cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15275592
title: Enviro-HIRLAM model output for April 2020 air pollution case study

description: Case study: wildfires and dust storm air pollution events occured in April 2020 in the norther part of Ukraine (including the abandoned Chornobyl Exclusion Zone).The presented dataset contains the seamless Environment – HIgh-Resolution Limited Area Model (Enviro-HIRLAM) model output with a 1.5 km horizontal resolution. Period of study cover 5-30 April 2020. The model domain consists of 410×410 grid points in a rotated system of coordinates. Extracted for the 11 lowest Enviro-HIRLAM model levels. The model description can be found by the following link: https://doi.org/10.5194/gmd-10-2971-2017

Model configurations: (1) reference (REF) run without aerosol effects; (2) run with direct aerosol effects (DAE) included; (3) run with indirect aerosol effects (IDAE); and (4) run with combined direct and indirect aerosol effects (COMB).

Domain and rotated system characteristics:- number of grid points along longitude = 410; - number of grid points along latitude = 410; - south boundary in rotated system of coordinates (deg) =-27.484;- north boundary in rotated system of coordinates = -21.349;- west boundary in rotated system of coordinates = -35.450;- east boundary in rotated system of coordinates = -29.315;- coordinates of South pole - latitude (deg) = 0.0;- coordinates of South pole - longitude =80.0

File format: NetCDF (converted from GRIB)

Example of file names: "met_fc20200405_00+003.nc", "metflux_fc20200405_00+003.nc", "aer_fc20200405_00+003.nc", where "20200405" is 5 April 2020; "00+003" is 03UTC.

Aerosols data description:var138 - sulfur Aitken solublevar139 - sulfur accumulation solublevar144 - sulfur coarse solublevar145 - black carbon Aitken solublevar146 - black carbon accumulation solublevar147 - black carbon coarse solublevar148 - black carbon Aitken insolublevar149 - organic carbon Aitken solublevar150 - organic carbon accumulation solublevar151 - organic carbon coarse solublevar250 - organic carbon Aitken insolublevar153 - sea salt accumulation solublevar154 - sea salt coarse solublevar155 - dust accumulation solublevar156 - dust coarse solublevar157 - dust accumulation insolublevar158 - dust coarse insoluble

Meteorological data description:var11 - temperaturevar33 - u-wind var34 - v-windvar51 - specific humidityvar58 - specific cloud icevar61 - total precipitationvar71 - total cloud covervar76 - specific cloud liquid watervar111 - net surface short-wave radiationvar112 - net surface long-wave radiationvar115 - downwelling surface long-wave radiationvar117 - downwelling global short-wave radiationvar200 - turbulent kinetic energy
DOI: 10.5281/zenodo.15275593
title: Enviro-HIRLAM model output for April 2020 air pollution case study

description: Case study: wildfires and dust storm air pollution events occured in April 2020 in the norther part of Ukraine (including the abandoned Chornobyl Exclusion Zone).The presented dataset contains the seamless Environment – HIgh-Resolution Limited Area Model (Enviro-HIRLAM) model output with a 1.5 km horizontal resolution. Period of study cover 5-30 April 2020. The model domain consists of 410×410 grid points in a rotated system of coordinates. Extracted for the 11 lowest Enviro-HIRLAM model levels. The model description can be found by the following link: https://doi.org/10.5194/gmd-10-2971-2017

Model configurations: (1) reference (REF) run without aerosol effects; (2) run with direct aerosol effects (DAE) included; (3) run with indirect aerosol effects (IDAE); and (4) run with combined direct and indirect aerosol effects (COMB).

Domain and rotated system characteristics:- number of grid points along longitude = 410; - number of grid points along latitude = 410; - south boundary in rotated system of coordinates (deg) =-27.484;- north boundary in rotated system of coordinates = -21.349;- west boundary in rotated system of coordinates = -35.450;- east boundary in rotated system of coordinates = -29.315;- coordinates of South pole - latitude (deg) = 0.0;- coordinates of South pole - longitude =80.0

File format: NetCDF (converted from GRIB)

Example of file names: "met_fc20200405_00+003.nc", "metflux_fc20200405_00+003.nc", "aer_fc20200405_00+003.nc", where "20200405" is 5 April 2020; "00+003" is 03UTC.

