cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.53x58n
title: Occurrence Download

description: A dataset containing 10412 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Phyllanthus emblica L."
 ]
}

 The dataset includes 10412 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022383-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13683420
title: Predictors of Substorm Onset Conjugate Displacement (Dataset)

description: We provide the mediated list containing the onset locations of substorm onsets in the northern and southern hemisphere. The northern hemisphere onsets have been obtained from Frey et al (2004), who use IMAGE WIC and SI13, and the southern hemisphere onsets have been selected in the accompanying paper using Polar VIS.
DOI: 10.15468/dl.xujm33
title: Occurrence Download

description: A dataset containing 178 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Austria",
 "TaxonKey is Dendrobaena platyura (Fitzinger, 1833)"
 ]
}

 The dataset includes 178 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022384-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14793315
title: Integrating Formal Surveys and Local Knowledge: Insights into the Subterranean Fauna of Apulia

description: Background

The study of hypogean fauna is critical to preserve subterranean biodiversity and ecosystem functioning in spite of climate change. However, underground habitats, often hosting unique and endemic species, present significant challenges for traditional biodiversity assessments due to their inaccessibility and the specialised nature of their inhabitants, which results in paucity of academic studies. Furthermore, even when these studies exist, data is often held in personal notes and databases,  which are not interoperable according to current standards, making it less usable for research purposes. Reawakening this dormant data, standardising and sharing it according to modern criteria offers enormous opportunities to expand existing knowledge and provide support for future studies.

Novel Information

In the Apulian region of Southern Italy, a biodiversity hotspot for subterranean life, the paucity of recent systematic surveys and the reliance on expert knowledge pose both opportunities and challenges for ecological research. By integrating data from various sources, this study provides an overview of the subterranean faunal assemblages documented in this region. Overall, the dataset is comprehensive of 109 species (29 of which are considered endemic of Apulia) and 224 sites, totalling 631 presence-only records. Since our records expand over 93 years,  this dataset represents a unique resource for elucidating the characteristics of Apulian subterranean ecosystems and, potentially, their changes over time. Integrating observations already published in previous studies with unpublished records, this is the first complete data collection on Apulian subterranean fauna  organised according to modern standards of data sharing.
DOI: 10.5281/zenodo.14793316
title: Integrating Formal Surveys and Local Knowledge: Insights into the Subterranean Fauna of Apulia

description: Background

The study of hypogean fauna is critical to preserve subterranean biodiversity and ecosystem functioning in spite of climate change. However, underground habitats, often hosting unique and endemic species, present significant challenges for traditional biodiversity assessments due to their inaccessibility and the specialised nature of their inhabitants, which results in paucity of academic studies. Furthermore, even when these studies exist, data is often held in personal notes and databases,  which are not interoperable according to current standards, making it less usable for research purposes. Reawakening this dormant data, standardising and sharing it according to modern criteria offers enormous opportunities to expand existing knowledge and provide support for future studies.

Novel Information

In the Apulian region of Southern Italy, a biodiversity hotspot for subterranean life, the paucity of recent systematic surveys and the reliance on expert knowledge pose both opportunities and challenges for ecological research. By integrating data from various sources, this study provides an overview of the subterranean faunal assemblages documented in this region. Overall, the dataset is comprehensive of 109 species (29 of which are considered endemic of Apulia) and 224 sites, totalling 631 presence-only records. Since our records expand over 93 years,  this dataset represents a unique resource for elucidating the characteristics of Apulian subterranean ecosystems and, potentially, their changes over time. Integrating observations already published in previous studies with unpublished records, this is the first complete data collection on Apulian subterranean fauna  organised according to modern standards of data sharing.
DOI: 10.5063/f1qz28gz
title: Burrow Morphology and Burrowing Behaviour of Trypaea australiensis.

