cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.4001454
title: Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific

description: Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on <em>Pocillopora damicornis</em> sensu stricto (or <em>Pocillopora </em>PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. <em>Pocillopora </em>PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region. This dataset contains the microsatellite genotypes analysed (458 <em>Pocillopora</em> PSH04 colonies × 13 loci).
description: {"references": ["Oury N., G\u00e9lin P. and Magalon H. (2020) Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific. Marine Biology. doi: 10.1007/s00227-020-03757-z"]}
DOI: 10.6084/m9.figshare.11364104
title: MOESM16 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 16. Unique genes list. For each fungal genome, a list of the protein coding genes that were not found in the other four fungi, their annotations and expression values.
DOI: 10.6084/m9.figshare.11364110.v1
title: MOESM5 of Visit-to-visit variability of glycemia and vascular complications: the Hoorn Diabetes Care System cohort

description: Additional file 5: Figure S3. Characterization of individuals based on their HbA1c-CV. Unadjusted outcome against the five quintiles with the fifth quintile being the group with the highest FG-CV against (a) sex (% males) (b) age at diagnosis (c) BMI (d) % smokers (e) total cholesterol levels (f) HDL-C levels (g) triglycerides levels (h) DBP (i) SBP (j) eGFR. Lines represent loess smoothed levels over 5-year average values of outcomes.
DOI: 10.6084/m9.figshare.11364104.v1
title: MOESM16 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 16. Unique genes list. For each fungal genome, a list of the protein coding genes that were not found in the other four fungi, their annotations and expression values.
DOI: 10.5281/zenodo.4001453
title: Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific

description: Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on <em>Pocillopora damicornis</em> sensu stricto (or <em>Pocillopora </em>PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. <em>Pocillopora </em>PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region. This dataset contains the microsatellite genotypes analysed (458 <em>Pocillopora</em> PSH04 colonies × 13 loci).
description: {"references": ["Oury N., G\u00e9lin P. and Magalon H. (2020) Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific. Marine Biology. doi: 10.1007/s00227-020-03757-z"]}
DOI: 10.6084/m9.figshare.11364092
title: MOESM3 of Visit-to-visit variability of glycemia and vascular complications: the Hoorn Diabetes Care System cohort

description: Additional file 3: Table S2. Characteristics of individuals across HbA1c-CV quintiles in the first interval.
DOI: 10.6084/m9.figshare.11364086
title: MOESM14 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 14. Cliques report with protein abundances. Data summary that was obtained from Additional file 1, and Additional file 12 (‘selected pathways’ tab). These data were used to generate the heatmaps in Fig. 3 and Additional file 15.
DOI: 10.6084/m9.figshare.11364092.v1
title: MOESM3 of Visit-to-visit variability of glycemia and vascular complications: the Hoorn Diabetes Care System cohort

description: Additional file 3: Table S2. Characteristics of individuals across HbA1c-CV quintiles in the first interval.
DOI: 10.6084/m9.figshare.11364086.v1
title: MOESM14 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 14. Cliques report with protein abundances. Data summary that was obtained from Additional file 1, and Additional file 12 (‘selected pathways’ tab). These data were used to generate the heatmaps in Fig. 3 and Additional file 15.
DOI: 10.6084/m9.figshare.11364071
title: MOESM12 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 12. Protein expression among homologs in all fungi. Annotated proteins and their expression (fold change under each culture condition compared to sucrose control). The tab ‘common pathways’ includes proteins found in all five fungal genomes. ‘Selected pathways’ includes proteins with the most interesting changes in expression. ‘Not common pathways’ lists proteins with expression changes that were not present in all five fungal genomes.
DOI: 10.6084/m9.figshare.11364071.v1
title: MOESM12 of Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

description: Additional file 12. Protein expression among homologs in all fungi. Annotated proteins and their expression (fold change under each culture condition compared to sucrose control). The tab ‘common pathways’ includes proteins found in all five fungal genomes. ‘Selected pathways’ includes proteins with the most interesting changes in expression. ‘Not common pathways’ lists proteins with expression changes that were not present in all five fungal genomes.
DOI: 10.6084/m9.figshare.11364041
title: MOESM6 of The genomic diversification of grapevine clones

description: Additional file 6: Bioinformatic pipeline for SNV, INDEL, and SV calling.
DOI: 10.6084/m9.figshare.11364035
title: MOESM5 of The genomic diversification of grapevine clones

description: Additional file 5: Settings and data used for Zin03 genome assembly, annotation, variant calling, and validation procedure.
DOI: 10.6084/m9.figshare.11364041.v1
title: MOESM6 of The genomic diversification of grapevine clones

