cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.6828475
title: CATH Structural domains in AlphaFold2 models for 21 model organisms

description: CATH structural domain assignments for AlphaFold2 models in 21 model organisms. The table cath-v4_3_0.alphafold-v2.2022-11-22.tsv contains the domain assignments with information on model quality, CATH superfamily and Class, organism, average pLDDT, percentage of residues not in secondary structure, globularity and domain origin (CATH-PDB, CATH-HMM,Pfam,newfams). Organisms included: Arabidopsis thaliana Caenorhabditis elegans Candida albicans Danio rerio Dictyostelium discoideum Drosophila melanogaster Escherichia coli Glycine max Homo sapiens Leishmania infantum Methanocaldococcus jannaschii Mus musculus Mycobacterium tuberculosis Oryza sativa Plasmodium falciparum Rattus norvegicus Saccharomyces cerevisiae Schizosaccharomyces pombe Staphylococcus aureus Trypanosoma cruzi Zea mays The archive <pre>cath-v4_3_0.alphafold-v2.2022-11-22.by_superfamily.tgz</pre> contains all domains assigned by CATH in the dataset as PDB files, divided by superfamily. Alternatively, if you're interested in a particular organism, an individual tarball containing all CATH domains as PDB files is available e.g. cath-v4_3_0.alphafold-v2.2022-11-22.arabidopsis_thaliana.tgz All domains included in this release are named as af_[UniProt_ID]_[start]_[stop].
DOI: 10.5281/zenodo.7624085
title: Data and code for "The immune regulation and epidemiological consequences of specific immune priming in Drosophila"

description: Raw data and R code used to analyse and generate all figures in the above manuscript.
DOI: 10.5281/zenodo.7624084
title: Data and code for "The immune regulation and epidemiological consequences of specific immune priming in Drosophila"

description: Raw data and R code used to analyse and generate all figures in the above manuscript.
DOI: 10.6084/m9.figshare.22059083
title: Revealing the relationship between nitrogen use efficiency-related QTLs and carbon and nitrogen metabolism regulation in poplar

description: <strong>Supporting information</strong> <strong>Figure S1. </strong>KEGG functional annotation of QTL candidate genes. <strong>Figure S2.</strong> Correlation analysis of 60 transcriptome sample data. <strong>Figure S3.</strong> Expression confirmation using quantitative real-time PCR. <strong>(a)</strong> Fragments per kilobase of exon model per million mapped fragments of target genes.<strong> (b)</strong> Relative expression of target genes by qRT‒PCR. <strong>Figure S4.</strong> Analysis of nitrogen response DEGs of 10 clones under high- and low-nitrogen conditions. <strong>(a) </strong>Statistical analysis of up- and downregulated genes in 10 clones under high- and low-nitrogen conditions.<strong> (b) </strong>Functional enrichment analysis of KEGG for all DEGs of 10 clones under high- and low-nitrogen conditions. The colour scale represents the adjusted <em>P</em> value (padj). The high-nitrogen condition is represented by the letters A, and the low-nitrogen condition is represented by the letters B. <strong>Figure S5.</strong> Difference analysis of carbon and nitrogen metabolism of 10 clones under high- and low-nitrogen conditions. <strong>(a)</strong> Comparison of differences in total nitrogen, total carbon, and the carbon to nitrogen ratio in the xylem.<strong> (b)</strong> Comparison of differences in total nitrogen, total carbon, and the carbon to nitrogen ratio in the bark. S1 is ‘Danhong’. S2 is ‘Tongliao 1’. S3-S10 are F1 offspring. <strong>Figure S6.</strong> Difference analyses of cellulose, hemicellulose, and lignin contents in the xylems of 10 clones under high- and low-nitrogen conditions. <strong>Figure S7. </strong>Difference analysis of hydrolysed amino acid content in the bark of 10 clones under high- and low-nitrogen conditions. <strong>Figure S8. </strong>Difference analysis of hydrolysed amino acid content in the xylems of 10 clones under low- and high-nitrogen conditions. <strong>Figure S9. </strong>WGCNA of 10 clones under high- and low-nitrogen conditions. Queue selection of WGCNA. <strong>(a) </strong>WGCNA power value testing and determination. <strong>(b) </strong>Module hierarchical clustering tree of WGCNA. <strong>Table S1. </strong>The original data of ground diameter, plant height, and stem biomass of the hybrid population. The original data were averaged. <strong>Table S2. </strong>Summary of QTL mapping results for NUE-related traits. <strong>Table S3. </strong>Functional annotation of candidate genes for QTLs. <strong>Table S4.</strong> Summary of the RNA-Seq results. The high-nitrogen condition is represented by the letters A, and the low-nitrogen condition is represented by the letters B. <strong>Table S5.</strong> The primers used in this study.
DOI: 10.6084/m9.figshare.22059083.v1
title: Revealing the relationship between nitrogen use efficiency-related QTLs and carbon and nitrogen metabolism regulation in poplar

