cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26180/5e79a4dbec8dd
title: Consolidated survey results for phase I and phase II of the Occupational Violence and Aggression in the Emergency Department investigation.

description: Consolidated survey results for phase I and phase II of the Occupational Violence and Aggression in the Emergency Department investigation.<br>Pouryahya P, Lim A, Meyer A, Warburton E, Quahe A. Risk factors for Occupational Violence and Aggression in the Emergency Department 2020. Submitted to the Mediterranean Journal of Emergency Medicine and awaiting peer review.<br>Original survey and methods described in:<br>Pouryahya P, Meyer AD, Sherington S. Violence and Abuse against Staff in the Emergency Department, a Descriptive Analysis of a Two-Centre Staff Survey. Journal of General and Emergency Medicine 2019;4:2.<b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.12022047
title: Additional file 3 of Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study

description: Additional file 3. Raw sequence data.
DOI: 10.6084/m9.figshare.12022047.v1
title: Additional file 3 of Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study

description: Additional file 3. Raw sequence data.
DOI: 10.6084/m9.figshare.12022041
title: Additional file 2 of MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

description: Additional file 2: Table S2. Metadata associated with individual helminth-infected and -uninfected samples (n = 732) included in the meta-analysis. Information provided was derived from the original publication or following personal communication with the corresponding author.
DOI: 10.6084/m9.figshare.12022041.v1
title: Additional file 2 of MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

description: Additional file 2: Table S2. Metadata associated with individual helminth-infected and -uninfected samples (n = 732) included in the meta-analysis. Information provided was derived from the original publication or following personal communication with the corresponding author.
DOI: 10.6084/m9.figshare.12022032
title: Additional file 1 of MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

description: Additional file 1: Table S1. Studies investigating the relationships between helminth parasites and vertebrate gut microbiota included in the MICrobiome HELminth INteractions database (MICHELINdb). Studies from which datasets included in the meta-analysis were retrieved are indicated in green.
DOI: 10.6084/m9.figshare.12022032.v1
title: Additional file 1 of MICHELINdb: a web-based tool for mining of helminth-microbiota interaction datasets, and a meta-analysis of current research

