cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.94rjdf
title: Occurrence Download

description: A dataset containing 21450 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Castilla elastica Cerv., Castilla ulei Warb., Helicostylis pedunculata Benoist, Helicostylis tomentosa (Poepp. & Endl.) J.F.Macbr., Maquira calophylla (Poepp. & Endl.) C.C.Berg, Maquira costaricana (Standl.) C.C.Berg, Maquira guianensis Aubl., Naucleopsis caloneura (Huber) Ducke, Naucleopsis guianensis (Mildbr.) C.C.Berg, Naucleopsis krukovii (Standl.) C.C.Berg, Naucleopsis naga Pittier, Naucleopsis ternstroemiiflora (Mildbr.) C.C.Berg, Naucleopsis ulei (Warb.) Ducke, Perebea angustifolia (Poepp. & Endl.) C.C.Berg, Perebea guianensis Aubl., Perebea humilis C.C.Berg, Perebea longepedunculata C.C.Berg, Perebea rubra (Trécul) C.C.Berg, Perebea xanthochyma H.Karst., Poulsenia armata (Miq.) Standl., Pseudolmedia laevigata Trécul, Pseudolmedia laevis (Ruiz & Pav.) J.F.Macbr., Pseudolmedia macrophylla Trécul, Pseudolmedia spuria (Sw.) Griseb.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 {
 "not" : {
 "EstablishmentMeans" : [
 "is one of (MANAGED, INTRODUCED)"
 ]
 }
 },
 "EstablishmentMeans is null"
 ]
 }
 ]
}

 The dataset includes 21450 records from 352 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011678-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26992837
title: Additional file 2 of In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code

description: Additional file 2: Table S1. Glycosomes and glycolysis-related proteins. Table S2. Acidocalcisomes. Table S3. Mitochondrial translocation machinery. Table S4. OXPHOS subunits and ubiquinone synthesis. Table S5. Mitochondrial metabolism. Table S6. Amino acid metabolism. Table S7. Serine-driven 1C, folate, and biopterine metabolism. Table S8. Urea cycle. Table S9. Pyrimidine biosynthesis and purine salvage. Table S10. Synthesis of sugar nucleotides. Table S11. RNA interference. Table S12. Lipid metabolism. Table S13. Mevalonate and sterol synthesis. Table S14. Phospholipids and phospholipases. Table S15. Vitamins and cofactors. Table S16. Heme biosynthesis and iron uptake system.
DOI: 10.6084/m9.figshare.26992843
title: Additional file 2 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.26992852.v1
title: Additional file 5 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 5
DOI: 10.6084/m9.figshare.26992855
title: Additional file 6 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.26992837.v1
title: Additional file 2 of In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code

description: Additional file 2: Table S1. Glycosomes and glycolysis-related proteins. Table S2. Acidocalcisomes. Table S3. Mitochondrial translocation machinery. Table S4. OXPHOS subunits and ubiquinone synthesis. Table S5. Mitochondrial metabolism. Table S6. Amino acid metabolism. Table S7. Serine-driven 1C, folate, and biopterine metabolism. Table S8. Urea cycle. Table S9. Pyrimidine biosynthesis and purine salvage. Table S10. Synthesis of sugar nucleotides. Table S11. RNA interference. Table S12. Lipid metabolism. Table S13. Mevalonate and sterol synthesis. Table S14. Phospholipids and phospholipases. Table S15. Vitamins and cofactors. Table S16. Heme biosynthesis and iron uptake system.
DOI: 10.6084/m9.figshare.26992849.v1
title: Additional file 4 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.26992855.v1
title: Additional file 6 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.26992858.v1
title: Additional file 7 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.26992861
title: Additional file 8 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.26992861.v1
title: Additional file 8 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.26992858
title: Additional file 7 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 7
DOI: 10.6084/m9.figshare.26992879.v1
title: Additional file 1 of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

description: Additional file 1: Supplementary Table 1. All rpS3 groups. Supplementary Table 2. rpS3 gene coverage. Supplementary Table 3. All xoxF sequences identified in the metagenomes. Supplementary Table 4. Whole-rock elemental composition ICP-MS data. Supplementary Table 5. All BGCs (&gt;10kbp) identified in the metagenomes. Supplementary Table 6. All BGCs (&gt;10kbp) from the dereplicated genome set. Supplementary Table 7. EDX data for minerals in Fig. 6.
DOI: 10.6084/m9.figshare.26992879
title: Additional file 1 of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

