cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21227/ts5t-nx64
title: "transcription factor binding site prediction"

description: "Accurate prediction of transcription factor binding sites (TFBSs) is crucial for understanding gene regulatory mechanisms. However, existing computational methods typically rely on linear sequence modeling, overlooking the potential complex structures and semantic information within DNA sequences, which limits their ability to capture key binding regions. Therefore, we propose MSGSNet, a computational framework for TFBS prediction that integrates linear sequence features with graph topological structures. MSGSNet encodes DNA sequences using stacked codon encoding and extracts deep semantic features via multi-scale convolutions and Bi-LSTM, with hierarchical bidirectional attention enhancing regulatory feature learning. To further capture topological dependencies among k-mers, MSGSNet constructs multi-scale De Bruijn graphs and leverages graph convolutional and attention mechanisms to effectively learn graph structural representations. Experimental results on 165 ChIP-seq (chromatin immunoprecipitation sequencing) benchmark datasets demonstrate that MSGSNet outperforms existing computational methods. Cross-cell line and cross-transcription factor evaluations further demonstrate that MSGSNet maintains superior robustness under conditions of high data heterogeneity and weak peak signals. In addition, we conducted both global and local interpretability analyses of the latent representations learned by MSGSNet using SHAP values and LIME, and further examined the sequence regions attended to by the model through hierarchical bidirectional attention analysis. The results demonstrate that MSGSNet can effectively identify biologically meaningful core motifs and long-range contextual regions."
DOI: 10.5281/zenodo.15864196
title: ADAM10 FAST sampling POPC-POPS

description: This repository contains all the trajectories and input files related to simulations of ADAM10 in a membrane composed of POPC:POPS(7:3). The xtc trajectories are downsampled 10 times to allow for their publication on zenodo (frames recorded every ns).As a starting point for the simulations, we used the x-ray structure of ADAM10 (PDB:6BE6). The missing residues (670-748) were reconstructed using Alphafold2 43,44 , resulting in a single transmembrane helix with 2 juxtamembrane helices from residues 654 to 677, that we are calling Stalk Domain. The initial systems were built using CHARMM-GUI 45 . The final ADAM10 model was embedded in a lipid bilayer composed of a mixture of POPC:POPS(7:3). The system was then solvated in a box of explicit water molecules and neutralized in 150 mM KCl. To increase the sampling of POPC-POPS systems, we generated 20 differents initial membrane repartitions by using the membrane mixer plugin in VMD. Molecular dynamics simulations of the membrane protein were performed using GROMACS 2023.2. The CHARMM36 force field was employed in combination with the TIP3P water model. The systems underwent energy minimization using the steepest descent algorithm until the energy gradient converged to a threshold of 0.01 kcal/mol/Å. The solvent and membrane were then allowed to relax in the NVT ensemble at 300K for 625ps. The system then underwentNPT equilibration during 3ns, first increasing the timestep from 1fs to 2fs, then progressively removing all constraints applied on protein and lipids. The LINCS algorithm was used for bond constraints. During equilibration, the Berendsen thermostat and barostat (when applicable) were used. For production, the v-rescale thermostat and c-rescale barostat were used for temperature and pressure control, respectively. For equilibration as well as production runs, a cutoff distance fornon-bonded interactions was set at 1.2 nm, utilizing a cut-off van der Waals (vdW) type with a force-switch modifier. The switching distance was configured to 1.0 nm.The Coulombicinteractions were calculated using the Particle Mesh Ewald (PME) method, with a cutoff distance of 1.2 nm.We performed adaptive sampling based on the Fluctuation Amplification of Specific Traits (FAST) method to enhance the exploration of the conformational landscape. Briefly, the method consists of setting up a swarm of short simulations, clustering structures among the resulting trajectories, and selecting new structures among them to set up a new swarm. The new structures were chosen based on a reward function defined as the sum of 127 pairwise distances spread among 4 interfaces between the catalytic domain of ADAM10 and the other subdomains(See publication). We then generated 16 generations of 20 simulations, each with a length of 50 ns. Once the overall sampling done, simulations from all seeds were extended to ensure a better sampling, amounting to 32µs of sampling for each system.
DOI: 10.5281/zenodo.15864195
title: ADAM10 FAST sampling POPC-POPS

