cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.11397463
title: Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing

description: Abstract:  The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.

This data sets contains:

Tab. S1 - Significant genes results

Tab. S2 - Enriched pathways_GO_Biological Processes

Tab. S3 - Enriched pathways_GO_Cellular Components

Tab. S4 - Enriched pathways_GO_Molecular Function

Tab. S5 - Enriched pathways_KEGG

Tab. S6 - EnrichEnriched pathways_Panther

Tab. S7 - Enriched pathways_Reactome

Tab. S8 - Gene counts

Tab. S9 - Gene selection for targeted analysis
DOI: 10.15468/dl.wtg36l
title: Occurrence Download

description: A dataset containing 36346 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Coenonympha tullia Müller, 1764"
 ]
}

 The dataset includes 36346 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000315-180508205500799/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j1jt8v
title: Occurrence Download

description: A dataset containing 7500 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Calothorax G.R.Gray, 1840"
 ]
}

 The dataset includes 7500 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003631-181003121212138/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.54ntrc
title: Occurrence Download

description: A dataset containing 2066 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Molossus molossus (Pallas, 1766)"
 ]
}

 The dataset includes 2066 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0073937-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ddwb5a
title: Occurrence Download

description: A dataset containing 758 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "HasCoordinate is true",
 "TaxonKey is Salix lapponum L.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 758 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003631-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qlicgp
title: Occurrence Download

description: A dataset containing 1882 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Schoenoplectiella mucronata (L.) J.Jung & H.K.Choi",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 1882 records from 76 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000315-180730143533302/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.0gtqvv
title: Occurrence Download

description: A dataset containing 2858015 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-10.48782 39.91249,-4.61179 39.91249,-4.61179 43.90107,-10.48782 43.90107,-10.48782 39.91249))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 2858015 records from 433 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003105-180412121330197/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwz2xb
title: Occurrence Download

description: A dataset containing 1177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia deltoidea (Torr.) W.W.Payne",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1177 records from 37 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056765-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sdef4l
title: Occurrence Download

description: A dataset containing 1574 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Tabebuia aurea (Silva Manso) Benth. & Hook.fil. ex S.Moore"
 ]
}

 The dataset includes 1574 records from 97 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003631-170627171947987/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b8b1rk
title: Occurrence Download

description: A dataset containing 18856 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Museo Nacional de Ciencias Naturales, Colección de Malacología: MNCN-Malac"
 ]
}

 The dataset includes 18856 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003105-190307172214381/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ekyb3a
title: Occurrence Download

description: A dataset containing 4017 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ambrosia dumosa (A.Gray) W.W.Payne",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 4017 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056766-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.twuhn0
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cyathea catacampta Alston"
 ]
}

 The dataset includes 28 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0036966-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hfigzu
title: Occurrence Download

description: A dataset listing the 3 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "TaxonKey is Jatropha integerrima Jacq."
 ]
}

 The dataset's 3 records were derived from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0034992-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pv73f6
title: Occurrence Download

description: A dataset containing 19388 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is UEL - Coleção de Peixes - Museu de Zoologia da Universidade Estadual de Londrina"
 ]
}

 The dataset includes 19388 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000315-180920211646547/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrpezg
title: Occurrence Download

description: A dataset containing 305 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Daboia palaestinae (Werner, 1938)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 305 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050598-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4a8v9h
title: Occurrence Download

description: A dataset containing 281 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polygonatum kingianum Collett & Hemsl."
 ]
}

 The dataset includes 281 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0056132-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rzhswp
title: Occurrence Download

