cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3644234_d10
title: Additional file 8: Table S6. of Lactation undernutrition leads to multigenerational molecular programming of hypothalamic gene networks controlling reproduction

description: Upstream regulators suggested by Ingenuity Pathway Analysis for genes showing differential expression in hypothalamus of control (CON) vs. LUN mice. Ingenuity’s Upstream Regulator Analysis tool predicts upstream regulators from gene expression data based on the literature and compiled in the Ingenuity Knowledge Base. Activation z-score infer the activation state of predicted transcriptional regulator (Th = +/− 1). A Fisher’s exact test p-value is calculated to assess the significance of enrichment of the gene expression data for the genes downstream of an upstream regulator. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3644234_d7
title: Additional file 3: Table S1. of Lactation undernutrition leads to multigenerational molecular programming of hypothalamic gene networks controlling reproduction

description: Molecular changes in the hypothalami of 10- (D10) and 21-day (D21) old female (A) and male (B) F1 and F2 progeny assessed by real-time RT-PCR. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3644234_d8
title: Additional file 12: Table S7. of Lactation undernutrition leads to multigenerational molecular programming of hypothalamic gene networks controlling reproduction

description: Names, primers and probes sequences or assay IDs, RefSeq numbers of genes selected for real-time RT-PCR analysis. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3644234_d12
title: Additional file 6: Table S4. of Lactation undernutrition leads to multigenerational molecular programming of hypothalamic gene networks controlling reproduction

description: Top 25 Combined (A) and Single (B) Biofunction Categories enriched with genes showing differential expression in the hypothalamus of control (CON) vs. LUN mice. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.c.3644306_d1
title: Additional file 1 of CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements

description: Supplementary Tables. Table S1. The complete list of the biological processes that the predicted SREs are involved in. Table S2. MCSsets generated by CoSREM. Table S3. Exon skipping events identified for the SRE set (GAGGAC,GGGAGG). Table S4. The list of the biological processes that the predicted SREs are involved in. Table S5. Combinatorial SRE sets detected in both exonic flanking regions. (xlsx 73.7kb)
DOI: 10.6084/m9.figshare.c.3644324_d1
title: Additional file 1: Table S1. of Fusion of the HMGA2 and C9orf92 genes in myolipoma with t(9;12)(p22;q14)

description: Cases of myolipomas which have been reported from 1991 until October 20, 2015. They were found searching pubmed ( http://www.ncbi.nlm.nih.gov/pubmed/ ) using the term â  myolipomaâ  . (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3644438_d4
title: Additional file 4: Table S1. of Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs

description: Top-ranked results from EWAS of 15 cancer discordant MZ twin-pairs prior to diagnosis. (XLSX 42Â kb)
DOI: 10.6084/m9.figshare.c.3644525_d2
title: MOESM3 of Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array

description: Additional file 3: Table S2. Summary table of the correspondence between the QTL and SNP associations identified in the present study and other studies previously reported for parasite resistance traits in sheep. This table shows the correspondences found for all the QTL identified in this study (by LA, LDLA and GWAS) (indicated in green cells) with QTL previously reported based on microsatellite-based studies (compiled in the SheepQTLdb; indicated in light orange cells) and SNP chip-based studies (indicated in orange cells).
DOI: 10.6084/m9.figshare.c.3644525_d1
title: MOESM4 of Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array

description: Additional file 4: Table S3. Total list of annotated genes extracted from the Sheep Genome Assembly v3.1 using the BioMart web-tool for the significant QTL regions and SNP associations identified for the two parasite resistance traits analyzed in the present study. Among the total list of genes extracted, we identified 205 functional candidate genes involved in the immune response, based on our candidate gene survey, which are indicated in blue font colour. The colour of the rows refer to genes extracted based on the results of the Linkage Analysis (LA; green), Combined Linkage Disequilibrium and Linkage Analysis (LDLA; yellow) and Genome-wise Association Study (GWAS; blue).
DOI: 10.6084/m9.figshare.c.3644537_d1
title: Additional file 1: of Germline mutations in BRCA1 and BRCA2 in epithelial ovarian cancer patients in Brazil