description: Additional file 1: Table S1. Studies investigating the relationships between helminth parasites and vertebrate gut microbiota included in the MICrobiome HELminth INteractions database (MICHELINdb). Studies from which datasets included in the meta-analysis were retrieved are indicated in green.
DOI: 10.6084/m9.figshare.12021990
title: Additional file 9 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 9: Table S4. Core mycobiome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars in non-inoculated conditions. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021990.v1
title: Additional file 9 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 9: Table S4. Core mycobiome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars in non-inoculated conditions. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021963
title: Additional file 4 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 4: Table S3. Core bacteriome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars upon Verticillium dahliae inoculation. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021963.v1
title: Additional file 4 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 4: Table S3. Core bacteriome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars upon Verticillium dahliae inoculation. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021954
title: Additional file 3 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 3: Table S2. Core bacteriome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars in non-inoculated conditions. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021948
title: Additional file 9 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 9 : Table S4: Analysis of type IIb fibers from the EDL, TA, and Gast. S4_Summary: MaxQuant summary.txt table of the proteomics analysis in pooled type IIb muscle fibers of the EDL, GAST, and TA, related to Fig.ure 3a. S4_protein groups_ident: Protein groups output table of identified proteins in type IIb fibers of the EDL, TA, and GAST, related to Fig.ure 3a. S4_protein groups_quant: Protein groups output table of quantified proteins in type IIb fibers of the EDL, TA, and GAST, related to Figure 3a. S4_Fisher: Summary of Fisher’s exact tests of type IIb fibers, related to Figure 3b. S4_IHC: Quantification of TPM1, DES and TTN signal intensities on soleus cross-sections related to Figure 3d-e and Suppl. Figure 3A-D
DOI: 10.6084/m9.figshare.12021954.v1
title: Additional file 3 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 3: Table S2. Core bacteriome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars in non-inoculated conditions. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021942
title: Additional file 8 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 8 : Table S3: Fiber profiling data and protein groups output table of type I and type IIa fibers. S3_ProFiTvsIHC: Summary of fiber-type profiling of the soleus and EDL using either ProFiT or immunohistochemistry, related to Figure 2a. S3_protein groups ProFiT: Protein groups output table of single muscle fiber proteomes analyzed by ProFiT, related to Figure 2a. S3_Summary: MaxQuant summary.txt table of the proteomics analysis of pooled soleus type I and type IIa muscle fiber, related to Figure 2b. S3_protein groups_ident: Protein groups output table for proteins identified in type I and IIa fibers, related to Figure 2b. S3_protein groups_quant: Protein groups output table for type I and IIa quantification, related to Figure 2b. S3 _1DannotEnrich: 1D protein annotation of proteins identified in soleus type I and IIa fibers, related to Fig.ure 2c. S3_TMEM_IHC: Quantification of TMEM65 signal intensities on soleus and EDL cross-sections, related to Suppl. Figureure 2E-I. S3_CSP1_IHC: Quantification of CPS1 signal intensities on soleus cross-sections related to Figure 2d-e. S3_protein groups_MTNorm: Protein groups output table of type I and IIa quantification with OXPHOS-normalized mitochondrial protein abundances, related to Suppl. Figureure3 A-B.
DOI: 10.6084/m9.figshare.12021942.v1
title: Additional file 8 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 8 : Table S3: Fiber profiling data and protein groups output table of type I and type IIa fibers. S3_ProFiTvsIHC: Summary of fiber-type profiling of the soleus and EDL using either ProFiT or immunohistochemistry, related to Figure 2a. S3_protein groups ProFiT: Protein groups output table of single muscle fiber proteomes analyzed by ProFiT, related to Figure 2a. S3_Summary: MaxQuant summary.txt table of the proteomics analysis of pooled soleus type I and type IIa muscle fiber, related to Figure 2b. S3_protein groups_ident: Protein groups output table for proteins identified in type I and IIa fibers, related to Figure 2b. S3_protein groups_quant: Protein groups output table for type I and IIa quantification, related to Figure 2b. S3 _1DannotEnrich: 1D protein annotation of proteins identified in soleus type I and IIa fibers, related to Fig.ure 2c. S3_TMEM_IHC: Quantification of TMEM65 signal intensities on soleus and EDL cross-sections, related to Suppl. Figureure 2E-I. S3_CSP1_IHC: Quantification of CPS1 signal intensities on soleus cross-sections related to Figure 2d-e. S3_protein groups_MTNorm: Protein groups output table of type I and IIa quantification with OXPHOS-normalized mitochondrial protein abundances, related to Suppl. Figureure3 A-B.
DOI: 10.6084/m9.figshare.12021945
title: Additional file 1 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 1: Table S1. Codes and description of the studied samples. The same codes were used for bacterial and fungal communities.
DOI: 10.6084/m9.figshare.12021948.v1
title: Additional file 9 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 9 : Table S4: Analysis of type IIb fibers from the EDL, TA, and Gast. S4_Summary: MaxQuant summary.txt table of the proteomics analysis in pooled type IIb muscle fibers of the EDL, GAST, and TA, related to Fig.ure 3a. S4_protein groups_ident: Protein groups output table of identified proteins in type IIb fibers of the EDL, TA, and GAST, related to Fig.ure 3a. S4_protein groups_quant: Protein groups output table of quantified proteins in type IIb fibers of the EDL, TA, and GAST, related to Figure 3a. S4_Fisher: Summary of Fisher’s exact tests of type IIb fibers, related to Figure 3b. S4_IHC: Quantification of TPM1, DES and TTN signal intensities on soleus cross-sections related to Figure 3d-e and Suppl. Figure 3A-D
DOI: 10.6084/m9.figshare.12021945.v1
title: Additional file 1 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 1: Table S1. Codes and description of the studied samples. The same codes were used for bacterial and fungal communities.
DOI: 10.6084/m9.figshare.12021933
title: Additional file 7 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 7 : Table S2: Data for short LC-MS gradients related to Suppl. Figure 1. S2_AbsProtCopyNr: Absolute protein copy numbers per muscle fiber nucleus either calculated using the Proteomics Dynamic Range Standard (UPS2) kit or the proteomic ruler approach, related to Suppl. Figure 1A-B. S2_Identifications-1-7: Peptide and protein groups output table of different LC-MS gradients measured with the Easy nLC II-LTQ-Orbitrap Discovery system, related to Suppl. Figure 1C – E. S2_proteingroups_CAPvsnLC: Protein groups output table of single fiber ProFiT runs using the Easy nLC II - LTQ Orbitrap and capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1F. S2_peptides_CAPvsnLC: Peptide output table of single fiber ProFiT runs using the Easy nLC II - LTQ Orbitrap and capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1G. S2_CarryOver: List of log2 LFQ intensities of short gradients with six muscle fibers and blank runs to test for potential carryover, related to Suppl. Figure 1H. S2_Top5MyHCPeptides: List of MyHC peptides analyzed with ProFit with its mass, retention time and peptide scores measured on an Easy nLC II - LTQ Orbitrap or a capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1I-J
DOI: 10.6084/m9.figshare.12021933.v1
title: Additional file 7 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 7 : Table S2: Data for short LC-MS gradients related to Suppl. Figure 1. S2_AbsProtCopyNr: Absolute protein copy numbers per muscle fiber nucleus either calculated using the Proteomics Dynamic Range Standard (UPS2) kit or the proteomic ruler approach, related to Suppl. Figure 1A-B. S2_Identifications-1-7: Peptide and protein groups output table of different LC-MS gradients measured with the Easy nLC II-LTQ-Orbitrap Discovery system, related to Suppl. Figure 1C – E. S2_proteingroups_CAPvsnLC: Protein groups output table of single fiber ProFiT runs using the Easy nLC II - LTQ Orbitrap and capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1F. S2_peptides_CAPvsnLC: Peptide output table of single fiber ProFiT runs using the Easy nLC II - LTQ Orbitrap and capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1G. S2_CarryOver: List of log2 LFQ intensities of short gradients with six muscle fibers and blank runs to test for potential carryover, related to Suppl. Figure 1H. S2_Top5MyHCPeptides: List of MyHC peptides analyzed with ProFit with its mass, retention time and peptide scores measured on an Easy nLC II - LTQ Orbitrap or a capillary LC/quadrupole Orbitrap system, related to Suppl. Figure 1I-J
DOI: 10.6084/m9.figshare.12021927
title: Additional file 6 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 6 : Table S1: Data for comparison of whole muscle and single fiber proteomes related to Fig.ure 1. S1_proteingroups.txt: Protein groups output table of whole muscle and single muscle fiber (n = 48) lysates for Venn diagram representation. S1_ident_protgroups: Number of identified proteingroups in 1x, 5x, 10x, 20x, 48x and 96x fibers as well as whole muscle lysate, related to Fig.ure 1d. S1_Proteinranking: Ranking of protein intensities, identified in muscle fibers (n = 48) and whole muscle lysates, related to Figure 1c. S1_GO-enrichment: GO-annotation enrichment of protein groups only identified in whole muscle lysates or single muscle fibers (48x), related to Figure 1a
DOI: 10.6084/m9.figshare.12021927.v1
title: Additional file 6 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 6 : Table S1: Data for comparison of whole muscle and single fiber proteomes related to Fig.ure 1. S1_proteingroups.txt: Protein groups output table of whole muscle and single muscle fiber (n = 48) lysates for Venn diagram representation. S1_ident_protgroups: Number of identified proteingroups in 1x, 5x, 10x, 20x, 48x and 96x fibers as well as whole muscle lysate, related to Fig.ure 1d. S1_Proteinranking: Ranking of protein intensities, identified in muscle fibers (n = 48) and whole muscle lysates, related to Figure 1c. S1_GO-enrichment: GO-annotation enrichment of protein groups only identified in whole muscle lysates or single muscle fibers (48x), related to Figure 1a
DOI: 10.6084/m9.figshare.12021903
title: Additional file 10 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 10: Table S5. Core mycobiome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars upon Verticillium dahliae inoculation. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021903.v1
title: Additional file 10 of Linking belowground microbial network changes to different tolerance level towards Verticillium wilt of olive