description: This repository contains all the trajectories and input files related to simulations of ADAM10 in a membrane composed of POPC:POPS(7:3). The xtc trajectories are downsampled 10 times to allow for their publication on zenodo (frames recorded every ns).As a starting point for the simulations, we used the x-ray structure of ADAM10 (PDB:6BE6). The missing residues (670-748) were reconstructed using Alphafold2 43,44 , resulting in a single transmembrane helix with 2 juxtamembrane helices from residues 654 to 677, that we are calling Stalk Domain. The initial systems were built using CHARMM-GUI 45 . The final ADAM10 model was embedded in a lipid bilayer composed of a mixture of POPC:POPS(7:3). The system was then solvated in a box of explicit water molecules and neutralized in 150 mM KCl. To increase the sampling of POPC-POPS systems, we generated 20 differents initial membrane repartitions by using the membrane mixer plugin in VMD. Molecular dynamics simulations of the membrane protein were performed using GROMACS 2023.2. The CHARMM36 force field was employed in combination with the TIP3P water model. The systems underwent energy minimization using the steepest descent algorithm until the energy gradient converged to a threshold of 0.01 kcal/mol/Å. The solvent and membrane were then allowed to relax in the NVT ensemble at 300K for 625ps. The system then underwentNPT equilibration during 3ns, first increasing the timestep from 1fs to 2fs, then progressively removing all constraints applied on protein and lipids. The LINCS algorithm was used for bond constraints. During equilibration, the Berendsen thermostat and barostat (when applicable) were used. For production, the v-rescale thermostat and c-rescale barostat were used for temperature and pressure control, respectively. For equilibration as well as production runs, a cutoff distance fornon-bonded interactions was set at 1.2 nm, utilizing a cut-off van der Waals (vdW) type with a force-switch modifier. The switching distance was configured to 1.0 nm.The Coulombicinteractions were calculated using the Particle Mesh Ewald (PME) method, with a cutoff distance of 1.2 nm.We performed adaptive sampling based on the Fluctuation Amplification of Specific Traits (FAST) method to enhance the exploration of the conformational landscape. Briefly, the method consists of setting up a swarm of short simulations, clustering structures among the resulting trajectories, and selecting new structures among them to set up a new swarm. The new structures were chosen based on a reward function defined as the sum of 127 pairwise distances spread among 4 interfaces between the catalytic domain of ADAM10 and the other subdomains(See publication). We then generated 16 generations of 20 simulations, each with a length of 50 ns. Once the overall sampling done, simulations from all seeds were extended to ensure a better sampling, amounting to 32µs of sampling for each system.
DOI: 10.5281/zenodo.18255843
title: Replication material for paper "Rudolph, Gomm (2024): How does an economic shock affect environmental attitudes, preferences and issue importance? Evidence from Switzerland. Climatic Change. DOI: 10.1007/s10584-024-03709-2"

description: Replication material for paper "Rudolph, Gomm (2024): How does an economic shock affect environmental attitudes, preferences and issue importance? Evidence from Switzerland. Climatic Change. DOI: 10.1007/s10584-024-03709-2"
DOI: 10.5281/zenodo.18255842
title: Replication material for paper "Rudolph, Gomm (2024): How does an economic shock affect environmental attitudes, preferences and issue importance? Evidence from Switzerland. Climatic Change. DOI: 10.1007/s10584-024-03709-2"

description: Replication material for paper "Rudolph, Gomm (2024): How does an economic shock affect environmental attitudes, preferences and issue importance? Evidence from Switzerland. Climatic Change. DOI: 10.1007/s10584-024-03709-2"
DOI: 10.15468/dl.yzuu2j
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"CHN.28.1_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 22 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011524-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18255889
title: Coleataenia prionitis (Nees) Soreng. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18255890
title: Coleataenia prionitis (Nees) Soreng. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.15468/dl.nsfxz8
title: Occurrence Download

description: A dataset containing 652 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chaenodraco wilsoni",
 "Year 1995-2010"
 ]
}

