cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.mp5rc5
title: Occurrence Download

description: A dataset containing 1257 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Sympterygia lima (Poeppig, 1835))"
 ]
}

 The dataset includes 1257 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033927-241126133413365/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.c.3618224_d2
title: Additional file 1: Table S1. of The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1

description: Primer information of all markers used in the study for genetic mapping, quantitative real-time PCR, allelic diversity study in natural populations. Table S2. Names, locations and predicted functions of 12 annotated genes in 68.4Â kb region harboring the CsGL3 locus. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3618299_d1
title: Additional file 1: of Prevalence, barriers and factors associated with parental disclosure of their HIV positive status to children: a cross-sectional study in an urban clinic in Kampala, Uganda

description: Disclosure data set. Parental disclosure of their HIV status to children. The data set contains information on all the variables investigated in this study. (XLS 647Â kb)
DOI: 10.6084/m9.figshare.c.3618482_d1
title: Additional file 1: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: FASTA file of LSK composite reference transcriptome. Includes 20,152 contigs containing an open reading frame greater than 100 amino acids. (FASTA 45736 kb)
DOI: 10.6084/m9.figshare.c.3618482_d2
title: Additional file 3: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of 66,909 SNPs that differentiate between LSK and rowi. Includes SNP position within the reference assembly, reference and alternative alleles, if SNP is untranslated or causes synonymous or non-synonymous substitutions, and predicted chicken chromosome synteny. (CSV 2607 kb)
DOI: 10.6084/m9.figshare.c.3618482_d3
title: Additional file 7: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of 3084 transcripts differentially expressed between LSK and rowi. Includes the Î˛-statistic, magnitude of expression difference, and direction of regulation (CSV 100 kb)
DOI: 10.6084/m9.figshare.c.3618482_d4
title: Additional file 4: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of 12,384 SNPs that differentiate among LSK. Includes SNP position within the reference assembly, reference and alternative alleles, if SNP is untranslated or causes synonymous or non-synonymous substitutions, predicted chicken chromosome synteny, and the SNP frequency in each LSK sequenced. (CSV 921 kb)
DOI: 10.6084/m9.figshare.c.3618431_d15
title: Additional file 10 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S10. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 25, h 2=0.8, 0.75 of explained ratio by QTL Ă  genetic background interactions to the total genetic variance, each of 25 QTLs interacted with 10 background markers with 25 replications. (TXT 2078 kb)
DOI: 10.6084/m9.figshare.c.3618482_d5
title: Additional file 2: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of BLAST results and alignment with the North Island brown kiwi genome. Includes the top BLAST hit for each LSK reference contig against NCBI-NR, chicken Ensembl, human Ensembl database, as well as the contig of the kiwi genome assembly to which each transcript mapped and the percent length mapped. (CSV 6520 kb)
DOI: 10.6084/m9.figshare.c.3618482_d6
title: Additional file 6: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of raw expression levels. The number of reads mapped to each LSK reference contig for all kiwi sampled (CSV 1820 kb)
DOI: 10.6084/m9.figshare.c.3618431_d16
title: Additional file 2 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S20. Genotypes for the 51 parental inbreds at the original SNPs. (TXT 186 kb)
DOI: 10.6084/m9.figshare.c.3618482_d7
title: Additional file 8: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of 150 transcripts differentially expressed between male and female kiwi. Includes the Î˛-statistic, magnitude of expression difference, direction of regulation (given in males relative to females), and synteny to the chicken genome (where available) (CSV 5 kb)
DOI: 10.6084/m9.figshare.c.3618431_d17
title: Additional file 5 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S4. Marker name and its position at chromosome for the simulated 10 K SNPs. (XLSX 3133 kb)
DOI: 10.6084/m9.figshare.c.3618482_d8
title: Additional file 5: of Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds

description: Comma separated file (.csv) of 29,313 SNPs that differentiate among rowi. Includes SNP position within the reference assembly, reference and alternative alleles, if SNP is untranslated or causes synonymous or non-synonymous substitutions, predicted chicken chromosome synteny, and the SNP frequency in each rowi sequenced. (CSV 2237 kb)
DOI: 10.6084/m9.figshare.c.3618431_d18
title: Additional file 17 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S18. Phenotypes for the 29 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.5 with 25 replications. (TXT 1208 kb)
DOI: 10.6084/m9.figshare.c.3618431_d19
title: Additional file 4 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S3. Genotypes for the simulated 51 parental inbreds at the simulated 10 K SNPs. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3618719_d1
title: Additional file 2: Table S1. of Evidence of positive selection associated with placental loss in tiger sharks

