cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3639932_d2
title: Additional file 1:  of Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

description: Table S1. Breed and population details and within-population genetic diversity parameters. Table S1 provides, for each considered population, information concerning the species, the geographical origin, the membership of breeds to four groups, as specified in the Methods section, the number of individuals (N), the proportion of polymorphic loci (P p l ), a measure of gene diversity (H e ), and the inbreeding coefficient (F). Table S2. Within-population genetic diversity parameters estimated for rarefied samples. Table S2 provides the proportion of polymorphic loci (P p l ), a measure of gene diversity (H e ), and the inbreeding coefficient (F) for population samples rarefied to N = 10 each. The membership of breeds to four groups, as specified in the Methods section, is also indicated. Table S3. Breeds and populations involved in the migration events inferred by TREEMIX. Table S3 provides a list of breeds and populations for which TREEMIX detected possible migration events. The analysis was carried out using the dataset of 671 samples from 37 populations, assuming M = 40. Relative migration weights are indicated. Branches of trees are shown in the Newick format. Only migrations with weights greater than 0.1 are shown. Table S4. Groups of populations involved in the migration events inferred by TREEMIX. Table S4 shows the results of the TREEMIX analysis carried out after removal of the Merino-derived breeds (Chinese Merino, Merinolandschaf, Sopravissana, Gentile di Puglia and Merinizzata) and clustering of the considered breeds and populations into six arbitrary groups, as specified in the Methods section. Relative migration weights are indicated. Table S5. Groups of populations involved in the migration events inferred by TREEMIX, after removal of the Andalusian Merino, Arapawa and Macarthur Merino populations. Table S5 shows the results of the TREEMIX analysis carried out after removal of Andalusian Merino, Arapawa, Macarthur Merino and the Merino-derived breeds (Chinese Merino, Merinolandschaf, Sopravissana, Gentile di Puglia and Merinizzata) and clustering of the considered breeds and populations into six arbitrary groups, as specified in the Methods section. Relative migration weights are indicated. Table S6. Z-scores from the f4 test on the aggregated dataset. Table S6 shows the results of the f4 test carried out using the dataset aggregated into six arbitrary groups (wild, WIL; feral, FER; primitive, PRIM; Merino, MER; Spanish non-Merino, SPA; Italian non-Merino; ITA). Only trees with significant Z-scores (&gt;3) are shown. For each tree, the three possible four-population topologies are reported.
DOI: 10.15468/dl.nnht7g
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Cannabis sativa L.",
 "Year 1981-2024"
 ]
}

 The dataset includes 32 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033967-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b6av56
title: Occurrence Download

description: A dataset containing 286 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "OccurrenceStatus is Present",
 "TaxonKey is Acropora cervicornis (Lamarck, 1816)",
 "Year 1990-2024"
 ]
}

 The dataset includes 286 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033968-241126133413365/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.3640121_d2
title: Additional file 2: of Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

description: Supplementary data files. Pathways.zip full set model predictions for all metabolites during transcription factor induction based on genome-wise expression. Pathways_specific.zip full set model predictions for all metabolites during transcription factor induction based on TF regulon specific expression. Model.xml: Genome scale MTB metabolic model used. Table S1 the binding network used for the transcription factor overexpression analyses and median-scaled metabolite abundance values for normoxic and hypoxic conditions. (ZIP 2706Â kb)
DOI: 10.6084/m9.figshare.c.3640133_d1
title: Additional file 3: of Behavioural responses to heat in desert birds: implications for predicting vulnerability to climate warming

description: Raw data as presented in Table S1 and Table S2. (XLSX 63 kb)
DOI: 10.6084/m9.figshare.c.3640133_d2
title: Additional file 2: of Behavioural responses to heat in desert birds: implications for predicting vulnerability to climate warming

description: Behavioural observation data of birds collected during the austral summers (November-March) of 2009/2010 and 2010/2011. (XLSX 1.09 mb)
DOI: 10.6084/m9.figshare.c.3640136_d2
title: Additional file 19: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate CRNs of Pl. halstedii, predictions based on ORFs generated from the un-masked genome. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d5
title: Additional file 16: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Kazal-like domain features among the different genomes. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3640136_d6
title: Additional file 18: of Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora

