cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fdy5pv
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "ScientificName is Rhizophora mangle",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002381-250424135625364/datasets/export for details.
DOI: 10.5281/zenodo.14941390
title: MERFISH output data for "Spatial Transcriptomics Reveals Human Cortical Layer and Area Specification"

description: The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas. These layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH), augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing over 18 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, three months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification in the mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior-posterior axis, and (2) a discrete, abrupt boundary uniquely identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week 20. This sharp binary transition in V1-V2 neuronal subtypes challenges the notion that continuous morphogen gradients dictate mid-gestation cortical arealization. Furthermore, integrating single-nucleus RNA-sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, implicating a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study provides a valuable resource for the field and establishes a spatially resolved single-cell analysis paradigm, paving the way for a comprehensive developmental atlas of the human brain.
DOI: 10.5281/zenodo.14941391
title: Spatial Transcriptomics Reveals Human Cortical Layer and Area Specification

description: The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas. These layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH), augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing over 18 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, three months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification in the mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior-posterior axis, and (2) a discrete, abrupt boundary uniquely identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week 20. This sharp binary transition in V1-V2 neuronal subtypes challenges the notion that continuous morphogen gradients dictate mid-gestation cortical arealization. Furthermore, integrating single-nucleus RNA-sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, implicating a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study provides a valuable resource for the field and establishes a spatially resolved single-cell analysis paradigm, paving the way for a comprehensive developmental atlas of the human brain.
DOI: 10.5281/zenodo.15127709
title: MERFISH output data for "Spatial Transcriptomics Reveals Human Cortical Layer and Area Specification"

description: The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas. These layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH), augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing over 18 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, three months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification in the mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior-posterior axis, and (2) a discrete, abrupt boundary uniquely identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week 20. This sharp binary transition in V1-V2 neuronal subtypes challenges the notion that continuous morphogen gradients dictate mid-gestation cortical arealization. Furthermore, integrating single-nucleus RNA-sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, implicating a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study provides a valuable resource for the field and establishes a spatially resolved single-cell analysis paradigm, paving the way for a comprehensive developmental atlas of the human brain.
DOI: 10.5281/zenodo.14681250
title: Supporting data for: "Preventive Effect of Upland Pigmented Potatoes Against LPS-Induced Inflammation in THP-1 Macrophages"

description: In this repository we deposited the docking poses and the target proteins for the paper "Preventive Effect of Upland Pigmented Potatoes Against LPS-Induced Inflammation in THP-1 Macrophages", Toccaceli M et al, 2025.

The file "toccaceli_et_al.zip" contains:

GLUT1

CGA

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -11.791

pose_2.pdb                                   # docking score -11.726

pose_3.pdb                                   # docking score -10.952

lig

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -10.795

pose_2.pdb                                   # docking score -10.549

pose_3.pdb                                   # docking score -10.401

Pg3G

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -13.017

pose_2.pdb                                   # docking score -12.810

pose_3.pdb                                   # docking score -12.750

Pn3G

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -14.210

pose_2.pdb                                   # docking score -13.768

pose_3.pdb                                   # docking score -13.391

GLUT3

CGA

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -10.371

pose_2.pdb                                   # docking score -9.794

pose_3.pdb                                   # docking score -9.476

lig

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -13.108

pose_2.pdb                                   # docking score -12.478

pose_3.pdb                                   # docking score -11.762

Pg3G

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -9.738

pose_2.pdb                                   # docking score -9.305

pose_3.pdb                                   # docking score -9.089

Pn3G

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -11.594

pose_2.pdb                                   # docking score -11.082

pose_3.pdb                                   # docking score -9.736

SGLT1

CGA

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -12.719

pose_2.pdb                                   # docking score -10.476

pose_3.pdb                                   # docking score -10.329

Pg3G

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -8.979

pose_2.pdb                                   # docking score -8.816

pose_3.pdb                                   # docking score -8.571

Pn3G

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -9.427

pose_2.pdb                                   # docking score -9.240

pose_3.pdb                                   # docking score -7.423
DOI: 10.5281/zenodo.14681251
title: Supporting data for: "Preventive Effect of Upland Pigmented Potatoes Against LPS-Induced Inflammation in THP-1 Macrophages"

description: In this repository we deposited the docking poses and the target proteins for the paper "Preventive Effect of Upland Pigmented Potatoes Against LPS-Induced Inflammation in THP-1 Macrophages", Toccaceli M et al, 2025.

