cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5834814
title: Additional file 1 of Identifying factors influencing contraceptive use in Bangladesh: evidence from BDHS 2014 data

description: 2014 Bangladesh Demographic and Health Survey data. Description of data: The Bangladesh Demographic Health Survey (BDHS) 2014 was a nationally representative cross sectional survey conducted between June and November 2014, covering the entire population of Bangladesh. The survey was based on a two-stage stratified sample of households. In the first stage, 600 enumerations areas (EAs) were selected with probability proportional to EA size, with 207 EAs from urban areas and 393 from rural areas, where an EA is either a village, a group of small villages, or a part of a large village. In the second stage, a systematic sample of 30 households on average was selected per EA to provide statistically reliable estimates of the key demographic and health variables for the country as a whole, for urban and rural areas separately and each of the seven divisions which are the administrative regions of Bangladesh. The 2014 BDHS used three types of questionnaires: a household questionnaire, a women questionnaire and a community questionnaire. For the women questionnaire, a total of 18,000 ever married and 16858 currently married (when conducting the interview) women aged between 15-49 years were interviewed. For our study, we considered only currently married women to ensure similar prevalence as BDHS 2014 reported. Further details about the data set can be found from Methods Section. (CSV 24,064 kb)
DOI: 10.6084/m9.figshare.5834814.v1
title: Additional file 1 of Identifying factors influencing contraceptive use in Bangladesh: evidence from BDHS 2014 data

description: 2014 Bangladesh Demographic and Health Survey data. Description of data: The Bangladesh Demographic Health Survey (BDHS) 2014 was a nationally representative cross sectional survey conducted between June and November 2014, covering the entire population of Bangladesh. The survey was based on a two-stage stratified sample of households. In the first stage, 600 enumerations areas (EAs) were selected with probability proportional to EA size, with 207 EAs from urban areas and 393 from rural areas, where an EA is either a village, a group of small villages, or a part of a large village. In the second stage, a systematic sample of 30 households on average was selected per EA to provide statistically reliable estimates of the key demographic and health variables for the country as a whole, for urban and rural areas separately and each of the seven divisions which are the administrative regions of Bangladesh. The 2014 BDHS used three types of questionnaires: a household questionnaire, a women questionnaire and a community questionnaire. For the women questionnaire, a total of 18,000 ever married and 16858 currently married (when conducting the interview) women aged between 15-49 years were interviewed. For our study, we considered only currently married women to ensure similar prevalence as BDHS 2014 reported. Further details about the data set can be found from Methods Section. (CSV 24,064 kb)
DOI: 10.6084/m9.figshare.5834808
title: Additional file 16: Table S15. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT4. Identified unique genes in the metatranscriptome of sample AT4, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 1219Â kb)
DOI: 10.6084/m9.figshare.5834808.v1
title: Additional file 16: Table S15. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT4. Identified unique genes in the metatranscriptome of sample AT4, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 1219Â kb)
DOI: 10.6084/m9.figshare.5834805
title: Additional file 11: of Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)

description: List of all miRNAs (known and novel) expressed in our data with a base mean value â Ľ10 reads. (XLSX 202 kb)
DOI: 10.6084/m9.figshare.5834805.v1
title: Additional file 11: of Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)

description: List of all miRNAs (known and novel) expressed in our data with a base mean value â Ľ10 reads. (XLSX 202 kb)
DOI: 10.6084/m9.figshare.5834802
title: Additional file 3: of Commensal microbiota modulate gene expression in the skin

description: Dataset S1. Results from differential expression analysis. Rows contain the 15,448 features analyzed. Columns contain Ensembl feature id, mean expression of GF samples, mean expression of SPF samples, the NOISeq differential expression statistic theta, the probability of differential expression (equal to 1-FDR-corrected p value when using NOISeqBio, DEGs defined as those with prob. &gt; 0.9), the log2 fold change in expression (upregulated in GF &gt; 0, downregulated in GF
DOI: 10.6084/m9.figshare.5834802.v1
title: Additional file 3: of Commensal microbiota modulate gene expression in the skin

description: Dataset S1. Results from differential expression analysis. Rows contain the 15,448 features analyzed. Columns contain Ensembl feature id, mean expression of GF samples, mean expression of SPF samples, the NOISeq differential expression statistic theta, the probability of differential expression (equal to 1-FDR-corrected p value when using NOISeqBio, DEGs defined as those with prob. &gt; 0.9), the log2 fold change in expression (upregulated in GF &gt; 0, downregulated in GF
DOI: 10.6084/m9.figshare.5834799
title: MOESM1 of Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization

description: Additional file 1. Primers used in study.
DOI: 10.6084/m9.figshare.5834799.v1
title: MOESM1 of Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization

description: Additional file 1. Primers used in study.
DOI: 10.6084/m9.figshare.5834790
title: Additional file 15: Table S14. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT3. Identified unique genes in the metatranscriptome of sample AT3, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 1326Â kb)
DOI: 10.6084/m9.figshare.5834790.v1
title: Additional file 15: Table S14. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT3. Identified unique genes in the metatranscriptome of sample AT3, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 1326Â kb)
DOI: 10.6084/m9.figshare.5834787
title: Additional file 10: of Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)

description: KEGG pathways associated with genes that were differentially expressed between Texel and F1 ewes on a flushing diet. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5834787.v1
title: Additional file 10: of Integrated ovarian mRNA and miRNA transcriptome profiling characterizes the genetic basis of prolificacy traits in sheep (Ovis aries)

description: KEGG pathways associated with genes that were differentially expressed between Texel and F1 ewes on a flushing diet. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.5834766
title: Additional file 14: Table S13. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT2. Identified unique genes in the metatranscriptome of sample AT2, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 8417Â kb)
DOI: 10.6084/m9.figshare.5834766.v1
title: Additional file 14: Table S13. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Metatranscriptomic gene annotation of sample AT2. Identified unique genes in the metatranscriptome of sample AT2, using transcripts assembled using Trinity and annotating using the Trinotate pipeline. Swissprot was used as reference database. (XLSX 8417Â kb)
DOI: 10.6084/m9.figshare.5834760
title: Additional file 1: Table S1. of Commensal microbiota modulate gene expression in the skin

description: Sample summary statistics. Rows contain the 16 samples analyzed; with columns containing associated sequencing statistics and metadata. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.5834760.v1
title: Additional file 1: Table S1. of Commensal microbiota modulate gene expression in the skin

description: Sample summary statistics. Rows contain the 16 samples analyzed; with columns containing associated sequencing statistics and metadata. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.5834757
title: MOESM12 of Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization

description: Additional file 12. GO Analysis on gene-list of genes which are regulated by E2 and targeted by TDG in response to E2.
DOI: 10.6084/m9.figshare.5834757.v1
title: MOESM12 of Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization

description: Additional file 12. GO Analysis on gene-list of genes which are regulated by E2 and targeted by TDG in response to E2.
DOI: 10.6084/m9.figshare.5834736
title: Additional file 13: of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Narrowed-down database containing all predicted and annotated genes of all organisms used in the specialised data analysis of this study. (FASTA 46859Â kb)
DOI: 10.6084/m9.figshare.5834736.v1
title: Additional file 13: of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Narrowed-down database containing all predicted and annotated genes of all organisms used in the specialised data analysis of this study. (FASTA 46859Â kb)
DOI: 10.6084/m9.figshare.5834712
title: Additional file 12: Table S12. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Constructed bacterial genomes of this study. List of constructed genomes based on metagenomic read binning using the MetaBat software, their assigned genera and ID used in this study, and corresponding CheckM software analysis results. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5834712.v1
title: Additional file 12: Table S12. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Constructed bacterial genomes of this study. List of constructed genomes based on metagenomic read binning using the MetaBat software, their assigned genera and ID used in this study, and corresponding CheckM software analysis results. (XLSX 10Â kb)
DOI: 10.6084/m9.figshare.5834694
title: Additional file 11: Table S11. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Common core metagenome of non-symptomatic samples. Genes identified in all non-symptomatic samples (AT2, AT3 and AT4), and in no symptomatic samples. Based on MG-RAST annotation using Swissprot as reference database. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.5834694.v1
title: Additional file 11: Table S11. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Common core metagenome of non-symptomatic samples. Genes identified in all non-symptomatic samples (AT2, AT3 and AT4), and in no symptomatic samples. Based on MG-RAST annotation using Swissprot as reference database. (XLSX 64Â kb)
DOI: 10.6084/m9.figshare.5834679
title: Additional file 10: Table S10. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Common core metagenome of AOD symptomatic tissue. Genes identified in all symptomatic samples (AT5, AT8, ROW1, ROW1â 2 and ROW2), and in no non-symptomatic samples. Based on MG-RAST annotation using Swissprot as reference database. (XLSX 105Â kb)
DOI: 10.6084/m9.figshare.5834679.v1
title: Additional file 10: Table S10. of Integrated multi-omic analysis of host-microbiota interactions in acute oak decline