Aerosols data description:var138 - sulfur Aitken solublevar139 - sulfur accumulation solublevar144 - sulfur coarse solublevar145 - black carbon Aitken solublevar146 - black carbon accumulation solublevar147 - black carbon coarse solublevar148 - black carbon Aitken insolublevar149 - organic carbon Aitken solublevar150 - organic carbon accumulation solublevar151 - organic carbon coarse solublevar250 - organic carbon Aitken insolublevar153 - sea salt accumulation solublevar154 - sea salt coarse solublevar155 - dust accumulation solublevar156 - dust coarse solublevar157 - dust accumulation insolublevar158 - dust coarse insoluble

Meteorological data description:var11 - temperaturevar33 - u-wind var34 - v-windvar51 - specific humidityvar58 - specific cloud icevar61 - total precipitationvar71 - total cloud covervar76 - specific cloud liquid watervar111 - net surface short-wave radiationvar112 - net surface long-wave radiationvar115 - downwelling surface long-wave radiationvar117 - downwelling global short-wave radiationvar200 - turbulent kinetic energy
DOI: 10.4121/96642016-963c-427d-bcd7-bd6d990fc264
title: Supplementary data for the paper: Walk along: An experiment on controlling the mobile robot "Spot’" with voice and gestures

description: Robots are becoming more capable and can autonomously perform tasks such as navigating between locations. However, human oversight remains crucial. This study compared two touchless methods for directing mobile robots: voice control and gesture control, to investigate the efficiency of these methods and the preference of users. We tested these methods in two conditions: one in which participants remained stationary and one in which they walked freely alongside the robot. We hypothesized that walking alongside the robot would result in higher intuitiveness ratings and improved task performance, based on the idea that walking promotes spatial alignment and reduces the effort required for mental rotation. In a 2×2 within-subject design, 218 participants guided the quadruped robot Spot along a circuitous route with multiple 90° turns using rotate left, rotate right, and walk forward commands. After each trial, participants rated the intuitiveness of the command mapping, while post-experiment interviews were used to gather the participants’ preferences. Results showed that voice control combined with walking with Spot was the most favored and intuitive, whereas gesture control while standing caused confusion for left/right commands. Nevertheless, 29% of participants preferred gesture control, citing increased task engagement and visual congruence as reasons. An odometry-based analysis revealed that participants often followed behind Spot, particularly in the gesture control condition, when they were allowed to walk. In conclusion, voice control with walking produced the best outcomes. Improving physical ergonomics and adjusting gesture types could make gesture control more effective.
DOI: 10.4121/96642016-963c-427d-bcd7-bd6d990fc264.v1
title: Supplementary data for the paper: Walk along: An experiment on controlling the mobile robot "Spot’" with voice and gestures

description: Robots are becoming more capable and can autonomously perform tasks such as navigating between locations. However, human oversight remains crucial. This study compared two touchless methods for directing mobile robots: voice control and gesture control, to investigate the efficiency of these methods and the preference of users. We tested these methods in two conditions: one in which participants remained stationary and one in which they walked freely alongside the robot. We hypothesized that walking alongside the robot would result in higher intuitiveness ratings and improved task performance, based on the idea that walking promotes spatial alignment and reduces the effort required for mental rotation. In a 2×2 within-subject design, 218 participants guided the quadruped robot Spot along a circuitous route with multiple 90° turns using rotate left, rotate right, and walk forward commands. After each trial, participants rated the intuitiveness of the command mapping, while post-experiment interviews were used to gather the participants’ preferences. Results showed that voice control combined with walking with Spot was the most favored and intuitive, whereas gesture control while standing caused confusion for left/right commands. Nevertheless, 29% of participants preferred gesture control, citing increased task engagement and visual congruence as reasons. An odometry-based analysis revealed that participants often followed behind Spot, particularly in the gesture control condition, when they were allowed to walk. In conclusion, voice control with walking produced the best outcomes. Improving physical ergonomics and adjusting gesture types could make gesture control more effective.
DOI: 10.15468/dl.xembhx
title: Occurrence Download

description: A dataset containing 4958 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample, Living Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Psathyromyia shannoni (Dyar, 1929)"
 ]
}

 The dataset includes 4958 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012943-250515123054153/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.28952606.v27
title: Logic innovation NEW

description: Logic innovation
DOI: 10.15468/dl.y6xs8n
title: Occurrence Download

description: A dataset containing 1594 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nylanderia bourbonica (Forel, 1886)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1594 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010991-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mtz6qv
title: Occurrence Download

description: A dataset containing 4911 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Neomyia cornicina (Fabricius, 1775)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4911 records from 134 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010990-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5518/1746
title: Influence of wettability on diffusion limited nanoparticle adsorption at gas-liquid interfaces - Dataset

description: Data related to study into the influence of hydrophobicity on particle adsorption by examining the behavior of hydrophobized silica particles at air-water interfaces. Langmuir-Blodgett (LB) trough studies of butanol (‘SiO-butane’) and hexanol (‘SiO-hexane’) esterified particles provided contrasting behavior. The SiO-butane particles formed weaker particle layers that underwent partial collapse with compression, leading to formations significantly below hexagonal close-packed estimates. In contrast, the SiO-hexane particles exhibited improved monolayer behavior and longer-range stability. Droplet surface tensions demonstrated that the hydrophobic particles significantly altered the dynamic tension during adsorption, when methyl isobutyl carbinol (MIBC) was added as a co-surfactant. Short-term modeling elucidated the role of diffusion and energy barriers on adsorption dynamics, with SiO-hexane having reduced diffusion coefficients with respect to SiO-butane and unmodified particles. Long-term modelling allowed calculation of specific adsorption rates.
DOI: 10.5281/zenodo.18231269
title: Constructing the ensemble of representative structures for a protein via neural-surrogate-guided MSA recombination

description: ProCEDiS – Data package

This record provides the datasets and analysis artifacts used in the ProCEDiS study.Files are distributed as ZIP archives for convenient download and sharing. After downloading, please unzip and keep the folder structure unchanged.

