cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3623231_d9
title: MOESM9 of “Gap hunting” to characterize clustered probe signals in Illumina methylation array data

description: Additional file 9: Table S3. Group distributions of 3 different classifications of gap signals. We compared the group distribution for the three groups—mapping measured SNP, mapping annotated SNP, and no mapping SNP—of gap signals. The two groups with mapping SNPs had a very similar relative proportion of groups, while the group with no mapping SNPs was comparatively enriched for distributions with 2 clusters or groups. This result lends additional rationale to a different mechanism besides SNPs as leading the gap signal behavior.
DOI: 10.6084/m9.figshare.c.3623261_d1
title: Additional file 3: Table S3. of Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage

description: RT-qPCR results for validation of RNAseq results. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.c.3623264_d1
title: Additional file 1: of Investigations of immunogenic, allergenic and adjuvant properties of Cry1Ab protein after intragastric exposure in a food allergy model in mice

description: The Excel datafile “FOTS 4534_all datasets” includes all datasets supporting the conclusions of this article: Clinical endpoints, serum MCPT-1, serum total IgE, serum lupin-specific IgG1, splenocyte IL-2, IL-5, IL-10, IL-13 and IFNγ, serum Cry1Ab-specific IgE, IgG1 and IgG2a, and gene expression of TNFα, Hsp70 and IL-6 in the small intestine. (XLSX 124 kb)
DOI: 10.6084/m9.figshare.c.3623261_d2
title: Additional file 2: Table S2. of Adaptation of Propionibacterium freudenreichii to long-term survival under gradual nutritional shortage

description: List of genes induced in the stationary phase (3d post-inoculation) compared to the exponential phase (1d post-inoculation) (P value adjusted ≤0.05). (XLSX 98 kb)
DOI: 10.15468/dl.hbu9hj
title: Occurrence Download

description: A dataset containing 11 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 Aedes tarsalis (Newstead, 1907)"
 ]
}

 The dataset includes 11 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033753-241126133413365/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.3623231_d11
title: MOESM10 of “Gap hunting” to characterize clustered probe signals in Illumina methylation array data

description: Additional file 10: Table S4. Alternatives to gap hunting do not correctly identify polymorphism-affected clusters. For the probes shown in Fig. 7 and the gap signal in Fig. 1, we explored other ways of identifying clusters. Specifically we examined a Gaussian mixture model clustering algorithm that selects an optimal number of clusters based on the Bayesian information criterion, and the dip test for unimodality (alternative hypothesis is that distribution is multi-modal). We recorded the number of clusters selected by the mixture model algorithm and the dip test p value.
DOI: 10.6084/m9.figshare.c.3623258_d6
title: MOESM2 of A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data

description: Additional file 2. Set of promoters mapping to putatively regulated eggNOG/COGs after adjusting for sensitivity with θ = 6.65. The table reports the eggNOG/COG identifier, the MetaHIT IGC gene identifier, composed of sample and gene identifiers, the gene strand and its promoter region sequence, and the gene and protein sequences.
DOI: 10.6084/m9.figshare.c.3623327_d1
title: MOESM2 of Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

description: Additional file 2. Documentation for all stoichiometric models used in this study.
DOI: 10.6084/m9.figshare.c.3623357_d7
title: Additional file 1: of Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintles-1 (Li
                     
                1
              ) and â  2 (Li
                     
                2
              ) revealed a role for miRNAs and their targets in cotton fiber elongation

description: miRPlan predicted miRNAs from all mappable reads in 3 small RNA libraries. (TXT 7525Â kb)
DOI: 10.6084/m9.figshare.c.3623393_d1
title: MOESM6 of What evidence exists for the effectiveness of on-farm conservation land management strategies for preserving ecosystem services in developing countries? A systematic map

description: Additional file 6. Systematic map database on on-farm conservation land management and ecosystem services.
DOI: 10.6084/m9.figshare.c.3623387_d2
title: Additional file 6: of Insights into the human mesenchymal stromal/stem cell identity through integrative transcriptomic profiling

description: Output summary of the meta-analysis differential expression. Notations: BM-MSC = Bone Marrow MSC; HPC = Hematopoietic progenitor cells; FIB = fibroblasts; OSTB = Osteoblasts; dOST = MSC in-vitro derived osteoblasts; stOST = stimulated osteoblasts. The ”n” refers to the number of microarrays. (XLSX 39 kb)
DOI: 10.15468/dl.rnrw7g
title: Occurrence Download

description: A dataset containing 9 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 Aedes taylori Edwards, 1936"
 ]
}

