cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3618287_d13
title: Additional file 1: of Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

description: Solanum incanum and S. aethiopicum assembled transcripts (compressed folder). The file provides the fasta sequences of the 108,322 S. incanum and 106,660 S. aethiopicum transcripts. (7Z 38772 kb)
DOI: 10.6084/m9.figshare.c.3618344_d3
title: Additional file 7: of 
                     In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes

description: Parameters applied for SSR identification. (XLSX 32Â kb)
DOI: 10.6084/m9.figshare.c.3618344_d4
title: Additional file 5: of 
                     In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes

description: Sequence context of the 55 VNSSRs associated to strong candidate genes. (XLSX 58Â kb)
DOI: 10.6084/m9.figshare.c.3618431_d3
title: Additional file 20 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S12. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8, 0.15 of explained ratio by QTL Ă  genetic background interactions to the total genetic variance with 25 replications. (TXT 2088 kb)
DOI: 10.6084/m9.figshare.c.3618431_d4
title: Additional file 18 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S19. Phenotypes for the 29 BC-NAM subpopulations in a scenario where QTLs = 100, h 2=0.5 with 25 replications. (TXT 1208 kb)
DOI: 10.6084/m9.figshare.c.3618428_d6
title: Additional file 3: of Genetic variants in the upstream region of activin receptor IIA are associated with female fertility in Japanese Black cattle

description: Genes on BTA2 in the ANAI 4 -associated region. The positions are based on the UMD3.1 assembly of the bovine genome. (XLSX 36Â kb)
DOI: 10.6084/m9.figshare.c.3618431_d6
title: Additional file 21 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S113. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8, 0.25 of explained ratio by QTL Ă  genetic background interactions to the total genetic variance with 25 replications. (TXT 2088 kb)
DOI: 10.6084/m9.figshare.c.3618431_d13
title: Additional file 11 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

description: Table S6. Genotypes for the 50 DH-NAM subpopulations, where 0 and 2 denote the homozygous gentoypes of parents, respectively. (TXT 88,883 kb)
DOI: 10.6084/m9.figshare.c.3618548_d1
title: Additional file 5: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Experimentally captured RNA-binding proteins at the trophozoite and schizont stages, including mass spectrometry data. (XLSX 1361 kb)
DOI: 10.6084/m9.figshare.c.3618545_d2
title: Additional file 3: Table S2. of Differences in procedural knowledge after a “spaced” and a “massed” version of an intensive course in emergency medicine, investigating a very short spacing interval

description: Raw data (English titles). (XLS 305 kb)
DOI: 10.6084/m9.figshare.c.3618548_d2
title: Additional file 7: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Proteins associated with polysomes during the IDC, including mass spectrometry data. (XLSX 1246 kb)
DOI: 10.6084/m9.figshare.c.3618548_d4
title: Additional file 6: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: Enriched GO terms and enrichment of mRNA-binding domains among experimentally captured RNA-binding proteins. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3618548_d5
title: Additional file 1: of The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum

description: List of RNA-binding domains used for HMM searches. (XLSX 67 kb)
DOI: 10.6084/m9.figshare.c.3618581_d10
title: Additional file 5: Table S4. of Transcriptome analysis in calorie-restricted rats implicates epigenetic and post-translational mechanisms in neuroprotection and aging

description: All DE miRNAs for all diets and ages. (XLSX 17 kb)
DOI: 10.15468/dl.cvaacw
title: Occurrence Download

description: A dataset containing 519 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Croomia pauciflora (Nutt.) Torr."
 ]
}

 The dataset includes 519 records from 58 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033721-241126133413365/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.3618659_d5
title: Additional file 9: Table S6. of Skin fungal community and its correlation with bacterial community of urban Chinese individuals

description: Significant SparCC correlations between OTUs of fungal and bacterial origins divided by body sites. (XLSX 32215Â kb)
DOI: 10.17632/5h9h7ssbpm.1
title: UNDERREPRESENTATION OF FEMALE SPEAKERS AT ONLINE AND IN-PERSON DENTISTRY CONFERENCES-UVMX-BICC

description: These are the raw data from the manuscript UNDERREPRESENTATION OF FEMALE SPEAKERS AT ONLINE AND IN-PERSON DENTISTRY CONFERENCES. The file includes the data that we have used to get the results of our study that explored the underrepresentation of female speakers at online and in-person dentistry conferences.
DOI: 10.6084/m9.figshare.c.3618659_d6
title: Additional file 1: Table S1. of Skin fungal community and its correlation with bacterial community of urban Chinese individuals

