decoder-based_approaches/with_context?ref_type=heads
DOI: 10.5281/zenodo.18502380
title: Subset of WRF/MPAS outputs supporting the publication "Development of the TCWA2 Bulk Cloud Microphysics Scheme and Its Integration with a Dual-Polarization Radar Operator for Forecasting Applications" in JAMES

description: This dataset contains subsets of model outputs generated using the TCWA2 microphysics scheme. The wrfout subset includes microphysical variables for each precipitating hydrometeor category (raindrops, pristine ice, snow-aggregates, and rimed ice), including bulk mean volume diameter (MVDX), spectral shape parameter (AFAX), hydrometeor density (RHOX), aspect ratio (XASPR), fall speed (VTQX), and dual-polarization radar variables (DBZX, ZDRX, and KDPX) for two-dimensional idealized squall-line simulations in the WRF model. The mpasout subset contains simulated dual-polarization radar products, including horizontal reflectivity (DBZ), differential reflectivity (ZDR), and specific differential phase (KDP) for a real-case simulation of an afternoon convective event using the MPAS model. These data were processed to reproduce the primary figures and analyses presented in the manuscript entitled “Development of the TCWA2 Bulk Cloud Microphysics Scheme and Its Integration with a Dual-Polarization Radar Operator for Forecasting Applications,” submitted to the Journal of Advances in Modeling Earth Systems (JAMES).
DOI: 10.5281/zenodo.18502379
title: Subset of WRF/MPAS outputs supporting the publication "Development of the TCWA2 Bulk Cloud Microphysics Scheme and Its Integration with a Dual-Polarization Radar Operator for Forecasting Applications" in JAMES

description: This dataset contains subsets of model outputs generated using the TCWA2 microphysics scheme. The wrfout subset includes microphysical variables for each precipitating hydrometeor category (raindrops, pristine ice, snow-aggregates, and rimed ice), including bulk mean volume diameter (MVDX), spectral shape parameter (AFAX), hydrometeor density (RHOX), aspect ratio (XASPR), fall speed (VTQX), and dual-polarization radar variables (DBZX, ZDRX, and KDPX) for two-dimensional idealized squall-line simulations in the WRF model. The mpasout subset contains simulated dual-polarization radar products, including horizontal reflectivity (DBZ), differential reflectivity (ZDR), and specific differential phase (KDP) for a real-case simulation of an afternoon convective event using the MPAS model. These data were processed to reproduce the primary figures and analyses presented in the manuscript entitled “Development of the TCWA2 Bulk Cloud Microphysics Scheme and Its Integration with a Dual-Polarization Radar Operator for Forecasting Applications,” submitted to the Journal of Advances in Modeling Earth Systems (JAMES).
DOI: 10.15468/dl.buzddv
title: Occurrence Download

description: A dataset containing 4060 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "Year is greater than or equal to 1900",
 "TaxonKey is Atriplex praecox"
 ]
}

 The dataset includes 4060 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007654-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.q2byyy
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Daubenya aurea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 32 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007655-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16900763
title: Context-Specific Genotoxicity in Therapeutic Base Editing for Genetic Hyperinflammation - Part 2

description: Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform– and cell type–specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62–89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type–specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR–Cas9, particularly in HSCs. While off-target sequence edits persisted, CBE-induced chromosomal translocations largely resolved in vivo. These findings establish therapeutic base editing for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide clinical translation of genome editors.
description: Murine T cells, HSCs and MEF cells were edited using Cas9 nuclease or evoCDA1-BE4max at the Unc13D locus. CAST-Seq was performed to assess the formation of chromosomal translocations between the on-target site and potential off-target sites.
DOI: 10.5281/zenodo.16900764
title: Context-Specific Genotoxicity in Therapeutic Base Editing for Genetic Hyperinflammation - Part 2