description: Additional file 6: Bioinformatic pipeline for SNV, INDEL, and SV calling.
DOI: 10.6084/m9.figshare.11364029
title: MOESM4 of The genomic diversification of grapevine clones

description: Additional file 4: Table S1. a summary of the alignment of Illumina libraries to Zin03, Table S2. a summary of variants relative to the Zinfandel primary assembly, and Table S3. a summary of the SnpEff analysis of variants, with mean values Â± SEM shown.
DOI: 10.6084/m9.figshare.11364035.v1
title: MOESM5 of The genomic diversification of grapevine clones

description: Additional file 5: Settings and data used for Zin03 genome assembly, annotation, variant calling, and validation procedure.
DOI: 10.6084/m9.figshare.11364020
title: MOESM3 of The genomic diversification of grapevine clones

description: Additional file 3: Results of technical (Table S1, Figure S1) and Sanger sequencing (Table S2) validation of variant calls by GATK.
DOI: 10.6084/m9.figshare.11364029.v1
title: MOESM4 of The genomic diversification of grapevine clones

description: Additional file 4: Table S1. a summary of the alignment of Illumina libraries to Zin03, Table S2. a summary of variants relative to the Zinfandel primary assembly, and Table S3. a summary of the SnpEff analysis of variants, with mean values Â± SEM shown.
DOI: 10.6084/m9.figshare.11364005
title: MOESM2 of The genomic diversification of grapevine clones

description: Additional file 2: Zinfandel genes intersecting structural variations identified between haplotypes (4459) with associated Gene Ontology categories.
DOI: 10.6084/m9.figshare.11364020.v1
title: MOESM3 of The genomic diversification of grapevine clones

description: Additional file 3: Results of technical (Table S1, Figure S1) and Sanger sequencing (Table S2) validation of variant calls by GATK.
DOI: 10.6084/m9.figshare.11364005.v1
title: MOESM2 of The genomic diversification of grapevine clones

description: Additional file 2: Zinfandel genes intersecting structural variations identified between haplotypes (4459) with associated Gene Ontology categories.
DOI: 10.6084/m9.figshare.11363966
title: MOESM1 of The efficacy of lyticase and β-glucosidase enzymes on biofilm degradation of Pseudomonas aeruginosa strains with different gene profiles

description: Additional file 1. Supplementary data.
DOI: 10.6084/m9.figshare.11363966.v1
title: MOESM1 of The efficacy of lyticase and β-glucosidase enzymes on biofilm degradation of Pseudomonas aeruginosa strains with different gene profiles

description: Additional file 1. Supplementary data.
DOI: 10.6084/m9.figshare.11363951
title: MOESM2 of From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

description: Additional file 2: Table S1 Description of the flower bud samples used for RNA-seq and RT-qPCR. Table S2. ‘Garnet’ differentially expressed genes and their assigned clusters. Table S3 Transcription factors with enriched targets in the different clusters. Table S4 Enrichments in gene ontology terms in the transcription factors targets. Table S5 Contribution of differentially expressed genes to the PCA dimensions 1 and 2. Table S6 RNA-seq mapped reads and gene count information. Table S7 Primers used for RT-qPCR.
DOI: 10.6084/m9.figshare.11363951.v1
title: MOESM2 of From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy

description: Additional file 2: Table S1 Description of the flower bud samples used for RNA-seq and RT-qPCR. Table S2. ‘Garnet’ differentially expressed genes and their assigned clusters. Table S3 Transcription factors with enriched targets in the different clusters. Table S4 Enrichments in gene ontology terms in the transcription factors targets. Table S5 Contribution of differentially expressed genes to the PCA dimensions 1 and 2. Table S6 RNA-seq mapped reads and gene count information. Table S7 Primers used for RT-qPCR.
DOI: 10.13016/tlmm-vtrd
title: Data from: Neural speech restoration at the cocktail party

description: This dataset is incremental to http://hdl.handle.net/1903/21109 and contains independent component analysis (ICA) used for additional preprocessing, gammatone stimulus representations, and STRFs that were used to generate the figures. The ICA is stored in MNE *-ica.fif files which can be opened with MNE-Python (http://mne.tools). Gammatone spectrograms and STRFs are stored in Python pickle files which require the Eelbrain library to be opened (http://eelbrain.readthedocs.io).
description: Data from the article titled: Neural speech restoration at the cocktail party: Auditory cortex recovers masked speech of both attended and ignored speakers.
DOI: 10.6084/m9.figshare.11363855
title: Unique responses of three highly salt-tolerant wild <i>Vigna</i> species against salt stress

