cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10020663
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 1967

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 1967.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.17864/1947.000501
title: Dataset for 'Electrical measurements during fog in the United Arab Emirates'

description: This dataset contains potential gradient and visibility data used in the paper 'Electrical measurements during fog in the United Arab Emirates' by Alkamali, A., Ambaum, M.H.P., Nicoll, K.A. The measurements were obtained at Sanad Academy, Dubai, United Arab Emirates (UAE) (24°56' N, 55°30' E) in the year 2021; and from Reading University Atmospheric Observatory (RUAO), UK in the year 2020-21 (December-January). The data has been used within this paper to study and compare the electrical properties of fog in the UAE and the UK.
DOI: 10.17909/n9pc-1q14
title: MIRI/MRS Data of II Zw 096 from the ERS 1328 Program

description: JWST MIRI/MRS data (all 12 sub-bands) of the local luminous infrared galaxy II Zw 096
DOI: 10.5281/zenodo.10020662
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 1967

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 1967.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.5281/zenodo.10020678
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 1968

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 1968.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.5281/zenodo.10020679
title: ERA5-Land selected indicators daily aggregates for the Latin America region, 1968

description: This deposit contains NetCDF files with daily aggregates from Copernicus Era5-Land eight selected indicators, covering the Latin America region, for 1968.
Each file represents one indicator aggregation for one month of the year. Inside each NetCDF file, the layers contain the daily aggregates.
For 2m dewpoint pressure, 10m u component of wind, 10m v component of wind, surface pressure, the mean function was used for aggregation. For total precipitation, the sum function was used for aggregation. For 2m temperature, the functions maximum, mean and minimum were used for aggregation.
Those files were created using the KrigR package.
DOI: 10.5281/zenodo.10008305
title: FKK6-ADME

description: Source data for figures in paper:
Dvorak Z et al: In Vitro Safety Signals for Potential Clinical Development of the Anti-Inflammatory Pregnane X Receptor Agonist FKK6
DOI: 10.5281/zenodo.10008306
title: FKK6-ADME

description: Source data for figures in paper:
Dvorak Z et al: In Vitro Safety Signals for Potential Clinical Development of the Anti-Inflammatory Pregnane X Receptor Agonist FKK6
DOI: 10.5281/zenodo.8355293
title: Data related to "An Antibiotic-Loaded Silicone-Hydrogel IPN for the Prevention of Surgical Site Infections"

description: Data related to "An Antibiotic Loaded Silicone Hydrogel IPN for the Prevention of Surgical Site Infections". The article is published in Gels as part of the Special Issue Antibacterial Gels.
DOI: 10.5281/zenodo.8355292
title: Data related to "An Antibiotic-Loaded Silicone-Hydrogel IPN for the Prevention of Surgical Site Infections"

description: Data related to "An Antibiotic Loaded Silicone Hydrogel IPN for the Prevention of Surgical Site Infections". The article is published in Gels as part of the Special Issue Antibacterial Gels.
DOI: 10.6084/m9.figshare.24356497
title: PRSComp Disease/trait database

description: The Disease/trait database is constructed based on GWAS Catalog summary statistics data of genetic risk score of diseases and traits accessed in June 2022 [13]. GWAS Catalog records were curated to fulfill the following criteria: biallelic single nucleotide variant, SNP containing information on effect size, genotyped at 1KG3 and HGDP (see Reference genotyped dataset) and not ambiguous. From them, SNP with conditional effect were excluded. A threshold of P-value lower than 1x10<sup>-8</sup> for the associated SNP was also established. In addition, OR values were transformed to their corresponding ln(OR) and SNPs were coded by their risk allele.The curated set of GWAS Catalog records were grouped into a set of query entries by using GWAS Catalog fields: “DISEASE/TRAIT”, “MAPPED_TRAIT”, “STUDY ACCESSION”, ancestry population and the unit measure of the SNP effect, extracted from “95% CI(TEXT)” field to describe a specific disease/trait study. Each query entry was then assigned to one of these main categories: Cancer/Neoplasm (514 entries, 2,211 SNPs), Disorder/Diseases (2,320 entries, 18,085 SNPs), Processes/measurements (7,037 entries, 52,337 SNPs) and Trait/conditions (203 entries, 2,423 SNPs). Then, each category was subdivided into additional subcategories according to the “Experimental Factor Ontology” field assigned at GWAS Catalog and complemented by querying the Open Targets Platform to refine the phenotype under study if necessary.We have incorporated the GWASROC-ID (https://gwasrocs.ca) to those <i>PRScomp</i> entries included in the GWASROC database (matching at PUBMEDID and rsID).
DOI: 10.25345/c53776564
title: MassIVE MSV000093151 - GNPS-Pinellia ternata20231019 samples
title: To investigate network of compounds in Pinellia ternata after derivatization by UPLC-MS/MS
DOI: 10.5517/ccdc.csd.cc2b51td
title: CCDC 2149813: Experimental Crystal Structure Determination