The file "toccaceli_et_al.zip" contains:

GLUT1

CGA

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -11.791

pose_2.pdb                                   # docking score -11.726

pose_3.pdb                                   # docking score -10.952

lig

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -10.795

pose_2.pdb                                   # docking score -10.549

pose_3.pdb                                   # docking score -10.401

Pg3G

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -13.017

pose_2.pdb                                   # docking score -12.810

pose_3.pdb                                   # docking score -12.750

Pn3G

GLUT1_4PYP_prepared.pdb

pose_1.pdb                                   # docking score -14.210

pose_2.pdb                                   # docking score -13.768

pose_3.pdb                                   # docking score -13.391

GLUT3

CGA

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -10.371

pose_2.pdb                                   # docking score -9.794

pose_3.pdb                                   # docking score -9.476

lig

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -13.108

pose_2.pdb                                   # docking score -12.478

pose_3.pdb                                   # docking score -11.762

Pg3G

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -9.738

pose_2.pdb                                   # docking score -9.305

pose_3.pdb                                   # docking score -9.089

Pn3G

GLUT3_4ZWC_prepared.pdb

pose_1.pdb                                   # docking score -11.594

pose_2.pdb                                   # docking score -11.082

pose_3.pdb                                   # docking score -9.736

SGLT1

CGA

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -12.719

pose_2.pdb                                   # docking score -10.476

pose_3.pdb                                   # docking score -10.329

Pg3G

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -8.979

pose_2.pdb                                   # docking score -8.816

pose_3.pdb                                   # docking score -8.571

Pn3G

SGLT1_7SLA_prepared.pdb

pose_1.pdb                                   # docking score -9.427

pose_2.pdb                                   # docking score -9.240

pose_3.pdb                                   # docking score -7.423
DOI: 10.15468/dl.jvcqz7
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is BRA.10.33_2",
 "TaxonKey is Aves"
 ]
}

 The dataset includes 4 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002388-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15277101
title: BACDAC supporting processed data for publication

description: Processed data for 36 TCGA samples and samples represented in figure 1 and figure 2 of the BACDAC publication: Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot. 

For each sample 3 types of files are included, 1) segmentation file (.csv), 2) read depth counts binned over 30kb and 100kb windows (.Rds) and 3) ref/alt counts for reference snp positions, one file for each chromosome 1 - 22 and X (.Rds). Total number of files for each sample is 26. For the TCGA samples, files are available for both the high coverage (as available from TCGA) and the low-pass (down-sampled) samples presented in the BACDAC publication.
DOI: 10.5281/zenodo.15277102
title: BACDAC supporting processed data for publication

description: Processed data for 36 TCGA samples and samples represented in figure 1 and figure 2 of the BACDAC publication: Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot. 

For each sample 3 types of files are included, 1) segmentation file (.csv), 2) read depth counts binned over 30kb and 100kb windows (.Rds) and 3) ref/alt counts for reference snp positions, one file for each chromosome 1 - 22 and X (.Rds). Total number of files for each sample is 26. For the TCGA samples, files are available for both the high coverage (as available from TCGA) and the low-pass (down-sampled) samples presented in the BACDAC publication.
DOI: 10.15468/dl.89cp2z
title: Occurrence Download

description: A dataset containing 183 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Didunculus strigirostris (Jardine, 1845)"
 ]
}

 The dataset includes 183 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002389-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wvgswy
title: Occurrence Download

description: A dataset containing 367785 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paspalum L."
 ]
}

 The dataset includes 367785 records from 1913 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002382-250424135625364/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x6nuj5
title: Occurrence Download

description: A dataset containing 1561 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Bolborhynchus ferrugineifrons)",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "License is one of (CC-BY 4.0, CC0 1.0)"
 ]
}

 The dataset includes 1561 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0083899-250717081556266/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.1594/pangaea.964952
title: Pre-rainfall experiment calibration to determine droplet diameter at 15 different positions within an area of 1.21 m²

description: We provide data from experiments with artificial rain over a 5100-liter basin with a retractable roof, where temperature and conductivity (to calculate salinity) were measured at different depths in the upper sea surface, as well as rain properties (intensity, rain temperature, droplet size and velocity). Three different nozzle types were used to investigate the impacts of droplet properties on temperature and salinity anomalies at the sea surface. To measure droplet sizes and velocities, we made calibration measurements with an optical laser disdrometer before the actual experiments. In the first experiments, we excluded external influences such as wind-driven mixing to show on a very small vertical and horizontal scale how very different rainfall intensities and properties such as droplet sizes and velocities affect sea surface temperature and salinity. In a second series of experiments, we used different stages of a flow pump to add turbulence to the basin and find out how quickly the rain water mixes with the seawater at the near-surface layer. The duration of the artificial rain was 15 minutes for all experiments. We used an acoustic doppler velocimeter (ADV) to calculate turbulent kinetic energy at two different depths (14 and 44 cm) within the basin. Additional samples from the sea surface microlayer (SML) were collected before and after the artificial rain in both experiments.
description: Before performing the experiments, we performed a calibration of the different nozzle types and rain intensities to see what droplet properties were produced. We measured the droplet diameter and velocity at 15 different positions within an area of 1.21 m². Location of the mesocosm experiment: Sea-SurFace Facility (SURF), Institute of Chemistry and Biology of the marine Environment, Schleusenstraße 1, 26382 Wilhelmshaven, Coordinates: 53.5148, 8.1463
DOI: 10.1594/pangaea.964909
title: Rainfall experiment 1 conducted in a large seawater tank with three different nozzle types and three different precipitation intensities - air temperature measurement

