cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7612421.v1
title: Additional file 4: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Figure S4a. Growth curves of Salinispora strains in DMM without sulfur sources. Sulfur source was not included in the medium to examine the ability of strains to store sulfur as was observed in the case of S. tropica CNB-440T by Contador et al. 2015. Sulfur must be supplemented to the medium after the depletion of the accumulated sulfur. All experiments were done in duplicate. Error bars represent standard deviation. Figure S4b. Growth curves of Salinispora strains in DMM without carbon sources. (ZIP 214 kb)
DOI: 10.6084/m9.figshare.7612415
title: Additional file 2: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Excel files with list of reactions, metabolites, and genes included in each reconstruction with corresponding references, associated GPR, E.C. numbers and notes. Mat files for each Salinispora model built in this work. (MAT). (ZIP 1303 kb)
DOI: 10.6084/m9.figshare.7612415.v1
title: Additional file 2: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Excel files with list of reactions, metabolites, and genes included in each reconstruction with corresponding references, associated GPR, E.C. numbers and notes. Mat files for each Salinispora model built in this work. (MAT). (ZIP 1303 kb)
DOI: 10.6084/m9.figshare.7612418.v1
title: Additional file 3: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Details of biomass equations used for Core (worksheet1), Salinispora arenicola (worksheet2) and Salinispora pacifica (worksheet3) models. References are included in the file. (XLSX 67 kb)
DOI: 10.7284/125132
title: Anemometer data collected during research cruise EN588 using a RM Young 05103 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612409
title: Additional file 1: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Table S1. contains ortholog data used to build the Core model (worksheet1). Table S2. contains a heat map of InParanoid scores (worksheet2). Table S3. contains genome and available isolation metadata of Salinispora strains in Core (worksheet3). References used to extract data related to isolation metadata are listed in the table. Table S4. contains list of conserved and not conserved reactions in each mode (worksheet4). Tables S5, S6 and S7. contain reactions associated to essential genes in ST-CNB440, SA-CNH643 and SP-CNR114 models under DMM growth conditions, respectively (worksheet5). Table S8, S9 and S10. contain reactions associated to essential genes in ST-CNB440, SA-CNH643 and SP-CNR114 models under CM growth conditions, respectively (worksheet6). Table S11. contains growth rate ratio between deletion strain and wild type strains for each model under DMM and CM growth conditions (worksheet7). (XLSX 2620 kb)
DOI: 10.6084/m9.figshare.7612409.v1
title: Additional file 1: of Use of genome-scale models to get new insights into the marine actinomycete genus Salinispora