description: Related Article: Veera Babu Gudise, Shaik Anwar|2023|RSC Advances|13|27456|doi:10.1039/D3RA04996E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2b526t
title: CCDC 2149825: Experimental Crystal Structure Determination

description: Related Article: Veera Babu Gudise, Shaik Anwar|2023|RSC Advances|13|27456|doi:10.1039/D3RA04996E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2c0b1s
title: CCDC 2175054: Experimental Crystal Structure Determination

description: Related Article: Veera Babu Gudise, Shaik Anwar|2023|RSC Advances|13|27456|doi:10.1039/D3RA04996E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fh010
title: CCDC 2248741: Experimental Crystal Structure Determination

description: Related Article: Lucas G. Fachini, Gabriel B. Baptistella, Kahoana Postal, Francielli S. Santana, Emanuel M. de Souza, Ronny R. Ribeiro, Giovana G. Nunes, Eduardo L. Sá|2023|RSC Advances|13|27997|doi:10.1039/D3RA02130K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fh021
title: CCDC 2248742: Experimental Crystal Structure Determination

description: Related Article: Lucas G. Fachini, Gabriel B. Baptistella, Kahoana Postal, Francielli S. Santana, Emanuel M. de Souza, Ronny R. Ribeiro, Giovana G. Nunes, Eduardo L. Sá|2023|RSC Advances|13|27997|doi:10.1039/D3RA02130K
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2frhxm
title: CCDC 2256921: Experimental Crystal Structure Determination

description: Related Article: A. Bouzina, Y. Bououne, M. Ibrahim-Ouali, N-E, Aouf|2023|CSD Communication|||
description: Related Article: Yousra Ouafa Bouone, Abdeslem Bouzina, Rayene Sayad, Abdelhak Djemel, Farouk Benaceur, Abdelhalim Zoukel, Malika Ibrahim-Ouali, Nour-Eddine Aouf, Fouzia Bouchareb|2023|RSC Advances|13|28030|doi:10.1039/D3RA05289C
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg56b
title: CCDC 2277731: Experimental Crystal Structure Determination

description: Related Article: Ming-Yi Lee, Chih-Hsiang Liao, Hsiu-Yu Hung, Jhen-Yi Lee, Hon Man Lee|2023|RSC Advances|13|27434|doi:10.1039/D3RA05016E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg616
title: CCDC 2277757: Experimental Crystal Structure Determination

description: Related Article: Ming-Yi Lee, Chih-Hsiang Liao, Hsiu-Yu Hung, Jhen-Yi Lee, Hon Man Lee|2023|RSC Advances|13|27434|doi:10.1039/D3RA05016E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg627
title: CCDC 2277758: Experimental Crystal Structure Determination

description: Related Article: Ming-Yi Lee, Chih-Hsiang Liao, Hsiu-Yu Hung, Jhen-Yi Lee, Hon Man Lee|2023|RSC Advances|13|27434|doi:10.1039/D3RA05016E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg638
title: CCDC 2277759: Experimental Crystal Structure Determination

description: Related Article: Ming-Yi Lee, Chih-Hsiang Liao, Hsiu-Yu Hung, Jhen-Yi Lee, Hon Man Lee|2023|RSC Advances|13|27434|doi:10.1039/D3RA05016E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gg649
title: CCDC 2277760: Experimental Crystal Structure Determination

description: Related Article: Ming-Yi Lee, Chih-Hsiang Liao, Hsiu-Yu Hung, Jhen-Yi Lee, Hon Man Lee|2023|RSC Advances|13|27434|doi:10.1039/D3RA05016E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.23851572
title: Supplementary_tables - Prenatal programming in dairy cattle

description: Supplementary material : file containing supplementary tables 1 to 11.
DOI: 10.6084/m9.figshare.23851572.v1
title: Supplementary_tables - Prenatal programming in dairy cattle