description: Orthologues Under Positive Selection Across All Species. The 95 orthologues exhibiting signatures of positive selection across all species based on the CodeML maximum-likelihood site test and Bayes Empirical Bayes method. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3618716_d3
title: Additional file 1: of Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

description: TOP2B interactome, and statistically over-represented biological processes in the TOP2B interactome. (XLSX 158 kb)
DOI: 10.6084/m9.figshare.c.3618725_d1
title: Additional file 2 of Computational modeling of sphingolipid metabolism

description: SMBL file with the model implementation of homoeostasis.
DOI: 10.6084/m9.figshare.c.3618725_d3
title: Additional file 3 of Computational modeling of sphingolipid metabolism

description: SMBL file with the model implementation of AD.
DOI: 10.6084/m9.figshare.c.3618755_d4
title: Additional file 1 of Identification of nuclear genes controlling chlorophyll synthesis inÂ barley by RNA-seq

description: Table of FPKM values for each transcribed genome fragment for each of six libraries, as derived from TopPat2 mappings; lists of differentially expressed genes obtained with EdgeR and Cufflinks tools. (XLSX 3393Â kb)
DOI: 10.6084/m9.figshare.c.3618995_d2
title: Additional file 2: of MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing

description: OTU-analysis commands. (TXT 6 kb)
DOI: 10.6084/m9.figshare.c.3619001_d1
title: Additional file 2: of Ultrasound-guided gastrocnemius recession: a new ultra–minimally invasive surgical technique

description: Clinical and functional data: Range of motion, AOFAS, VAS, and complications after gastrocnemius lengthening. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3619010_d1
title: MOESM10 of A rapid passage through a two-active-X-chromosome state accompanies the switch of imprinted X-inactivation patterns in mouse trophoblast stem cells

description: Additional file 10: Name and chromosomal position of X-linked RNA-FISH probes used in the study.
DOI: 10.6084/m9.figshare.c.3619025_d3
title: Additional file 4: Table S3. of Exploiting single-cell expression to characterize co-expression replicability

description: Correlation between node degree and median expression for model co-expression networks with varying input. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3619202_d5
title: Additional file 3: Table S3. of Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum

description: Pips identified by Yeast two-hybrid screening. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3619205_d5
title: Additional file 3: of Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii

description: Muscle protein alignments; visualize with MEGA [ 117 ]. (ZIP 46 kb)
DOI: 10.6084/m9.figshare.c.3619205_d6
title: Additional file 4: of Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii

description: Gblock edited alignments, FA-GBÂ files in .txt format. (ZIP 20 kb)
DOI: 10.6084/m9.figshare.c.3619205_d7
title: Additional file 1: of Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii

description: Distance matrices (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3619202_d7
title: Additional file 2: Table S2. of Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum

description: Common Pips between P. falciparum and other species. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3619205_d8
title: Additional file 8: of Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii

description: Contig and singleton annotations. (XLSX 8403 kb)
DOI: 10.6084/m9.figshare.c.3619208_d4
title: Additional file 18: Table S6. of Altered gut microbiota in Rett syndrome

description: Correspondences among deposited metagenomics data and samples, unrarefied OTU tables and taxonomic classifications of the 16S and ITS1 datasets. (XLSX 449Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d1
title: Additional file 5: Table S5 of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Counts of the putative genes per CAZy family in the 9 genomes used in this study. Table S6. Counts of the putative genes per Plant Polysaccharide Degradation (PDD)-related CAZy family in the 9 genomes used in this study. Table S7. Functional annotation of the PDD-related genes (with orthologues) for A. westerdijkiae. Table S8. Functional annotation of the PDD-related genes (without orthologues) for A. westerdijkiae. Table S9. Counts of the putative genes involved in plant polysaccharide degradation in the nine Aspergillus species. (XLSX 79Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d2
title: Additional file 1: Table S1. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Statistics of the Aspergillus genomes used in this study. Table S2. Scaffolds greater than 100Â kb in the A. westerdijkiae genome sequences. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d3
title: Additional file 7: Table S11. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Putative secondary metabolism clusters. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3619427_d8
title: MOESM3 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

description: Additional file 3: Figure S3. Phylogenetic trees of gp120 sequences from transmission pairs. Neighbor joining trees of gp120 sequences from transmitters (red) and recipients (blue). Sequences derived from single genome amplification are displayed with filled circles and those inferred from cloning with open circles. Next generation sequencing haplotypes (frequency above 1 %) of plasma and primary virus isolates are indicated by filled and empty squares, respectively. X indicates the majority haplotype and the asterisks the consensus sequence. Not for all patients next generation sequencing data is present due to limitations in sample availability, failure of amplification or haplotype reconstruction. Triangles depict sequences that were used as Env-pseudoviruses for follow-up experiments. Branch lengths are drawn to scale and HIV-1 HXB2 was used as a subtype B reference.
DOI: 10.6084/m9.figshare.c.3619427_d9
title: MOESM4 of Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