description: <strong>Supporting information</strong> <strong>Figure S1. </strong>KEGG functional annotation of QTL candidate genes. <strong>Figure S2.</strong> Correlation analysis of 60 transcriptome sample data. <strong>Figure S3.</strong> Expression confirmation using quantitative real-time PCR. <strong>(a)</strong> Fragments per kilobase of exon model per million mapped fragments of target genes.<strong> (b)</strong> Relative expression of target genes by qRT‒PCR. <strong>Figure S4.</strong> Analysis of nitrogen response DEGs of 10 clones under high- and low-nitrogen conditions. <strong>(a) </strong>Statistical analysis of up- and downregulated genes in 10 clones under high- and low-nitrogen conditions.<strong> (b) </strong>Functional enrichment analysis of KEGG for all DEGs of 10 clones under high- and low-nitrogen conditions. The colour scale represents the adjusted <em>P</em> value (padj). The high-nitrogen condition is represented by the letters A, and the low-nitrogen condition is represented by the letters B. <strong>Figure S5.</strong> Difference analysis of carbon and nitrogen metabolism of 10 clones under high- and low-nitrogen conditions. <strong>(a)</strong> Comparison of differences in total nitrogen, total carbon, and the carbon to nitrogen ratio in the xylem.<strong> (b)</strong> Comparison of differences in total nitrogen, total carbon, and the carbon to nitrogen ratio in the bark. S1 is ‘Danhong’. S2 is ‘Tongliao 1’. S3-S10 are F1 offspring. <strong>Figure S6.</strong> Difference analyses of cellulose, hemicellulose, and lignin contents in the xylems of 10 clones under high- and low-nitrogen conditions. <strong>Figure S7. </strong>Difference analysis of hydrolysed amino acid content in the bark of 10 clones under high- and low-nitrogen conditions. <strong>Figure S8. </strong>Difference analysis of hydrolysed amino acid content in the xylems of 10 clones under low- and high-nitrogen conditions. <strong>Figure S9. </strong>WGCNA of 10 clones under high- and low-nitrogen conditions. Queue selection of WGCNA. <strong>(a) </strong>WGCNA power value testing and determination. <strong>(b) </strong>Module hierarchical clustering tree of WGCNA. <strong>Table S1. </strong>The original data of ground diameter, plant height, and stem biomass of the hybrid population. The original data were averaged. <strong>Table S2. </strong>Summary of QTL mapping results for NUE-related traits. <strong>Table S3. </strong>Functional annotation of candidate genes for QTLs. <strong>Table S4.</strong> Summary of the RNA-Seq results. The high-nitrogen condition is represented by the letters A, and the low-nitrogen condition is represented by the letters B. <strong>Table S5.</strong> The primers used in this study.
DOI: 10.5519/qd.5cjlfix9
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1830 records)
DOI: 10.5281/zenodo.7623944
title: Supplying renewable energy to Central European research facilities: A techno-economic comparison of electricity and hydrogen (Dataset)