description: A dataset listing the 18296 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry MULTIPOLYGON (((-58.9 47.6, -59.25 47.55, -59.4 47.95, -58.45 48.45, -58.7 48.55, -58.65 48.8, -58.4 49.15, -58.15 49.05, -58.25 49.4, -57.95 49.55, -57.35 50.7, -56.95 50.9, -57.1 51.05, -56.9 51, -56.75 51.35, -55.4 51.65, -55.6 51.3, -56.1 51.35, -55.65 51.15, -56.2 50.75, -56.1 50.65, -56.75 50.05, -56.8 49.65, -56.1 50.15, -55.85 49.95, -55.5 50, -56 49.7, -55.85 49.7, -55.85 49.5, -55.7 49.65, -55.55 49.45, -55.15 49.55, -55.25 49.25, -54.9 49.4, -54.8 49.3, -54.7 49.5, -54.9 49.6, -54.75 49.7, -54.5 49.65, -54.45 49.4, -54.05 49.5, -53.5 49.3, -53.8 48.55, -53.25 48.5, -53.2 48.65, -53 48.55, -53.55 48.25, -53.85 47.7, -53.55 47.55, -53.35 48, -52.9 48.15, -53.25 47.6, -53.1 47.4, -52.75 47.8, -52.6 47.5, -52.85 47.3, -53.05 46.65, -53.6 46.6, -53.6 47.1, -54.2 46.8, -53.9 47.5, -54.05 47.85, -54.5 47.35, -54.95 47.35, -55.4 46.85, -55.85 46.85, -56 47, -55.45 47.15, -55.25 47.45, -54.9 47.5, -54.85 47.65, -55.1 47.55, -55.4 47.65, -55.55 47.4, -55.9 47.45, -56.05 47.7, -56.7 47.55, -57.35 47.65, -57.7 47.55, -57.9 47.7, -58.9 47.6), (-53.8 48.85, -53.75 49, -53.95 48.9, -53.8 48.85)), ((-54.15 49.75, -54.05 49.65, -54.3 49.55, -54.3 49.8, -54.15 49.75)), ((-56.4 47.15, -56.25 46.8, -56.4 46.8, -56.4 47.15)), ((-59.1 48.6, -58.8 48.5, -59.25 48.45, -59.1 48.6)), ((-62.6 49.15, -63.55 49.35, -63.8 49.65, -64.5 49.9, -63.35 49.85, -61.7 49.2, -61.8 49.05, -62.6 49.15)), ((-62.95 46.2, -63.15 46.25, -63.15 46.1, -63.65 46.2, -63.75 46.4, -64.15000000000001 46.4, -64.05 46.6, -64.40000000000001 46.6, -64.40000000000001 46.75, -64 47.05, -64.05 46.8, -63.8 46.65, -63.8 46.45, -62 46.45, -62.6 46.2, -62.45 46.1, -62.5 45.95, -62.85 45.95, -62.95 46.2)))",
 "HasCoordinate is true",
 "Year is greater than or equal to 1960",
 "HasGeospatialIssue is false"
 ]
}

 The dataset's 18296 records were derived from 273 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048947-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11617741
title: Dataset from the paper "The boring history of GAIA BH3 from isolated binary evolution": I - initial conditions & run scripts

description: This repository contains the initial condition files and the run scripts to reproduce the results in Iorio et al., 2024.

Content

Files XXX.ic

Ascii files containing the initial conditions of 2e7 binary systems. The files do not contain a header, and the columns report (from left to right):



Mass of the primary [Msun]

Absolute metallicity of the primary 

Initial spin (angular velocity over critical angular velocity)

Supernova model for the primary

Initial age of the star (Myr or special keywords)

Mass of the secondary [Msun]

Absolute metallicity of the secondary

Initial spin (angular velocity over critical angular velocity)

Supernova model for the secondary

Initial age of the star (Myr or special keywords)

Initial semimajor axis [Rsun]

Initial Eccentricity 

Ending time or condition of the simulation [Myr or special keyword]

Output frequency [Myr or special]

Random seed


Some columns contains the special placeorder keyword XXX. In this case, the values are undefined and they are set at runtime using the value on the runscripts. For additional information see the SEVN Userguide.

The initial conditions are:



SEVNIC20M_qmin0005.in, initial conditions used in all the simuations of  Iorio et al., 2024 except for the model fiducial_ICthermal (see Table 1) e partially for the model fiducial2E8 (see below).

SEVNIC20M_qmin0005_ethermal.in, initial conditions for the simulation set fiducial_ICthermal

SEVNIC20M_X.in (where X ranges from 1 to 9), initial conditions (split in different chuncks) used for the simulation set fiducial2e8. This set is also complemetned by the SEVNIC20M_qmin0005.in initial conditions. 


Runscripts

The runscripts are contained in the archive runscripts.zip. See the README in the archive for additional information. 

