cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21253540
title: Exploring preferences of at-risk individuals for preventive treatments for rheumatoid arthritis

description: Some immunomodulatory drugs have been shown to delay the onset of, or lower the risk of developing, rheumatoid arthritis (RA), if given to individuals at risk. Several trials are ongoing in this area; however, little evidence is currently available about the views of those at risk of RA regarding preventive treatment. Three focus groups and three interviews explored factors that are relevant to first degree relatives (FDRs) of RA patients and members of the general public when considering taking preventive treatment for RA. The semi-structured qualitative interview prompts explored participant responses to hypothetical attributes of preventive RA medicines. Transcripts of focus group/interview proceedings were inductively coded and analysed using a framework approach. Twenty-one individuals (five FDRs, 16 members of the general public) took part in the study. Ten broad themes were identified describing factors that participants felt would influence their decisions about whether to take preventive treatment if they were at increased risk of RA. These related either directly to features of the specific treatment or to other factors, including personal characteristics, attitude towards taking medication, and an individual’s actual risk of developing RA. This research highlights the importance of non-treatment factors in the decision-making process around preventive treatments, and will inform recruitment to clinical trials as well as information to support shared decision making by those considering preventive treatment. Studies of treatment preferences in individuals with a confirmed high risk of RA would further inform clinical trial design.
DOI: 10.6084/m9.figshare.21253540.v1
title: Exploring preferences of at-risk individuals for preventive treatments for rheumatoid arthritis

description: Some immunomodulatory drugs have been shown to delay the onset of, or lower the risk of developing, rheumatoid arthritis (RA), if given to individuals at risk. Several trials are ongoing in this area; however, little evidence is currently available about the views of those at risk of RA regarding preventive treatment. Three focus groups and three interviews explored factors that are relevant to first degree relatives (FDRs) of RA patients and members of the general public when considering taking preventive treatment for RA. The semi-structured qualitative interview prompts explored participant responses to hypothetical attributes of preventive RA medicines. Transcripts of focus group/interview proceedings were inductively coded and analysed using a framework approach. Twenty-one individuals (five FDRs, 16 members of the general public) took part in the study. Ten broad themes were identified describing factors that participants felt would influence their decisions about whether to take preventive treatment if they were at increased risk of RA. These related either directly to features of the specific treatment or to other factors, including personal characteristics, attitude towards taking medication, and an individual’s actual risk of developing RA. This research highlights the importance of non-treatment factors in the decision-making process around preventive treatments, and will inform recruitment to clinical trials as well as information to support shared decision making by those considering preventive treatment. Studies of treatment preferences in individuals with a confirmed high risk of RA would further inform clinical trial design.
DOI: 10.6084/m9.figshare.21431053
title: Exploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies

description: The chemical structure of a compound directly affects its biological activity, as different functional groups can change a compound’s activity. With this in mind, the current study aims to predict the likely mechanism of action of several podophyllotoxin derivatives whose biological activities have already been documented. The interactions of the derivatives of podophyllotoxin with tubulin (PDB ID: 6NNG) and topoisomerase II (PDB ID: 3QX3), the two recognised targets of podophyllotoxin, were examined using molecular docking experiments. According to the molecular docking result, tubulin, and the investigated variants of podophyllotoxin interact more effectively than topoisomerase. The greatest docking score of the compounds was −12.200 against tubulin and −4.511 against topoisomerase, indicating that tubulin is the target of these drugs. Further to ascertain the strength of the interaction between the best-docked derivatives and the target protein, additional molecular dynamics investigations were also incorporated. With tubulin, the derivatives engage steadily, while with topoisomerase, the ligands shift from the protein’s initial binding site to its DNA binding site. MMPBSA analysis was used to examine the stability of their relationship. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21431053.v1
title: Exploring the mechanism of action of podophyllotoxin derivatives through molecular docking, molecular dynamics simulation and MM/PBSA studies