 The dataset includes 9 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033754-241126133413365/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.3623468_d2
title: Additional file 5: Table S5. of Characterization of the cytokinin-responsive transcriptome in rice

description: Genes differentially regulated in response to cytokinin in shoots. (XLSX 1485Â kb)
DOI: 10.6084/m9.figshare.c.3623468_d3
title: Additional file 4: Table S4. of Characterization of the cytokinin-responsive transcriptome in rice

description: Genes differentially regulated in response to cytokinin in roots. (XLSX 10749Â kb)
DOI: 10.6084/m9.figshare.c.3623468_d4
title: Additional file 7: Figure S1. of Characterization of the cytokinin-responsive transcriptome in rice

description: Regulation of genes involved in cytokinin biosynthesis, signaling, response, and degradation. Figure S2. Cytokinin regulation of orthologous genes in rice and Arabidopsis. Figure S3. Characterization of rice type-B RRs OsRR27 and OsRR29 through use of protein binding microarrays. Figure S4. GO categorization of genes induced by cytokinin in both the root and the shoot. Figure S5. GO categorization of genes repressed by cytokinin in both the root and the shoot. Figure S6. GO categorization of genes induced by cytokinin in the root. Figure S7. GO categorization of genes induced by cytokinin in the shoot. Figure S8. GO categorization of genes repressed by cytokinin in the shoot. Figure S9. MapMan overviews of metabolism, cellular response and regulation of cytokinin-regulated genes in shoots in rice. (XLSX 220Â kb)
DOI: 10.6084/m9.figshare.c.3623468_d5
title: Additional file 8: Table S7. of Characterization of the cytokinin-responsive transcriptome in rice

description: Genes that were DE in roots and shoots in opposite directions. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3623468_d6
title: Additional file 3: Table S3. of Characterization of the cytokinin-responsive transcriptome in rice

description: Genes that were DE between roots and shoots in rice. (XLSX 3612Â kb)
DOI: 10.6084/m9.figshare.c.3623612_d2
title: Additional file 2: of 
                     P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis

description: File S1 (annotated_tss_P16Dnmt-Myc.fq_macs_peaksFile). (XLSX 1943 kb)
DOI: 10.15468/dl.aa33ss
title: Occurrence Download

description: A dataset containing 330 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 Aedes togoi (Theobald, 1907)"
 ]
}

 The dataset includes 330 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033757-241126133413365/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.3623621_d1
title: Additional file 4: of A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveilsÂ novel thermoalkaliphilic enzymes

description: Complete gene annotation of fosmid insert T4-1. (XLS 43 kb)
DOI: 10.6084/m9.figshare.c.3623612_d3
title: Additional file 5: of 
                     P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis

description: File S4 (P16-Dnmt induced methylation sites). (XLSX 4152 kb)
DOI: 10.6084/m9.figshare.c.3623621_d2
title: Additional file 6: of A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveilsÂ novel thermoalkaliphilic enzymes

description: Complete gene annotation of fosmid insert NT18-21. (XLS 39 kb)
DOI: 10.6084/m9.figshare.c.3623612_d4
title: Additional file 6: of 
                     P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis

description: File S5 (450 K RawSignal). (CSV 46821 kb)
DOI: 10.6084/m9.figshare.c.3623624_d1
title: Additional file 1: of Effect of herd size on subclinical infection of swine in Vietnam with influenza A viruses

description: Isolate_IDs and virus names deposited in GISAID Epiful database. (XLS 48Â kb)
DOI: 10.6084/m9.figshare.c.3623567_d8
title: Additional file 2: of Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

description: PathVisioRPC jar files. This zip archive contains both the plugin and standalone versions of the PathVisioRPC program packaged as jar files. The plugin can be installed in the PathVisio program and the standalone jar can be run in the command line to launch the PathVisioRPC server. The jar files are being provided for archival purposes, for use please obtain a recent version of the software from the project websites. (ZIP 11950Â kb)
DOI: 10.6084/m9.figshare.c.3623621_d3
title: Additional file 2: of A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveilsÂ novel thermoalkaliphilic enzymes

description: Complete gene annotation of fosmid insert T5-5. (XLS 42 kb)
DOI: 10.15468/dl.c8j3g6
title: Occurrence Download

description: A dataset containing 7512 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Geococcyx velox (Wagner, 1836)"
 ]
}

