cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5721796
title: Additional file 1: of TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps

description: Example script for generating linkage maps with TSPmap. (R 2Â kb)
DOI: 10.6084/m9.figshare.5721793
title: Additional file 18: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: phylo_anova.R. Phylogenetic ANOVA and MANOVA Code. This is the phylogenetic ANOVA/MANOVA code we used to test for relationships between dimensions and habitat specializations under different evolutionary models. Has not been extensively tested with other datasets. See code for details. (R 4 kb)
DOI: 10.6084/m9.figshare.5721796.v1
title: Additional file 1: of TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps

description: Example script for generating linkage maps with TSPmap. (R 2Â kb)
DOI: 10.6084/m9.figshare.5721793.v1
title: Additional file 18: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: phylo_anova.R. Phylogenetic ANOVA and MANOVA Code. This is the phylogenetic ANOVA/MANOVA code we used to test for relationships between dimensions and habitat specializations under different evolutionary models. Has not been extensively tested with other datasets. See code for details. (R 4 kb)
DOI: 10.6084/m9.figshare.5721781
title: Additional file 17: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_alignment.phy. The alignment used in maximum likelihood analyses. The alignment used in maximum likelihood analyses from more than 200 aedines in phylip format. (PHY 1606 kb)
DOI: 10.6084/m9.figshare.5721781.v1
title: Additional file 17: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_alignment.phy. The alignment used in maximum likelihood analyses. The alignment used in maximum likelihood analyses from more than 200 aedines in phylip format. (PHY 1606 kb)
DOI: 10.6084/m9.figshare.5721769
title: MOESM1 of A 3D subject-specific model of the spinal subarachnoid space with anatomically realistic ventral and dorsal spinal cord nerve rootlets

description: Additional file 1. 3D computer aided design files for the spinal cord, dura and nerve roots in .OBJ and .STL file format. Summary of geometric and hydrodynamic results for the spinal cord, dura and nerve roots in .XLSX format.
DOI: 10.6084/m9.figshare.5721769.v1
title: MOESM1 of A 3D subject-specific model of the spinal subarachnoid space with anatomically realistic ventral and dorsal spinal cord nerve rootlets

description: Additional file 1. 3D computer aided design files for the spinal cord, dura and nerve roots in .OBJ and .STL file format. Summary of geometric and hydrodynamic results for the spinal cord, dura and nerve roots in .XLSX format.
DOI: 10.6084/m9.figshare.5721766
title: Additional file 16: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_ml_3ormore.nwk. Newick file for the maximum likelihood phylogeny of the Aedini generated from taxa with three or more markers. The maximum likelihood phylogeny generated in this study for taxa with three or more markers, representing taxa for which we have high confidence in sequence identity, in newick format. (NWK 7 kb)
DOI: 10.6084/m9.figshare.5721766.v1
title: Additional file 16: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_ml_3ormore.nwk. Newick file for the maximum likelihood phylogeny of the Aedini generated from taxa with three or more markers. The maximum likelihood phylogeny generated in this study for taxa with three or more markers, representing taxa for which we have high confidence in sequence identity, in newick format. (NWK 7 kb)
DOI: 10.6084/m9.figshare.5721751
title: Additional file 15: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_calibrated.nwk. Newick file for the calibrated phylogeny of the Aedini. The maximum likelihood phylogeny of the Aedini was rendered ultrametric and calibrated for usage in comparative analyses, and presented here in newick format. (NWK 14 kb)
DOI: 10.6084/m9.figshare.5721751.v1
title: Additional file 15: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_calibrated.nwk. Newick file for the calibrated phylogeny of the Aedini. The maximum likelihood phylogeny of the Aedini was rendered ultrametric and calibrated for usage in comparative analyses, and presented here in newick format. (NWK 14 kb)
DOI: 10.6084/m9.figshare.5721739
title: Additional file 14: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_ml.nwk. Newick file for the maximum likelihood phylogeny of the Aedini. The maximum likelihood phylogeny generated in this study presented in newick format. (NWK 18 kb)
DOI: 10.6084/m9.figshare.5721739.v1
title: Additional file 14: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_ml.nwk. Newick file for the maximum likelihood phylogeny of the Aedini. The maximum likelihood phylogeny generated in this study presented in newick format. (NWK 18 kb)
DOI: 10.6084/m9.figshare.5721718
title: Additional file 13: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_alignment_parts.txt. Partition scheme for the nucleotide alignment. The best partition scheme was determined using PartitionFinder 2, and is listed here. (TXT 389 bytes)
DOI: 10.6084/m9.figshare.5721718.v1
title: Additional file 13: of From ground pools to treeholes: convergent evolution of habitat and phenotype in Aedes mosquitoes