description: OTU counts and taxonomic information of all samples included in this study. (XLSX 579Â kb)
DOI: 10.6084/m9.figshare.c.3618716_d1
title: Additional file 2: of Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders

description: Supplementary tables and figures. (XLSX 193 kb)
DOI: 10.15468/dl.2dh3zq
title: Occurrence Download

description: A dataset containing 301 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Melanophryniscus moreirae (Miranda-Ribeiro, 1920))",
 "BasisOfRecord is one of (Specimen, Occurrence evidence, Material sample)",
 "Country is one of (Brazil, Argentina, Bolivia (Plurinational State of), Chile, Colombia, Ecuador, Guyana, French Guiana, Paraguay, Peru, Suriname, Uruguay, Venezuela (Bolivarian Republic of))"
 ]
}

 The dataset includes 301 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033722-241126133413365/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.3618755_d6
title: Additional file 3 of Identification of nuclear genes controlling chlorophyll synthesis inÂ barley by RNA-seq

description: Table of differentially expressed gene isoforms as derived from Cufflinks pipeline results. (XLSX 11200Â kb)
DOI: 10.6084/m9.figshare.c.3618755_d7
title: Additional file 2 of Identification of nuclear genes controlling chlorophyll synthesis inÂ barley by RNA-seq

description: Plastid genome expressed fragments with respective annotated genes, location in plastid genome, FPKM levels for lines i:BwAlm and Bowman and log2 for expression level fold changes. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3618755_d8
title: Additional file 8 of Identification of nuclear genes controlling chlorophyll synthesis inÂ barley by RNA-seq

description: Sequences generated by Trinity from Bowman libraries that did not align to H. vulgare reference genome. (FASTA 337Â kb)
DOI: 10.6084/m9.figshare.c.3618773_d2
title: Additional file 8: of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

description: FASTA alignments of catalase proteins (related to Fig. 4). (FASTA 157 kb)
DOI: 10.6084/m9.figshare.c.3618773_d3
title: Additional file 3: Table S3. of Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

description: List of photoprotective and antioxidant genes of P. rhodozyma. (XLS 1304 kb)
DOI: 10.5281/zenodo.13870492
title: Scenario data for KEC 5.0

description: Data as input for the KEC 5.0 calculations (RWS-WVL)
DOI: 10.5281/zenodo.13870493
title: Scenario data for KEC 5.0

description: Data as input for the KEC 5.0 calculations (RWS-WVL)
DOI: 10.5281/zenodo.13870696
title: Scenario data for KEC 5.0

description: Data as input for the KEC 5.0 calculations (RWS-WVL)
DOI: 10.6084/m9.figshare.c.3618878_d2
title: Additional file 4 of Reconstruction of gene networks using prior knowledge

description: List of the edges for B.subtilis data with a l p h a =0 . 5. (TEXT 115 KB)
DOI: 10.6084/m9.figshare.c.3618884_d2
title: Additional file 4: Table S4. of Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex

description: Correlation analysis between miR-142 expression levels and DNA methylation of miR-142 promoter. (XLSX 8.93 KB)
DOI: 10.6084/m9.figshare.c.3618878_d3
title: Additional file 3 of Reconstruction of gene networks using prior knowledge

description: List of the edges for E. coli data with a l p h a =0 . 5. (TEXT 82 KB)
DOI: 10.6084/m9.figshare.c.3618884_d3
title: Additional file 1: Table S1. of Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex

description: Information on all individuals used in this analysis, including age, sex, and postmortem interval. (XLSX 10.0 KB)
DOI: 10.6084/m9.figshare.c.3618896_d1
title: Additional file 2: Table S1. of Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats

description: Limma DE gene table of the spots with foreground different to background. Table S2. EdgeR DE gene table. Table S3. Comparison between PINARRA3 and RNA-Seq data. Table S4. Mapman categories from DE genes. Table S5. Contig ID for Reference transcriptome. Table S6. Primers used for qPCR. (XLSX 4413 kb)
DOI: 10.6084/m9.figshare.c.3618884_d4
title: Additional file 3: Table S3. of Hypomethylation of miR-142 promoter and upregulation of microRNAs that target the oxytocin receptor gene in the autism prefrontal cortex