description: Candidate CRNs of Pl. halstedii, predictions based on gene models. (XLSX 46Â kb)
DOI: 10.6084/m9.figshare.c.3640178_d1
title: Additional file 1: of Countrywide serological evaluation of canine prevalence for Anaplasma spp., Borrelia burgdorferi (sensu lato), Dirofilaria immitis and Ehrlichia canis in Mexico

description: Dataset supporting the conclusions of this article. (XLSX 227 kb)
DOI: 10.6084/m9.figshare.c.3640181_d1
title: Additional file 1: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

description: R script used to generate figures, tables and numbers used in the described analysis of Hi-C data. (RMD 7 kb)
DOI: 10.6084/m9.figshare.c.3640181_d2
title: Additional file 2: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

description: R script used to generate figures, tables and numbers used in the described analysis of ChIA-PET data. (RMD 14 kb)
DOI: 10.6084/m9.figshare.c.3640184_d1
title: Additional file 1: Table S1. of Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

description: This table is derived from the MaxQuant output table ProteinGroups and contains the complete list of identified proteins/protein groups including the ones that we did not accept after application of criteria described in Materials and Methods. This table also contains additional data such as the complete set of accession numbers forming one group, the distribution of peptides among the 20 PAGE sections analyzed separately, the calculated molecular weight of each entry, the iBAQ intensity and the percentages calculated from it. (XLSX 265Â kb)
DOI: 10.6084/m9.figshare.c.3640184_d2
title: Additional file 2: Table S2. of Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

description: Table S2, derived from MaxQuant output table Peptides, contains all identified peptide sequences belonging to the proteins of Table S1 in alphabetic order starting with the first amino acid: It also contains other relevant data such as scores, charge states, and mass accuracy. (XLSX 2472Â kb)
DOI: 10.6084/m9.figshare.c.3640184_d4
title: Additional file 5: Table S4. of Proteomic analysis of quail calcified eggshell matrix: a comparison to chicken and turkey eggshell proteomes

description: Curated version of the MaxQuant output file Phospho (STY) sites with phosphopeptide sequences, localization probabilities, scores, mass errors and other relevant data. Also included are phosphopeptides with site probabilities lower than 0.75, which were not included into TableÂ 2. (XLS 99Â kb)
DOI: 10.6084/m9.figshare.c.3640316_d9
title: Additional file 5: Table S4. of Decoding breast cancer tissueâ  stroma interactions using species-specific sequencing

description: Gene lists from in vitro comparisons. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3640331_d1
title: Additional file 3: Table S2. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 1,807 experiment 2 only senDMPs. (CSV 539 kb)
DOI: 10.6084/m9.figshare.c.3640331_d2
title: Additional file 8: Table S6. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 1,807 experiment 2 only senDMPs. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3640331_d3
title: Additional file 2: Table S1. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 969 experiment 1 only senDMPs. (CSV 290 kb)
DOI: 10.6084/m9.figshare.c.3640331_d5
title: Additional file 4: Table S3. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the annotated information of the 725 agree senDMPs. (CSV 244 kb)
DOI: 10.6084/m9.figshare.c.3640331_d6
title: Additional file 7: Table S5. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 969 experiment 1 only senDMPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640331_d7
title: Additional file 6: Table S7. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Panther DB pathway analysis of the 725 agree senDMPs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640331_d8
title: Additional file 5: Table S8. of The senescent methylome and its relationship with cancer, ageing and germline genetic variation in humans

description: Table containing the P values for the difference in methylation between the EP cells and each of the FACs sorted populations as well as the FACs sorted populations against each other. (CSV 89758 kb)
DOI: 10.6084/m9.figshare.c.3640409_d3
title: Additional file 2: Table S1. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

description: Calculated gene copy numbers. Sheet 1: RPKM counts for all genes, modal values and calculated gene copy numbers. Sheet 2 Calculated gene copy numbers (RPKM divided by modal RPKM) for the unique gene list [39]. (XLS 3352 kb)
DOI: 10.6084/m9.figshare.c.3640409_d4
title: Additional file 3: Table S2. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

description: SNPs and indels for the new isolates. The first sheet is a summary, the others are as labelled on the tabs. (XLSX 12654 kb)
DOI: 10.6084/m9.figshare.c.3640409_d7
title: Additional file 4: Table S3. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