description: This dataset contains central input assumptions and results related to the publication "Supplying renewable energy to Central European research facilities: A techno-economic comparison of electricity and hydrogen". Result files are contained in the <strong> results.zip</strong> archive file. The file contains for each scenario, as indicated by the folder structure, the following files: <strong>results.csv</strong>: Central scenario results exported as <em>character separated value</em> <em>(csv)</em> file, with a semicolon (<strong>;</strong>) as field separator. All fields are quoted using double quotation marks <strong>"..."</strong>. Can be explored using standard office software like Microsoft Excel/Libre Office or other tools. <strong>network.nc</strong>: PyPSA network file containing the optimized scenario with all input and unprocessed outputs (results). Can be explored using the PyPSA software package. <strong>lcoes.csv</strong>: Levelised Cost of Electricity used to construct the renewable energy source (RES) based supply curve for each scenario. The dataset further contains the following files which represent central input assumptions to the model and scenarios, both as <em>CSV</em> files: <strong>efficiencies.csv</strong>: Technology process and conversion efficiencies<em> </em>including more details on the assumptions and information on which references the assumptions are based. <strong>costs_2030.csv</strong>: Technology cost assumptions for 2030 including more details on the assumptions and information on which references the assumptions are based. This data is based on this Technology Data repository on GitHub.
DOI: 10.5281/zenodo.7623943
title: Supplying renewable energy to Central European research facilities: A techno-economic comparison of electricity and hydrogen (Dataset)

description: This dataset contains central input assumptions and results related to the publication "Supplying renewable energy to Central European research facilities: A techno-economic comparison of electricity and hydrogen". Result files are contained in the <strong> results.zip</strong> archive file. The file contains for each scenario, as indicated by the folder structure, the following files: <strong>results.csv</strong>: Central scenario results exported as <em>character separated value</em> <em>(csv)</em> file, with a semicolon (<strong>;</strong>) as field separator. All fields are quoted using double quotation marks <strong>"..."</strong>. Can be explored using standard office software like Microsoft Excel/Libre Office or other tools. <strong>network.nc</strong>: PyPSA network file containing the optimized scenario with all input and unprocessed outputs (results). Can be explored using the PyPSA software package. <strong>lcoes.csv</strong>: Levelised Cost of Electricity used to construct the renewable energy source (RES) based supply curve for each scenario. The dataset further contains the following files which represent central input assumptions to the model and scenarios, both as <em>CSV</em> files: <strong>efficiencies.csv</strong>: Technology process and conversion efficiencies<em> </em>including more details on the assumptions and information on which references the assumptions are based. <strong>costs_2030.csv</strong>: Technology cost assumptions for 2030 including more details on the assumptions and information on which references the assumptions are based. This data is based on this Technology Data repository on GitHub.
DOI: 10.5281/zenodo.7561734
title: MCL-1 promiscuity and the structural resilience of its binding partners - DATA

description: Data supporting: "MCL-1 promiscuity and the structural resilience of its binding partners"; Journal of Chemical Physics (JCP); 2023.
DOI: 10.6084/m9.figshare.21908964.v1
title: Biodiversity mitigates trade-offs among species functional traits underpinning multiple ecosystem services

description: <strong>Biodiversity mitigates trade-offs among species functional traits underpinning multiple ecosystem services</strong>
DOI: 10.6084/m9.figshare.22047263.v1
title: Dose response

description: Data and code for Figure 2 of Earth Commission synthesis paper
DOI: 10.5281/zenodo.7624429
title: Raw Data for the article: Atrial fibrillation ablation improves late survival after concomitant cardiac surgery

description: <strong>Objective: </strong>Preoperative atrial fibrillation (AF) increases risk of stroke, heart failure, and all-cause mortality after cardiac surgery. Despite encouraging results and guideline recommendations, surgical ablation (SA) for AF concomitant with other heart surgery remains low. In the current study we aimed to address the long-term mortality after SA concomitant with cardiac surgery. <strong>Methods: </strong>This report pertains to the HEart surgery In atrial fibrillation and Supraventricular Tachycardia (HEIST) registry. We identified 20,765 adult patients (62% male) with preoperative AF who underwent conventional sternotomy heart surgery between 2010 and 2021 in 8 tertiary centers in Poland, Netherlands, and Italy. We used Cox proportional hazards models for computations and propensity score matching to minimize differences in baseline characteristics. <strong>Results: </strong>Of included patients, 2755 (13.4%) underwent SA for AF. The highest rates of SA were observed for mitral interventions (mitral valve repair or replacement and tricuspid intervention, 25.2%), lowest for isolated coronary artery bypass grafting (6.2%). Patients in the SA group were younger (mean age 64.5 ± 9.0 years vs 68.7 ± 16.0 years; P &lt; .001) and lower risk (mean European System for Cardiac Operative Risk Evaluation [EuroSCORE] II, 4.1 vs 5.7; P &lt; .001). During the 11-year study period, there was a mortality reduction associated with SA (hazard ratio, 0.57; 95% CI, 0.52-0.62; P &lt; .001). After propensity matching, 2750 pairs with similar baseline characteristics were identified. SA was associated with 16% mortality decline (hazard ratio, 0.84; 95% CI, 0.75-0.94; P = .003). <strong>Conclusions: </strong>In this multicenter, retrospective, propensity matched study, SA concomitant with other cardiac surgery was associated with improved long-term survival regardless of baseline surgical risk.
DOI: 10.5281/zenodo.7624428
title: Raw Data for the article: Atrial fibrillation ablation improves late survival after concomitant cardiac surgery