description: soghigian_et_al_alignment_parts.txt. Partition scheme for the nucleotide alignment. The best partition scheme was determined using PartitionFinder 2, and is listed here. (TXT 389 bytes)
DOI: 10.6084/m9.figshare.5721697
title: Additional file 6: Excel S1. of Structural, expression and evolutionary analysis of the non-specific phospholipase C gene family in Gossypium hirsutum

description: Analysis of cis-elements in GhNPC gene promoters (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5721697.v1
title: Additional file 6: Excel S1. of Structural, expression and evolutionary analysis of the non-specific phospholipase C gene family in Gossypium hirsutum

description: Analysis of cis-elements in GhNPC gene promoters (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5721619
title: Additional file 1: of Chemotherapy diminishes lipid storage capacity of adipose tissue in a preclinical model of colon cancer

description: Lipid metabolism proteins differentially expressed in tumour-bearing animals compared to the reference animals. (XLS 43Â kb)
DOI: 10.6084/m9.figshare.5721619.v1
title: Additional file 1: of Chemotherapy diminishes lipid storage capacity of adipose tissue in a preclinical model of colon cancer

description: Lipid metabolism proteins differentially expressed in tumour-bearing animals compared to the reference animals. (XLS 43Â kb)
DOI: 10.6084/m9.figshare.5721595
title: MOESM1 of The impact of antiretroviral therapy on iron homeostasis and inflammation markers in HIV-infected patients with mild anemia

description: Additional file 1. Pearson correlation analysis. Pearson correlation analysis between variables considered in this study (Hb, HIV-related factors, markers of iron homeostasis, of immune activation and inflammation). In bold Pearson correlation coefficients with rho &gt; |0.7| and p values
DOI: 10.6084/m9.figshare.5721595.v1
title: MOESM1 of The impact of antiretroviral therapy on iron homeostasis and inflammation markers in HIV-infected patients with mild anemia