description: Additional file 10: Table S5. Core mycobiome of 'Frantoio' (yellow cells) and 'Picual' (green cells) cultivars upon Verticillium dahliae inoculation. The shared core bacteriome is shown with light brown cells. Genera in red color belong to the RNA (functional community) core. In bold type letters main genera with relative abundance &gt; 1% (sum of both cultivars).
DOI: 10.6084/m9.figshare.12021891
title: Additional file 10 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 10 : Table S5: Analysis of Lys-6 incorporation rates into muscle fiber types. S5_ProFiT: Protein groups output table of muscle fibers analyzed with ProFiT, related to Figure 4b-c. S5_ProtIncorp_Ttest:T-test of Lys-6 incorporation rates for proteins in different muscle fiber types analyzed with ProFiT, related to Figure 4b. S5_MyHCIncorp_TtestT-test of Lys-6 incorporation rates into MyHC isoforms in different muscle fiber types analyzed with ProFiT, related to Figure 4c. S5_protein groups_HL-ratios: Protein group output table of H/L ratios (Lys6/Lys0) in pooled muscle fiber types, related to Figure 4d-l. S5_protein groups_IncorpRates: Protein group output table of Lys-6 incorporation rates in pooled muscle fiber types, related to Figure 4d-l. S5_Complex I_Testing:T-test of Lys-6 incorporation rates into respiratory chain complex I modules, related to Figure 4l. S5_HL ratio Liver: protein groups output table of H/L ratios of Lys-6 to Lys-0 in liver tissue, related to suppl. Figure 4B. S5_protein groups_Lys6_Tissue: Protein groups output table of Lys-6 incorporation rates in different mouse tissues, related to Figure 4m. S5_T-test_ComplexIV:T-test of Lys-6 incorporation rates into respiratory chain complex IV subunits, related to Figure 4m
DOI: 10.6084/m9.figshare.12021894
title: Additional file 11 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 11 : Table S6: Muscle fiber type-specific analysis of phosphosites. S6_Phospho(STY)_Ident: Phospho (STY) sites output table of identified phosphorylation sites in soleus type I and type IIa fibers, related to Figure 5b-f. S6_Phospho(STY)_Quant: Phospho (STY) sites output table of quantified phosphorylation sites in soleus type I and type IIa fibers, related to Figure 5b-f. S6_proteingroups_Ident: Fiber type-specific phosphorylation patterns on the giant protein titin (TTN), related to Figure 5f. S6_proteingroups_Quant: Protein groups output table of protein intensities in soleus type I and IIa fibers, related to Figure 5c-e
DOI: 10.6084/m9.figshare.12021894.v1
title: Additional file 11 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 11 : Table S6: Muscle fiber type-specific analysis of phosphosites. S6_Phospho(STY)_Ident: Phospho (STY) sites output table of identified phosphorylation sites in soleus type I and type IIa fibers, related to Figure 5b-f. S6_Phospho(STY)_Quant: Phospho (STY) sites output table of quantified phosphorylation sites in soleus type I and type IIa fibers, related to Figure 5b-f. S6_proteingroups_Ident: Fiber type-specific phosphorylation patterns on the giant protein titin (TTN), related to Figure 5f. S6_proteingroups_Quant: Protein groups output table of protein intensities in soleus type I and IIa fibers, related to Figure 5c-e
DOI: 10.6084/m9.figshare.12021876
title: Additional file 8 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 8. Genes used for methanogenic pathway reconstructions in five archaeal MAGs and their regulation towards external hydrogen.
DOI: 10.6084/m9.figshare.12021891.v1
title: Additional file 10 of High-throughput proteomics fiber typing (ProFiT) for comprehensive characterization of single skeletal muscle fibers