description: The genus <i>Vigna</i> contains important crops such as cowpea and mungbean. Wild <i>Vigna</i> showing higher salt tolerance than <i>Vigna</i> crops were screened and their tolerance mechanisms are discussed. Primary screening using 7 <i>Vigna</i> crops and 23 wild <i>Vigna</i> under 300 mM NaCl selected <i>V. luteola, V. marina</i> and <i>V. vexillata</i>. A study under different salt concentrations revealed the highest survival ability of <i>V. marina</i>. Diversity of salt tolerance in each species was revealed using a total of 230 accessions. Growth and physiological responses under 150 mM NaCl were then compared using two selected accessions from each species. The pattern of Na<sup>+</sup> accumulation in roots, stems and leaves suggested that <i>V. vexillata</i> (V1) and <i>V. luteola</i> (L8, L9) are ‘Na<sup>+</sup> excluder’ type, while <i>V. marina</i> (M1, M4) is ‘Na<sup>+</sup> includer’ type. <i>V. luteola</i> (L8, L9) showed the highest dry matter production under control condition and well-maintained shoot dry weight under salt stress. Interestingly, <i>V. luteola</i> (L9) accumulated the highest Na<sup>+</sup> in roots (3000 μM g<sup>−1</sup>) and increased root dry weight under salt stress, which might work as Na<sup>+</sup> reservoir restricting Na<sup>+</sup> transition to the leaves, leading to the increased photosynthetic rate. <i>V. luteola</i> has great potential in areas where moderate salt damage occurs. <i>V. marina</i> (M1, M4) accumulated Na<sup>+</sup> at high level in roots, stem, and leaves. Under salt stress, they increased stomatal conductance, transpiration rate, and photosynthetic rate, which suggested the adaptational regulation of aquaporin gene expression. <i>V. marina</i> will be useful as food, pasture and phytoremediation legumes in highly salt-damaged areas.
DOI: 10.6084/m9.figshare.11363885
title: MOESM1 of Analysis of the Health Product Profile Directory — a new tool to inform priority-setting in global public health

description: Additional file 1. Download of data contained in the Health Product Profile Directory, 5 May 2019.
DOI: 10.6084/m9.figshare.11363852
title: EDGAR temporal profiles (r1)

description: The file 'EDGAR_temporal_profiles_r1.xls' contains the EDGAR temporal profiles developed in this work to disaggregate annual emissions into monthly data.
DOI: 10.6084/m9.figshare.11363855.v1
title: Unique responses of three highly salt-tolerant wild <i>Vigna</i> species against salt stress

description: The genus <i>Vigna</i> contains important crops such as cowpea and mungbean. Wild <i>Vigna</i> showing higher salt tolerance than <i>Vigna</i> crops were screened and their tolerance mechanisms are discussed. Primary screening using 7 <i>Vigna</i> crops and 23 wild <i>Vigna</i> under 300 mM NaCl selected <i>V. luteola, V. marina</i> and <i>V. vexillata</i>. A study under different salt concentrations revealed the highest survival ability of <i>V. marina</i>. Diversity of salt tolerance in each species was revealed using a total of 230 accessions. Growth and physiological responses under 150 mM NaCl were then compared using two selected accessions from each species. The pattern of Na<sup>+</sup> accumulation in roots, stems and leaves suggested that <i>V. vexillata</i> (V1) and <i>V. luteola</i> (L8, L9) are ‘Na<sup>+</sup> excluder’ type, while <i>V. marina</i> (M1, M4) is ‘Na<sup>+</sup> includer’ type. <i>V. luteola</i> (L8, L9) showed the highest dry matter production under control condition and well-maintained shoot dry weight under salt stress. Interestingly, <i>V. luteola</i> (L9) accumulated the highest Na<sup>+</sup> in roots (3000 μM g<sup>−1</sup>) and increased root dry weight under salt stress, which might work as Na<sup>+</sup> reservoir restricting Na<sup>+</sup> transition to the leaves, leading to the increased photosynthetic rate. <i>V. luteola</i> has great potential in areas where moderate salt damage occurs. <i>V. marina</i> (M1, M4) accumulated Na<sup>+</sup> at high level in roots, stem, and leaves. Under salt stress, they increased stomatal conductance, transpiration rate, and photosynthetic rate, which suggested the adaptational regulation of aquaporin gene expression. <i>V. marina</i> will be useful as food, pasture and phytoremediation legumes in highly salt-damaged areas.
DOI: 10.6084/m9.figshare.11363885.v1
title: MOESM1 of Analysis of the Health Product Profile Directory — a new tool to inform priority-setting in global public health

description: Additional file 1. Download of data contained in the Health Product Profile Directory, 5 May 2019.
DOI: 10.6084/m9.figshare.11363852.v1
title: EDGAR temporal profiles (r1)

description: The file 'EDGAR_temporal_profiles_r1.xls' contains the EDGAR temporal profiles developed in this work to disaggregate annual emissions into monthly data.
DOI: 10.6084/m9.figshare.11363837
title: Python and sql scripts to disaggregate annual emissions into high time resolution data

description: The file named 'Python_sql_codes_to_implement_temp_profiles.zip' contains the Python codes and some sql scripts used to apply temporal profiles to disaggregate EDGAR annual emissions into higher time resolution data. These scripts were applied to the EDGAR database but can adapted to any other emission database or model.
DOI: 10.6084/m9.figshare.11363840
title: R codes to calculate agricultural profiles

description: The file named 'R_codes_for_agriculture_temp_profiles.zip' includes the scripts developed in the software R used to calculate the monthly profiles for the agricultural sector based on the IRRI Rice Atlas.
DOI: 10.6084/m9.figshare.11363834
title: IDL codes to compute heating degree days

description: The file named 'IDL_codes_to_process_ERA5_data_for_HDD.zip' contains the IDL scripts to compute heating degree days based on the ERA5 atmospheric reanalysis of global climate produced by ECMWF.
DOI: 10.6084/m9.figshare.11363834.v1
title: IDL codes to compute heating degree days

description: The file named 'IDL_codes_to_process_ERA5_data_for_HDD.zip' contains the IDL scripts to compute heating degree days based on the ERA5 atmospheric reanalysis of global climate produced by ECMWF.
DOI: 10.6084/m9.figshare.11363837.v1
title: Python and sql scripts to disaggregate annual emissions into high time resolution data

description: The file named 'Python_sql_codes_to_implement_temp_profiles.zip' contains the Python codes and some sql scripts used to apply temporal profiles to disaggregate EDGAR annual emissions into higher time resolution data. These scripts were applied to the EDGAR database but can adapted to any other emission database or model.
DOI: 10.6084/m9.figshare.11363840.v1
title: R codes to calculate agricultural profiles

description: The file named 'R_codes_for_agriculture_temp_profiles.zip' includes the scripts developed in the software R used to calculate the monthly profiles for the agricultural sector based on the IRRI Rice Atlas.
DOI: 10.6084/m9.figshare.11363738
title: N2 fixation rates, primary production and other oceanographic parameters in the Bay of Bengal

description: N2 fixation rates, primary production and other oceanographic parameters in the Bay of Bengal
DOI: 10.6084/m9.figshare.11363777
title: Summarising biometrics from the SAFRING database for southern African birds

description: Biometrics form a key characteristic of a species. Here, we provide a summary of biometrics held by the South African Bird Ringing Scheme (SAFRING), which was initiated in 1948, including measures of mass and lengths of the tarsus, head, culmen, tail and wing. We include all species in southern Africa for which there was sufficient data. Accordingly, we present biometric data for 674 of the 904 southern African bird species. We also investigated whether there were sex-specific differences for each species, and provide summaries for species where values significantly differed between the sexes. We found 376 species with significant sex-specific differences for at least one measure (e.g. mass). Although SAFRING holds data entries for many ringed individuals, a sizeable proportion of the entries was not useable as biometric data. Therefore, in this article, we aim to: 1) present a complete, standardised reference of summarised biometric data for the birds of southern Africa; 2) provide ringers with benchmark values that could guide data-capturing; 3) identify data-deficient species; and 4) highlight the importance of collecting and capturing biometric data carefully and consistently.
DOI: 10.6084/m9.figshare.11363738.v1
title: N2 fixation rates, primary production and other oceanographic parameters in the Bay of Bengal

description: N2 fixation rates, primary production and other oceanographic parameters in the Bay of Bengal
DOI: 10.6084/m9.figshare.11363777.v2
title: Summarising biometrics from the SAFRING database for southern African birds

description: Biometrics form a key characteristic of a species. Here, we provide a summary of biometrics held by the South African Bird Ringing Scheme (SAFRING), which was initiated in 1948, including measures of mass and lengths of the tarsus, head, culmen, tail and wing. We include all species in southern Africa for which there was sufficient data. Accordingly, we present biometric data for 674 of the 904 southern African bird species. We also investigated whether there were sex-specific differences for each species, and provide summaries for species where values significantly differed between the sexes. We found 376 species with significant sex-specific differences for at least one measure (e.g. mass). Although SAFRING holds data entries for many ringed individuals, a sizeable proportion of the entries was not useable as biometric data. Therefore, in this article, we aim to: 1) present a complete, standardised reference of summarised biometric data for the birds of southern Africa; 2) provide ringers with benchmark values that could guide data-capturing; 3) identify data-deficient species; and 4) highlight the importance of collecting and capturing biometric data carefully and consistently.