cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/fd7y24vfdm
title: Data and Code for: Low-Cost, High-Accuracy Reactivity Modeling: Integrating Genetic Algorithms and Machine Learning with Multilevel DFT calculations

description: This document provides the necessary data, software, and workflow information to reproduce the results presented in the manuscript: “Low-Cost, High-Accuracy Reactivity Modeling: Integrating Genetic Algorithms and Machine Learning with Multilevel DFT calculations”. The contents include self-contained, ready-to-run sub-directories with the necessary Python scripts, input files, and key outputs for verification.
This repository is structured for both demonstration and full reproducibility. It provides "ready-to-run" examples for direct application and foundational code templates for more complex methods (such as the GA2, GA3, and GA4 models), allowing users to reconstruct, adapt, and build upon the work.
The repository's content is organized into the following three computational levels:
Level 1: GA-ML Calibration & MLR (01_test_720LoT): Calibrates the initial hybrid framework integrating a genetic algorithm and machine learning (GA-ML) with the full 24x720 matrix and subsequently fits a Multiple Linear Regression (MLR) model.
Level 2: Reduced-Matrix GA-ML Models (02_test_576LoT): Proposes five GA-ML-based models (GA1–GA5) to optimize the selection of DFT LoTs from a reduced 24x576 matrix. This includes templates for advanced models (GA2–GA4) that use techniques such as Bayesian optimization and simultaneous regression analysis.
Level 3: Dynamic Generalization-Driven Transfer Learning (03_DGDTL): Implements a two-stage DGDTL protocol designed to enhance generalization, avoid overfitting, and find an optimal solution.
DOI: 10.17632/fd7y24vfdm.1
title: Data and Code for: Low-Cost, High-Accuracy Reactivity Modeling: Integrating Genetic Algorithms and Machine Learning with Multilevel DFT calculations

description: This document provides the necessary data, software, and workflow information to reproduce the results presented in the manuscript: “Low-Cost, High-Accuracy Reactivity Modeling: Integrating Genetic Algorithms and Machine Learning with Multilevel DFT calculations”. The contents include self-contained, ready-to-run sub-directories with the necessary Python scripts, input files, and key outputs for verification.
This repository is structured for both demonstration and full reproducibility. It provides "ready-to-run" examples for direct application and foundational code templates for more complex methods (such as the GA2, GA3, and GA4 models), allowing users to reconstruct, adapt, and build upon the work.
The repository's content is organized into the following three computational levels:
Level 1: GA-ML Calibration & MLR (01_test_720LoT): Calibrates the initial hybrid framework integrating a genetic algorithm and machine learning (GA-ML) with the full 24x720 matrix and subsequently fits a Multiple Linear Regression (MLR) model.
Level 2: Reduced-Matrix GA-ML Models (02_test_576LoT): Proposes five GA-ML-based models (GA1–GA5) to optimize the selection of DFT LoTs from a reduced 24x576 matrix. This includes templates for advanced models (GA2–GA4) that use techniques such as Bayesian optimization and simultaneous regression analysis.
Level 3: Dynamic Generalization-Driven Transfer Learning (03_DGDTL): Implements a two-stage DGDTL protocol designed to enhance generalization, avoid overfitting, and find an optimal solution.
DOI: 10.17632/tpndx2k6vp
title: Hidradenitis suppurativa project

description: Hidradenitis suppurativa is reportedly associated with increased cardiovascular risk. However, it is difficult to separate the role of the disease from the one of often coexisting cardiovascular risk factors. 
We tested whether patients with a low prevalence of cardiovascular risk factors displayed endothelial damage and pathological vessels’ remodelling as compared to a matched control population. 
Circulating endothelial cells were assessed in 17 HS patients and 19 matched controls. Retinal vascular changes were evaluated using optical coherence tomography angiography. Plasma levels of inflammatory and endothelial biomarkers were measured. 
Our results indicate that hidradenitis suppurativa is associated with a significant reduction in alive circulating endothelial progenitor cells, with no signs of acute endothelial damage. Affected subjects present narrower arteriolar diameter and wider venular diameter in the retinal microcirculation. 
At a median disease duration of 10 years from the diagnosis, patients display altered endothelial repair and microvascular remodelling. This calls for rigorous cardiovascular assessment in this specific cohort.
DOI: 10.17632/tpndx2k6vp.1
title: Hidradenitis suppurativa project