description: Base editors enable precise correction of point mutations without requiring DNA double-strand breaks, yet platform– and cell type–specific genotoxicities remain incompletely characterized. Here, we applied cytosine base editing (CBE) to disrupt a cryptic splice-site mutation in the Unc13d locus of Jinx mice, a model of familial hemophagocytic lymphohistiocytosis type 3 (FHL3). Efficient editing (62–89%) in fibroblasts, T cells, and hematopoietic stem cells (HSCs) restored Unc13d splicing, reconstituted cytotoxic T cell function, and protected mice from virus-triggered hyperinflammation after transplantation of edited HSCs. Comparative genotoxicity profiling revealed distinct platform- and cell type–specific patterns: hyperactive CBE induced broader off-target activity and more structural variants than CRISPR–Cas9, particularly in HSCs. While off-target sequence edits persisted, CBE-induced chromosomal translocations largely resolved in vivo. These findings establish therapeutic base editing for a genetically predisposed hyperinflammatory syndrome and underscore the importance of context-specific safety profiling to guide clinical translation of genome editors.
description: Murine T cells, HSCs and MEF cells were edited using Cas9 nuclease or evoCDA1-BE4max at the Unc13D locus. CAST-Seq was performed to assess the formation of chromosomal translocations between the on-target site and potential off-target sites.
DOI: 10.17605/osf.io/zfau9
title: END-IT NH

description: The END-IT NH project was a feasibility cluster randomized controlled trial aimed at testing an intervention to favor benzodiazepine receptor agonists deprescribing in Belgian nursing homes residents (NHR). In total, 61 NHR participated, within 6 nursing homes (NH), each NH being a cluster.
DOI: 10.15468/dl.6q6mxk
title: Occurrence Download

description: A dataset containing 102 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Myloplus lobatus",
 "DecimalLatitude is not null",
 "DecimalLongitude is not null"
 ]
}

 The dataset includes 102 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007656-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15151/esrf-es-2286110233
title: Cryo-electron microscopy EPN/Grenoble BAG

description: ESRF is privileged to host two state-of-the-art microscopes. Our BAG unites the majority of local labs that utilise cryo-EM to address their diverse structural biology questions, including researchers from the EPN campus (IBS, ESRF, ILL and EMBL) and its vicinity (Cell & Plant Physiology Laboratory LPCV, Grenoble Institut des Neurosciences - GIN, Institute for Advanced Biosciences - IAB).
In a nutshell, approximately 30 principal investigators would greatly benefit from Krios time, with 100 different samples proposed. The high demand for EM beamtime is partially met by two Glacios microscopes available on the campus, currently charged with the pre-screening, but also frequently yielding satisfactory structural insights. Nonetheless, the use of a Krios is indispensable for challenging samples (with heterogeneity or limited concentration requiring a large number of images, small proteins, etc.). Only such “difficult cases” will be selected for Krios time at the BAG level.
DOI: 10.6084/m9.figshare.31313352
title: Pharmacist-Led Fentanyl Test Strip Education and Distribution for Veterans in Substance Use Treatment: A Quality Improvement Project

description: Unregulated fentanyl use is driving overdose deaths, and fentanyl test strips (FTS) are a tool to support overdose risk reduction. This quality improvement project assessed a novel pharmacist-led model of FTS education and distribution Veterans Affairs (VA) substance use disorder (SUD) care and its association with fentanyl-related knowledge and overdose risk reduction behaviors (ORRBs). This prospective single-arm cohort project was completed in outpatient SUD clinics at a VA Medical Center. A pharmacist delivered education (fentanyl, opioid overdose risk, FTS use) and offered Veterans FTS and intranasal naloxone. Veterans completed surveys pre-/post-education and at one-month. Pre-/post-changes in fentanyl knowledge, concerns, and planned ORRBs were analyzed using paired t-tests with Cohen’s <i>d</i> for effect size. Fifty-seven Veterans (mean age 59.3 years, 100% male) participated (January-October 2020). Most (<i>n</i> = 56, 98.2%) accepted at least one FTS kit, and 25 (43.9%) accepted naloxone. Significant pre-post improvements were observed in knowledge of carfentanil potency (<i>p</i> &lt; 0.001, <i>d</i> = 1.21), fentanyl potency (<i>p</i> &lt; 0.001, <i>d</i> = 0.74), and concern about fentanyl contamination (<i>p</i> &lt; 0.001, <i>d</i> = 0.59). Planned ORRBs improved: keeping naloxone nearby (<i>p</i> &lt; 0.001, <i>d</i> = 0.67); testing non-prescribed opioids for fentanyl (<i>p</i> &lt; 0.001, <i>d</i> = 0.61). Eleven (22.2%) reported using at least one FTS; most positive results were followed by ORRBs. A brief, pharmacist-led FTS education and distribution model was feasible in outpatient VA SUD care and associated with improved knowledge and ORRBs among Veterans. This model may reach Veterans who do not access conventional community-based harm reduction services and supports broader integration of FTS education and distribution in Veteran-focused SUD care to reduce overdose risk.
DOI: 10.6084/m9.figshare.31313352.v1
title: Pharmacist-Led Fentanyl Test Strip Education and Distribution for Veterans in Substance Use Treatment: A Quality Improvement Project