description: Supplementary material : file containing supplementary tables 1 to 10.
DOI: 10.6084/m9.figshare.23851572.v2
title: Supplementary_tables - Prenatal programming in dairy cattle

description: Supplementary material : file containing supplementary tables 1 to 11.
DOI: 10.5281/zenodo.8385519
title: Dataset for "Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase"

description: This data set contains files related to the article "Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase" by Alba Nin-Hill, Albert Ardèvol, Xevi Biarnés, Antoni Planas and Carme Rovira. 
ABSTRACT
Bacterial β-glycosidases are hydrolytic enzymes that depolymerize polysaccharides such as β-cellulose, β-glucans and β-xylans from different sources are used in a myriad of biomedical and industrial applications. It has been shown that a conformational change of the substrate, from a relaxed 4C1 conformation to a distorted 1S3/1,4B conformation of the reactive sugar, is necessary for catalysis. However, the molecular determinants that stabilize the substrate's distortion are poorly understood. Here we use quantum mechanics/molecular mechanics (QM/MM)-based molecular dynamics methods to assess the impact of the interaction between the reactive sugar, i.e. the one at subsite -1, and the catalytic nucleophile (a glutamate) on substrate conformation. We show that the hydrogen bond involving the C2 exocyclic group and the nucleophile controls substrate conformation: its presence preserves sugar distortion, whereas its absence (e.g. in an enzyme mutant) knocks it out. We also show that 2-deoxy-2-fluoro derivatives, widely used to trap the reaction intermediates by X-ray crystallography, reproduce the conformation of the hydrolysable substrate at the experimental conditions. These results highlight the importance of the 2-OH···nucleophile interaction in substrate recognition and catalysis in endo-glycosidases and can inform mutational campaigns aimed to search for more efficient enzymes.
 
DESCRIPTION OF THE DATASET
The data is compressed in a .rar file in where we would find the following folders:

Model1_WT
Model2_2deoxy2F_lowpH
Model3_2deoxy2F_neutralpH
Model4_Glu105Gln_lowpH
Model5_Glu105Gln_neutralpH
Model6_Glu105Asp_neutralpH
Model7_Glu105Ala_lowpH
Model8_Glu105Ile_lowpH
Model8_Glu105Ile_lowpH
Model10_Glu105Ile_neutralpH
scripts
Each folder contains the first frame of the production phase of the QM/MM MD simulations in a .pdb format and the representative structures of the whole simulation obtained by clustering in a .nc format.
In the scripts folder we can find the scripts used to calculate and analyze the QM/MM MD simulations and a README.txt file with their proper descriptions.
 
More data can be made available upon reasonable request.
DOI: 10.5281/zenodo.8385518
title: Dataset for "Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase"

description: This data set contains files related to the article "Control of Substrate Conformation by Hydrogen Bonding in a Retaining β-Endoglycosidase" by Alba Nin-Hill, Albert Ardèvol, Xevi Biarnés, Antoni Planas and Carme Rovira. 
ABSTRACT
Bacterial β-glycosidases are hydrolytic enzymes that depolymerize polysaccharides such as β-cellulose, β-glucans and β-xylans from different sources are used in a myriad of biomedical and industrial applications. It has been shown that a conformational change of the substrate, from a relaxed 4C1 conformation to a distorted 1S3/1,4B conformation of the reactive sugar, is necessary for catalysis. However, the molecular determinants that stabilize the substrate's distortion are poorly understood. Here we use quantum mechanics/molecular mechanics (QM/MM)-based molecular dynamics methods to assess the impact of the interaction between the reactive sugar, i.e. the one at subsite -1, and the catalytic nucleophile (a glutamate) on substrate conformation. We show that the hydrogen bond involving the C2 exocyclic group and the nucleophile controls substrate conformation: its presence preserves sugar distortion, whereas its absence (e.g. in an enzyme mutant) knocks it out. We also show that 2-deoxy-2-fluoro derivatives, widely used to trap the reaction intermediates by X-ray crystallography, reproduce the conformation of the hydrolysable substrate at the experimental conditions. These results highlight the importance of the 2-OH···nucleophile interaction in substrate recognition and catalysis in endo-glycosidases and can inform mutational campaigns aimed to search for more efficient enzymes.
 