description: Raw poly(A)+ mRNA transcriptome data and calculations based on reads per million (RPM). Sheet 1: Alignment statistics and correlations between the different datasets, calculated from RPM using the unique gene set only. cBS: cultured Lister 427 bloodstream forms expressing the tet repressor from pHD1313. BT1-3: Tbr729; LW - new isolates; PC - cultured Lister 427 procyclic forms. Sheet 2: Read counts for all genes. Sheet 3: Data for unique gene list [39] with reads per million (RPM). Column R shows the regulation pattern according to a custom script. Samples giving significantly peak RPMs (relative to other samples) are indicated by “max” and troughs are indicated by “min”. The threshold was set at 2-fold. Sheet 4: Sheet 3 results, filtered to remove genes for which the maximum RPM value was less than 10. Column T shows correlation coefficients of the RPM results with PIP39 (Tb927.9.6090). Colour code for ratios: Blue is less than 0.25×, green is less than 0.5×, orange is greater than 2× and red is greater than 4×. Comparisons with other datasets are indicated as follows: ST/SL Kabani; stumpy/slender ratio from [6]; ST/SL BS Jensen - stumpy/slender ratio from [7]; SLvST mRNA Capewell and ST polysomes/mRNA Capewell - data from [13]; SG/cBS: salivary gland trypanosomes relative to cultured bloodstream forms from [30]; SG/PC: salivary gland trypanosomes [30] relative to our results for cultured Lister 427 procyclic forms. Sheet 5: calculated RPMs for selected recognised stumpy-form markers. Reads for the ESAG9s and the PAD genes are not unique and precise allocation to a particular variant was not attempted. Sheet 6: Genes showing increased RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. Sheet 7: Genes showing reduced RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. (XLSX 3928 kb)
DOI: 10.6084/m9.figshare.c.3640412_d2
title: Additional file 1: of Significance of soluble triggering receptor expressed on myeloid cells-1 elevation in patients admitted to the intensive care unit with sepsis

description: Whole data set used for statistical analysis evaluating prognostic value of biomarkers and severity scores. (XLSX 129Â kb)
DOI: 10.6084/m9.figshare.c.3640424_d1
title: MOESM1 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 1. Feature set VARSEL RF.
DOI: 10.6084/m9.figshare.c.3640424_d2
title: MOESM2 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 2. Feature set SVM RFE.
DOI: 10.6084/m9.figshare.c.3640424_d3
title: MOESM5 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 5. Feature set SVM.
DOI: 10.6084/m9.figshare.c.3640424_d4
title: MOESM4 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 4. Feature set RF.
DOI: 10.6084/m9.figshare.c.3640424_d5
title: MOESM6 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 6. Feature set LASSO.
DOI: 10.6084/m9.figshare.c.3640424_d6
title: MOESM3 of Feature selection and validated predictive performance in the domain of Legionella pneumophila: a comparative study

description: Additional file 3. Feature set CART.
DOI: 10.6084/m9.figshare.c.3640433_d1
title: Additional file 10: Table S9. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: GO â  condensed nuclear chromosomeâ   table of DE genes in df/+ Bl6 MEFs. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3640433_d2
title: Additional file 7: Table S6. of Quantitative analysis of chromatin interaction changes upon a 4.3 Mb deletion at mouse 4E2

description: Sequencing LAD (sLAD) positions detected for the terminal part of chromosome 4. Data derived from 3 T3 MEFs40. Marked in yellow is the extensive sequence stretch bordering the CNV devoid of sLADs. Marked in green are the sLAD regions inside the CNV. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3640538_d1
title: Additional file 5: Table S5. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Relative abundance of microbial taxa at phylum level in various samples collected from the three hot springs (83.6, 81 and 45.1 °C) of L. Magadi and Little Magadi. ‘No blast hit/Others’ represent unclassified sequences in both data sets. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3640538_d2
title: Additional file 3: Table S3. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Total diversity Sequence Read Archive metadata sheet of the samples collected from the hot springs of L. Magadi and Little Magadi (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3640538_d4
title: Additional file 4: Table S4. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Active diversity Sequence Read Archive metadata sheet of the samples collected from the hot springs of L. Magadi and Little Magadi. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3640538_d5
title: Additional file 7: Table S7. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Active diversity relative abundance of microbial taxa at family level in various samples collected from the three hot springs (83.6, 81 and 45.1 °C) of L. Magadi and Little Magadi. ‘No blast hit/Others’ represent unclassified sequences in both data sets. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3640538_d6
title: Additional file 2: Table S2. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Active diversity environmental data sheet of the samples collected from the hot springs of L. Magadi and Little Magadi (XLS 24 kb)
DOI: 10.6084/m9.figshare.c.3640538_d7
title: Additional file 6: Table S6. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Total diversity relative abundance of microbial taxa at family level in various samples collected from the three hot springs (83.6, 81 and 45.1 °C) of L. Magadi and Little Magadi. ‘No blast hit/Others’ represent unclassified sequences in both data sets. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3640538_d9
title: Additional file 1: Table S1. of Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya

description: Total diversity environmental data sheet of the samples collected from the hot springs of L. Magadi and Little Magadi (XLS 25 kb)
DOI: 10.6084/m9.figshare.c.3640541_d2
title: Additional file 6: of Impact of flanking chromosomal sequences on localization and silencing by the human non-coding RNA XIST

description: Table of primers. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3640604_d4
title: Additional file 5: Table S1. of Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

description: The highly conserved genes among R. ferrugineus, D. ponderosae and I. typographus. (XLSX 130Â kb)
DOI: 10.6084/m9.figshare.c.3640604_d7
title: Additional file 10: Table S3. of Identification of the genes involved in odorant reception and detection in the palm weevil Rhynchophorus ferrugineus, an important quarantine pest, by antennal transcriptome analysis

description: GenBank accession numbers of the GR and OR proteins used for the tree construction (Figures 9 and 5). (XLSX 25Â kb)
DOI: 10.6084/m9.figshare.c.3640727_d1
title: MOESM1 of 
                     Aspergillus nidulans protein kinase A plays an important role in cellulase production

description: Additional file 1: Table S1. List of CAZymes.
DOI: 10.6084/m9.figshare.c.3640727_d4
title: MOESM3 of 
                     Aspergillus nidulans protein kinase A plays an important role in cellulase production

description: Additional file 3: Table S3. MIPS FunCat 24 h.
DOI: 10.6084/m9.figshare.c.3640727_d5
title: MOESM2 of 
                     Aspergillus nidulans protein kinase A plays an important role in cellulase production

description: Additional file 2: Table S2. MIPS FunCat 8 h.
DOI: 10.15468/dl.defaqe
title: Occurrence Download

description: A dataset containing 2631 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 "TaxonKey is Anopheles barbirostris Wulp, 1884"
 ]
}

 The dataset includes 2631 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033969-241126133413365/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.3640751_d1
title: Additional file 1: of Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

description: A list of altered genes identified along with the days on which they were differentially expressed. (XLS 1332 kb)
DOI: 10.6084/m9.figshare.c.3640763_d1
title: Additional file 3: Table S2. of The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence

description: rs6693105 (ie, linked with L CE3BC deletion) a llele frequency in ancient human samples. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3640763_d2
title: Additional file 4: Table S3. of The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence

description: Tajimaâ  s D, Pi, Fst, Î iHH for Neutral, ancient and Target regions. (XLSX 7546 kb)
DOI: 10.6084/m9.figshare.c.3640763_d3
title: Additional file 5: of The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence

description: File S1. Codes. (TXT 2 kb)
DOI: 10.6084/m9.figshare.c.3640763_d4
title: Additional file 2: Table S1. of The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence

description: Linkage disequilibrium between LCE3 BC deletion and adjacent SNPs. (XLSX 64 kb)
DOI: 10.6084/m9.figshare.c.3640763_d6
title: Additional file 6: of The psoriasis-associated deletion of late cornified envelope genes LCE3B and LCE3C has been maintained under balancing selection since Human Denisovan divergence

description: FIle S2. Input file for generating the World Map. (TXT 1 kb)
DOI: 10.6084/m9.figshare.c.3640766_d1
title: MOESM3 of Baseline susceptibility of different European lepidopteran and coleopteran pests to Bt proteins expressed in Bt maize: a systematic review

description: Additional file 3: Table S3. Articles without duplicates.
DOI: 10.6084/m9.figshare.c.3640766_d2
title: MOESM4 of Baseline susceptibility of different European lepidopteran and coleopteran pests to Bt proteins expressed in Bt maize: a systematic review

description: Additional file 4: Table S4. Articles after title screening.
DOI: 10.6084/m9.figshare.c.3640862_d2
title: Additional file 5: Table S4. of Serological diagnosis of pulmonary Mycobacterium tuberculosis infection by LIPS using a multiple antigen mixture

description: Raw LIPS data from the seven antigen mixture test with cohorts 2 and 3. (XLS 15Â kb)