description: Unregulated fentanyl use is driving overdose deaths, and fentanyl test strips (FTS) are a tool to support overdose risk reduction. This quality improvement project assessed a novel pharmacist-led model of FTS education and distribution Veterans Affairs (VA) substance use disorder (SUD) care and its association with fentanyl-related knowledge and overdose risk reduction behaviors (ORRBs). This prospective single-arm cohort project was completed in outpatient SUD clinics at a VA Medical Center. A pharmacist delivered education (fentanyl, opioid overdose risk, FTS use) and offered Veterans FTS and intranasal naloxone. Veterans completed surveys pre-/post-education and at one-month. Pre-/post-changes in fentanyl knowledge, concerns, and planned ORRBs were analyzed using paired t-tests with Cohen’s <i>d</i> for effect size. Fifty-seven Veterans (mean age 59.3 years, 100% male) participated (January-October 2020). Most (<i>n</i> = 56, 98.2%) accepted at least one FTS kit, and 25 (43.9%) accepted naloxone. Significant pre-post improvements were observed in knowledge of carfentanil potency (<i>p</i> &lt; 0.001, <i>d</i> = 1.21), fentanyl potency (<i>p</i> &lt; 0.001, <i>d</i> = 0.74), and concern about fentanyl contamination (<i>p</i> &lt; 0.001, <i>d</i> = 0.59). Planned ORRBs improved: keeping naloxone nearby (<i>p</i> &lt; 0.001, <i>d</i> = 0.67); testing non-prescribed opioids for fentanyl (<i>p</i> &lt; 0.001, <i>d</i> = 0.61). Eleven (22.2%) reported using at least one FTS; most positive results were followed by ORRBs. A brief, pharmacist-led FTS education and distribution model was feasible in outpatient VA SUD care and associated with improved knowledge and ORRBs among Veterans. This model may reach Veterans who do not access conventional community-based harm reduction services and supports broader integration of FTS education and distribution in Veteran-focused SUD care to reduce overdose risk.
DOI: 10.15468/dl.g8ydfy
title: Occurrence Download

description: A dataset containing 66 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "TaxonKey is Anelasmocephalus pyrenaicus"
 ]
}

 The dataset includes 66 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007658-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18605581
title: scacac
DOI: 10.5281/zenodo.18605582
title: scacac
DOI: 10.15468/dl.cy4v63
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dichopogon fimbriatus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 712 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007659-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15023691
title: De novo transcriptome assembly and annotation of the Moroccan fir (Abies marocana)

description: The Moroccan fir (Abies marocana Trab.) is an endangered conifer endemic to the western Rif Mountains. Despite its ecological and economic significance, no transcriptomic data was previously available for the species. We present the first de novo transcriptome assembly for A. marocana, generated from RNA-seq data obtained from three organs (leaf, stem, and root) subjected to different stress treatments (drought, heat, cold, hormones, and physical damage), using both short- and long-read sequencing technologies, to achieve a comprehensive representation of the species' transcriptome. The assembly achieved a completeness value of 92.1% according to BUSCO, with 279,439 final transcripts, of which approximately 45.2% were functionally annotated. This high-quality transcriptome provides a valuable resource for advancing genetic research and supporting conservation efforts for this vulnerable species.
DOI: 10.5281/zenodo.15023692
title: De novo transcriptome assembly and annotation of the Moroccan fir (Abies marocana)