description: Additional file 1. Pearson correlation analysis. Pearson correlation analysis between variables considered in this study (Hb, HIV-related factors, markers of iron homeostasis, of immune activation and inflammation). In bold Pearson correlation coefficients with rho &gt; |0.7| and p values
DOI: 10.6084/m9.figshare.5721562
title: MOESM8 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 8. List of substrate samples and Caenorhabditis isolates collected in the Nouragues National Reserve (2013â 2015).
DOI: 10.6084/m9.figshare.5721562.v1
title: MOESM8 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 8. List of substrate samples and Caenorhabditis isolates collected in the Nouragues National Reserve (2013â 2015).
DOI: 10.6084/m9.figshare.5721535
title: MOESM6 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 6. Micro-habitat colonization and age-dependent incidence: Population census and developmental stages of Caenorhabditis colonizing Clusia flowers. In addition to the Clusia colonization assessment (Fig. 4, Additional file 4), we collected 21 Clusia flower samples containing Caenorhabditis (N=21) and immediately placed them on NGM plates seeded with E. coli to determine number and stages of individuals 5–7 h later.
DOI: 10.6084/m9.figshare.5721535.v1
title: MOESM6 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 6. Micro-habitat colonization and age-dependent incidence: Population census and developmental stages of Caenorhabditis colonizing Clusia flowers. In addition to the Clusia colonization assessment (Fig. 4, Additional file 4), we collected 21 Clusia flower samples containing Caenorhabditis (N=21) and immediately placed them on NGM plates seeded with E. coli to determine number and stages of individuals 5–7 h later.
DOI: 10.6084/m9.figshare.5721529
title: Additional file 4: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S3 (DF+miRNAs model). (XML 163Â kb)
DOI: 10.6084/m9.figshare.5721529.v1
title: Additional file 4: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S3 (DF+miRNAs model). (XML 163Â kb)
DOI: 10.6084/m9.figshare.5721520
title: MOESM5 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 5. Micro-habitat colonization and age-dependent incidence: Caenorhabditis colonization as a function of substrate age (Clusia flowers). To estimate Caenorhabditis colonization as a function of substrate age, we haphazardly collected 70 flower samples of each of three clearly distinct, progressive stages of decay (N=210) at a single locality. Labelling of samples is arbitrary. See also Fig.Â 4.
DOI: 10.6084/m9.figshare.5721520.v1
title: MOESM5 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 5. Micro-habitat colonization and age-dependent incidence: Caenorhabditis colonization as a function of substrate age (Clusia flowers). To estimate Caenorhabditis colonization as a function of substrate age, we haphazardly collected 70 flower samples of each of three clearly distinct, progressive stages of decay (N=210) at a single locality. Labelling of samples is arbitrary. See also Fig.Â 4.
DOI: 10.6084/m9.figshare.5721514
title: Additional file 3: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S2 (DF model). (XML 158Â kb)
DOI: 10.6084/m9.figshare.5721514.v1
title: Additional file 3: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S2 (DF model). (XML 158Â kb)
DOI: 10.6084/m9.figshare.5721505
title: MOESM4 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 4. Micro-habitat colonization and age-dependent incidence: Caenorhabditis colonization of bait samples at spots with high fruit/flower density. We selected five localities near the Parare station and 18 localities near the Inselberg station (Nouragues Natural Reserve). At each locality, we collected five native fruit/flower samples as well as five (5-day old) bait samples within an area of approximately 5m2. See also Additional file 4.
DOI: 10.6084/m9.figshare.5721505.v1
title: MOESM4 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 4. Micro-habitat colonization and age-dependent incidence: Caenorhabditis colonization of bait samples at spots with high fruit/flower density. We selected five localities near the Parare station and 18 localities near the Inselberg station (Nouragues Natural Reserve). At each locality, we collected five native fruit/flower samples as well as five (5-day old) bait samples within an area of approximately 5m2. See also Additional file 4.
DOI: 10.6084/m9.figshare.5721502
title: Additional file 2: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S1 (SF model). (XML 158Â kb)
DOI: 10.6084/m9.figshare.5721502.v1
title: Additional file 2: of Dynamic modeling of folliculogenesis signaling pathways in the presence of miRNAs expression