description: The chemical structure of a compound directly affects its biological activity, as different functional groups can change a compound’s activity. With this in mind, the current study aims to predict the likely mechanism of action of several podophyllotoxin derivatives whose biological activities have already been documented. The interactions of the derivatives of podophyllotoxin with tubulin (PDB ID: 6NNG) and topoisomerase II (PDB ID: 3QX3), the two recognised targets of podophyllotoxin, were examined using molecular docking experiments. According to the molecular docking result, tubulin, and the investigated variants of podophyllotoxin interact more effectively than topoisomerase. The greatest docking score of the compounds was −12.200 against tubulin and −4.511 against topoisomerase, indicating that tubulin is the target of these drugs. Further to ascertain the strength of the interaction between the best-docked derivatives and the target protein, additional molecular dynamics investigations were also incorporated. With tubulin, the derivatives engage steadily, while with topoisomerase, the ligands shift from the protein’s initial binding site to its DNA binding site. MMPBSA analysis was used to examine the stability of their relationship. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21370840
title: Pharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics

description: Studies have established that proteolytic enzyme inhibition holds significant promise in cancer prevention and treatment. Cathepsin C (CatC) is conserved lysosomal cysteine dipeptidyl aminopeptidase, which is the key for pro-inflammatory neutrophil serine protease activation and biological functioning. This makes CatC as a promising therapeutic drug target for the management of different cancer types. Considering this, using a wide range of computer aided drug-designing applications, several inhibitors are shortlisted against CatC active pocket, which interact with the enzyme with high affinity and form strong intermolecular interaction network. Compared to control, three molecules ASN_06916232, ASN_06917112 and ASN_06916892 are filtered as best binders of the CatC active pocket with binding energy value of −10.9 kcal/mol, −10.9 kcal/mol and −10.7 kcal/mol, respectively. These compounds interact with several important active side residues of CatC such as Ser233, Cys234, Gly277, Asn380 and His38. Furthermore, the complexes of these compounds with CatC reveal very stable dynamics with average RMSD value less than 3 Å. The binding energy analysis further indicates the compounds to have very stable van der Waals and electrostatic energies. In conclusion, these molecules are promising and require experimental validation to prove them as anti-CatC molecules. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.21370840.v1
title: Pharmacological inhibition of cathepsin C (CatC) as a potential approach for cancer therapeutics

description: Studies have established that proteolytic enzyme inhibition holds significant promise in cancer prevention and treatment. Cathepsin C (CatC) is conserved lysosomal cysteine dipeptidyl aminopeptidase, which is the key for pro-inflammatory neutrophil serine protease activation and biological functioning. This makes CatC as a promising therapeutic drug target for the management of different cancer types. Considering this, using a wide range of computer aided drug-designing applications, several inhibitors are shortlisted against CatC active pocket, which interact with the enzyme with high affinity and form strong intermolecular interaction network. Compared to control, three molecules ASN_06916232, ASN_06917112 and ASN_06916892 are filtered as best binders of the CatC active pocket with binding energy value of −10.9 kcal/mol, −10.9 kcal/mol and −10.7 kcal/mol, respectively. These compounds interact with several important active side residues of CatC such as Ser233, Cys234, Gly277, Asn380 and His38. Furthermore, the complexes of these compounds with CatC reveal very stable dynamics with average RMSD value less than 3 Å. The binding energy analysis further indicates the compounds to have very stable van der Waals and electrostatic energies. In conclusion, these molecules are promising and require experimental validation to prove them as anti-CatC molecules. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137823
title: Developing human olfactory network and exploring olfactory receptor-odorant interaction