For source code and detailed instructions on usage, please refer to our github .

 

scores.zip

Contains evaluation outputs (TM-score–based) for all methods. After unzipping, each method has one folder, and inside each method folder each PDB-ID subfolder provides score_list.csv (TM-scores of every generated structure against each reference label) plus representative-set index files rep_*_indices*.npy that map directly to the row indices of score_list.csv (for ProCEDiS variants, the extra suffix indicates the episode).

dataset_77proteins.zip

Contains the 77-protein benchmark inputs, including per-target sequences (.fasta) and MSAs (.a3m), plus ground-truth conformational pairs from the PDB under pair/. For analyses that require matched lengths, homologous_modeling/ provides length-aligned reference models generated by homology modeling.

procedis_sample.zip

Provides sample ProCEDiS outputs for the 77-protein benchmark (standard and high-temperature variants). For each target, msa_pool/ contains all MSAs explored during the search and structure_pool/ contains all corresponding predicted structures—both are raw, non-deduplicated pools.

parallel_md_npy.zip

Contains the parallel MD simulation outputs for selected systems and seeds: each seed folder includes the minimized system structure (*_minimized.cif), equilibration and production logs (*_npt_eq.log, *_npt_prod.log), and the production trajectory saved as Cα-only coordinates (*_npt_prod_prot_ca.npy) to reduce file size.

ncbi_tax_species.zip

Contains a single taxonomy lineage table (ncbi_tax_species.csv) that maps each NCBI tax_id to major ranks (superkingdom→species), used for taxonomic annotation in our Taxo-seq clustering. It was generated from the NCBI taxonomy files using the ncbitax2lin workflow (GitHub repo: zyxue/ncbitax2lin).
DOI: 10.5281/zenodo.18231270
title: Constructing the ensemble of representative structures for a protein via neural-surrogate-guided MSA recombination

description: ProCEDiS – Data package

This record provides the datasets and analysis artifacts used in the ProCEDiS study.Files are distributed as ZIP archives for convenient download and sharing. After downloading, please unzip and keep the folder structure unchanged.

For source code and detailed instructions on usage, please refer to our github .

 

scores.zip

Contains evaluation outputs (TM-score–based) for all methods. After unzipping, each method has one folder, and inside each method folder each PDB-ID subfolder provides score_list.csv (TM-scores of every generated structure against each reference label) plus representative-set index files rep_*_indices*.npy that map directly to the row indices of score_list.csv (for ProCEDiS variants, the extra suffix indicates the episode).

dataset_77proteins.zip

Contains the 77-protein benchmark inputs, including per-target sequences (.fasta) and MSAs (.a3m), plus ground-truth conformational pairs from the PDB under pair/. For analyses that require matched lengths, homologous_modeling/ provides length-aligned reference models generated by homology modeling.

procedis_sample.zip

Provides sample ProCEDiS outputs for the 77-protein benchmark (standard and high-temperature variants). For each target, msa_pool/ contains all MSAs explored during the search and structure_pool/ contains all corresponding predicted structures—both are raw, non-deduplicated pools.

parallel_md_npy.zip

Contains the parallel MD simulation outputs for selected systems and seeds: each seed folder includes the minimized system structure (*_minimized.cif), equilibration and production logs (*_npt_eq.log, *_npt_prod.log), and the production trajectory saved as Cα-only coordinates (*_npt_prod_prot_ca.npy) to reduce file size.