description: Common core metagenome of AOD symptomatic tissue. Genes identified in all symptomatic samples (AT5, AT8, ROW1, ROW1â 2 and ROW2), and in no non-symptomatic samples. Based on MG-RAST annotation using Swissprot as reference database. (XLSX 105Â kb)
DOI: 10.6084/m9.figshare.5834664
title: Additional file 1: Figure S1. of Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history

description: Venn diagram of gene orthologs across the 3 bacteria. Figure S2. Symbiotic plasmids syntenies and differentially regulated genes. Figure S3. Summary of RNAseq results per replicate and condition. Figure S4. Comparison of pVal and Fold Change values on the number of DEG. Figure S5. Genes targeted 5 for qPCR (A) & primers used (B). Figure S6. Comparison of gene expression between RNAseq counts and qPCR. Table S1. Excel tables of all DEG data shared or specific. Figure S8. Myo-inositol catabolism operons in BP, RM and CT. Figure S9. Biolog GN20 API galleries results for BP, CT and RM. Figure S10. Annotation of the putative rhizobitoxine biosynthesis operon in BP. Figure S11. Up-regulated (A) and down-regulated (B) T6SS in B. phymatum (BP). Figure S12. T4SS of B. phymatum STM815. Figure S13. Elution profiles of C. taiwanensis RNA samples. Figure S14. Scatter plots (A) & Volcano plot (B) of RNAseq data. (ZIP 15222 kb)
DOI: 10.6084/m9.figshare.5834664.v1
title: Additional file 1: Figure S1. of Transcriptomic profiling of Burkholderia phymatum STM815, Cupriavidus taiwanensis LMG19424 and Rhizobium mesoamericanum STM3625 in response to Mimosa pudica root exudates illuminates the molecular basis of their nodulation competitiveness and symbiotic evolutionary history

description: Venn diagram of gene orthologs across the 3 bacteria. Figure S2. Symbiotic plasmids syntenies and differentially regulated genes. Figure S3. Summary of RNAseq results per replicate and condition. Figure S4. Comparison of pVal and Fold Change values on the number of DEG. Figure S5. Genes targeted 5 for qPCR (A) & primers used (B). Figure S6. Comparison of gene expression between RNAseq counts and qPCR. Table S1. Excel tables of all DEG data shared or specific. Figure S8. Myo-inositol catabolism operons in BP, RM and CT. Figure S9. Biolog GN20 API galleries results for BP, CT and RM. Figure S10. Annotation of the putative rhizobitoxine biosynthesis operon in BP. Figure S11. Up-regulated (A) and down-regulated (B) T6SS in B. phymatum (BP). Figure S12. T4SS of B. phymatum STM815. Figure S13. Elution profiles of C. taiwanensis RNA samples. Figure S14. Scatter plots (A) & Volcano plot (B) of RNAseq data. (ZIP 15222 kb)
DOI: 10.6084/m9.figshare.5834658
title: Additional file 1: of Variations of circulating cardiac biomarkers during and after anthracycline-containing chemotherapy in breast cancer patients

description: Statistical analyses. (A) Correlations Spearman tests between the fold change of cTnT, NT-proBNP, sST2, miR-126-3p, miR-199a-3p, miR-423-5p and miR-34a-5p at different time point of the neoadjuvant chemotherapy in 45 breast cancer patients. (B) Comparison between the increase of the markers at the end of the chemotherapy (NA1 vs. D8 and NA1 vs. 3 M) in patients treated (n = 17) or not (n = 28) with HER2 targeted therapy, using Mann-Whitney tests. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.5834658.v1
title: Additional file 1: of Variations of circulating cardiac biomarkers during and after anthracycline-containing chemotherapy in breast cancer patients

description: Statistical analyses. (A) Correlations Spearman tests between the fold change of cTnT, NT-proBNP, sST2, miR-126-3p, miR-199a-3p, miR-423-5p and miR-34a-5p at different time point of the neoadjuvant chemotherapy in 45 breast cancer patients. (B) Comparison between the increase of the markers at the end of the chemotherapy (NA1 vs. D8 and NA1 vs. 3 M) in patients treated (n = 17) or not (n = 28) with HER2 targeted therapy, using Mann-Whitney tests. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.5834631
title: Additional file 1: of Does a provider payment method affect membership retention in a health insurance scheme? a mixed method study of Ghanaâ s capitation payment for primary care