description: Primers used in our analysis. (XLSX 9.48 KB)
DOI: 10.6084/m9.figshare.c.3619049_d1
title: MOESM14 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 14: Table S9. Organization of chromosome 7. A. Genes on core and accessory chromosomes according to our updated annotation [12]. Overall gene density is clearly lower for accessory compared to core chromosomes. B. Same analyses for the whole chromosome 7, the core segment (Tel7L to 1.8Â Mb) and the right, accessory segment (1.8Â Mb to Tel7R). Even though the right-most segment shows hallmarks of an accessory chromosome gene density is higher than on the left segment.
DOI: 10.6084/m9.figshare.c.3619049_d2
title: MOESM13 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 13: Table S8. Correlation analyses of ChIP-seq data obtained for different histone modifications. Correlation analyses were performed on coverage data along core or accessory chromosomes alone and on all chromosomes combined. The coverage of transposable elements (TE) or coding sequences (CDS) for each histone modification (H3K4me2, H3K9me3, H3K27me3) was considered. Two biological replicates (Replicate 1 and 2) were generated and analyzed separately. The Kendallâ  s Tau correlation test was applied [107], as provided in the R statistical package.
DOI: 10.6084/m9.figshare.c.3619046_d3
title: Additional file 3: of Extending digital PCR analysis by modelling quantification cycle data

description: Collated Cq data GE. The data used in this paper, collated from dPCR output data files. (CSV 7402 kb)
DOI: 10.6084/m9.figshare.c.3619049_d6
title: MOESM11 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 11: Table S7. Repetitive DNA at the subtelomeric regions. Percentage of TE-families and repetitive elements is shown for each subtelomeric region. The length of the subtelomeric region, TE-families/repeats with a coverage &gt; 10 % and the total amount of TE/repeats (%) are shown. Categorized TE-families are labeled according to nomenclature proposed recently [34]. “NoCat” means that repetitive DNA does not match TE sequences.
DOI: 10.6084/m9.figshare.c.3619049_d7
title: MOESM2 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 2: Table S1. Statistics of ChIP-seq experiments. Number of total reads after filtering and mapping is shown. Percentage of reads mapping uniquely, in more than one position or that remained unmapped is based on the total amount of reads. Data were submitted to SRA under accession number SRP059394.
DOI: 10.6084/m9.figshare.c.3619049_d15
title: MOESM7 of Histone modifications rather than the novel regional centromeres of Zymoseptoria tritici distinguish core and accessory chromosomes

description: Additional file 7: Table S3. Centromeres are not located in the longest AT-rich region of the chromosome. A. The number of AT-rich regions in all chromosomes, including the length of the AT-rich region, the coordinates of the AT-rich regions and the percentage of repetitive DNA (mostly TEs) are listed. B. Number of AT-rich regions in all centromeres, including the length of the AT-rich region, the coordinates of the AT-rich regions and the percentage of repetitive DNA (mostly TEs). In total there are 847 AT-rich regions, from 2 kb to 86.3 kb in size and covering 7.383 Mb of the genome. The median size is 7.1 kb and the mean AT-content is 55 %. In chromosomes 4 and 10 two AT-rich regions partially overlap the centromeres, on chromosome 4 this is 1.905 kb of 86.31 kb and on chromosomes 10 this is 1.77 kb of 11.8 kb; these regions are indicated by an asterisk (*).
DOI: 10.6084/m9.figshare.c.3619121_d12
title: Additional file 7: File S1. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

description: Clusters and normalised expression tables. (XLSX 956 kb)
DOI: 10.6084/m9.figshare.c.3619121_d14
title: Additional file 13: Table S5. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

description: Variants summary. (XLSX 11 kb)
DOI: 10.3886/e213341
title: A Longitudinal Portrait of California’s Kindergarten English Learners & Their Learning Outcomes

description: California’s K-12 funding and instructional policies for English learners have changed significantly over the past two decades. This paper uses student-level longitudinal data from 2006 to 2019 to examine the learning outcomes of successive cohorts of students who were classified as English learners in kindergarten as they progressed through California’s changing public school system. First, we find ELs grew more diverse linguistically over time. Second, we find that their third-grade achievement improved in math and English Language Arts, and achievement gaps narrowed in both subjects. Third, we find that more recent cohorts reported slightly higher rates of English proficiency acquisition by the end of grade-5. Finally, we find that the proportion who were reclassified by grade-5 increased dramatically for the first two cohorts of our study but then remained constant for the next five years. In the most recent cohort we can observe, only 53% of students who entered kindergarten as ELs were reclassified by the end of grade-5.
DOI: 10.3886/e213341v1
title: A Longitudinal Portrait of California’s Kindergarten English Learners & Their Learning Outcomes