description: Supplementary Methods. Table S1. Clinical and pathological characteristics, BRCA sequencing and MLPA results. Table S2. BRCA1 gene variants. Table S3. BRCA2 gene variants. (ZIP 73.7 kb)
DOI: 10.6084/m9.figshare.c.3644546_d1
title: Additional file 2 of Multi-objective optimization for RNA design with multiple target secondary structures

description: Supplementary Tables S10 â   S15. The detailed results of the single-target RNA design by MODENA. (XLSX 70.8 kb)
DOI: 10.6084/m9.figshare.c.3644546_d2
title: Additional file 1 of Multi-objective optimization for RNA design with multiple target secondary structures

description: Supplementary Tables S1 â   S9. The detailed results of the RNA sequences designed by MODENA. The results for two-, three-, four-target designs with and without sequence constraints are included. (XLSX 71.7 kb)
DOI: 10.6084/m9.figshare.c.3644666_d1
title: MOESM1 of Using biological networks to integrate, visualize and analyze genomics data

description: Additional file 1: Table S1. Case study gene expression data. Description: 514 genes from Lawless et al. [30] that were found to be significantly up-regulated more than threefold in monocytes isolated from milk at either 36 or 48Â h post-infection (hpi) with the pathogen Streptococcus uberis that causes mastitis in cattle.
DOI: 10.6084/m9.figshare.c.3644747_d2
title: Additional file 2: of The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata)

description: Peptides. This table contains all peptides of identifications in Additional file 1 in alphabetic order starting with the first amino acid. It also contains additional data such as scores, charge state, and mass accuracy. (XLS 2094 kb)
DOI: 10.6084/m9.figshare.c.3644747_d1
title: Additional file 1: of The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata)

description: ProteinGroups. This table contains MaxQuant ProteinGroup output and contains the complete list of identifications, including those not accepted after manual validation or because they did not match the thresholds defined in Materials and Methods. The table also includes relevant additional data such as the complete set of accession numbers forming one group, the calculated molecular weight of each accession, iBAQ intensities and scores. (XLS 687 kb)
DOI: 10.6084/m9.figshare.c.3644747_d4
title: Additional file 4: of The calcified eggshell matrix proteome of a songbird, the zebra finch (Taeniopygia guttata)

description: Phospho(STY)sites. This file contains the MaxQuant output for phosphopeptides and also includes peptides not accepted after manual validation. The data include phosphopeptide sequences, localization probabilities and scores. (XLS 95 kb)
DOI: 10.6084/m9.figshare.c.3644750_d3
title: Additional file 3: File S2. of The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria

description: KEGG weblinks with the functional conservation of metabolic maps in Gammaproteobacteria. (TXT 56Â kb)
DOI: 10.6084/m9.figshare.c.3644750_d5
title: Additional file 1: Table S1. of The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria

description: Statistics of construction of ESS per metabolic map. Number of reactions, genes, and ESS produced for each metabolic map per organism. (TAB 230Â kb)
DOI: 10.6084/m9.figshare.c.3644750_d6
title: Additional file 5: File S1. of The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria

description: Enzymatic Step Sequence database. (ZIP 1300Â kb)
DOI: 10.6084/m9.figshare.c.3644753_d1
title: Additional file 2: of Evidence-based practice, research utilization, and knowledge translation in chiropractic: a scoping review

description: Data Abstraction Table. (XLSX 213 kb)
DOI: 10.6084/m9.figshare.c.3644753_d2
title: Additional file 3: of Evidence-based practice, research utilization, and knowledge translation in chiropractic: a scoping review

description: Thematic analysis of articles*. (XLSX 24 kb)
DOI: 10.6084/m9.figshare.c.3644759_d4
title: MOESM1 of Lytic polysaccharide monooxygenases and other oxidative enzymes are abundantly secreted by Aspergillus nidulans grown on different starches

description: Additional file 1: Table S1. Proteins identified in the secretome of Aspergillus nidulans. The table shows the MaxQuant output of identified proteins and the quantitative LFQ intensities associated with all replicates and conditions. Prediction of secretion was done as a combination of SignalP, Phobius and WoLF PSORT. CAZy annotation was done with dbCAN.
DOI: 10.6084/m9.figshare.c.3644765_d2
title: Additional file 1: of Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis

description: Supplementary tables. (XLSX 1072 kb)
DOI: 10.6084/m9.figshare.c.3644870_d2
title: Additional file 2: of ProClaT, a new bioinformatics tool for in silico protein reclassification: case study of DraB, a protein coded from the draTGB operon in Azospirillum brasilense

description: List of bacterial species having at least 5 genes nif and the presence of the genes nif, nifO, draT and draG. In the list below are all bacterial species that contain at least five essential nif genes according to ProClaT, analyzing the complete genomes of bacteria. The columns indicate the presence of nifHDK, nifENB, nifO, draT and draG genes. (XLSX 14Â kb)
DOI: 10.6084/m9.figshare.c.3644897_d1
title: Additional file 3 of SwitchFinder â   a novel method and query facility for discovering dynamic gene expression patterns

description: Additional file A-H. These files contain the fitting results for the genes from the groups A-H, deduced by SwitchFinder, which represent eight dynamic patterns of the gene expression response to ATRA in neuroblastoma cell line. (ZIP 2457 kb)
DOI: 10.6084/m9.figshare.c.3644873_d4
title: Additional file 1: of 
                     Acanthamoeba containing endosymbiotic chlamydia isolated from hospital environments and its potential role in inflammatory exacerbation

description: Accession numbers of nucleotide sequences used for the phylogenetic analysis. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.c.3644903_d1
title: Additional file 1: Table S1. of Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat

description: Chromosomal locations and genotypic data for GBS markers. (XLSX 924Â kb)
DOI: 10.6084/m9.figshare.c.3644903_d2
title: Additional file 2: Table S2. of Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat

description: QTL detected by Single QTL mapping methods. (XLSX 17Â kb)
DOI: 10.6084/m9.figshare.c.3644972_d7
title: Additional file 2: of Reproducibility of Illumina platform deep sequencing errors allows accurate determination of DNA barcodes in cells

description: The file ‘testartificialdata.txt’ contains example artificial data to which the clean-up procedure (i.e., the script ‘barcodecleanup.R’) can be applied. (TXT 399 bytes)
DOI: 10.6084/m9.figshare.c.3645017_d3
title: MOESM1 of Complete genome sequence of Peptoclostridium difficile strain Z31

description: Additional file 1. Â Assembler software (Mira, Newbler and SPAdes) parameters.
DOI: 10.6084/m9.figshare.c.3645017_d2
title: MOESM2 of Complete genome sequence of Peptoclostridium difficile strain Z31

description: Additional file 2. Â Primer sets used on in silico PCRÂ for genes related to virulence factor, antibiotic resistance, and other known toxins.
DOI: 10.5281/zenodo.14461984
title: Leveraging Fitness Tracker Applications for Sustainable Exercise Habits

description: Dataset
DOI: 10.5281/zenodo.14461985
title: Leveraging Fitness Tracker Applications for Sustainable Exercise Habits

description: Dataset
DOI: 10.6084/m9.figshare.c.3645122_d1
title: Additional file 1: of The balance between Foxp3 and Ror-Îłt expression in peripheral blood is altered by tocilizumab and abatacept in patients with rheumatoid arthritis

description: The expression levels of master regulator genes and clinical responses to ABT or TCZ. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3645125_d1
title: Additional file 5: of An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

description: List of GDSL sequences from lycophyte S. moellendorffii and selected green algae identified here by motif scanning methods. Lists of GDSL sequences from different proteomes are given in separate sheets. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3645125_d2
title: Additional file 4: of An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

description: List of sequences from Pfam family PF00657. GDSL lipases are shown in red while sequences missing one or more blocks are in blue. (XLSX 31 kb)
DOI: 10.6084/m9.figshare.c.3645125_d4
title: Additional file 3: of An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

description: Revised list of GDSL sequences. Analyses of GDSL sequences from different proteomes are given in separate sheets. In each sheet, table A shows GDSL sequences from the RefSeq proteomes identified in this study; table B shows previously reported GDSL sequences not identified in our study but traced in RefSeq via provided gene loci [9]; and table C shows previously reported GDSL sequences [9] that could not be traced since standard gene identifiers were not provided. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.c.3645125_d7
title: Additional file 6: of An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom

description: List of GDSL sequences used for the phylogenetic analysis. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.c.3645149_d2
title: MOESM2 of Assigning breed origin to alleles in crossbred animals

description: Additional file 2. Figure S1: Percentages of correct allelic assignments with a relaxation factor equal to 20 % when breeds are distantly related. Minimum (grey) and maximum (black) percentages of correct allelic assignments, for the chromosome 2 and averaged across A(BC) animals of distantly related breeds, as a function of the number of offset and non-offset phasing analyses selected based on a forward selection. Reported results are averages and SD across all replicates. Figure S2: Percentages of correct allelic assignments with a relaxation factor equal to 0 % when breeds are distantly related. Minimum (grey) and maximum (black) percentages of correct allelic assignments, for the chromosome 2 and averaged across A(BC) animals of distantly related breeds, as a function of the number of offset and non-offset phasing analyses selected based on a forward selection. Reported results are averages and SD across all replicates. Figure S3: Percentages of correct allelic assignments with a relaxation factor equal to 20 % when breeds are unrelated. Minimum (grey) and maximum (black) percentages of correct allelic assignments, for the chromosome 2 and averaged across A(BC) animals of unrelated breeds, as a function of the number of offset and non-offset phasing analyses selected based on a forward selection. Reported results are averages and SD across all replicates. Figure S4: Breed origin of the two alleles for each SNP of the chromosome SSC2 in 20 EF animals using BOA and the additional rules. Alleles from breeds E and F are in green and blue, respectively. Grey regions are unassigned alleles. Relaxation factor was equal to 0 %. Figure S5: Breed origin of the two alleles for each SNP of the chromosome SSC2 in 20 D(EF) animals using BOA and the additional rules. Alleles from breeds D, E, and F are in brown, green, and blue, respectively. Grey regions are unassigned alleles. Relaxation factor was equal to 0 %.
DOI: 10.6084/m9.figshare.c.3645152_d1
title: Additional file 2: of A longitudinal study on the information needs and preferences of patients after an acute coronary syndrome

description: DATABASE. (XLS 191 kb)
DOI: 10.6084/m9.figshare.c.3645257_d5
title: Additional file 2: of Systematic review of outcome domains and instruments used in clinical trials of tinnitus treatments in adults

description: TINNET WG5 master file. An editable version of the data master file. (XLSX 313 kb)
DOI: 10.6084/m9.figshare.c.3645269_d4
title: Additional file 20: Table S2. of Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

description: Spearman's correlation coefficients and Spearman's partial correlations controlling for mRNA abundance to assess an association between codon optimality and mRNA synthesis rates. (XLS 31 kb)
DOI: 10.6084/m9.figshare.c.3645269_d11
title: Additional file 23: Table S5. of Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe

description: Presence (1) and absence (0) of DNA/RNA sequence motifs in S. pombe. (XLS 538 kb)
DOI: 10.6084/m9.figshare.c.3645371_d1
title: Additional file 1: Figures S1A, S1B, and S1C. of PML-RAR alpha induces the downmodulation of HHEX: a key event responsible for the induction of an angiogenetic response

description: Figure S1A Analysis of HHEX (top panel) and VEGF-A (middle panel) reported in 176 primary AMLs on the TCGA platform. The HHEX/VEGF-A ratio is reported in the bottom panel. Figure S1B Correlation between HHEX and VEGF-A levels observed in 18 primary APLs in the present study (p = 0.0484) and in 16 primary APLs in the TCGA data (p = 0.0284). Figure S1C Correlation between HHEX and VEGF-A levels observed in 18 primary APLs (p = 00484) and in 20 primary M5 AMLs in the TCGA data (p = 0.0174). (ZIP 689 kb)
DOI: 10.6084/m9.figshare.c.3645392_d1
title: Additional file 1: of Mapping areas of spatial-temporal overlap from wildlife tracking data

description: Derivation of biased correlated random walks (BCRW) as implemented in the simulation study. (ZIP 26.5 kb)
DOI: 10.6084/m9.figshare.c.3645395_d2
title: MOESM3 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