description: SBML S1 (SF model). (XML 158Â kb)
DOI: 10.6084/m9.figshare.5721484
title: MOESM3 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 3. Micro-habitat colonization and age-dependent incidence: Caenorhabditis colonization of orange bait samples distributed at 72 spots along trail system. At each of the 72 spots (Parare, Nouragues Natural Reserve), three baits were distributed (i.e. subsamples, labelled a, b, c) approximately 1 meter apart from each other. See also Additional file 7.
DOI: 10.6084/m9.figshare.5721472
title: MOESM2 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 2. Substrate incidence of Caenorhabditis (Inselberg site, Nouragues Natural Reserve). Raw and summary data that were used to estimate quantitative differences in the incidence of Caenorhabditis in decaying leaf litter versus rotting fruit. For labelling of intersections of sampled area, see Fig.Â 3.
DOI: 10.6084/m9.figshare.5721472.v1
title: MOESM2 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 2. Substrate incidence of Caenorhabditis (Inselberg site, Nouragues Natural Reserve). Raw and summary data that were used to estimate quantitative differences in the incidence of Caenorhabditis in decaying leaf litter versus rotting fruit. For labelling of intersections of sampled area, see Fig.Â 3.
DOI: 10.6084/m9.figshare.5721454
title: MOESM1 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 1. List of Caenorhabditis isolates and associated sampling information (French Guiana 2013–2015). Summary file listing all 626 Caenorhabditis isolates collected for this study. The column “Type of sampling” refers to the different sampling experiments performed: “Inselberg—substrate incidence” (see Substrate incidence of Caenorhabditis, Fig. 2, Additional file 2);“Bait transect” (see Micro-habitat colonization and age-dependent incidence, Additional file 3), “Bait Fruit/Flower spot“(see Micro-habitat colonization and age-dependent incidence, Additional file 4); “Clusia in-depth sampling“(see Micro-habitat colonization and age-dependent incidence, Fig. 4 and Additional file 5). For complete list of substrate samples collected during opportunistic sampling, including negative samples, see Additional file 8 (all samples collected in Nouragues National Reserve) and Additional file 11 (all samples collected in French Guiana outside of Nouragues National Reserve).
DOI: 10.6084/m9.figshare.5721454.v1
title: MOESM1 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 1. List of Caenorhabditis isolates and associated sampling information (French Guiana 2013–2015). Summary file listing all 626 Caenorhabditis isolates collected for this study. The column “Type of sampling” refers to the different sampling experiments performed: “Inselberg—substrate incidence” (see Substrate incidence of Caenorhabditis, Fig. 2, Additional file 2);“Bait transect” (see Micro-habitat colonization and age-dependent incidence, Additional file 3), “Bait Fruit/Flower spot“(see Micro-habitat colonization and age-dependent incidence, Additional file 4); “Clusia in-depth sampling“(see Micro-habitat colonization and age-dependent incidence, Fig. 4 and Additional file 5). For complete list of substrate samples collected during opportunistic sampling, including negative samples, see Additional file 8 (all samples collected in Nouragues National Reserve) and Additional file 11 (all samples collected in French Guiana outside of Nouragues National Reserve).
DOI: 10.6084/m9.figshare.5721403
title: MOESM1 of Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus

description: Additional file 1: Table S1. Alignment results for transcriptomes of A. robustus, N. californiae, and P. finnis [5]. Shown are # of transcripts (% of transcriptome) in the transcriptome of the fungus listed on the left side successfully aligned to the transcriptome of the fungus listed across the top row using blastn analysis. Table S2. Alignment of scaffoldin amino acid sequences from P. finnis [13] to the transcriptome of C. churrovis by tblastn identifies scaffoldin transcripts. Only results with an alignment E value of 0 are shown. Figure S1. ITS1 Phylogeny of Caecomyces strains shows C. churrovis is significantly different compared to other strains. ITS1 phylogeny of only Caecomyces fungal strains identified a clear separation of C. churrovis from other isolated strains. Figure S2. Full ITS Phylogeny confirms observations about C. churrovis. Phylogeny of ITS1-5.8S-ITS2 regions confirmed the observations that C. churrovis represents a new species in the Caecomyces genus. Figure S3. Catabolic pathways for biomass derived sugars were reconstructed using transcriptome annotations. Enzyme commission numbers and BLAST alignments were used to identify complete sugar pathways present in the transcriptome of C. churrovis. This analysis revealed catabolic routes for glucose, xylose, and fructose, but not mannose, sucrose, and arabinose. Catabolism of Îą-d-galactose was identified using BLAST annotations, but not EC numbers. Figure S4. The secretomes of anaerobic gut fungi display free enzymes and multi enzymes complexes (cellulosomes). The same amount of secreted proteins (determined by BCA assay) of P. finnis (F), N. californiae (G1), A. robustus (S4) and C. churrovis (C) were loaded on Native (A) and SDS (B) PAGE. While the Native PAGE (stained by silver staining) shows strong bands indicative of cellulosomes around 1200Â kDa, the SDS PAGE (stained by SYPRO Ruby) shows many bands in dissociated cellulosome complexes.
DOI: 10.6084/m9.figshare.5721403.v1
title: MOESM1 of Transcriptomic characterization of Caecomyces churrovis: a novel, non-rhizoid-forming lignocellulolytic anaerobic fungus