description: <strong>Objective: </strong>Preoperative atrial fibrillation (AF) increases risk of stroke, heart failure, and all-cause mortality after cardiac surgery. Despite encouraging results and guideline recommendations, surgical ablation (SA) for AF concomitant with other heart surgery remains low. In the current study we aimed to address the long-term mortality after SA concomitant with cardiac surgery. <strong>Methods: </strong>This report pertains to the HEart surgery In atrial fibrillation and Supraventricular Tachycardia (HEIST) registry. We identified 20,765 adult patients (62% male) with preoperative AF who underwent conventional sternotomy heart surgery between 2010 and 2021 in 8 tertiary centers in Poland, Netherlands, and Italy. We used Cox proportional hazards models for computations and propensity score matching to minimize differences in baseline characteristics. <strong>Results: </strong>Of included patients, 2755 (13.4%) underwent SA for AF. The highest rates of SA were observed for mitral interventions (mitral valve repair or replacement and tricuspid intervention, 25.2%), lowest for isolated coronary artery bypass grafting (6.2%). Patients in the SA group were younger (mean age 64.5 ± 9.0 years vs 68.7 ± 16.0 years; P &lt; .001) and lower risk (mean European System for Cardiac Operative Risk Evaluation [EuroSCORE] II, 4.1 vs 5.7; P &lt; .001). During the 11-year study period, there was a mortality reduction associated with SA (hazard ratio, 0.57; 95% CI, 0.52-0.62; P &lt; .001). After propensity matching, 2750 pairs with similar baseline characteristics were identified. SA was associated with 16% mortality decline (hazard ratio, 0.84; 95% CI, 0.75-0.94; P = .003). <strong>Conclusions: </strong>In this multicenter, retrospective, propensity matched study, SA concomitant with other cardiac surgery was associated with improved long-term survival regardless of baseline surgical risk.
DOI: 10.5281/zenodo.7624051
title: NMR Relaxometry data for publication "Engineered Nonviral Protein Cages Modified for MR Imaging"

description: NMRD profiles collected with field-cycling NMR relaxometry of a water solution of Gd-C4-IA, and of AaLS-13 and OP protein cages labeled with the gadolinium(III) complex. Published in: https://doi.org/10.1021/acsabm.2c00892 NMRD data acquisition and analysis was performed with the support of the PRIN 2017A2KEPL project “Rationally designed nanogels embedding paramagnetic ions as MRI. probes”, and the European Commision through H2020 FET-Open project HIRES-MULTIDYN<br> award no. 899683 and H2020 INFRAIA iNEXT-Discovery (Structural Biology Research Infrastructures for Translational Research and Discovery) award no. 871037.
DOI: 10.5281/zenodo.7624050
title: NMR Relaxometry data for publication "Engineered Nonviral Protein Cages Modified for MR Imaging"

description: NMRD profiles collected with field-cycling NMR relaxometry of a water solution of Gd-C4-IA, and of AaLS-13 and OP protein cages labeled with the gadolinium(III) complex. Published in: https://doi.org/10.1021/acsabm.2c00892 NMRD data acquisition and analysis was performed with the support of the PRIN 2017A2KEPL project “Rationally designed nanogels embedding paramagnetic ions as MRI. probes”, and the European Commision through H2020 FET-Open project HIRES-MULTIDYN<br> award no. 899683 and H2020 INFRAIA iNEXT-Discovery (Structural Biology Research Infrastructures for Translational Research and Discovery) award no. 871037.
DOI: 10.5281/zenodo.7586231
title: UNIX@H5P_Dataset