ncbi_tax_species.zip

Contains a single taxonomy lineage table (ncbi_tax_species.csv) that maps each NCBI tax_id to major ranks (superkingdom→species), used for taxonomic annotation in our Taxo-seq clustering. It was generated from the NCBI taxonomy files using the ncbitax2lin workflow (GitHub repo: zyxue/ncbitax2lin).
DOI: 10.17028/rd.lboro.13286012
title: Supplementary information files for "A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications"

description: Supplementary files for article "A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications." <br><br>Xenogeneic pericardium-based substitutes are employed for several surgical indications after chemical shielding, limiting their biocompatibility and therapeutic durability. Adverse responses to these replacements might be prevented by tissue decellularization, ideally removing cells and preserving the original extracellular matrix (ECM). The aim of this study was to compare the mostly applied pericardia in clinics, i.e., bovine and porcine tissues, after their decellularization, and obtain new insights for their possible surgical use. Bovine and porcine pericardia were submitted to TRICOL decellularization, based on osmotic shock, detergents and nuclease treatment. TRICOL procedure resulted in being effective in cell removal and preservation of ECM architecture of both species’ scaffolds. Collagen and elastin were retained but glycosaminoglycans were reduced, significantly for bovine scaffolds. Tissue hydration was varied by decellularization, with a rise for bovine pericardia and a decrease for porcine ones. TRICOL significantly increased porcine pericardial thickness, while a non-significant reduction was observed for the bovine counterpart. The protein secondary structure and thermal denaturation profile of both species’ scaffolds were unaltered. Both pericardial tissues showed augmented biomechanical compliance after decellularization. The ECM bioactivity of bovine and porcine pericardia was unaffected by decellularization, sustaining viability and proliferation of human mesenchymal stem cells and endothelial cells. In conclusion, decellularized bovine and porcine pericardia demonstrate possessing the characteristics that are suitable for the creation of novel scaffolds for reconstruction or replacement: differences in water content, thickness and glycosaminoglycans might influence some of their biomechanical properties and, hence, their indication for surgical use.
DOI: 10.17028/rd.lboro.13286012.v1
title: Supplementary information files for A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications

description: Supplementary files for article A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications. Xenogeneic pericardium-based substitutes are employed for several surgical indications after chemical shielding, limiting their biocompatibility and therapeutic durability. Adverse responses to these replacements might be prevented by tissue decellularization, ideally removing cells and preserving the original extracellular matrix (ECM). The aim of this study was to compare the mostly applied pericardia in clinics, i.e., bovine and porcine tissues, after their decellularization, and obtain new insights for their possible surgical use. Bovine and porcine pericardia were submitted to TRICOL decellularization, based on osmotic shock, detergents and nuclease treatment. TRICOL procedure resulted in being effective in cell removal and preservation of ECM architecture of both species’ scaffolds. Collagen and elastin were retained but glycosaminoglycans were reduced, significantly for bovine scaffolds. Tissue hydration was varied by decellularization, with a rise for bovine pericardia and a decrease for porcine ones. TRICOL significantly increased porcine pericardial thickness, while a non-significant reduction was observed for the bovine counterpart. The protein secondary structure and thermal denaturation profile of both species’ scaffolds were unaltered. Both pericardial tissues showed augmented biomechanical compliance after decellularization. The ECM bioactivity of bovine and porcine pericardia was unaffected by decellularization, sustaining viability and proliferation of human mesenchymal stem cells and endothelial cells. In conclusion, decellularized bovine and porcine pericardia demonstrate possessing the characteristics that are suitable for the creation of novel scaffolds for reconstruction or replacement: differences in water content, thickness and glycosaminoglycans might influence some of their biomechanical properties and, hence, their indication for surgical use.<br>
DOI: 10.17028/rd.lboro.13286012.v2
title: Supplementary information files for "A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications"

description: Supplementary files for article "A comprehensive comparison of bovine and porcine decellularized pericardia: new insights for surgical applications." <br><br>Xenogeneic pericardium-based substitutes are employed for several surgical indications after chemical shielding, limiting their biocompatibility and therapeutic durability. Adverse responses to these replacements might be prevented by tissue decellularization, ideally removing cells and preserving the original extracellular matrix (ECM). The aim of this study was to compare the mostly applied pericardia in clinics, i.e., bovine and porcine tissues, after their decellularization, and obtain new insights for their possible surgical use. Bovine and porcine pericardia were submitted to TRICOL decellularization, based on osmotic shock, detergents and nuclease treatment. TRICOL procedure resulted in being effective in cell removal and preservation of ECM architecture of both species’ scaffolds. Collagen and elastin were retained but glycosaminoglycans were reduced, significantly for bovine scaffolds. Tissue hydration was varied by decellularization, with a rise for bovine pericardia and a decrease for porcine ones. TRICOL significantly increased porcine pericardial thickness, while a non-significant reduction was observed for the bovine counterpart. The protein secondary structure and thermal denaturation profile of both species’ scaffolds were unaltered. Both pericardial tissues showed augmented biomechanical compliance after decellularization. The ECM bioactivity of bovine and porcine pericardia was unaffected by decellularization, sustaining viability and proliferation of human mesenchymal stem cells and endothelial cells. In conclusion, decellularized bovine and porcine pericardia demonstrate possessing the characteristics that are suitable for the creation of novel scaffolds for reconstruction or replacement: differences in water content, thickness and glycosaminoglycans might influence some of their biomechanical properties and, hence, their indication for surgical use.