description: Additional file 4: Figure S4. Highlighter plots of transmitter and recipient Env sequences. The consensus of the single genome amplification (SGA) sequences of recipients were used as master sequences indicated on top and Env sequences of recipients (R) and transmitters (T) were aligned to it. Amino acid mismatches are illustrated by a colored bar. Sequences are derived from single genome amplification (SGA_X), cloning (cl_X) and from next generation sequencing of primary virus isolate and plasma virus. Note that haplotypes for primary virus isolates and plasma are only spanning gp120 and only those at a frequency above 1 % are depicted. Clones indicated in blue and red were used in follow up experiments for recipient and transmitter, respectively.
DOI: 10.6084/m9.figshare.c.3619418_d10
title: Additional file 7: of Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis â   a rich resource to identify new transcripts, proteins and to study gene regulation

description: Table S5 - List of all detected proteins; Table S6 - Comparison of our proteomics data to ref. [61]. (XLS 3565 kb)
DOI: 10.6084/m9.figshare.c.3619451_d1
title: Additional file 5: of Cognition in chronic kidney disease: a systematic review and meta-analysis

description: Meta-analysis for eGFR 45. (XLSX 52.4 kb)
DOI: 10.6084/m9.figshare.c.3619364_d16
title: Additional file 15: Table S9. of Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

description: The assignment of the patients from TCGA ovarian cancer study [2] into four subtypes based on the INSPIRE latent variables. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3619451_d3
title: Additional file 6: of Cognition in chronic kidney disease: a systematic review and meta-analysis

description: Meta-analysis for eGFR 30. (XLSX 47.5 kb)
DOI: 10.6084/m9.figshare.c.3619364_d21
title: Additional file 8: Table S3. of Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

description: The properties of the modules learned by INSPIRE. Column A: ID of the module. Column B: The number of the neighbor modules in the learned module network. Column C: IDs of the neighbor modules. Column D: The number of genes the module contains. Column E: The names of the genes the module contains. Column F: The number of MSigDB C2 categories for which the module is significantly enriched (Bonferroni-corrected p &lt;0.05) based on a Fisher’s exact test. Column G: The MSigDB C2 categories for which the module is significantly enriched and the corresponding Bonferroni-corrected − log10 p values. The enriched categories are ordered from most significant to least significant. Columns H–L: The p value from the Pearson’s correlation of the feature corresponding to the module with six phenotypes: percent stroma (column H), percent tumor (column I), vessel formation and abundance (column J), stroma type (column K), invasion pattern (column L), residual tumor (column M), and survival (column N). As in Fig. 5a, we highlight modules 5, 6, 53, 54, 60, 78, and 81 that are significantly correlated with at least three of the six phenotypes in red. We also highlight module 30 since it is the only module that has a significant correlation with the vessel formation phenotype. (XLSX 258 kb)
DOI: 10.6084/m9.figshare.c.3619484_d2
title: Additional file 6: of Transcript profiling for early stages during embryo development in Scots pine

description: Transcription factors (TFs) differentially expressed, with a fold-change higher that 2, in any of the pairwise comparison between embryos and megagametophytes. A list of differentially expressed TFs (DETFs) in embryos and megagametophytes respectively, resulting from the pairwise comparisons E1 vs M1, E2 vs M2, E3DO vs M3, E3SU vs M3 and E4 vs M4 is included in this file. TF name (Transcript ID), TF family, and the best match against TAIR database (At locus ID, At name and At annotation) are indicated. The number of all DETFs detected for each family during seed development in embryos and megagametophytes is also included. (XLSX 200 kb)
DOI: 10.6084/m9.figshare.c.3619697_d1
title: Additional file 1: of A novel method of measuring passive quasi-stiffness in the first metatarsophalangeal joint

description: MTPJ quasi-stiffness supporting data. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3619700_d1
title: Additional file 1: of MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

description: Supplementary text, figures, and data files. All text and materials were formated as a small self-contained website (1 HTML file with necessary figures and data files). Data files include input and result files of the case study including the fold change of expression values between tumor vs. normal conditions (in log2FC), average expression value of each gene in 4 GBM subtypes, GBM-altered subnetworks (nodes and edges) weighted by expression correlations between each pair of genes, and gene sets in 2 critical modules and their functional annotations. (ZIP 4315kb)
DOI: 10.6084/m9.figshare.c.3619661_d6
title: MOESM8 of Mechanism of lignin inhibition of enzymatic biomass deconstruction