description: A dataset from a quasi-experimental pilot study, that examined effects of immediately available feedback in a CBA on the learning motivation of first-year students. Pilot study took place at the University of Potsdam from 18-10-2022 to 09-11-2022.
DOI: 10.5281/zenodo.7624464
title: Raw Data for the article: Clinical Insights to Complete and Incomplete Surgical Revascularization in Atrial Fibrillation and Multivessel Coronary Disease

description: <strong>Objectives: </strong>Although endorsed by international guidelines, complete revascularization (CR) with Coronary Artery Bypass Grafting (CABG) remains underused. In higher-risk patients such as those with pre-operative atrial fibrillation (AF), the effects of CR are not well studied. <strong>Methods: </strong>We analyzed patients' data from the HEIST (HEart surgery In AF and Supraventricular Tachycardia) registry. Between 2012 and 2020 we identified 4770 patients with pre-operative AF and multivessel coronary artery disease who underwent isolated CABG. We divided the cohort according to the completeness of the revascularization and used propensity score matching (PSM) to minimize differences between baseline characteristics. The primary endpoint was all-cause mortality. <strong>Results: </strong>Median follow-up was 4.7 years [interquartile range (IQR) 2.3-6.9]. PSM resulted in 1,009 pairs of complete and incomplete revascularization. Number of distal anastomoses varied, accounting for 3.0 + -0.6 vs. 1.7 + -0.6, respectively. Although early (&lt; 24 h) and 30-day post-operative mortalities were not statistically different between non-CR and CR patients [Odds Ratio (OR) and 95% Confidence Intervals (CIs): 1.34 (0.46-3.86); <em>P</em> = 0.593, Hazard Ratio (HR) and 95% CIs: 0.88 (0.59-1.32); <em>P</em> = 0.542, respectively] the long term mortality was nearly 20% lower in the CR cohort [HR (95% CIs) 0.83 (0.71-0.96); <em>P</em> = 0.011]. This benefit was sustained throughout subgroup analyses, yet most accentuated in low-risk patients (younger i.e., &lt; 70 year old, with a EuroSCORE II &lt; 2%, non-diabetic) and when off-pump CABG was performed. <strong>Conclusion: </strong>Complete revascularization in patients with pre-operative AF is safe and associated with improved survival. Particular survival benefit with CR was observed in low-risk patients undergoing off-pump CABG.
DOI: 10.5281/zenodo.7624463
title: Raw Data for the article: Clinical Insights to Complete and Incomplete Surgical Revascularization in Atrial Fibrillation and Multivessel Coronary Disease

description: <strong>Objectives: </strong>Although endorsed by international guidelines, complete revascularization (CR) with Coronary Artery Bypass Grafting (CABG) remains underused. In higher-risk patients such as those with pre-operative atrial fibrillation (AF), the effects of CR are not well studied. <strong>Methods: </strong>We analyzed patients' data from the HEIST (HEart surgery In AF and Supraventricular Tachycardia) registry. Between 2012 and 2020 we identified 4770 patients with pre-operative AF and multivessel coronary artery disease who underwent isolated CABG. We divided the cohort according to the completeness of the revascularization and used propensity score matching (PSM) to minimize differences between baseline characteristics. The primary endpoint was all-cause mortality. <strong>Results: </strong>Median follow-up was 4.7 years [interquartile range (IQR) 2.3-6.9]. PSM resulted in 1,009 pairs of complete and incomplete revascularization. Number of distal anastomoses varied, accounting for 3.0 + -0.6 vs. 1.7 + -0.6, respectively. Although early (&lt; 24 h) and 30-day post-operative mortalities were not statistically different between non-CR and CR patients [Odds Ratio (OR) and 95% Confidence Intervals (CIs): 1.34 (0.46-3.86); <em>P</em> = 0.593, Hazard Ratio (HR) and 95% CIs: 0.88 (0.59-1.32); <em>P</em> = 0.542, respectively] the long term mortality was nearly 20% lower in the CR cohort [HR (95% CIs) 0.83 (0.71-0.96); <em>P</em> = 0.011]. This benefit was sustained throughout subgroup analyses, yet most accentuated in low-risk patients (younger i.e., &lt; 70 year old, with a EuroSCORE II &lt; 2%, non-diabetic) and when off-pump CABG was performed. <strong>Conclusion: </strong>Complete revascularization in patients with pre-operative AF is safe and associated with improved survival. Particular survival benefit with CR was observed in low-risk patients undergoing off-pump CABG.