description: Additional file 10 : Table S5: Analysis of Lys-6 incorporation rates into muscle fiber types. S5_ProFiT: Protein groups output table of muscle fibers analyzed with ProFiT, related to Figure 4b-c. S5_ProtIncorp_Ttest:T-test of Lys-6 incorporation rates for proteins in different muscle fiber types analyzed with ProFiT, related to Figure 4b. S5_MyHCIncorp_TtestT-test of Lys-6 incorporation rates into MyHC isoforms in different muscle fiber types analyzed with ProFiT, related to Figure 4c. S5_protein groups_HL-ratios: Protein group output table of H/L ratios (Lys6/Lys0) in pooled muscle fiber types, related to Figure 4d-l. S5_protein groups_IncorpRates: Protein group output table of Lys-6 incorporation rates in pooled muscle fiber types, related to Figure 4d-l. S5_Complex I_Testing:T-test of Lys-6 incorporation rates into respiratory chain complex I modules, related to Figure 4l. S5_HL ratio Liver: protein groups output table of H/L ratios of Lys-6 to Lys-0 in liver tissue, related to suppl. Figure 4B. S5_protein groups_Lys6_Tissue: Protein groups output table of Lys-6 incorporation rates in different mouse tissues, related to Figure 4m. S5_T-test_ComplexIV:T-test of Lys-6 incorporation rates into respiratory chain complex IV subunits, related to Figure 4m
DOI: 10.6084/m9.figshare.12021870
title: Additional file 7 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 7. The expression level of acetate kinase, acyl-CoA synthetase and formyltetrahydrofolate synthetase genes.
DOI: 10.6084/m9.figshare.12021876.v1
title: Additional file 8 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 8. Genes used for methanogenic pathway reconstructions in five archaeal MAGs and their regulation towards external hydrogen.
DOI: 10.6084/m9.figshare.12021870.v1
title: Additional file 7 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 7. The expression level of acetate kinase, acyl-CoA synthetase and formyltetrahydrofolate synthetase genes.
DOI: 10.6084/m9.figshare.12021864
title: Additional file 6 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 6. The correspondence among methane yield, expression of mrcA gene, overall archaeal relative abundance and activity.
DOI: 10.6084/m9.figshare.12021858
title: Additional file 5 of Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

description: Additional file 5. The average RPKM and relative activity of each MAG in 9 samples.