 The dataset includes 7512 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033756-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s4f4bt
title: Occurrence Download

description: A dataset containing 16857 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Geococcyx californianus (Lesson, 1829)"
 ]
}

 The dataset includes 16857 records from 82 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033755-241126133413365/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.3623663_d2
title: Additional file 2: Table S2. of Changes in malaria burden and transmission in sentinel sites after the roll-out of long-lasting insecticidal nets in Papua New Guinea

description: Description of study population by site. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3623681_d1
title: Additional file 1: of Risk prediction model for epithelial ovarian cancer using molecular markers and clinical characteristics

description: Table S1. Prognostic molecular markers in published studies. Table S2. The relationship between molecular markers and clinicopathologic characteristics. Figure S1. Single immunostaining of 15 molecular markers in epithelial ovarian cancer. Figure S2. Kaplan-Meier overall survival analyses of 15 molecular markers inepithelial ovarian cancer. (ZIP 108 kb)
DOI: 10.6084/m9.figshare.c.3623768_d3
title: Additional file 1: Table S1. of Distribution of the DNA transposon family, Pokey in the Daphnia pulex species complex

description: Details of Daphnia isolates analyzed in this study. Table S2. CT values from qPCR analysis of Pokey, mPok, and rRNA gene number in 45 isolates from the Daphnia pulex complex. Table S3. Estimates of Pokey, mPok, and rRNA gene number in 45 isolates of the Daphnia pulex complex. (XLSX 51Â kb)
DOI: 10.6084/m9.figshare.c.3623777_d1
title: Additional file 1 of Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates

description: An R script which provides a user made function to implement the Q-Gen methodology. The original QuSAGE package is all that is needed. Example code of how to implement the function is provided as well. (TXT 2.61 KB)
DOI: 10.6084/m9.figshare.c.3623780_d1
title: Additional file 2: Table S1. of Exploring the genomic traits of fungus-feeding bacterial genus Collimonas

description: Gene locus of the flagellar biosynthetic gene cluster of the Collimonas strains. Table S2. Gene locus of the secretion systems of the Collimonas strains. Table S3. Genomic distribution of signal transduction proteins in six Collimonas genomes. Table S4. Presence of quorum-sensing proteins in six Collimonas genomes. Table S5. Gene locus of the collimomycin biosynthetic gene cluster of the Collimonas strains. Table S6. Gene locus of the chitinase biosynthetic gene clusters of the Collimonas strains. Table S7. Gene locus of the phopholipase genes of the Collimonas strains. Table S8. Antimicrobial activities of the Collimonas strains. Table S9. Genes encoding secondary metabolites and secretion systems in Collimonas strains. Table S10. Strains and mutants used in this study. Table S11. Summary of Illumina paired-end sequences assembly data. Table S12. Summary of PacBio sequences assembly data. Table S13. Sequences of characterized bacterial terpene synthases used in the phylogenetic analysis. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.c.3623780_d2
title: Additional file 3: of Exploring the genomic traits of fungus-feeding bacterial genus Collimonas

description: The IGS annotation of Collimonas fungivorans Ter331 genome. (GBF 10511Â kb)
DOI: 10.6084/m9.figshare.c.3623801_d8
title: Additional file 2: Table S1. of SABRE: a method for assessing the stability of gene modules in complex tissues and subject populations

description: Patient demographics. Demographic characteristics of the 238 COPD patients. (CSV 495 bytes)
DOI: 10.15468/dl.thv7ep
title: Occurrence Download

description: A dataset containing 20423 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 Aedes triseriatus (Say, 1823)"
 ]
}

 The dataset includes 20423 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033758-241126133413365/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.3623924_d2
title: Additional file 3: Table S14. of Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

description: Subcellular localization evidence of host digestive proteins. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3623939_d1
title: MOESM1 of ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins

description: Additional file 1: Table S1. Amino acid composition distribution between proinflammatory and non-proinflammatory data.
DOI: 10.6084/m9.figshare.c.3623933_d1
title: Additional file 1: of Rituximab induces phenotypical and functional changes of NK cells in a non-malignant experimental setting

description: Figure S1a. NK cells and serum cooperate in mediating rituximab-induced B cell depletion. Same experiment as shown in Fig. 3; all samples and controls are shown. -/+ RTX, without/with rituximab. Figure S1b.Â The extent of rituximab-induced B cell depletion correlates with theÂ size of NK cell proportions. Same experiment as shown in Fig. 4a; the complete experiment with all negative controls including proof of successfull NK cell depletion is shown. -/+ RTX, without/with rituximab. (ZIP 421 kb)
DOI: 10.6084/m9.figshare.c.3624026_d3
title: Additional file 5: Table S3. of Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae

description: All predicted genes within the mapped locus, Pfin 7. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3624017_d10
title: Additional file 16: of Modeling hormonal and inflammatory contributions to preterm and term labor using uterine temporal transcriptomics

description: Loadings values derived from the OSC-PLS modeling of the 357 humanâ  mouse gene orthologs. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3624017_d11
title: Additional file 15: of Modeling hormonal and inflammatory contributions to preterm and term labor using uterine temporal transcriptomics

description: Ensembl gene annotation for the 357 gene orthologs differentially expressed across murine gestation and during human labor. (XLSX 72 kb)
DOI: 10.6084/m9.figshare.c.3624026_d5
title: Additional file 3: Table S1. of Association mapping by pooled sequencing identifies TOLL 11 as a protective factor against Plasmodium falciparum in Anopheles gambiae

description: Fd03 Infection Prevalence Association and Table S2. Fd03 Infection Intensity Association (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3624068_d1
title: Additional file 2: Table S6. of Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection

description: List of RT-PCR primers used in this study. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.c.3624134_d1
title: Additional file 1: Table S1. of Allergic reactions to milk appear sooner than reactions to henâ  s eggs: a retrospective study

description: Grading symptoms. (XSLX 11kb)
DOI: 10.6084/m9.figshare.c.3624122_d3
title: Additional file 2: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Annotation of the 100 most abundant transcriptâ  s coding sequence for each of the aphids investigated. Top BLAST hit annotation for each of the identified coding sequences. (XLSX 27 kb)
DOI: 10.6084/m9.figshare.c.3624134_d2
title: Additional file 2: Table S2. of Allergic reactions to milk appear sooner than reactions to henâ  s eggs: a retrospective study

description: Clinicodemographic features of the study patients. (XSLX 10kb)
DOI: 10.6084/m9.figshare.c.3624122_d4
title: Additional file 7: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Proteins identified in aphid saliva using LC-MS/MS. Proteins identified in aphid saliva using LC-MS/MS when searching against the de novo transcriptomes and against NCBI NR database. The corresponding sequences of the proteins identified, and the raw LC-MS/MS coverage data for each dataset investigated. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3624134_d3
title: Additional file 3: Table S3. of Allergic reactions to milk appear sooner than reactions to henâ  s eggs: a retrospective study

description: Data related to induced reactions and treatments for positive challenges. (XSLX 10kb)
DOI: 10.6084/m9.figshare.c.3624122_d5
title: Additional file 15: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Predicted nucleotide coding sequences for Myzus persicae genotype J. (GZ 11406 kb)
DOI: 10.6084/m9.figshare.c.3624122_d13
title: Additional file 17: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Predicted nucleotide coding sequences for Rhopalosiphum padi and Aphis glycines. (GZ 8032 kb)
DOI: 10.6084/m9.figshare.c.3624122_d14
title: Additional file 4: of Comparative transcriptomics and proteomics of three different aphid species identifies core and diverse effector sets

description: Expression profiles of constitutively expressed genes. TMM-FPKM expression profile for transcripts constitutively expressed. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3624239_d8
title: Additional file 6: of Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins

description: Performance of HyPe on independent genomic dataset. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3624260_d2
title: Additional file 5 of Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies

description: List of primate tRNAs. Tab-separated table including positions and sequences of the tRNAs and translations to other genome versions. These tRNAs are used for the comparisons of the MSA block based approach and the orthologous proteins (OP) approach. (TXT 217 kb)
DOI: 10.15468/dl.9g5zed
title: Occurrence Download

description: A dataset containing 36956 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 Aedes trivittatus (Coquillett, 1902)"
 ]
}

 The dataset includes 36956 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033759-241126133413365/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.3624239_d9
title: Additional file 5: of Prediction of peptidoglycan hydrolases- a new class of antibacterial proteins

description: Comparison of performance of all the three approaches on a Metagenomic dataset. (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.c.3624260_d5
title: Additional file 6 of Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies

description: List of drosophilid tRNAs. Tab-separated table including positions and sequences of the tRNAs and translations to other genome versions and FlyBase IDs. This list is used in the comparison of the MSA block based approach and the work of [20]. (TXT 305 kb)