description: Additional file 1: Supplementary Table 1. All rpS3 groups. Supplementary Table 2. rpS3 gene coverage. Supplementary Table 3. All xoxF sequences identified in the metagenomes. Supplementary Table 4. Whole-rock elemental composition ICP-MS data. Supplementary Table 5. All BGCs (&gt;10kbp) identified in the metagenomes. Supplementary Table 6. All BGCs (&gt;10kbp) from the dereplicated genome set. Supplementary Table 7. EDX data for minerals in Fig. 6.
DOI: 10.6084/m9.figshare.26992882.v1
title: Additional file 2 of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

description: Additional file 2: Supplementary Data 1. Ribosomal protein S3 tree file.
DOI: 10.6084/m9.figshare.26992888
title: Additional file 4 of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

description: Additional file 4: Supplementary Data 2. Multiple alignment of lanmodulin.
DOI: 10.25403/upresearchdata.25213754.v1
title: Newly qualified social workers' readiness in providing services to families and children

description: The goal of the study was to describe and explore newly qualified social workers (NQSW) s’ experiences regarding their work readiness to provide social work services to families and children in the Gauteng province. The research followed a qualitative research approach, and interpretivism paradigm that was underpinned by applied research. The research focused on exploring and describing the experiences of NQSWs readiness to provide services to children and families. An instrumental case study design was employed. The study population involved NQSW who provide services to children and families. Non-probability sampling was used, specifically purposive sampling, where 9 participants for the study were recruited, as this number of participants was found sufficient to reach data saturation. Semi structured interviews were used and guided by the interview schedule, as a data collection method. Thematic analysis was used for data analysis, using an inductive and latent approach for coding.
DOI: 10.6084/m9.figshare.26992882
title: Additional file 2 of Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes

description: Additional file 2: Supplementary Data 1. Ribosomal protein S3 tree file.
DOI: 10.6084/m9.figshare.26992846
title: Additional file 3 of Distinct regulatory networks control toxin gene expression in elapid and viperid snakes