 The dataset includes 652 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011525-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/14506514
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5281/zenodo.15863909
title: ADAM10 FAST sampling POPC

description: This repository contains all the trajectories and input files related to simulations of ADAM10 in a membrane composed of POPC. The xtc trajectories are downsampled 10 times to allow for their publication on zenodo (frames recorded every ns) .As a starting point for the simulations, we used the x-ray structure of ADAM10 (PDB:6BE6). The missing residues (670-748) were reconstructed using Alphafold2 43,44 , resulting in a single transmembrane helix with 2 juxtamembrane helices from residues 654 to 677, that we are calling Stalk Domain. The initial systems were built using CHARMM-GUI 45 . The final ADAM10 model was embedded in a lipid bilayer composed of of POPC. The system was then solvated in a box of explicit water molecules and neutralized in 150 mM KCl. Molecular dynamics simulations of the membrane protein were performed using GROMACS 2023.2. The CHARMM36 force field was employed in combination with the TIP3P water model. The systems underwent energy minimization using the steepest descent algorithm until the energy gradient converged to a threshold of 0.01 kcal/mol/Å. The solvent and membrane were then allowed to relax in the NVT ensemble at 300K for 625ps. The system then underwentNPT equilibration during 3ns, first increasing the timestep from 1fs to 2fs, then progressively removing all constraints applied on protein and lipids. The LINCS algorithm was used for bond constraints. During equilibration, the Berendsen thermostat and barostat (when applicable) were used. For production, the v-rescale thermostat and c-rescale barostat were used for temperature and pressure control, respectively. For equilibration as well as production runs, a cutoff distance fornon-bonded interactions was set at 1.2 nm, utilizing a cut-off van der Waals (vdW) type with a force-switch modifier. The switching distance was configured to 1.0 nm.The Coulombicinteractions were calculated using the Particle Mesh Ewald (PME) method, with a cutoff distance of 1.2 nm.We performed adaptive sampling based on the Fluctuation Amplification of Specific Traits (FAST) method to enhance the exploration of the conformational landscape. Briefly, the method consists of setting up a swarm of short simulations, clustering structures among the resulting trajectories, and selecting new structures among them to set up a new swarm. The new structures were chosen based on a reward function defined as the sum of 127 pairwise distances spread among 4 interfaces between the catalytic domain of ADAM10 and the other subdomains(See publication). We then generated 16 generations of 20 simulations, each with a length of 50 ns. Once the overall sampling done, simulations from all seeds were extended to ensure a better sampling, amounting to 32µs of sampling for each system.
DOI: 10.5281/zenodo.15863910
title: ADAM10 FAST sampling POPC

description: This repository contains all the trajectories and input files related to simulations of ADAM10 in a membrane composed of POPC. The xtc trajectories are downsampled 10 times to allow for their publication on zenodo (frames recorded every ns) .As a starting point for the simulations, we used the x-ray structure of ADAM10 (PDB:6BE6). The missing residues (670-748) were reconstructed using Alphafold2 43,44 , resulting in a single transmembrane helix with 2 juxtamembrane helices from residues 654 to 677, that we are calling Stalk Domain. The initial systems were built using CHARMM-GUI 45 . The final ADAM10 model was embedded in a lipid bilayer composed of of POPC. The system was then solvated in a box of explicit water molecules and neutralized in 150 mM KCl. Molecular dynamics simulations of the membrane protein were performed using GROMACS 2023.2. The CHARMM36 force field was employed in combination with the TIP3P water model. The systems underwent energy minimization using the steepest descent algorithm until the energy gradient converged to a threshold of 0.01 kcal/mol/Å. The solvent and membrane were then allowed to relax in the NVT ensemble at 300K for 625ps. The system then underwentNPT equilibration during 3ns, first increasing the timestep from 1fs to 2fs, then progressively removing all constraints applied on protein and lipids. The LINCS algorithm was used for bond constraints. During equilibration, the Berendsen thermostat and barostat (when applicable) were used. For production, the v-rescale thermostat and c-rescale barostat were used for temperature and pressure control, respectively. For equilibration as well as production runs, a cutoff distance fornon-bonded interactions was set at 1.2 nm, utilizing a cut-off van der Waals (vdW) type with a force-switch modifier. The switching distance was configured to 1.0 nm.The Coulombicinteractions were calculated using the Particle Mesh Ewald (PME) method, with a cutoff distance of 1.2 nm.We performed adaptive sampling based on the Fluctuation Amplification of Specific Traits (FAST) method to enhance the exploration of the conformational landscape. Briefly, the method consists of setting up a swarm of short simulations, clustering structures among the resulting trajectories, and selecting new structures among them to set up a new swarm. The new structures were chosen based on a reward function defined as the sum of 127 pairwise distances spread among 4 interfaces between the catalytic domain of ADAM10 and the other subdomains(See publication). We then generated 16 generations of 20 simulations, each with a length of 50 ns. Once the overall sampling done, simulations from all seeds were extended to ensure a better sampling, amounting to 32µs of sampling for each system.
DOI: 10.5281/zenodo.18255899
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS260115k Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS260115k Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.5281/zenodo.18255900
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS260115k Preliminary