description: Additional file 8. PDB file of a single copy of the enzyme taken from the trajectory where the average lignin-enzyme contact numberis provided in the beta column.
DOI: 10.6084/m9.figshare.c.3619661_d7
title: MOESM10 of Mechanism of lignin inhibition of enzymatic biomass deconstruction

description: Additional file 10. A file containing the initial coordinates for the simulation system for independent analysis.
DOI: 10.6084/m9.figshare.c.3619706_d3
title: Additional file 1: of Low levels of IgM antibodies recognizing oxidation-specific epitopes are associated with human non-alcoholic fatty liver disease

description: Data NAFLD cohort. (XLSX 1353Â kb)
DOI: 10.6084/m9.figshare.c.3619706_d4
title: Additional file 3: of Low levels of IgM antibodies recognizing oxidation-specific epitopes are associated with human non-alcoholic fatty liver disease

description: Data IBD cohort. (XLS 44Â kb)
DOI: 10.6084/m9.figshare.c.3619661_d8
title: MOESM11 of Mechanism of lignin inhibition of enzymatic biomass deconstruction

description: Additional file 11. A zip archive containing a gallery of each of the cellulases that bound to cellulose in the context of their environment. Each image within the gallery is one snapshot taken from the end of the trajectory showing the relative position of each enzyme (green) that makes contact with the cellulose (red). Nearby lignins are shown in blue, and the substrate tunnel is a yellow surface to orient the viewer. The three tyrosine residues are shown in orange. Note that for each protein, there are 4 images, taken from different relative orientations to the cellulose fibril (0, 90, 180, and 270), and are labeled accordingly in their filenames.
DOI: 10.6084/m9.figshare.c.3619706_d5
title: Additional file 2: of Low levels of IgM antibodies recognizing oxidation-specific epitopes are associated with human non-alcoholic fatty liver disease

description: Data HepC cohort. (XLSX 28Â kb)
DOI: 10.6084/m9.figshare.c.3619661_d9
title: MOESM7 of Mechanism of lignin inhibition of enzymatic biomass deconstruction

description: Additional file 7. PDB file of a single copy of the enzyme taken from the trajectory where the average enzyme-enzyme contactnumber is provided in the beta column.
DOI: 10.6084/m9.figshare.c.3619757_d2
title: Additional file 3: of Diet may influence the oral microbiome composition in cats

description: Nutritional data concerning commercially available wet and dry extruded rations available in Australia. The nutritional data provided include the metabolisable energy (ME), the percentage of carbohydrate in the food (% CHO), the percentage of carbohydrate on a dry matter basis (DM % CHO), and the amount of carbohydrate (CHO), fat and protein in the food in grams per 100Â kcal. This information was collated meticulously by Dr. Linda Fleeman. Abbreviations: metabolisable energy (ME), carbohydrate (CHO) and dry matter (DM). (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3619757_d3
title: Additional file 1: of Diet may influence the oral microbiome composition in cats

description: Relative frequency (%) of OTUs per cat and per diet group. Abbreviations: non-assigned (NA) and standard deviation (SD). (XLSX 133 kb)
DOI: 10.6084/m9.figshare.c.3619757_d4
title: Additional file 2: of Diet may influence the oral microbiome composition in cats

description: Alpha diversity metrics per cat. The alpha diversity metrics presented include the Abundance Coverage Estimator (ACE), which estimates species richness, and the Simpsonâ  s Index that estimates species evenness. Abbreviations: Abundance Coverage Estimator (ACE) and standard error (SE). (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3619886_d4
title: Additional file 3: Table S3. of Association mapping of resistance to rice blast in upland field conditions

description: Blast disease scores measured on 18 differential lines in Andranomanelatra in 2011 and 2015. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3619877_d9
title: Additional file 5: of Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

description: Number of variants identified by GATK, SAMtools and freebayes in the layer chicken genome. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3619892_d3
title: Additional file 1: of Rapid change of fecal microbiome and disappearance of Clostridium difficile in a colonized infant after transition from breast milk to cow milk

description: QIIME commands used to generate the principal coordinate plots. (TXT 2 kb)
DOI: 10.6084/m9.figshare.c.3619880_d8
title: Additional file 3: of Identifying candidate drivers of drug response in heterogeneous cancer by mining high throughput genomics data

description: CNV data. (TXT 14949Â kb)
DOI: 10.6084/m9.figshare.c.3619880_d9
title: Additional file 2: of Identifying candidate drivers of drug response in heterogeneous cancer by mining high throughput genomics data

description: Expression data. (TXT 8662Â kb)