description: Additional file 3: Table S3. SNPs and Indels identified in the PF3D7_1222600 gene among P. falciparum field isolates from Africa and Asia.
DOI: 10.6084/m9.figshare.c.3645395_d4
title: MOESM7 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

description: Additional file 7: Table S5. A scan for motifs in gene sequences (coding and UTR regions).
DOI: 10.6084/m9.figshare.c.3645395_d5
title: MOESM4 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

description: Additional file 4: Table S4. Structural variants identified in the three lines 3D7A, A4 and F12.
DOI: 10.6084/m9.figshare.c.3645395_d3
title: MOESM1 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

description: Additional file 1: Table S1. SNPs identified in the three lines 3D7A, A4 and F12.
DOI: 10.6084/m9.figshare.c.3645395_d7
title: MOESM2 of Genomic variation in two gametocyte non-producing Plasmodium falciparum clonal lines

description: Additional file 2: Table S2. Insertions (INS) and deletions (DEL) identified in the three lines 3D7A, A4 and F12.
DOI: 10.6084/m9.figshare.c.3645500_d1
title: Additional file 1: of Comparison of sodium ion levels between an arterial blood gas analyzer and an autoanalyzer in preterm infants admitted to the neonatal intensive care unit: a retrospective study

description: The datasets supporting the conclusion of this study. (XLSX 820Â kb)
DOI: 10.6084/m9.figshare.c.3645512_d1
title: Additional file 5: Table S4. of Negative selection maintains transcription factor binding motifs in human cancer

description: Overview of DNase accessibility data analysis including mutation counts, motif predictions and data sources used to filter mutations in regulatory regions for breast cancer and lung adenocarcinoma. (XLSX 153 kb)
DOI: 10.6084/m9.figshare.c.3645512_d3
title: Additional file 4: Table S3. of Negative selection maintains transcription factor binding motifs in human cancer

description: Binding motifs under positive and negative selection. Data for separate motifs is shown, as well as aggregated data for the motifs grouped by family (number of significantly protected motifs is shown, family name and ID are given according to TFClass). (XLSX 30 kb)
DOI: 10.6084/m9.figshare.c.3645512_d4
title: Additional file 7: Table S5. of Negative selection maintains transcription factor binding motifs in human cancer

description: Binding motifs found under positive and negative selection in a basic test considering mutations overlapping and avoiding binding sites predictions. Raw data on binding sites predictions are given along with the resulting aggregated information for motif families. (XLSX 370 kb)
DOI: 10.6084/m9.figshare.c.3645512_d5
title: Additional file 2: Table S2. of Negative selection maintains transcription factor binding motifs in human cancer

description: Raw data on binding sites predictions across mutation-centered windows in all evaluated cancer data sets as well as the respective generated control data sets. (XLSX 624 kb)
DOI: 10.6084/m9.figshare.c.3645512_d7
title: Additional file 1: Table S1. of Negative selection maintains transcription factor binding motifs in human cancer

description: Mutation counts, frequencies of mutation contexts and relative control sizes for different cancer types. Initial as well as the final size (after binding sites predictions and equalizing the mutation contexts distribution) of each control set is shown. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3645611_d2
title: Additional file 2: of CNV analysis in the Lithuanian population

description: Summary of CNVs detected. Also includes CNV annotation results. (XLSX 368Â kb)
DOI: 10.6084/m9.figshare.c.3645620_d1
title: Additional file 1: Table S1. of Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map

description: Order and position of SNP markers in genetic map. (XLSX 234Â kb)
DOI: 10.6084/m9.figshare.c.3645620_d2
title: Additional file 3: Table S2. of Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map

description: Comparison of 38 SNP calls by GBS and resequencing data. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3645620_d3
title: Additional file 2: Table S3. of Molecular Dissection of Seedling Salinity Tolerance in Rice (Oryza sativa L.) Using a High-Density GBS-Based SNP Linkage Map

description: List of candidate genes contained in QTL intervals. (XLSX 84Â kb)
DOI: 10.6084/m9.figshare.c.3645647_d1
title: Additional file 1: of Difference in blood pressure between early and late menopausal transition was significant in healthy Korean women

description: Baseline characteristics of the study population excluding women taking antihypertensive drugs. (XLSX 11 kb)