Notes

The code used in Iorio et al., 2024 is SEVN (Iorio et al., 2023) version 2.10.1 (commit a4753f11).
DOI: 10.5281/zenodo.13142331
title: Gulag Memoirs

description: Memoirs used and analyzed by Gulag Echoes Team members.
DOI: 10.5281/zenodo.13142332
title: Gulag Memoirs

description: Memoirs used and analyzed by Gulag Echoes Team members.
DOI: 10.5281/zenodo.13142399
title: Gulag Memoirs

description: Memoirs used and analyzed by Gulag Echoes Team members.
DOI: 10.6084/m9.figshare.26243276.v1
title: Research on Control Methods for Automatic Drilling Robot Based on Visual Servoing

description: In the demolition blasting scene, a large number of humans are needed to drill the gun holes. Aiming at the problems of harsh blasting environment, high accuracy of drilling operation and large number of drilling holes, an automatic drilling robot is designed, and a visual servo drilling algorithm of cooperative manipulator with stable trajectory is proposed. This method is a control method based on visual feedback. The manipulator is calibrated by hand and eye, and the manipulator servo experiments of image-based visual servoing (IBVS) and position-based visual servoing (PBVS) are carried out based on Apriltag tag as the target object. In the experiment, three factors that may affect the robustness of visual servoing tasks, namely, different lighting conditions, different target object poses and hand-eye calibration, were tested in orthogonal experiments. The experimental results show that the robustness of the automatic drilling robot control method based on image visual servoing using point features is better than that of the position-based visual servoing control method. The visual error convergence curve, camera motion speed curve and camera motion trajectory of IBVS are better than those of PBVS, and the accuracy of visual error convergence can meet the drilling requirements of demolition.
DOI: 10.15468/dl.zy4paq
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Machaerium milleflorum Pittier)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 153 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043239-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnydbg
title: Occurrence Download

description: A dataset listing the 25168 species recorded in GBIF matching the query:
{
 "Country" : [
 "is Malawi"
 ]
}

 The dataset's 25168 records were derived from 687 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043227-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7y4q5p
title: Occurrence Download

description: A dataset containing 2285 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is Europe",
 "GadmGid is one of (GBR.3_1, GBR.4_1, GBR.1_1)",
 "Geometry POLYGON((-180 56,180 56,180 57,-180 57,-180 56))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Cepaea nemoralis (Linnaeus, 1758), Cepaea hortensis (O.F.Müller, 1774))"
 ]
}

 The dataset includes 2285 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043238-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dbjy4j
title: Occurrence Download

description: A dataset listing the 2242 species recorded in GBIF matching the query:
{
 "GadmGid" : [
 "is MWI.11_1"
 ]
}

 The dataset's 2242 records were derived from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043233-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jkwfmu
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Machaerium millei Standl.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 271 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043241-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.5345wu
title: Occurrence Download

description: A dataset containing 674 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-94.52867 37.34678,-124.74118 25.14271,-109.41168 -4.02799,-69.22756 -12.66013,-48.83783 5.94363,-67.29277 36.90029,-79.49683 40.02572,-94.52867 37.34678))",
 "TaxonKey is Ponthieva racemosa (Walter) C.Mohr"
 ]
}

 The dataset includes 674 records from 62 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043240-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.w8padj
title: Occurrence Download

description: A dataset containing 113 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Delias aurantia"
 ]
}

 The dataset includes 113 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043242-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xduxap
title: Occurrence Download

description: A dataset containing 271 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Machaerium pittieri J.F.Macbr.)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 271 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043243-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34777/9w2p-dx95
title: SkySoft ATM MALAT Vertical Rate

description: The dataset comprises detailed altitude tracking (`TRACK_ALTITUDE`) for over 25,000 flights across European airspace, amassed over four different weeks. Each flight track is matched with its corresponding cleared flight level (`CFL`) and supplemented with anonymized `AIRCRAFT_TYPE` and can be grouped using the `FLIGHT_ID` field.
DOI: 10.15468/dl.6tt9sy
title: Occurrence Download

description: A dataset containing 71 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Machaerium riparium Brandegee)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 71 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043244-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3v29k8
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Atrophaneura priapus (Boisduval, 1836)"
 ]
}

 The dataset includes 220 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043246-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.