description: Table S1. contains ortholog data used to build the Core model (worksheet1). Table S2. contains a heat map of InParanoid scores (worksheet2). Table S3. contains genome and available isolation metadata of Salinispora strains in Core (worksheet3). References used to extract data related to isolation metadata are listed in the table. Table S4. contains list of conserved and not conserved reactions in each mode (worksheet4). Tables S5, S6 and S7. contain reactions associated to essential genes in ST-CNB440, SA-CNH643 and SP-CNR114 models under DMM growth conditions, respectively (worksheet5). Table S8, S9 and S10. contain reactions associated to essential genes in ST-CNB440, SA-CNH643 and SP-CNR114 models under CM growth conditions, respectively (worksheet6). Table S11. contains growth rate ratio between deletion strain and wild type strains for each model under DMM and CM growth conditions (worksheet7). (XLSX 2620 kb)
DOI: 10.7284/125054
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN588 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612376
title: Additional file 9: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Individual/multi-locus ANOVA and post-hoc mean comparison tests of all associated markers on G BLUPs from the within-year model. *** shows p-value below 0.001, ** between 0.001 and 0.01,* between 0.01 and 0.05, and ‘ns’ indicates non-significant p-values. Significant results are indicated in red. Results with p-values slightly over the 5% significance level (noted as (.)) are indicated in italic. SS = ratio sum of squares (factor/total variation). For ‘multi-locus’ ANOVA, strict-sense heritability estimates h2 are indicated. Comparison of means between groups were performed for individual locus-ANOVA only on phenotypes associated to a unique locus. AA/BB = homozygotes major/minor allele. AB = heterozygous. Letters indicate means differencing significantly between groups (HSD post-hoc test α = 5%). Group sizes are indicated between brackets for HSD post-hoc tests. (XLSX 15 kb)
DOI: 10.7284/125040
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN588 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612376.v1
title: Additional file 9: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Individual/multi-locus ANOVA and post-hoc mean comparison tests of all associated markers on G BLUPs from the within-year model. *** shows p-value below 0.001, ** between 0.001 and 0.01,* between 0.01 and 0.05, and ‘ns’ indicates non-significant p-values. Significant results are indicated in red. Results with p-values slightly over the 5% significance level (noted as (.)) are indicated in italic. SS = ratio sum of squares (factor/total variation). For ‘multi-locus’ ANOVA, strict-sense heritability estimates h2 are indicated. Comparison of means between groups were performed for individual locus-ANOVA only on phenotypes associated to a unique locus. AA/BB = homozygotes major/minor allele. AB = heterozygous. Letters indicate means differencing significantly between groups (HSD post-hoc test α = 5%). Group sizes are indicated between brackets for HSD post-hoc tests. (XLSX 15 kb)
DOI: 10.7284/125041
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN588 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612361
title: Additional file 6: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Gene set enrichment results. For all KEGG, Reactome, and Biocarta gene sets, the proportion of genes that are up- and down-regulated with a FDRâ
DOI: 10.6084/m9.figshare.7612361.v1
title: Additional file 6: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Gene set enrichment results. For all KEGG, Reactome, and Biocarta gene sets, the proportion of genes that are up- and down-regulated with a FDRâ
DOI: 10.7284/125044
title: Gyrocompass data collected during research cruise EN588 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/125045
title: Gyrocompass data collected during research cruise EN588 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612331
title: Additional file 2: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Code and data for the validation dataset analyses. The R code and data used in the colorectal and endometrial/neuroendocrine validation analyses are included in this zip file. Code executes in the directory in which it is placed. (CSV 2 kb)
DOI: 10.7284/125133
title: Meteorological Station data collected during research cruise EN588 using a RM Young 26800 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612325
title: Additional file 13: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Genotypic data of the 63,236 SNPs used for GWAS. MAF: Minor Allele Frequency. Genotypes are coded according to minor allele dose. 0/2 = homozygous major/minor allele. 1 = heterozygous. Markers names are indicated as LG[chromosome number]_[physical position in bp]. (XLSX 17724 kb)
DOI: 10.6084/m9.figshare.7612331.v1