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.26992894.v1
title: Additional file 2 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 2: Supplementary Table 1. Summary metrics and NCBI identifiers for the generated genome (PacBio long-read) and transcriptome (PacBio long-read and Illumina short-read) sequences, and the complete annotation statistics. ^ tRNA pseudogenes are fragments of genes that were identified and not used for annotation. * Genes models that were predicted by but Stringtie no valid ORF was identified by Transdecoder and therefore not used in the annotation.
DOI: 10.6084/m9.figshare.26992897
title: Additional file 3 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 3: Supplementary Table 2. Biomphalaria sudanica orthologues to genes / genomic markers of 18 candidate immune loci that have been identified for their involvement in Schistosoma mansoni immunity in B. glabrata.*The Knight marker, qRS-5.1, and qRS-2.1, truly represent a marker and not a coding gene, hence putative function and mechanism are unknown.
DOI: 10.6084/m9.figshare.26992897.v1
title: Additional file 3 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 3: Supplementary Table 2. Biomphalaria sudanica orthologues to genes / genomic markers of 18 candidate immune loci that have been identified for their involvement in Schistosoma mansoni immunity in B. glabrata.*The Knight marker, qRS-5.1, and qRS-2.1, truly represent a marker and not a coding gene, hence putative function and mechanism are unknown.
DOI: 10.6084/m9.figshare.26992903.v1
title: Additional file 5 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 5: Supplementary Table 4. Complete list showing the genome positions and prediction scores of 919 tRNA genes predicted in the Biomphalaria sudanica genome by tRNAscan-SE 2.0 v2.0.9 [124].
DOI: 10.6084/m9.figshare.26992906
title: Additional file 6 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 6: Supplementary Table 5. Summary table of repeated elements composition of the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992906.v1
title: Additional file 6 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 6: Supplementary Table 5. Summary table of repeated elements composition of the Biomphalaria sudanica genome.
DOI: 10.6084/m9.figshare.26992909
title: Additional file 7 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 7: Supplementary Table 6. Predicted coding genes that overlap with repeated elements. For each one it is specified the contig/scaffold, gene and coordinates, and each overlapping repeated element and the features they compromise: Intron region, 5'UTR, 3'UTR and/or CDS.
DOI: 10.6084/m9.figshare.26992909.v1
title: Additional file 7 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 7: Supplementary Table 6. Predicted coding genes that overlap with repeated elements. For each one it is specified the contig/scaffold, gene and coordinates, and each overlapping repeated element and the features they compromise: Intron region, 5'UTR, 3'UTR and/or CDS.
DOI: 10.6084/m9.figshare.26992912
title: Additional file 8 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 8: Supplementary Table 7. Mitochondrial genome annotation of Biomphalaria sudanica and RNAseq read counts from the Illumina short-read datasets. For each feature, detail is given on the coordinates, encoding strand, source of the annotation and if their boundaries were manually adjusted based on the read mappings. The starting coordinate was selected to be the start of nad5 in order to be consistent with the already published mitochondrial genomes of Biomphalaria [56].
DOI: 10.6084/m9.figshare.26992912.v1
title: Additional file 8 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 8: Supplementary Table 7. Mitochondrial genome annotation of Biomphalaria sudanica and RNAseq read counts from the Illumina short-read datasets. For each feature, detail is given on the coordinates, encoding strand, source of the annotation and if their boundaries were manually adjusted based on the read mappings. The starting coordinate was selected to be the start of nad5 in order to be consistent with the already published mitochondrial genomes of Biomphalaria [56].
DOI: 10.6084/m9.figshare.26992915
title: Additional file 9 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 9: Supplementary Table 8. Summary table of the predicted location signals found in the Biomphalaria sudanica protein coding genes using the programs SignalP v6.0 [62] for the identification of Signal Peptides (SP), TargetP v2.0 [63] for the identification of mitochondrial transit peptide (mTP) and SecretomeP v1.0 [64] for proteins putatively secreted through other pathways. In addition to the total number of trans-membrane domains predicted by DeepTMHMM v1.0.13 [131] and the identified InterPro v5.56-89.0 [52] signals. Each isoform was putatively classified into 4 types: Secreted (SP identified or positive result with SecretomeP and no trans-membrane domains), Mitochondrial Cytoplasmatic (mTP identified and no trans-membrane domains), Membrane (SP identified or positive result with SecretomeP and at least one trans-membrane domain), Mitochondrial Membrane (mTP identified and at least one trans-membrane domain). When either an SP or a mTP was identified, its location and probability is included in the column Location Signal Details.
DOI: 10.6084/m9.figshare.26992915.v1
title: Additional file 9 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 9: Supplementary Table 8. Summary table of the predicted location signals found in the Biomphalaria sudanica protein coding genes using the programs SignalP v6.0 [62] for the identification of Signal Peptides (SP), TargetP v2.0 [63] for the identification of mitochondrial transit peptide (mTP) and SecretomeP v1.0 [64] for proteins putatively secreted through other pathways. In addition to the total number of trans-membrane domains predicted by DeepTMHMM v1.0.13 [131] and the identified InterPro v5.56-89.0 [52] signals. Each isoform was putatively classified into 4 types: Secreted (SP identified or positive result with SecretomeP and no trans-membrane domains), Mitochondrial Cytoplasmatic (mTP identified and no trans-membrane domains), Membrane (SP identified or positive result with SecretomeP and at least one trans-membrane domain), Mitochondrial Membrane (mTP identified and at least one trans-membrane domain). When either an SP or a mTP was identified, its location and probability is included in the column Location Signal Details.