description: Additional file 1: Table S1. Alignment results for transcriptomes of A. robustus, N. californiae, and P. finnis [5]. Shown are # of transcripts (% of transcriptome) in the transcriptome of the fungus listed on the left side successfully aligned to the transcriptome of the fungus listed across the top row using blastn analysis. Table S2. Alignment of scaffoldin amino acid sequences from P. finnis [13] to the transcriptome of C. churrovis by tblastn identifies scaffoldin transcripts. Only results with an alignment E value of 0 are shown. Figure S1. ITS1 Phylogeny of Caecomyces strains shows C. churrovis is significantly different compared to other strains. ITS1 phylogeny of only Caecomyces fungal strains identified a clear separation of C. churrovis from other isolated strains. Figure S2. Full ITS Phylogeny confirms observations about C. churrovis. Phylogeny of ITS1-5.8S-ITS2 regions confirmed the observations that C. churrovis represents a new species in the Caecomyces genus. Figure S3. Catabolic pathways for biomass derived sugars were reconstructed using transcriptome annotations. Enzyme commission numbers and BLAST alignments were used to identify complete sugar pathways present in the transcriptome of C. churrovis. This analysis revealed catabolic routes for glucose, xylose, and fructose, but not mannose, sucrose, and arabinose. Catabolism of Îą-d-galactose was identified using BLAST annotations, but not EC numbers. Figure S4. The secretomes of anaerobic gut fungi display free enzymes and multi enzymes complexes (cellulosomes). The same amount of secreted proteins (determined by BCA assay) of P. finnis (F), N. californiae (G1), A. robustus (S4) and C. churrovis (C) were loaded on Native (A) and SDS (B) PAGE. While the Native PAGE (stained by silver staining) shows strong bands indicative of cellulosomes around 1200Â kDa, the SDS PAGE (stained by SYPRO Ruby) shows many bands in dissociated cellulosome complexes.
DOI: 10.6084/m9.figshare.5721370
title: MOESM11 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 11. List of substrate samples and Caenorhabditis isolates collected in the coastal regions of French Guiana and in the area of Saul in central French Guiana (2013, 2015) (N=457).
DOI: 10.6084/m9.figshare.5721370.v1
title: MOESM11 of Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes

description: Additional file 11. List of substrate samples and Caenorhabditis isolates collected in the coastal regions of French Guiana and in the area of Saul in central French Guiana (2013, 2015) (N=457).
DOI: 10.6084/m9.figshare.5721364
title: Additional file 2: Table S2. of Proteomics analysis and proteogenomic characterization of different physiopathological human lenses

description: Identification of genetic variants and filtering analysis for the RLSC and CC groups. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5721364.v1
title: Additional file 2: Table S2. of Proteomics analysis and proteogenomic characterization of different physiopathological human lenses

description: Identification of genetic variants and filtering analysis for the RLSC and CC groups. (XLSX 22Â kb)
DOI: 10.6084/m9.figshare.5721358
title: Additional file 6: of Inferring defense-related gene families in Arabidopsis and wheat

description: The number of predicted SNPs for rust resistance in wheat and significant SNPs for 21 defense-related traits in Arabidopsis. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.5721358.v1
title: Additional file 6: of Inferring defense-related gene families in Arabidopsis and wheat

description: The number of predicted SNPs for rust resistance in wheat and significant SNPs for 21 defense-related traits in Arabidopsis. (XLSX 50Â kb)
DOI: 10.6084/m9.figshare.5721349
title: Additional file 1: Table S1. of Proteomics analysis and proteogenomic characterization of different physiopathological human lenses

description: Identification and quantification of total proteins across the RLSC, CC and ARC groups. (XLSX 217Â kb)
DOI: 10.6084/m9.figshare.5721349.v1
title: Additional file 1: Table S1. of Proteomics analysis and proteogenomic characterization of different physiopathological human lenses

description: Identification and quantification of total proteins across the RLSC, CC and ARC groups. (XLSX 217Â kb)