description: The Olfactory receptor (OR)-odorant interactions are perplexed. ORs can bind to structurally diverse odorants associated with one or more odor percepts. Various attempts have been made to understand the intricacies of OR-odorant interaction. In this study, experimentally documented OR-odorant interactions are investigated comprehensively to; (a) suggest potential odor percepts for ORs based on the OR-OR network; (b) determine how odorants interacting with specific ORs differ in terms of inherent pharmacophoric features and molecular properties, (c) identify molecular interactions that explained OR-odorant interactions of selective ORs; and (d) predict the probable role of ORs other than olfaction. Human olfactory receptor network (hORnet) is developed to study possible odor percepts for ORs. We identified six molecular properties which showed variation and significant patterns to differentiate odorants binding with five ORs. The pharmacophore analysis revealed that odorants subset of five ORs follow similar pharmacophore hypothesis, (one hydrogen acceptor and two hydrophobic regions) but differ in terms of distance and orientation of pharmacophoric features. To ascertain the binding site residues and key interactions between the selected ORs and their interacting odorants, 3D-structure modelling, docking and molecular dynamics studies were carried out. Lastly, the potential role of ORs beyond olfaction is explored. A human OR-OR network was developed to suggest possible odor percepts for ORs using empirically proven OR-odorant interactions. We sought to find out significant characteristics, molecular properties, and molecular interactions that could explain OR-odorant interactions and add to the understanding of the complex issue of odor perception. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.24137823.v1
title: Developing human olfactory network and exploring olfactory receptor-odorant interaction

description: The Olfactory receptor (OR)-odorant interactions are perplexed. ORs can bind to structurally diverse odorants associated with one or more odor percepts. Various attempts have been made to understand the intricacies of OR-odorant interaction. In this study, experimentally documented OR-odorant interactions are investigated comprehensively to; (a) suggest potential odor percepts for ORs based on the OR-OR network; (b) determine how odorants interacting with specific ORs differ in terms of inherent pharmacophoric features and molecular properties, (c) identify molecular interactions that explained OR-odorant interactions of selective ORs; and (d) predict the probable role of ORs other than olfaction. Human olfactory receptor network (hORnet) is developed to study possible odor percepts for ORs. We identified six molecular properties which showed variation and significant patterns to differentiate odorants binding with five ORs. The pharmacophore analysis revealed that odorants subset of five ORs follow similar pharmacophore hypothesis, (one hydrogen acceptor and two hydrophobic regions) but differ in terms of distance and orientation of pharmacophoric features. To ascertain the binding site residues and key interactions between the selected ORs and their interacting odorants, 3D-structure modelling, docking and molecular dynamics studies were carried out. Lastly, the potential role of ORs beyond olfaction is explored. A human OR-OR network was developed to suggest possible odor percepts for ORs using empirically proven OR-odorant interactions. We sought to find out significant characteristics, molecular properties, and molecular interactions that could explain OR-odorant interactions and add to the understanding of the complex issue of odor perception. Communicated by Ramaswamy H. Sarma
DOI: 10.5281/zenodo.8344258
title: AIS heatmap: North Sea and Dutch Inland Waterways for the months January, April, July, October in 2019

description: This dataset contains information on vessel movements in the North Sea and Dutch Inland Waterways for the months January, April, July, and October in 2019. It provides a heatmap representation of vessel traffic density during these specific months, which can be useful for various maritime and environmental analyses. 1. File Formats The dataset is provided in the following file formats: NetCDF : The primary data files are available in netcdf format. For each grid cell the variables sog (Speed Over Ground) and count (Number of AIS messages) are available GeoTIFF (Georeferenced Tagged Image File Format): Heatmap images are provided in GeoTIFF format, suitable for geographic visualization. The dataset is split into tiles. Each tile conforms to the OSM tiling naming scheme. 2. Variables The dataset includes the following key variables: <strong>Speed Over Ground (SOG)</strong>: The average vessel's speed over the ground for all the messages. <strong>Count</strong>: The number of AIS messages received in this location 3. Data Collection Method The AIS data used in this dataset was collected from AIS transponders on vessels operating in the North Sea and Dutch Inland Waterways. These transponders transmit information such as vessel position, speed, and identification. The dataset aggregates this information to create heatmap images for analysis. We did this on all the messages. Some ships emit more messages than others. Ships emit messages at higher frequency when sailing than when stationary. 4. Source of Original Data The original AIS data used to create this dataset was sourced from the AIS archive from Rijkswaterstaat. This dataset was analysed for the purpose of a storymap.
DOI: 10.5281/zenodo.8344257
title: AIS heatmap: North Sea and Dutch Inland Waterways for the months January, April, July, October in 2019