title: Additional file 2: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Code and data for the validation dataset analyses. The R code and data used in the colorectal and endometrial/neuroendocrine validation analyses are included in this zip file. Code executes in the directory in which it is placed. (CSV 2 kb)
DOI: 10.7284/125130
title: Radiometer data collected during research cruise EN588 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612319
title: Additional file 12: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Q ancestral covariates,G, G × Y BLUPs from the multi-year and G BLUPs from the within-year model of phenotypic data in the apricot core-collection. NA: missing values. Q1, Q2 and Q3 covariates are relative to ancestral fractions from (i) Central & Eastern Asia, (ii) Continental Europe and (iii) Irano-Caucasia & Mediterranean Basin, respectively. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.7612325.v1
title: Additional file 13: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Genotypic data of the 63,236 SNPs used for GWAS. MAF: Minor Allele Frequency. Genotypes are coded according to minor allele dose. 0/2 = homozygous major/minor allele. 1 = heterozygous. Markers names are indicated as LG[chromosome number]_[physical position in bp]. (XLSX 17724 kb)
DOI: 10.6084/m9.figshare.7612310
title: Additional file 11: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Information of plant material used in the study: geographical origin, name and number of year repetitions through 2013 to 2016 phenotyping period. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7612319.v1
title: Additional file 12: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Q ancestral covariates,G, G × Y BLUPs from the multi-year and G BLUPs from the within-year model of phenotypic data in the apricot core-collection. NA: missing values. Q1, Q2 and Q3 covariates are relative to ancestral fractions from (i) Central & Eastern Asia, (ii) Continental Europe and (iii) Irano-Caucasia & Mediterranean Basin, respectively. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.7612307
title: Additional file 10: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Marker haplotype composition of the apricot core-collection considering all detected loci. Groups of markers were constructed by considering all detected loci for each phenotype according to G and G × Y BLUPs. For markers, 0,1 and 2 are allelic codes according to minor allele dose. (i) Global G BLUPs from multi-year and within-year models associated with the haplotype. (ii) P-value of association between haplotype and trait. (iii) Number of accessions carrying the haplotype. (iv) Mean (± standard deviation) of associated trait per haplotype. (v) Post-hoc group mean comparison test (HSD α = 5%). HSD post-hoc tests were performed on G BLUPs from the multi-year and within-year models considering all haplotypes classes with n &gt; 2. Green and red cases: extreme group values related to partially resistant and susceptible accessions for each phenotype. For haplotypes carried by only one individual, assessment was performed in comparison with significantly different groups from HSD post-hoc tests. Bold values show outliers in individual haplotypes from the extreme groups (values over the mean ± standard deviation of the extreme significant groups issued from HSD post-hoc tests). (XLSX 19 kb)
DOI: 10.7284/125146
title: Radiometer data collected during research cruise EN588 using a Eppley RAD instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612307.v1
title: Additional file 10: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Marker haplotype composition of the apricot core-collection considering all detected loci. Groups of markers were constructed by considering all detected loci for each phenotype according to G and G × Y BLUPs. For markers, 0,1 and 2 are allelic codes according to minor allele dose. (i) Global G BLUPs from multi-year and within-year models associated with the haplotype. (ii) P-value of association between haplotype and trait. (iii) Number of accessions carrying the haplotype. (iv) Mean (± standard deviation) of associated trait per haplotype. (v) Post-hoc group mean comparison test (HSD α = 5%). HSD post-hoc tests were performed on G BLUPs from the multi-year and within-year models considering all haplotypes classes with n &gt; 2. Green and red cases: extreme group values related to partially resistant and susceptible accessions for each phenotype. For haplotypes carried by only one individual, assessment was performed in comparison with significantly different groups from HSD post-hoc tests. Bold values show outliers in individual haplotypes from the extreme groups (values over the mean ± standard deviation of the extreme significant groups issued from HSD post-hoc tests). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.7612310.v1
title: Additional file 11: of Genome-wide association multi-locus and multi-variate linear mixed models reveal two linked loci with major effects on partial resistance of apricot to bacterial canker