DOI: 10.6084/m9.figshare.26992918
title: Additional file 10 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 10: Supplementary Table 9. Phylogenetic Hierarchical Orthogroups (HOG) estimated by Orthofinder [68]. For each HOG, detail is provided on their ID, the original Orthogroup ID and the node in the gene tree from which the HOG was determined together with the protein ID for the eight genomes analyzed: B. glabrata strain BB02 (GCF_000457365.2 [5]), B. glabrata strain iBS90 (GCA_025434165.1 [6]), B. glabrata strain iM (GCA_025434175.1 [6]), and the species B. pfeifferi (GCA_030265305.1 [8]), B. straminea (GCA_021533235.1 [7]), with the planorbid snail Bulinus truncatus (GCA_021962125.1 [127]) and the Plakobranchidae Elysia marginata (GCA_019649035.1 [128]).
DOI: 10.6084/m9.figshare.26992921
title: Additional file 11 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 11: Supplementary Table 10. Gene Ontology (GO) terms assigned to each Phylogenetic Hierarchical Orthogroups (HOG) by eggNOG-mapper [71, 72].
DOI: 10.6084/m9.figshare.26992921.v1
title: Additional file 11 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 11: Supplementary Table 10. Gene Ontology (GO) terms assigned to each Phylogenetic Hierarchical Orthogroups (HOG) by eggNOG-mapper [71, 72].
DOI: 10.6084/m9.figshare.26992924
title: Additional file 12 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 12: Supplementary Table 11. Enriched gene ontology (GO) terms found in the protein families that significantly expanded or contracted in the CAFE 5 [69] analysis. At each node it is specified the IDs and total count of the Phylogenetic Hierarchical Orthogroups (HOG) identified to be either expanded or contracted, followed by the enrichment results produced by v2.48.0 [73]: the GO terms enriched, the total number of annotated HOGs with each GO terms, how many GO terms were observed, and the total number of GO terms expected given the list size and the p-value.
DOI: 10.6084/m9.figshare.26992924.v1
title: Additional file 12 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 12: Supplementary Table 11. Enriched gene ontology (GO) terms found in the protein families that significantly expanded or contracted in the CAFE 5 [69] analysis. At each node it is specified the IDs and total count of the Phylogenetic Hierarchical Orthogroups (HOG) identified to be either expanded or contracted, followed by the enrichment results produced by v2.48.0 [73]: the GO terms enriched, the total number of annotated HOGs with each GO terms, how many GO terms were observed, and the total number of GO terms expected given the list size and the p-value.
DOI: 10.6084/m9.figshare.26992927.v1
title: Additional file 13 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 13: Supplementary Table 12.Summary of the enriched gene ontology (GO) terms found in the protein families that significantly expanded or contracted in the CAFE 5 [69] analysis. For each group in the REVIGO [74] TreeMap summary (see Supplementary File 5) it is specified their member GO terms ID description, and the semantic similarity measurements calculated by REVIGO: Frequency of the term in the UniProt database (uniport.org/, database as of May 25th 2022), its semantical Uniqueness in the whole list and their Dispensability if the term was nested with another GO term. In the latter case (dispensable terms), the GO term number it is nested with is reported, or displayed as “-” otherwise.
DOI: 10.6084/m9.figshare.26992930
title: Additional file 14 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 14: Supplementary Table 13. Biomphalaria sudanica protein domain location and Signal Peptides (SP) found among the initial candidates identified for the protein families C-type lectin-related protein (CREP), Fibrinogen-related protein (FREP) or galectin-related protein (GREP), determined by the presence of C-type lectin, fibrinogen (FBD) and Galectin like domains, respectively. For each examined protein it is detailed to which of the three families it is considered a candidate for, and the details of each domain and SP, the analysis that identified it, the signature accession, score (e-value or probability depending on the analysis, domain coordinates, InterPro v5.56-89.0 [52] annotation and description (if applicable), and what type of signature it was classified as: C-type lectin like domain, FBD like domain, Galectin like domain, IgSF like domain, other immunoglobulin like domain or a secreted protein. If the protein was utilized in the phylogenetic analysis it is indicated with an “X” in the Final Selection column, and “.” otherwise.
DOI: 10.6084/m9.figshare.26992930.v1
title: Additional file 14 of The genome and transcriptome of the snail Biomphalaria sudanica s.l.: immune gene diversification and highly polymorphic genomic regions in an important African vector of Schistosoma mansoni

description: Additional file 14: Supplementary Table 13. Biomphalaria sudanica protein domain location and Signal Peptides (SP) found among the initial candidates identified for the protein families C-type lectin-related protein (CREP), Fibrinogen-related protein (FREP) or galectin-related protein (GREP), determined by the presence of C-type lectin, fibrinogen (FBD) and Galectin like domains, respectively. For each examined protein it is detailed to which of the three families it is considered a candidate for, and the details of each domain and SP, the analysis that identified it, the signature accession, score (e-value or probability depending on the analysis, domain coordinates, InterPro v5.56-89.0 [52] annotation and description (if applicable), and what type of signature it was classified as: C-type lectin like domain, FBD like domain, Galectin like domain, IgSF like domain, other immunoglobulin like domain or a secreted protein. If the protein was utilized in the phylogenetic analysis it is indicated with an “X” in the Final Selection column, and “.” otherwise.