description: This study examined the burrow morphology and burrowing behavior of the mud shrimp Trypaea australiensis to understand the role of burrows for these organisms. We quantified burrow size and shape using resin casts and 3D imagery at two field sites, Shoalhaven Heads and Port Hacking. We found burrow casts at Shoalhaven Heads were larger and more variable in length compared to those at Port Hacking. For shrimp burrow behaviour, laboratory experiments showed that the shrimp tend to spend considerable time maintaining their burrows, regardless of time of day or shrimp sex. Though it was found that shrimp size impacted their behaviour, with smaller shrimp spending more time sitting and less time ventilating their burrows than larger shrimp.
DOI: 10.2908/gov_rrf_fa
title: Recovery and resilience facility (RRF) financial flows
title: Flux financiers de la facilité pour la reprise et la résilience (FRR)
title: : Finanzierungsströme der Aufbau- und Resilienzfazilität (ARF)
DOI: 10.2908/gov_rrf_use
title: Recovery and resilience facility (RRF) uses
title: Emploi des fonds de la facilité pour la reprise et la résilience (FRR)
title: Mittelverwendung aus der Aufbau- und Resilienzfazilität (ARF)
DOI: 10.15468/dl.kyrf7u
title: Occurrence Download

description: A dataset containing 4701 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bidens subalternans DC., Bidens triangularis DC., Bidens platensis Manganaro, Bidens quadrangularis DC., Bidens subalternans var. typica Sherff)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 4701 records from 137 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022385-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/10711235
title: World Stock Prices ( Daily Updating )
DOI: 10.15468/dl.dnhdc4
title: Occurrence Download

description: A dataset containing 2814 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Données sur la biodiversité des récifs coralliens de Martinique (OMMM)"
 ]
}

 The dataset includes 2814 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022386-250127130748423/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.28374878
title: NeuRGI-OntoVAE

description: The dataset was used in OntoVAE of NeuRGI pipeline.
DOI: 10.6084/m9.figshare.28374878.v1
title: NeuRGI-OntoVAE

description: The dataset was used in OntoVAE of NeuRGI pipeline.
DOI: 10.15468/dl.pvctgw
title: Occurrence Download

description: A dataset listing the 4300 species recorded in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Italy",
 "GadmGid is ITA.10_1",
 "License is one of (CC0 1.0, CC-BY 4.0, CC-BY-NC 4.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset's 4300 records were derived from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022356-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vxffv8
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Geometry POLYGON((-2.94908 37.63555,-2.31705 37.63555,-2.31705 38.1763,-2.94908 38.1763,-2.94908 37.63555))",
 "HasGeospatialIssue is false",
 "TaxonKey is Taxus baccata L."
 ]
}

 The dataset includes 19 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022390-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zzcxgn
title: Occurrence Download

description: A dataset containing 862 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bidens vulgata Greene, Bidens vulgata f. vulgata, Bidens vulgata var. vulgata, Bidens vulgata var. dissectior Sherff, Bidens frondosa var. puberula Wiegand, Bidens puberula Wiegand, Bidens vulgata var. schizantha Lunell, Bidens vulgata f. puberula (Wiegand) Fernald, Bidens vulgata var. puberula (Wiegand) Greene, Bidens puberula (Wiegand) Rydb.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 862 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022391-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eyfskj
title: Occurrence Download

description: A dataset listing the 307 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "DatasetKey is EOD – eBird Observation Dataset",
 "GadmGid is CHN.10_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Month is one of (May, June, January, February, March, April, July, August, September, October, November, December)",
 "Year 2021-2021"
 ]
}

 The dataset's 307 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022375-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vx65ad
title: Occurrence Download

description: A dataset listing the 1008 species recorded in GBIF matching the query:
{
 "and" : [
 "Country is United Kingdom of Great Britain and Northern Ireland",
 "DatasetKey is one of (Macro-moth distribution records for the UK from Butterfly Conservation, up to 2019, BSBI data from several English counties, up to 2018, UK Butterfly Monitoring Scheme (UKBMS))",
 "OccurrenceStatus is Present",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset's 1008 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022371-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5epg45
title: Occurrence Download

description: A dataset containing 2055 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Entomophthora muscae (Cohn) Fresen.",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 2055 records from 85 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022392-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sjv457
title: Occurrence Download

description: A dataset containing 6098 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Boerhavia coccinea Mill., Boerhavia marlothiae Heimerl, Boerhavia patula Dombey, Boerhavia diffusa var. paniculata Kuntze, Boerhavia marlothii Heimerl, Boerhavia repens var. undulata Asch. & Schweinf., Boerhavia sonorae Rose, Boerhavia diffusa var. acrophila Domin, Boerhavia diffusa Engelm. & A.Gray, Boerhavia polymorpha Rich., Boerhavia coccinea f. parcehirsuta Heimerl, Boerhavia diandra Aubl., Boerhavia glandulosa Andersson, Boerhavia ixioides Standl., Boerhavia hirsuta L., Boerhavia diffusa var. hirta Balle, Boerhavia ramulosa M.E.Jones, Boerhavia diffusa Sw., Boerhavia squamata Raf., Boerhavia viscosa subsp. apiculata Standl., Boerhavia adscendens var. pubescens Choisy, Boerhavia nantocana Schauer, Boerhavia ixodes Standl., Boerhavia diffusa var. obtusifolia Choisy, Boerhavia hirsuta Jacq., Boerhavia viscosa Lag. & Rodr., Boerhavia viscosa f. oligadena Heimerl, Boerhavia patula Dombey ex Vahl, Boerhavia bracteata T.Cooke, Boerhavia diffusa var. xerophila Domin, Boerhavia obtusifolia Lam., Boerhavia diffusa f. crassifolia Domin, Boerhavia caribaea Jacq., Boerhavia diffusa var. obtusifolia Cordem., 1895, Boerhavia coccinea var. paniculata (Kuntze) Moscoso, Boerhavia diffusa var. undulata (Asch. & Schweinf.) Cufod., Boerhavia coccinea var. pubescens (Choisy) Cufod., Boerhavia diffusa var. hirsuta Heimerl, Boerhavia diffusa var. hirsuta (Jacq.) Kuntze, Boerhavia coccinea var. viscosa (Lag. & Rodr.) Moscoso, Boerhavia diffusa var. viscosa (Lag. & Rodr.) Heimerl)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 6098 records from 189 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022393-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cm53j7
title: Occurrence Download

description: A dataset containing 1319 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Specimen)",
 "Country is one of (Spain, Portugal)",
 "OccurrenceStatus is Present",
 "TaxonKey is Alnus lusitanica Vít, Douda & Mandák"
 ]
}

 The dataset includes 1319 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022394-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.czzqx4
title: Occurrence Download

description: A dataset containing 451 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anacardium occidentale L."
 ]
}

 The dataset includes 451 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022395-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14825440
title: Subset of the ZINC dataset used in paper 'Improving Structural Plausibility in 3D Molecule Generation via Property-Conditioned Training with Distorted Molecules'

description: Contains train, validation and test datasets in the format used for training EDM.
DOI: 10.15468/dl.byjj9u
title: Occurrence Download

description: A dataset containing 790 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "PublishingOrg is 396d5f30-dea9-11db-8ab4-b8a03c50a862",
 "TaxonKey is Bombus distinguendus Morawitz, 1869"
 ]
}

 The dataset includes 790 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022396-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14755800
title: Comparing randomized trial designs to estimate treatment effect in rare diseases with longitudinal models: a simulation study showcased by Autosomal Recessive Cerebellar Ataxias using the SARA score - code

description: This repository contains the scripts for the paper submitted to the BMC Medical Research Methodology Journal : Comparing randomized trial designs to estimate treatment effect in rare diseases with longitudinal models: a simulation study showcased by Autosomal Recessive Cerebellar Ataxias using the SARA score

 

Authors : Hendrickx N, Mentré F, Hamdan A, Karlsson M O, Hooker A C, Traschütz A, Gagnon C, Schüle R, ARCA Study Group, EVIDENCE-RND consortium, Synofzik M, Comets E.

 

This repository contains the NONMEM code to reproduce the simulation study of the manuscript for the slow progression case. It contains three folders, one for each design : parallel, crossover and delayed start. 

Each folder contains one .csv file describing the design of the simulation, 8 NONMEM model files and 2 .sh files for the simulation. There are three models : Logistic, Linear and Linear Sparse models, twice each (*_full.mod = drug effect estimated, *_red.mod = drug effect fixed to 0). The Logistic model is also present twice : *H0_* = with a simulated drug effect of 0; *H1_* = with a simulated drug effect of 0.5. There are two .sh files : *_H0.sh = simulated drug effect of 0, for type 1 error ;  *_H1.sh = simulated drug effect of 0.5, for power.

 

To get the type 1 error and power calculation, you will need to unzip the "m1.zip" folders present in "ARSACS_type1" and "ARSACS_power" to "m1_*(t1/power)*" in each design directory and run the "script_type1_power.R" script in the parent directory to get the type 1 error and corrected power for all designs, as well as the code to get the figures 4 and 5 from the manuscript.