DESCRIPTION OF THE DATASET
The data is compressed in a .rar file in where we would find the following folders:

Model1_WT
Model2_2deoxy2F_lowpH
Model3_2deoxy2F_neutralpH
Model4_Glu105Gln_lowpH
Model5_Glu105Gln_neutralpH
Model6_Glu105Asp_neutralpH
Model7_Glu105Ala_lowpH
Model8_Glu105Ile_lowpH
Model8_Glu105Ile_lowpH
Model10_Glu105Ile_neutralpH
scripts
Each folder contains the first frame of the production phase of the QM/MM MD simulations in a .pdb format and the representative structures of the whole simulation obtained by clustering in a .nc format.
In the scripts folder we can find the scripts used to calculate and analyze the QM/MM MD simulations and a README.txt file with their proper descriptions.
 
More data can be made available upon reasonable request.
DOI: 10.6084/m9.figshare.24356521
title: 珠江口流域碳酸盐的地球化学特征

description: FM-1至FM-8是碳酸盐的XRD数据。xlsx文件是碳和氧同位素和矿物数据。Txt是文石和方解石的拉曼数据。OPJU文件是碳酸盐在多个区域的碳和氧同位素值。
DOI: 10.6084/m9.figshare.24356521.v1
title: 珠江口流域碳酸盐的地球化学特征

description: FM-1至FM-8是碳酸盐的XRD数据。xlsx文件是碳和氧同位素和矿物数据。Txt是文石和方解石的拉曼数据。OPJU文件是碳酸盐在多个区域的碳和氧同位素值。
DOI: 10.6084/m9.figshare.24356548
title: Supplementary Material for: Thickened Perirenal Fat Predicts Poor Renal Outcome in Patients with IgA Nephropathy: A Population-Based Retrospective Cohort Study

description: Introduction: Perirenal fat is a pad that fills the retroperitoneal space outside the kidney, which affects kidney function in various ways. However, the association between perirenal fat and IgA nephropathy (IgAN) has not yet been elucidated. This study aimed to investigate the role of perirenal fat in predicting IgAN progression. Methods: A total of 473 patients with biopsy-proven IgAN were recruited, and perirenal fat thickness (PFT) was measured using color Doppler ultrasonography. Patients were divided into two groups according to the median PFT: low PFT group (PFT≤1.34 cm, n=239) and high PFT group (PFT&gt;1.35 cm, n=234). A total of 473 healthy participants were included in the control group. Basic clinical characteristics were assessed at the time of renal biopsy, and the relationship between PFT and combined endpoints was analyzed. The combined endpoints were defined as a two-fold increase in blood creatinine level, end-stage renal disease (ESRD), and dialysis over three months. KaplanMeier survival analysis was used to explore the role of PFT in the progression of IgAN. Three clinicopathological models of multivariate Cox regression analysis were established to evaluate the association between PFT and renal prognosis in patients with IgAN. Results: Compared to healthy subjects, patients with IgAN showed significantly higher PFT. After a median follow-up of 50 months, 75 of 473 patients (15.9%) with IgAN reached renal combined endpoints. Among these, 13 in 239 patients (5.4%) were in the low PFT group and 62 of 234 patients (26.5%) were in the high PFT group (p&lt;0.001). The results of three Cox regression models (including demographics, pathological and clinical indicators, and PFT) demonstrated that a higher PFT was significantly associated with a higher risk of reaching combined endpoints in patients with IgAN. Conclusion: This study indicated a positive relationship between PFT and renal progression in patients with IgAN, suggesting that perirenal fat might act as a marker of poor prognosis in patients with IgAN.
DOI: 10.5281/zenodo.10020777
title: ML System Development Processes Expert Interview Transcripts
DOI: 10.5281/zenodo.10020776
title: ML System Development Processes Expert Interview Transcripts
DOI: 10.5517/ccdc.csd.cc2cpmk8
title: CCDC 2195530: Experimental Crystal Structure Determination

description: Related Article: Kah Yean Lum, Jonathan M White, Daniel J G Johnson, Vicky M Avery, Rohan A Davis|2023|Beilstein J.Org.Chem.|19|107|doi:10.3762/bjoc.19.11
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cpml9
title: CCDC 2195531: Experimental Crystal Structure Determination

description: Related Article: Kah Yean Lum, Jonathan M White, Daniel J G Johnson, Vicky M Avery, Rohan A Davis|2023|Beilstein J.Org.Chem.|19|107|doi:10.3762/bjoc.19.11
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.