description: Hidradenitis suppurativa is reportedly associated with increased cardiovascular risk. However, it is difficult to separate the role of the disease from the one of often coexisting cardiovascular risk factors. 
We tested whether patients with a low prevalence of cardiovascular risk factors displayed endothelial damage and pathological vessels’ remodelling as compared to a matched control population. 
Circulating endothelial cells were assessed in 17 HS patients and 19 matched controls. Retinal vascular changes were evaluated using optical coherence tomography angiography. Plasma levels of inflammatory and endothelial biomarkers were measured. 
Our results indicate that hidradenitis suppurativa is associated with a significant reduction in alive circulating endothelial progenitor cells, with no signs of acute endothelial damage. Affected subjects present narrower arteriolar diameter and wider venular diameter in the retinal microcirculation. 
At a median disease duration of 10 years from the diagnosis, patients display altered endothelial repair and microvascular remodelling. This calls for rigorous cardiovascular assessment in this specific cohort.
DOI: 10.17632/5y8ywkfs9b
title: LINF_200013400

description: Pseudouridine synthase-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/5y8ywkfs9b.1
title: LINF_200013400

description: Pseudouridine synthase-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/xdtb6v3n8h.1
title: Biogeochemical Data from ODP Site 721A: Climatic Variability and Its Influence on the Indian Ocean Monsoon and on the NW Arabian Sea Oxygen Minimum Zone
DOI: 10.17632/pcjnbg5zjm
title: LINF_200013800

description: Elf1-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/pcjnbg5zjm.1
title: LINF_200013800

description: Elf1-like protein; Leishmania infantum (strain JPCM5)
DOI: 10.17632/rrcbybnrb7
title: LINF_200014000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.17632/rrcbybnrb7.1
title: LINF_200014000

description: Protein of unknown function - conserved; Leishmania infantum (strain JPCM5)
DOI: 10.15468/dl.hrzd5w
title: Occurrence Download

description: A dataset containing 11590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Glossophaga soricina (Pallas, 1766)"
 ]
}

 The dataset includes 11590 records from 284 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051476-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m24m87
title: Occurrence Download

description: A dataset containing 37279 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((10.6087 59.87921,10.87379 59.87921,10.87379 59.9722,10.6087 59.9722,10.6087 59.87921))",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Fulica atra Linnaeus, 1758, Anas platyrhynchos Linnaeus, 1758, Ardea cinerea Linnaeus, 1758)"
 ]
}

 The dataset includes 37279 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051480-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/cnbd274bxj
title: Boron isotopes in loess organic phase and the implication of terrestrial biomass on the Chinese Loess Plateau

description: [B] and B isotopic compositions of organic phase and the residual fraction in Yuanbao loess profile
DOI: 10.17632/cnbd274bxj.1
title: Boron isotopes in loess organic phase and the implication of terrestrial biomass on the Chinese Loess Plateau

description: [B] and B isotopic compositions of organic phase and the residual fraction in Yuanbao loess profile
DOI: 10.17632/gfv8nh5m52.1
title: Evaluation of SGLT2 inhibitor therapeutic efficacy and identification of IL-18/IL-18R1 signaling as a predictive biomarker in patients with T2DM

description: We hypothesised that circulating proteins predict inter-individual variability in the metabolic and cardiorenal benefits obtained from sodium-glucose co-transporter-2 inhibitor (SGLT2i) therapy in type 2 diabetes mellitus (T2DM). To test this, we combined longitudinal clinical phenotyping with plasma proteomics (Olink ® panels) and PBMC RNA-seq in up to 70 adults initiating SGLT2i treatment and followed for six months.

What the Data Show
- Clinical outcomes: Significant improvements in HbA1c (median −0.9 %), UACR (−26 %), body-weight (−1.8 kg) and related metabolic indices.
- Proteomics: Baseline IL-18R1 and its six-month reduction correlated with glycaemic change, fat-mass loss and albuminuria improvement (AUC = 0.75 for overall response). Macrophage-linked proteins (CD163, CHI3L1, CD93) and inflammasome‐related IL-1R2 also declined after therapy.
- Transcriptomics: RNA-seq of paired PBMC samples confirmed down-regulation of pro-inflammatory genes (CCR2, TNFAIP8L2, VIP) and up-regulation of reparative markers (SELENBP1, HIF1A), supporting an anti-inflammatory shift.
DOI: 10.17632/yhcf6787yp
title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. Bonine et al.

description: Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell-of-origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus data sets into a harmonized cell atlas covering 362,991 cells across 68 patient samples. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with new data and using it as a reference for data-driven cell-type annotation. 

seuratObj_NBAtlas_share_v20240130.rds: Seurat Object of the NBAtlas. Be aware, using this object requires roughly 14 GB of memory. 
SeuratObj_Share_50kSubset_NBAtlas_v20240130.rds: Light-weight version of the NBAtlas (50 k subset) for portable use. 
# v2: 
seuratObj_NBAtlas_share_v20241203.rds: Cleaned Seurat Object of the NBAtlas (doublets from the zooms filtered out). 
# v3:
SeuratMeta_TumorZoom_NBAtlas_v20250228.rds: Metadata of tumor zoom, for annotation use "clusters" or "cluster_nr", for umap coordinates use "scviUMAP_1" and "scviUMAP_2". This metadata can be used to subset the entire atlas Seurat object to obtain a tumor zoom Seurat object.
DOI: 10.17632/yhcf6787yp.3
title: NBAtlas: A harmonized single-cell transcriptomic reference atlas of human neuroblastoma tumors. Bonine et al.

description: Neuroblastoma, a rare embryonic tumor arising from neural crest development, is responsible for 15% of pediatric cancer-related deaths. Recently, several single-cell transcriptome studies were performed on neuroblastoma patient samples to investigate the cell-of-origin and tumor heterogeneity. However, these individual studies involved a small number of tumors and cells, limiting the conclusions that could be drawn. To overcome this limitation, we integrated seven single-cell or single-nucleus data sets into a harmonized cell atlas covering 362,991 cells across 68 patient samples. We use this atlas to decipher the transcriptional landscape of neuroblastoma at single-cell resolution revealing associations between transcriptomic profiles and clinical outcomes within the tumor compartment. In addition, we characterize the complex immune cell landscape and uncover considerable heterogeneity among tumor-associated macrophages. Finally, we showcase the utility of our atlas as a resource by expanding it with new data and using it as a reference for data-driven cell-type annotation. 

seuratObj_NBAtlas_share_v20240130.rds: Seurat Object of the NBAtlas. Be aware, using this object requires roughly 14 GB of memory. 
SeuratObj_Share_50kSubset_NBAtlas_v20240130.rds: Light-weight version of the NBAtlas (50 k subset) for portable use. 
# v2: 
seuratObj_NBAtlas_share_v20241203.rds: Cleaned Seurat Object of the NBAtlas (doublets from the zooms filtered out). 
# v3:
SeuratMeta_TumorZoom_NBAtlas_v20250228.rds: Metadata of tumor zoom, for annotation use "clusters" or "cluster_nr", for umap coordinates use "scviUMAP_1" and "scviUMAP_2". This metadata can be used to subset the entire atlas Seurat object to obtain a tumor zoom Seurat object.
DOI: 10.15468/dl.u5nswd
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Habenaria schlechteri Kraenzl.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((35.6306 -23.844,35.6007 -23.8125,35.6007 -24.0157,35.6306 -23.844))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0051481-250525065834625/datasets/export for details.
DOI: 10.17632/4kwh3zzrrz
title: Replication Package for "Climbing and Falling Off the Ladder: Asset Pricing Implications of Labor Market Event Risk"

description: Repository includes all source data and codes required to reproduce tables and figures from "Climbing and Falling Off the Ladder: Asset Pricing Implications of Labor Market Event Risk", which is forthcoming in the Journal of Financial Economics. 