description: We provide data from experiments with artificial rain over a 5100-liter basin with a retractable roof, where temperature and conductivity (to calculate salinity) were measured at different depths in the upper sea surface, as well as rain properties (intensity, rain temperature, droplet size and velocity). Three different nozzle types were used to investigate the impacts of droplet properties on temperature and salinity anomalies at the sea surface. To measure droplet sizes and velocities, we made calibration measurements with an optical laser disdrometer before the actual experiments. In the first experiments, we excluded external influences such as wind-driven mixing to show on a very small vertical and horizontal scale how very different rainfall intensities and properties such as droplet sizes and velocities affect sea surface temperature and salinity. In a second series of experiments, we used different stages of a flow pump to add turbulence to the basin and find out how quickly the rain water mixes with the seawater at the near-surface layer. The duration of the artificial rain was 15 minutes for all experiments. We used an acoustic doppler velocimeter (ADV) to calculate turbulent kinetic energy at two different depths (14 and 44 cm) within the basin. Additional samples from the sea surface microlayer (SML) were collected before and after the artificial rain in both experiments.
description: Data from the first experiment: the air temperature was measured. Location of the mesocosm experiment: Sea-SurFace Facility (SURF), Institute of Chemistry and Biology of the marine Environment, Schleusenstraße 1, 26382 Wilhelmshaven, Coordinates: 53.5148, 8.1463
DOI: 10.1594/pangaea.964911
title: Rainfall experiment 2 conducted in a large seawater tank with three different nozzle types and rain intensities, and added turbulence - CTD measurement

description: We provide data from experiments with artificial rain over a 5100-liter basin with a retractable roof, where temperature and conductivity (to calculate salinity) were measured at different depths in the upper sea surface, as well as rain properties (intensity, rain temperature, droplet size and velocity). Three different nozzle types were used to investigate the impacts of droplet properties on temperature and salinity anomalies at the sea surface. To measure droplet sizes and velocities, we made calibration measurements with an optical laser disdrometer before the actual experiments. In the first experiments, we excluded external influences such as wind-driven mixing to show on a very small vertical and horizontal scale how very different rainfall intensities and properties such as droplet sizes and velocities affect sea surface temperature and salinity. In a second series of experiments, we used different stages of a flow pump to add turbulence to the basin and find out how quickly the rain water mixes with the seawater at the near-surface layer. The duration of the artificial rain was 15 minutes for all experiments. We used an acoustic doppler velocimeter (ADV) to calculate turbulent kinetic energy at two different depths (14 and 44 cm) within the basin. Additional samples from the sea surface microlayer (SML) were collected before and after the artificial rain in both experiments.
description: Data from the second experiment: again with three different nozzle types and rain intensities, but this time we added turbulence in the tank with a large flow pump at three different levels (0 %, 0.5 %, and 1 %). Temperature and conductivity (for later calculation of salinity) were measured at different depths.Location of the mesocosm experiment: Sea-SurFace Facility (SURF), Institute of Chemistry and Biology of the marine Environment, Schleusenstraße 1, 26382 Wilhelmshaven, Coordinates: 53.5148, 8.1463
DOI: 10.6084/m9.figshare.29755771
title: Additional file 1 of Yeast culture in weaned lamb feed: a proteomic journey into enhanced rumen health and growth

description: Additional file 1: Downregulation of DEPs.
DOI: 10.6084/m9.figshare.29755771.v1
title: Additional file 1 of Yeast culture in weaned lamb feed: a proteomic journey into enhanced rumen health and growth

description: Additional file 1: Downregulation of DEPs.
DOI: 10.6084/m9.figshare.29755774
title: Additional file 2 of Yeast culture in weaned lamb feed: a proteomic journey into enhanced rumen health and growth

description: Additional file 2: Upregulation of DEPs.
DOI: 10.6084/m9.figshare.29755774.v1
title: Additional file 2 of Yeast culture in weaned lamb feed: a proteomic journey into enhanced rumen health and growth

description: Additional file 2: Upregulation of DEPs.