description: This dataset contains information on vessel movements in the North Sea and Dutch Inland Waterways for the months January, April, July, and October in 2019. It provides a heatmap representation of vessel traffic density during these specific months, which can be useful for various maritime and environmental analyses. 1. File Formats The dataset is provided in the following file formats: NetCDF : The primary data files are available in netcdf format. For each grid cell the variables sog (Speed Over Ground) and count (Number of AIS messages) are available GeoTIFF (Georeferenced Tagged Image File Format): Heatmap images are provided in GeoTIFF format, suitable for geographic visualization. The dataset is split into tiles. Each tile conforms to the OSM tiling naming scheme. 2. Variables The dataset includes the following key variables: <strong>Speed Over Ground (SOG)</strong>: The average vessel's speed over the ground for all the messages. <strong>Count</strong>: The number of AIS messages received in this location 3. Data Collection Method The AIS data used in this dataset was collected from AIS transponders on vessels operating in the North Sea and Dutch Inland Waterways. These transponders transmit information such as vessel position, speed, and identification. The dataset aggregates this information to create heatmap images for analysis. We did this on all the messages. Some ships emit more messages than others. Ships emit messages at higher frequency when sailing than when stationary. 4. Source of Original Data The original AIS data used to create this dataset was sourced from the AIS archive from Rijkswaterstaat. This dataset was analysed for the purpose of a storymap.
DOI: 10.57906/0mr2-we17
title: Workplace Employment Relations Survey - Great Britain
DOI: 10.21227/a3e9-f387
title: RFID Chinese sign language dataset

description: The dataset is the image data obtained after data conversion of the phases of six Chinese sign languages collected using RFID, the dataset includes the data of five people in environment 1, and also includes the data of user 1 in the previous environment, the dataset is converted into 1000×1000 pixel images to be saved in it, which is a total of 3,000 images. Inside this dataset, six Chinese sign languages are included, which are "come", "give", "have", " leave", "need", and "high", in which our phase data is generated by rearranging the data of each label, making the phase data more representative.
DOI: 10.57906/s5f5-nq13
title: Virus Watch - England and Wales
DOI: 10.57906/qwbe-x221
title: Universities and Colleges Admissions Service - UK
DOI: 10.6084/m9.figshare.23300345
title: <strong>Gingipains impair cognition: an animal study</strong>

description: <strong>Aims:</strong> Blood-brain barrier (BBB) disorder is one of the early findings in cognitive impairments. We have recently found that <em>Porphyromonas gingivalis</em> (<em>P. gingivalis</em>) bacteremia can cause cognitive impairment and increased BBB permeability. This study is aimed to find out the possible key virulence factors of <em>P. gingivalis</em> contributing to the pathological process. <strong>Materials and methods:</strong> C57/BL6 mice were infected with <em>P. gingivalis</em> or gingipains or <em>P. gingivalis</em> lipopolysaccharide (<em>P. gingivalis</em>LPS group) by tail vein injection for 8 weeks. The cognitive behavior changes of mice, the histopathological changes of the hippocampus and cerebral cortex, the alternations of BBB permeability, and the changes of Mfsd2a and Cav-1 levels were measured. The mechanisms of Ddx3x-induced regulation on Mfsd2a by Arginine-specific gingipain A (RgpA) in BMECs were explored. <strong>Results:</strong> <em>P. gingivalis</em> and gingipains significantly promoted mice cognitive impairment, pathological changes in the hippocampus and cerebral cortex, increased BBB permeability, inhibited Mfsd2a expression, and up-regulated Cav-1 expression. After RgpA stimulation, the permeability of the BBB model in vitro increased, and the Ddx3x / Mfsd2a / Cav-1 regulatory axis was activated. <strong>Conclusion:</strong> Gingipains may be one of the key virulence factors of <em>P</em>. <em>gingivalis</em> to impair cognition and enhance blood-brain barrier permeability by the Ddx3x / Mfsd2a / Cav-1 axis.
DOI: 10.57906/49pv-1r98
title: UK Gross Value Added for Lower Layer Super Output Areas
DOI: 10.57906/4snk-kf30
title: State-funded schools inspections and outcomes - England
DOI: 10.57906/2gpb-5009
title: Small Business Survey - UK
DOI: 10.6084/m9.figshare.23643669
title: CrysMMNet data