Paper Abstract: Administrative earnings data reveal that households are exposed to large, countercyclical idiosyncratic tail risks in labor earnings. I illustrate how these risks affect asset prices within an asset pricing framework with recursive preferences, heterogeneous agents and incomplete markets. Quantitatively, a model in which agents face a time-varying probability of experiencing a rare, idiosyncratic disaster, with parameters disciplined by data, matches the level and dynamics of the equity premium. Stock returns are highly informative about labor market event risk, and, consistent with model predictions, initial claims for unemployment, a proxy for labor market uncertainty, is a highly robust predictor of returns.
DOI: 10.15468/dl.tfyuf4
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gloeothece subtilis Skuja"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006186-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6hwc7n
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gloeothece tepidariorum (A.Braun) Lagerh."
 ]
}

 The dataset includes 41 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006187-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v9r2u6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gloeothece verrucosa"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006189-241024112534372/datasets/export for details.
DOI: 10.15468/dl.v6wn8u
title: Occurrence Download

description: A dataset containing 589493 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is EOD – eBird Observation Dataset",
 "Geometry POLYGON((-114 43,-110 43,-110 50,-114 50,-114 43))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Issue is Continent derived from coordinates",
 "OccurrenceStatus is Present",
 "TaxonKey is Aves",
 "Year 2020-2020"
 ]
}

 The dataset includes 589493 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006177-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h524ke
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Orobanche anatolica, Orobanche anatolica, Orobanche anatolica Boiss. & Reuter, Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut., Orobanche anatolica Boiss. & Reut. ex Reut., 1847, Orobanche leucopogon Boiss. & Hausskn., Orobanche leucopogon Boiss. & Hausskn., Orobanche leucopogon Boiss. & Hausskn., Orobanche leucopogon Boiss. & Hausskn., Orobanche leucopogon Boiss. & Hausskn.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 30 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006190-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.epj8yp
title: Occurrence Download

description: A dataset containing 151 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gloeotrichia echinulata P.G.Richt."
 ]
}

 The dataset includes 151 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006191-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8azbmm
title: Occurrence Download

description: A dataset listing the 1 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ritchiea capparoides var. capparoides"
 ]
}

 The dataset's 1 records were derived from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006183-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rfbk93
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Gloeotrichia intermedia (Lemmerm.) Geitler"
 ]
}

 The dataset includes 4 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006193-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.trtjqu
title: Occurrence Download

description: A dataset containing 6606 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Solanum diphyllum, Solanum diphyllum, Solanum diphyllum Osbeck, Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum Forssk., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum Forssk., Solanum diphyllum Linnaeus, Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum L., Solanum diphyllum Forssk., Solanum diphyllum Osbeck, Solanum diphyllum Osbeck, Solanum diphyllum Osbeck, Solanum diphyllum Forssk., Solanum diphyllum Banks, Solanum diphyllum Osbeck, Solanum diphyllum L., 1753, Solanum diphyllum Forssk., 1775, Solanum diphyllum L., 1753, Solanum diphyllum Linnaeus 1753, Solanum diphyllum Linnaeus 1753, Solanum diphyllum Sessé & Moc., 1894, Solanum diphyllum Sessé & Moc., 1894, Solanum diphyllum Banks ex Dunal, Solanum diphyllum Banks ex Dunal, 174972593, Solanum diphyllum Banks ex Dunal, Solanum diphyllum Banks ex Dunal, Solanum diphyllum L. in Linné & Salvius, Solanum diphyllum Banks ex Dunal, 1852, Solanum diphyllum L. in Linné & Salvius, Solanum pseudocapsicum L., Metochus abbreviatus Scott 1874, Metochus abbreviatus Scott, 1874, Pseudocapsicum diphyllum (L.) Medik., Pseudocapsicum diphyllum Medik., Pseudocapsicum diphyllum (L.) Medik., Pseudocapsicum diphyllum (L.) Medik.)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6606 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006192-241024112534372/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13433419
title: IPBES Invasive Alien Species Assessment, database for Chapter 4. Impact Evidence Database

description: This is a database described in the data management report for chapter 4 of IPBES thematic assessment on invasive alien species and their control.

 

The data is currently under restricted access. If you'd like to access the data, please request via Zenodo. 

Data were gathered on direct observations of impacts from published literature, including grey literature, in order to form a database on the evidence to which invasive alien species impact, negatively and positively, nature, nature's contributions to people and good quality of life for Chapter 4 of IPBES thematic assessment of invasive alien species and their control. The criteria for inclusion were a published direct evidence of an impact on native species, a change in ecosystem properties, nature's contributions to people and the extent to which humans were affected through changes in their constituents of well-being.