description: California’s K-12 funding and instructional policies for English learners have changed significantly over the past two decades. This paper uses student-level longitudinal data from 2006 to 2019 to examine the learning outcomes of successive cohorts of students who were classified as English learners in kindergarten as they progressed through California’s changing public school system. First, we find ELs grew more diverse linguistically over time. Second, we find that their third-grade achievement improved in math and English Language Arts, and achievement gaps narrowed in both subjects. Third, we find that more recent cohorts reported slightly higher rates of English proficiency acquisition by the end of grade-5. Finally, we find that the proportion who were reclassified by grade-5 increased dramatically for the first two cohorts of our study but then remained constant for the next five years. In the most recent cohort we can observe, only 53% of students who entered kindergarten as ELs were reclassified by the end of grade-5.
DOI: 10.6084/m9.figshare.c.3619163_d8
title: Additional file 4: of The hybrid non-ethylene and ethylene ripening response in kiwifruit (Actinidia chinensis) is associated with differential regulation of MADS-box transcription factors

description: Physiology of selected time points for mRNA-Seq, and depth of libraries. (XLSX 1091 kb)
DOI: 10.6084/m9.figshare.c.3619121_d17
title: Additional file 16: Table S7. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

description: SNP allele frequency correlation with virulence in non-effectors. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3619121_d25
title: Additional file 25: Table S12. of The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence

description: Microsatellite abundance. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3619202_d3
title: Additional file 6: Table S5. of Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum

description: Recombinant proteins produced. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3619205_d3
title: Additional file 6: of Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii

description: Gblock edited alignments, truncated for PhyML, .phyÂ files in .txt format. (ZIP 24 kb)
DOI: 10.6084/m9.figshare.c.3619202_d4
title: Additional file 1: Table S1. of Analysis of the interactome of the Ser/Thr Protein Phosphatase type 1 in Plasmodium falciparum

description: Pips identified by affinity chromatography/mass spectrometry. (XLSX 10 kb)
DOI: 10.15468/dl.hr2be7
title: Occurrence Download

description: A dataset containing 201 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 Grammangis Rchb.f."
 ]
}

 The dataset includes 201 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033724-241126133413365/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.3619241_d6
title: Additional file 2: of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Sequences and coordinates of the predicted proteins and transcripts of A. westerdijkiae. (ZIP 10770Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d7
title: Additional file 6: Table S10. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Putative proteases predicted by the batch Blast against the MEROPS database. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d8
title: Additional file 4: Table S4. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Putative secreted proteins involved in PHI, CAZy, Protease, and CYP450. (XLSX 134Â kb)
DOI: 10.6084/m9.figshare.c.3619256_d2
title: Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

description: A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 cells. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3619289_d5
title: Additional file 9: of South African HIV-1 subtype C transmitted variants with a specific V2 motif show higher dependence on α4β7 for replication

description: Univariate correlations between α4β7 dependence for replication and cytokine levels in CVL and plasma at transmission.
DOI: 10.6084/m9.figshare.c.3619415_d1
title: Additional file 8: of Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

description: Expanded data set for all novel genes. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.c.3619418_d1
title: Additional file 11: of Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

description: Table S13 - Plasmids used in this work; Table S14 – Oligonucleotides used in this work. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3619418_d2
title: Additional file 10: 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 S12 - Percentages of different types of TSSs above score cut-offs. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3619424_d1
title: Additional file 3: Table S2. of Infection with Plasmodium berghei ookinetes alters protein expression in the brain of Anopheles albimanus mosquitoes

description: Identification of differentially displayed proteins in Anopheles albimanus and orthologs in Anopheles darlingi and Drosophila melanogaster. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3619415_d4
title: Additional file 3: of Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

description: Gene Ontology terms predicted using Metastudent for the novel genes. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3619439_d1
title: MOESM1 of Malaria and large dams in sub-Saharan Africa: future impacts in a changing climate

description: Additional file 1. List of existing African dams used in the study. The data presents the location of the 1268 dams used in the present study.
DOI: 10.6084/m9.figshare.c.3619364_d12
title: Additional file 18: Table S10. of Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer

description: The enrichment of the marker modules that were selected by the Significance Analysis of Microarrays (SAM) procedure to be significantly differentially expressed in one of the four INSPIRE subtypes with MSigDB C5 categories of genes. Column A: ID of the module. Column B: The enriched MSigDB C5 category and − log10 p of the enrichment based on Fisher’s exact test. (XLSX 21 kb)