description: This is the multimodal (Graph+Text) dataset we propose in our recent work "CrysMMNet: Multimodal Representation for Crystal Property Prediction"
DOI: 10.5281/zenodo.8334053
title: Potential of Mean Force (PMFs) for Zerovalent Aluminium (100-110-111) NanoParticles

description: The dataset encompasses the potential of mean force data concerning three distinct fcc configurations of zero valent aluminum nanoparticles: (100), (110), and (111), in interaction with side-chain analogs of 22 diverse amino acids, which constitute the basic building blocks of proteins. The calculations employed the adaptive Well-Tempered Metadynamics method, a well-established technique previously utilized for assessing biomolecule adsorption on materials like Fe, TiO2 and Ag. To conduct these simulations, we utilized the GROMACS and PLUMED software packages, while the construction of the aluminium slabs was accomplished with the CHARMM-GUI/Nanomaterial Modeler. In the metadynamics biased simulation, the Surface Separation Distance (SSD) served as the primary reaction coordinate. This SSD quantifies the minimum separation between the center-of-mass (COM) of the side-chain analog (SCA) molecule and the surface atoms (ri) along the z-coordinate.
DOI: 10.5281/zenodo.8334052
title: Potential of Mean Force (PMFs) for Zerovalent Aluminium (100-110-111) NanoParticles

description: The dataset encompasses the potential of mean force data concerning three distinct fcc configurations of zero valent aluminum nanoparticles: (100), (110), and (111), in interaction with side-chain analogs of 22 diverse amino acids, which constitute the basic building blocks of proteins. The calculations employed the adaptive Well-Tempered Metadynamics method, a well-established technique previously utilized for assessing biomolecule adsorption on materials like Fe, TiO2 and Ag. To conduct these simulations, we utilized the GROMACS and PLUMED software packages, while the construction of the aluminium slabs was accomplished with the CHARMM-GUI/Nanomaterial Modeler. In the metadynamics biased simulation, the Surface Separation Distance (SSD) served as the primary reaction coordinate. This SSD quantifies the minimum separation between the center-of-mass (COM) of the side-chain analog (SCA) molecule and the surface atoms (ri) along the z-coordinate.
DOI: 10.25345/c5b853t9m
title: MassIVE MSV000092858 - honey quechers extract positive mode
title: Use CEN quechers method to extract 2.5g honey and use PSA to clean up matrix. Using ACN-water-0.01%HCOOH for compound separation and HRMS analysis with Thermo Orbitrap Exploris 120. Data was acquired in Full scan-ddms2 mode. This included a full scan over the m/z range 100- 1000 at full width at half maximum (FWHM) resolution of 60,000, and a data-dependent-MS2 scan at FWHM resolution of 15,000 on the top 4 ions. The ionization was performed in positive ESI with an inlusion list collated from OPPIN website, and to gain more information about fragment ions in the QC sample, we use an Automated Exclusion List Generation workflow, so one QC sample finally gave 3 injections.
DOI: 10.25345/c5g15tn30
title: MassIVE MSV000092859 - honey quechers extract positive mode
title: Use CEN quechers method to extract 2.5g honey and use PSA to clean up matrix. Using ACN-water-0.01%HCOOH for compound separation and HRMS analysis with Thermo Orbitrap Exploris 120. Data was acquired in Full scan-ddms2 mode. This included a full scan over the m/z range 100- 1000 at full width at half maximum (FWHM) resolution of 60,000, and a data-dependent-MS2 scan at FWHM resolution of 15,000 on the top 4 ions. The ionization was performed in positive ESI with an inlusion list collated from OPPIN website, and to gain more information about fragment ions in the QC sample, we use an Automated Exclusion List Generation workflow, so one QC sample finally gave 3 injections.