description: Information of plant material used in the study: geographical origin, name and number of year repetitions through 2013 to 2016 phenotyping period. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7612295
title: Additional file 2: of Limited developmental neurotoxicity from neonatal inhalation exposure to diesel exhaust particles in C57BL/6 mice

description: Raw Dataset. (XLSX 1310.72 kb)
DOI: 10.7284/125080
title: TSG (Thermosalinograph) data collected during research cruise EN588 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612295.v1
title: Additional file 2: of Limited developmental neurotoxicity from neonatal inhalation exposure to diesel exhaust particles in C57BL/6 mice

description: Raw Dataset. (XLSX 1310.72 kb)
DOI: 10.6084/m9.figshare.7612292
title: MOESM2 of What is the evidence that ecosystem components or functions have an impact on infectious diseases? A systematic review protocol

description: Additional file 2. Test lists, and number of articles from the test lists retrieved by the bibliographic search.
DOI: 10.6084/m9.figshare.7612283
title: Additional file 12: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Detailed summary of colorectal tumor samples used in algorithm validation studies. For the samples from the colorectal tumor validation dataset, relevant measurements from the NanoString platform, from immunohistochemistry, and from the qPCR MSI assay are provided. (CSV 3 kb)
DOI: 10.7284/125081
title: TSG (Thermosalinograph) data collected during research cruise EN588 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612277
title: Additional file 11: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Detailed summary of endometrial and neuroendocrine tumor samples used in algorithm validation studies. For the samples from the endometrial/neuroendocrine tumor validation dataset, relevant measurements from the NanoString platform, from immunohistochemistry, from qPCR, and from sequencing are provided. (CSV 2 kb)
DOI: 10.6084/m9.figshare.7612292.v1
title: MOESM2 of What is the evidence that ecosystem components or functions have an impact on infectious diseases? A systematic review protocol

description: Additional file 2. Test lists, and number of articles from the test lists retrieved by the bibliographic search.
DOI: 10.6084/m9.figshare.7612277.v1
title: Additional file 11: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Detailed summary of endometrial and neuroendocrine tumor samples used in algorithm validation studies. For the samples from the endometrial/neuroendocrine tumor validation dataset, relevant measurements from the NanoString platform, from immunohistochemistry, from qPCR, and from sequencing are provided. (CSV 2 kb)
DOI: 10.6084/m9.figshare.7612283.v1
title: Additional file 12: of A gene expression assay for simultaneous measurement of microsatellite instability and anti-tumor immune activity

description: Detailed summary of colorectal tumor samples used in algorithm validation studies. For the samples from the colorectal tumor validation dataset, relevant measurements from the NanoString platform, from immunohistochemistry, and from the qPCR MSI assay are provided. (CSV 3 kb)
DOI: 10.7284/125055
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN589 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612265
title: Additional file 2: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S2. Oxygen isotope data used for the interspecies correlation. (XLSX 11.4 kb)
DOI: 10.6084/m9.figshare.7612268
title: Additional file 3: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S3. Oxygen isotope values from the Anno Formation within the study area analyzed at the NIPR and KCC. Corrected Î´18O data represent the values after the interspecies correlation. Average Î´18O values are used for the oxygen isotope stratigraphy. (XLSX 22.6 kb)
DOI: 10.6084/m9.figshare.7612268.v1
title: Additional file 3: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S3. Oxygen isotope values from the Anno Formation within the study area analyzed at the NIPR and KCC. Corrected Î´18O data represent the values after the interspecies correlation. Average Î´18O values are used for the oxygen isotope stratigraphy. (XLSX 22.6 kb)
DOI: 10.6084/m9.figshare.7612259
title: Additional file 1: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S1. Directions of ChRM components and VGPs from the Anno Formation within the study area analyzed at the NMNS and KCC. Corrected declinations were estimated by correcting the back anomalies of declinations through rotation. (XLSX 29.9 kb)
DOI: 10.6084/m9.figshare.7612265.v1
title: Additional file 2: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S2. Oxygen isotope data used for the interspecies correlation. (XLSX 11.4 kb)
DOI: 10.7284/126786
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN590 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7612259.v1
title: Additional file 1: of Pliocene integrated chronostratigraphy from the Anno Formation, Awa Group, Boso Peninsula, central Japan, and its paleoceanographic implications

description: Table S1. Directions of ChRM components and VGPs from the Anno Formation within the study area analyzed at the NMNS and KCC. Corrected declinations were estimated by correcting the back anomalies of declinations through rotation. (XLSX 29.9 kb)
DOI: 10.7284/126793
title: Anemometer data collected during research cruise EN590 using a RM Young 05103 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126794
title: Anemometer data collected during research cruise EN590 using a RM Young 05103 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126787
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN590 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126784
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN590 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126785
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN590 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126788
title: Gyrocompass data collected during research cruise EN590 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/126789
title: Gyrocompass data collected during research cruise EN590 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition