cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20454658.v1
title: Additional file 11 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 11: Table S5. P metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454664
title: Additional file 13 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 13: Table S6. C fixation/photosynthesis. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454670
title: Additional file 15 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 15: Table S8. Compatible solutes and osmolytes. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454664.v1
title: Additional file 13 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 13: Table S6. C fixation/photosynthesis. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454667
title: Additional file 14 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 14: Table S7. Amino acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454667.v1
title: Additional file 14 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 14: Table S7. Amino acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454670.v1
title: Additional file 15 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 15: Table S8. Compatible solutes and osmolytes. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454673
title: Additional file 16 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 16: Table S9. Broad transporters, permeases, channels and uptake systems. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454673.v1
title: Additional file 16 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 16: Table S9. Broad transporters, permeases, channels and uptake systems. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454676
title: Additional file 17 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 17: Table S10. Glycerolipid/Fatty acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454676.v1
title: Additional file 17 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 17: Table S10. Glycerolipid/Fatty acid metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454685
title: Additional file 1 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 1: Table S1. Main genomic features of marine, brackish and freswhater culture-derived picocyanobacteria. An asterisk in the origin column indicates strains where euryhaline physiology is known.
DOI: 10.6084/m9.figshare.20454685.v1
title: Additional file 1 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 1: Table S1. Main genomic features of marine, brackish and freswhater culture-derived picocyanobacteria. An asterisk in the origin column indicates strains where euryhaline physiology is known.
DOI: 10.6084/m9.figshare.20454682
title: Additional file 19 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 19: Table S11. Reactive oxygen species (ROS). Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454682.v1
title: Additional file 19 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 19: Table S11. Reactive oxygen species (ROS). Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454691
title: Additional file 21 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 21: Table S12. Mobile genetic elements. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454691.v1
title: Additional file 21 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 21: Table S12. Mobile genetic elements. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454697
title: Additional file 3 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 3: Additional Dataset 1. Average and standard deviation genome size, median intergenic spacers, coding density and %GC of all culture-derived picocyanobacteria. Single pair ANOVA tests for each origin and sub-cluster and for different genomic features.
DOI: 10.6084/m9.figshare.20454697.v1
title: Additional file 3 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 3: Additional Dataset 1. Average and standard deviation genome size, median intergenic spacers, coding density and %GC of all culture-derived picocyanobacteria. Single pair ANOVA tests for each origin and sub-cluster and for different genomic features.
DOI: 10.6084/m9.figshare.20454703
title: Additional file 5 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 5: Additional Dataset 2. Pangenomic analysis between all picocyanobacterial isolates from SCs 5.1, 5.2 and 5.3. The total number of genes for each category (strict core, soft core, shell and cloud) and isolate are specified.
DOI: 10.6084/m9.figshare.20454703.v1
title: Additional file 5 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 5: Additional Dataset 2. Pangenomic analysis between all picocyanobacterial isolates from SCs 5.1, 5.2 and 5.3. The total number of genes for each category (strict core, soft core, shell and cloud) and isolate are specified.
DOI: 10.6084/m9.figshare.20454706
title: Additional file 6 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 6: Additional Dataset 3. 5.1-5.2-5.3 meta-pangenome. Core, strict-core, shell and cloud annotated genes with Cyanorak clusters (CK) and SEED.
DOI: 10.6084/m9.figshare.20454706.v1
title: Additional file 6 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 6: Additional Dataset 3. 5.1-5.2-5.3 meta-pangenome. Core, strict-core, shell and cloud annotated genes with Cyanorak clusters (CK) and SEED.
DOI: 10.6084/m9.figshare.20454709
title: Additional file 7 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 7: Table S2. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters.
DOI: 10.6084/m9.figshare.20454709.v1
title: Additional file 7 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 7: Table S2. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters.
DOI: 10.6084/m9.figshare.20454715.v1
title: Additional file 8 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 8: Additional Dataset 4. Non-clustered CK genes from all 132 analyzed picocyanobacteria. BLASTP results obtained with the closest taxon from the NCBI nr database.
DOI: 10.6084/m9.figshare.20454718.v1
title: Additional file 9 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 9: Table S3. S metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454715
title: Additional file 8 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 8: Additional Dataset 4. Non-clustered CK genes from all 132 analyzed picocyanobacteria. BLASTP results obtained with the closest taxon from the NCBI nr database.
DOI: 10.6084/m9.figshare.20454718
title: Additional file 9 of Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates

description: Additional file 9: Table S3. S metabolism. Gene/protein presence/absence between all 132 compared culture derived marine, brackish and freshwater picocyanobacteria. Annotation assessed by Cyanorak CK clusters. CDD was used to retrieve the PSSM-ids from best specific/non-specific hits covering &gt;50 % of the protein.
DOI: 10.6084/m9.figshare.20454719
title: Additional file 10 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 10: Supplementary Table 8. Data from the allelic expression imbalance (AEI) analysis of TMEM129 and SLBP. P-values calculated using Wilcoxon matched-pairs signed rank test.
DOI: 10.6084/m9.figshare.20454719.v1
title: Additional file 10 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 10: Supplementary Table 8. Data from the allelic expression imbalance (AEI) analysis of TMEM129 and SLBP. P-values calculated using Wilcoxon matched-pairs signed rank test.
DOI: 10.6084/m9.figshare.20454722
title: Additional file 1 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 1: Supplementary Table 1. Details of the 165 osteoarthritis patients included in this study.
DOI: 10.6084/m9.figshare.20454722.v1
title: Additional file 1 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 1: Supplementary Table 1. Details of the 165 osteoarthritis patients included in this study.
DOI: 10.6084/m9.figshare.20454725
title: Additional file 2 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 2: Supplementary Table 2. Primers used in this study. [Btn], biotin tag at the 5' end of the primer. n/a, not applicable. Lower case sequence represents restriction enzyme motifs for cloning applications: cctagg, AvrII; actagt, SpeI.
DOI: 10.6084/m9.figshare.20454725.v1
title: Additional file 2 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 2: Supplementary Table 2. Primers used in this study. [Btn], biotin tag at the 5' end of the primer. n/a, not applicable. Lower case sequence represents restriction enzyme motifs for cloning applications: cctagg, AvrII; actagt, SpeI.
DOI: 10.6084/m9.figshare.20454728
title: Additional file 3 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 3: Supplementary Table 3. The sequences of guide RNAs (gRNAs) used for dCas9-TET1 modulation of the epigenome.
DOI: 10.6084/m9.figshare.20454728.v1
title: Additional file 3 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 3: Supplementary Table 3. The sequences of guide RNAs (gRNAs) used for dCas9-TET1 modulation of the epigenome.
DOI: 10.6084/m9.figshare.20454731.v1
title: Additional file 4 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 4: Supplementary Table 4. Details of the pre-designed RT-qPCR assays used to quantify gene expression.
DOI: 10.6084/m9.figshare.20454731
title: Additional file 4 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 4: Supplementary Table 4. Details of the pre-designed RT-qPCR assays used to quantify gene expression.
DOI: 10.6084/m9.figshare.20454734
title: Additional file 5 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 5: Supplementary Table 5. Methylation data (β-values expressed as a percentage) used for mQTL analysis. P-values calculated by linear regression.
DOI: 10.6084/m9.figshare.20454734.v1
title: Additional file 5 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 5: Supplementary Table 5. Methylation data (β-values expressed as a percentage) used for mQTL analysis. P-values calculated by linear regression.
DOI: 10.6084/m9.figshare.20454746
title: Additional file 9 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 9: Supplementary Table 7. Data from the dCas9-TET1 experiment. P-values calculated using multiple paired t-tests with Holm-Šídák approach to account for multiple comparisons.
DOI: 10.6084/m9.figshare.20454743
title: Additional file 8 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 8: Supplementary Table 6. Lucia reporter analysis data. P-values calculated using unpaired t-test.
DOI: 10.6084/m9.figshare.20454743.v1
title: Additional file 8 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 8: Supplementary Table 6. Lucia reporter analysis data. P-values calculated using unpaired t-test.
DOI: 10.6084/m9.figshare.20454746.v1
title: Additional file 9 of Identification of TMEM129, encoding a ubiquitin-protein ligase, as an effector gene of osteoarthritis genetic risk

description: Additional file 9: Supplementary Table 7. Data from the dCas9-TET1 experiment. P-values calculated using multiple paired t-tests with Holm-Šídák approach to account for multiple comparisons.
DOI: 10.6084/m9.figshare.20454790
title: Additional file 5 of The use of co-design in developing physical activity interventions for older adults: a scoping review

description: Additional file 5. Characteristics of included studies.
DOI: 10.6084/m9.figshare.20454790.v1
title: Additional file 5 of The use of co-design in developing physical activity interventions for older adults: a scoping review

description: Additional file 5. Characteristics of included studies.
DOI: 10.5281/zenodo.6976116
title: Stiffness of randomly sampled stainless steel frames under gravity and gravity plus wind load scenarios

description: Data was generated using the general purpose finite element software ABAQUS and performing advanced nonlinear analyses. The database is comprised of vertical and lateral system stiffness values corresponding to different random samples of six different nominal stainless steel frames under gravity and gravity plus wind load combinations. The values of the random variable assignments are given for each case. The full details of the finite element model can be found in: Arrayago, I.; Rasmussen, K.J.R. Reliability of stainless steel frames designed using the Direct Design Method in serviceability limit states. Journal of Constructional Steel Research 196, 107425, 2022. DOI: https://doi.org/10.1016/j.jcsr.2022.107425 The data included in the dataset corresponds to the vertical & lateral stiffness of each frame under different load conditions. Although the data has been generated using the finite element software ABAQUS, no special software is required to read or interpret the data.
description: {"references": ["Arrayago I., Rasmussen K.J.R. Reliability of stainless steel frames designed using the Direct Design Method in serviceability limit states Journal of Constructional Steel Research 196, 107425, 2022. DOI: https://doi.org/10.1016/j.jcsr.2022.107425"]}
DOI: 10.5281/zenodo.6976115
title: Stiffness of randomly sampled stainless steel frames under gravity and gravity plus wind load scenarios

description: Data was generated using the general purpose finite element software ABAQUS and performing advanced nonlinear analyses. The database is comprised of vertical and lateral system stiffness values corresponding to different random samples of six different nominal stainless steel frames under gravity and gravity plus wind load combinations. The values of the random variable assignments are given for each case. The full details of the finite element model can be found in: Arrayago, I.; Rasmussen, K.J.R. Reliability of stainless steel frames designed using the Direct Design Method in serviceability limit states. Journal of Constructional Steel Research 196, 107425, 2022. DOI: https://doi.org/10.1016/j.jcsr.2022.107425 The data included in the dataset corresponds to the vertical & lateral stiffness of each frame under different load conditions. Although the data has been generated using the finite element software ABAQUS, no special software is required to read or interpret the data.
description: {"references": ["Arrayago I., Rasmussen K.J.R. Reliability of stainless steel frames designed using the Direct Design Method in serviceability limit states Journal of Constructional Steel Research 196, 107425, 2022. DOI: https://doi.org/10.1016/j.jcsr.2022.107425"]}
DOI: 10.6084/m9.figshare.20454899
title: Additional file 1 of Comparing the diagnostic accuracy of modified RIPASA and MASS in patients diagnosed with acute appendicitis in Suez Canal University Hospital Emergency Department: a cross-sectional study

description: Additional file 1.
DOI: 10.6084/m9.figshare.20454899.v1
title: Additional file 1 of Comparing the diagnostic accuracy of modified RIPASA and MASS in patients diagnosed with acute appendicitis in Suez Canal University Hospital Emergency Department: a cross-sectional study

description: Additional file 1.
DOI: 10.25919/78k0-py81
title: Pathling: analytics on FHIR - Supporting data

description: Supporting data for the reproduction of findings within the paper "Pathling: analytics on FHIR".
DOI: 10.5281/zenodo.5939241
title: Structure of an MHC I–tapasin–ERp57 editing complex defines chaperone promiscuity

description: Adaptive immunity depends on cell surface presentation of antigenic peptides by major histocompatibility complex class I (MHC I) molecules and on stringent ER quality control in the secretory pathway. The chaperone tapasin in conjunction with the oxidoreductase ERp57 is crucial for MHC I assembly and for shaping the epitope repertoire for high immunogenicity. However, how the tapasin–ERp57 complex engages MHC I clients has not yet been determined at atomic detail. Here, we present the 2.7 Å crystal structure of a tapasin–ERp57 heterodimer in complex with peptide-receptive MHC I. Our study unveils molecular details of client recognition by the multichaperone complex and highlights elements indispensable for peptide proofreading. The structure of this transient ER quality control complex provides the mechanistic basis for the selector function of tapasin and showcases how the numerous MHC I allomorphs are chaperoned during peptide loading and editing.