description: The Moroccan fir (Abies marocana Trab.) is an endangered conifer endemic to the western Rif Mountains. Despite its ecological and economic significance, no transcriptomic data was previously available for the species. We present the first de novo transcriptome assembly for A. marocana, generated from RNA-seq data obtained from three organs (leaf, stem, and root) subjected to different stress treatments (drought, heat, cold, hormones, and physical damage), using both short- and long-read sequencing technologies, to achieve a comprehensive representation of the species' transcriptome. The assembly achieved a completeness value of 92.1% according to BUSCO, with 279,439 final transcripts, of which approximately 45.2% were functionally annotated. This high-quality transcriptome provides a valuable resource for advancing genetic research and supporting conservation efforts for this vulnerable species.
DOI: 10.6084/m9.figshare.30870107
title: Dataset for: Pulsed evolution shaped extant angiosperm pollen disparity

description: This repository contains the primary data and scripts underlying the analyses presented in this study on angiosperm pollen morphological evolution and disparity. The files include the original morphological character matrix, time-calibrated phylogenetic trees, molecular sequence data, distance matrices, and all scripts required to reproduce the main results and figures.

Specifically, Data1_Original_coding_matrix.xlsx provides the genus-level discrete pollen character matrix used for morphospace, disparity, and evolutionary-rate analyses. Data2_MCCtrees.zip contains three time-calibrated angiosperm phylogenies (Triassic, Jurassic, and Cretaceous crown scenarios) in NEXUS format, which were used for disparity-through-time and rate analyses. Data3_Molecular_Dataset.nex includes the molecular alignment used to infer angiosperm phylogenetic relationships. Data4_Configuration file.txt contains the configuration file used for divergence-time estimation with TreePL. Data5_Distance_Matrix.zip provides the MORD morphological distance matrices (α = 0.5) used for ordination, disparity, and convergence analyses. Data6_Scripts.zip includes all R scripts used to perform ordinations (NMDS, PCoA), disparity calculations, bootstrap analyses, rate tests, and figure generation.
DOI: 10.6084/m9.figshare.30870107.v1
title: Dataset for: Pulsed evolution shaped extant angiosperm pollen disparity

description: This repository contains the primary data and scripts underlying the analyses presented in this study on angiosperm pollen morphological evolution and disparity. The files include the original morphological character matrix, time-calibrated phylogenetic trees, molecular sequence data, distance matrices, and all scripts required to reproduce the main results and figures.

Specifically, Data1_Original_coding_matrix.xlsx provides the genus-level discrete pollen character matrix used for morphospace, disparity, and evolutionary-rate analyses. Data2_MCCtrees.zip contains three time-calibrated angiosperm phylogenies (Triassic, Jurassic, and Cretaceous crown scenarios) in NEXUS format, which were used for disparity-through-time and rate analyses. Data3_Molecular_Dataset.nex includes the molecular alignment used to infer angiosperm phylogenetic relationships. Data4_Configuration file.txt contains the configuration file used for divergence-time estimation with TreePL. Data5_Distance_Matrix.zip provides the MORD morphological distance matrices (α = 0.5) used for ordination, disparity, and convergence analyses. Data6_Scripts.zip includes all R scripts used to perform ordinations (NMDS, PCoA), disparity calculations, bootstrap analyses, rate tests, and figure generation.
DOI: 10.15468/dl.ntrq35
title: Occurrence Download

description: A dataset containing 102618 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Medicago falcata",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is Fossil"
 ]
 }
 }
 ]
}

 The dataset includes 102618 records from 737 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007625-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fe6xz8
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "TaxonKey is Avicularia huriana"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008708-251025141854904/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.30493214
title: Zillow Housing price index, 2023 population, and 2023 median household income data for counties within Wyoming and surrounding states.

description: Time series Zillow Housing price index data and 2023 population and 2023 median household income data for counties within Wyoming and surrounding states.
DOI: 10.6084/m9.figshare.30493214.v1
title: Zillow Housing price index, 2023 population, and 2023 median household income data for counties within Wyoming and surrounding states.

description: Time series Zillow Housing price index data and 2023 population and 2023 median household income data for counties within Wyoming and surrounding states.