 

Please note that the computation time is long, especially if the commands are run locally. The commands in the .sh files are setup with 8 threads, and, depending on your CPU, the simulation study could take from 2 to 5 days per design and per simulation (Under H0 and H1) (with 500 replicates). Also, if you were to rerun the simulation, you should remove the "ARSACS_type_1" and "ARSACS_power" folders, or rename the target folder in the sse command and R script.

Softwares:

NONMEM 7.5.0PsN 5.3.1R 4.1.2
DOI: 10.5281/zenodo.14755801
title: Comparing randomized trial designs to estimate treatment effect in rare diseases with longitudinal models: a simulation study showcased by Autosomal Recessive Cerebellar Ataxias using the SARA score - code

description: This repository contains the scripts for the paper submitted to the BMC Medical Research Methodology Journal : Comparing randomized trial designs to estimate treatment effect in rare diseases with longitudinal models: a simulation study showcased by Autosomal Recessive Cerebellar Ataxias using the SARA score

 

Authors : Hendrickx N, Mentré F, Hamdan A, Karlsson M O, Hooker A C, Traschütz A, Gagnon C, Schüle R, ARCA Study Group, EVIDENCE-RND consortium, Synofzik M, Comets E.

 

This repository contains the NONMEM code to reproduce the simulation study of the manuscript for the slow progression case. It contains three folders, one for each design : parallel, crossover and delayed start. 

Each folder contains one .csv file describing the design of the simulation, 8 NONMEM model files and 2 .sh files for the simulation. There are three models : Logistic, Linear and Linear Sparse models, twice each (*_full.mod = drug effect estimated, *_red.mod = drug effect fixed to 0). The Logistic model is also present twice : *H0_* = with a simulated drug effect of 0; *H1_* = with a simulated drug effect of 0.5. There are two .sh files : *_H0.sh = simulated drug effect of 0, for type 1 error ;  *_H1.sh = simulated drug effect of 0.5, for power.

 

To get the type 1 error and power calculation, you will need to unzip the "m1.zip" folders present in "ARSACS_type1" and "ARSACS_power" to "m1_*(t1/power)*" in each design directory and run the "script_type1_power.R" script in the parent directory to get the type 1 error and corrected power for all designs, as well as the code to get the figures 4 and 5 from the manuscript.

 

Please note that the computation time is long, especially if the commands are run locally. The commands in the .sh files are setup with 8 threads, and, depending on your CPU, the simulation study could take from 2 to 5 days per design and per simulation (Under H0 and H1) (with 500 replicates). Also, if you were to rerun the simulation, you should remove the "ARSACS_type_1" and "ARSACS_power" folders, or rename the target folder in the sse command and R script.

Softwares:

NONMEM 7.5.0PsN 5.3.1R 4.1.2
DOI: 10.15468/dl.j82nwz
title: Occurrence Download

description: A dataset containing 2814 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Données sur la biodiversité des récifs coralliens de Martinique (OMMM)"
 ]
}

 The dataset includes 2814 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022397-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w86hq2
title: Occurrence Download

description: A dataset containing 790 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "PublishingOrg is 396d5f30-dea9-11db-8ab4-b8a03c50a862",
 "TaxonKey is Bombus distinguendus Morawitz, 1869"
 ]
}

 The dataset includes 790 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022398-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nb46du
title: Occurrence Download

description: A dataset containing 13568 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Flora of Sumatra: Vascular plant collection of selected families deposited at Herbarium of Andalas University (ANDA)"
 ]
}

 The dataset includes 13568 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022399-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14842958
title: Murine embryonic scRNA-seq data

description: These data sets contain scRNA-seq data of mouse embryos in Seurat object format.

The data are the result of a re-analysis of primary scRNA-seq data from:

 

 1. The lambdoid junction (lambdoid_junction_E11.5) 

GEO accession number: GSM3867275

Original publication: https://journals.biologists.com/dev/article/146/12/dev174888/19494/The-molecular-anatomy-of-mammalian-upper-lip-and

2. Whole embryos from the Mouse Organogenesis Cell Atlas (MOCA E9.5 - E13.5)

Original publication: https://www.nature.com/articles/s41586-019-0969-x

 

The re-analysis is described in:

Siewert A, Reiz B, Krug C, Heggemann J, Mangold E, Dickten H and Ludwig KU (2023) Analysis of candidate genes for cleft lip ± cleft palate using murine single-cell expression data. Front. Cell Dev. Biol. 11:1091666. doi: 10.3389/fcell.2023.1091666