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS260115k Preliminary. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.15468/dl.a4dtrc
title: Occurrence Download

description: A dataset containing 2439 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Orychophragmus violaceus"
 ]
}

 The dataset includes 2439 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011526-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18255907
title: Coleostephus Cass. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.5281/zenodo.18255908
title: Coleostephus Cass. In: Marchesi E., Mailhos A. & Bonifacino J.M. (Eds.). Flora Uruguaya: Flora Vascular del Uruguay. ISSN 3121-2050, V. 1.0.

description: Citable snapshot. Includes PDF and CSV of collections. Date: January 13th, 2026 at 16:44
DOI: 10.15468/dl.zcv8rd
title: Occurrence Download

description: A dataset containing 9 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_2_GID","value":"CHN.28.2_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011528-260108223611665/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.31073224
title: <b>INTERNAL MOBILITY INFLUENCE ON QUALITATIVE ASSURANCE OUTCOMES AS ENHANCEMENT OF </b><b>EMPLOYEE SKILLS AND COMPETENCIES</b>

description: <i>The attached dataset was utilised with purposive sampling to determine the 305 primarily sourced data points, which were collected through structured questionnaires shared among selected industries, including FMCG, Oil and Gas, Engineering Services, Construction, and Healthcare.</i>
DOI: 10.6084/m9.figshare.31073224.v1
title: <b>INTERNAL MOBILITY INFLUENCE ON QUALITATIVE ASSURANCE OUTCOMES AS ENHANCEMENT OF </b><b>EMPLOYEE SKILLS AND COMPETENCIES</b>

description: <i>The attached dataset was utilised with purposive sampling to determine the 305 primarily sourced data points, which were collected through structured questionnaires shared among selected industries, including FMCG, Oil and Gas, Engineering Services, Construction, and Healthcare.</i>
DOI: 10.6084/m9.figshare.31072855
title: Toffolo et al. (2026) Bulk Adsorption of Molecular Hydrogen in Crystalline SiO<sub>2</sub> at H<i>P</i>-H<i>T</i> Subduction Conditions: Implications for H<sub>2</sub> Storage and Release in the Earth’s Interior [Dataset]

description: This folder contains all the raw QMS mass spectrometric data used in the article: Toffolo et al. (2026) Bulk Adsorption of Molecular Hydrogen in Crystalline SiO<sub>2</sub> at H<i>P</i>-H<i>T</i> Subduction Conditions: Implications for H<sub>2</sub> Storage and Release in the Earth’s Interior
DOI: 10.6084/m9.figshare.31072855.v1
title: Toffolo et al. (2026) Bulk Adsorption of Molecular Hydrogen in Crystalline SiO<sub>2</sub> at H<i>P</i>-H<i>T</i> Subduction Conditions: Implications for H<sub>2</sub> Storage and Release in the Earth’s Interior [Dataset]

description: This folder contains all the raw QMS mass spectrometric data used in the article: Toffolo et al. (2026) Bulk Adsorption of Molecular Hydrogen in Crystalline SiO<sub>2</sub> at H<i>P</i>-H<i>T</i> Subduction Conditions: Implications for H<sub>2</sub> Storage and Release in the Earth’s Interior