description: NHIS membership dataset - new enrollment, renewal and total active membership data on NHIS subscribers in the Ashanti, Volta and Central regions of Ghana from 2009 to 2014. (XML 129 kb)
DOI: 10.6084/m9.figshare.5834631.v1
title: Additional file 1: of Does a provider payment method affect membership retention in a health insurance scheme? a mixed method study of Ghanaâ s capitation payment for primary care

description: NHIS membership dataset - new enrollment, renewal and total active membership data on NHIS subscribers in the Ashanti, Volta and Central regions of Ghana from 2009 to 2014. (XML 129 kb)
DOI: 10.6084/m9.figshare.5834592
title: Additional file 6: Table S5. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: IPA. Canonical pathways and upstream analysis for DE results: contrasts for c1 vs c3â 5, c2 vs c3â 5, c1 vs c2. (XLSX 203 kb)
DOI: 10.6084/m9.figshare.5834592.v1
title: Additional file 6: Table S5. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: IPA. Canonical pathways and upstream analysis for DE results: contrasts for c1 vs c3â 5, c2 vs c3â 5, c1 vs c2. (XLSX 203 kb)
DOI: 10.6084/m9.figshare.5834586
title: Additional file 3: of Development of a rapid point-of-care patient reported outcome measure for cataract surgery in India

description: Raw score to Rasch person-measure conversion. This worksheet allows researchers and clinicians to covert raw SF-IND-VFQ scores to interval scores without performing their own Rasch analysis. Caution should be exercised in applying this Rasch analysis to patient populations that are very different from the one in this study. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5834574
title: Additional file 5: Table S4. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Patient metadata and biomarker data. Clinical data summaries for patient groups and anonymized biomarker values for elite controllers and chronic progressors: CD4+ T cell counts, viral load, and CD64Hi,PD-L1Hi fractions before and after viral (VSV-g pseudotyped HIV-1) exposure. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.5834574.v1
title: Additional file 5: Table S4. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Patient metadata and biomarker data. Clinical data summaries for patient groups and anonymized biomarker values for elite controllers and chronic progressors: CD4+ T cell counts, viral load, and CD64Hi,PD-L1Hi fractions before and after viral (VSV-g pseudotyped HIV-1) exposure. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.5834556
title: Additional file 4: Table S3. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: DE Analysis. DE analysis results as described in “Methods,” including contrasts for c1 vs c3–5, c2 vs c3–5, c1 vs c2, and intra-c1 exposure differences. Numbers of cells in each comparison are printed above log-fold-change columns. Gene sets from Fig. 2c are included. (XLSX 3450 kb)
DOI: 10.6084/m9.figshare.5834556.v1
title: Additional file 4: Table S3. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: DE Analysis. DE analysis results as described in “Methods,” including contrasts for c1 vs c3–5, c2 vs c3–5, c1 vs c2, and intra-c1 exposure differences. Numbers of cells in each comparison are printed above log-fold-change columns. Gene sets from Fig. 2c are included. (XLSX 3450 kb)
DOI: 10.6084/m9.figshare.5834532
title: Additional file 3: Table S2. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Reproducible Modules and FastProject Analysis. Lists of genes exhibiting significantly high numbers of reproducible correlations as described in â Methods.â FastProject signature values and significance scores. (XLSX 408 kb)
DOI: 10.6084/m9.figshare.5834532.v1
title: Additional file 3: Table S2. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Reproducible Modules and FastProject Analysis. Lists of genes exhibiting significantly high numbers of reproducible correlations as described in â Methods.â FastProject signature values and significance scores. (XLSX 408 kb)
DOI: 10.6084/m9.figshare.5834523
title: Additional file 5: of Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

description: Supporting data. Raw supporting data for Figs. 2A,B1–B4,C, 3A,B, 7 F, and 8C. (XLS 215 kb)
DOI: 10.6084/m9.figshare.5834523.v1
title: Additional file 5: of Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

description: Supporting data. Raw supporting data for Figs. 2A,B1–B4,C, 3A,B, 7 F, and 8C. (XLS 215 kb)
DOI: 10.6084/m9.figshare.5834511
title: Additional file 2: Table S1. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Clusters and tSNE coordinates for 48-h cells. Cluster identifiers and tSNE coordinates from (Fig.Â 1c) as described in â Methods.â (XLSX 27 kb)
DOI: 10.6084/m9.figshare.5834511.v1
title: Additional file 2: Table S1. of A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

description: Clusters and tSNE coordinates for 48-h cells. Cluster identifiers and tSNE coordinates from (Fig.Â 1c) as described in â Methods.â (XLSX 27 kb)
DOI: 10.6084/m9.figshare.5834496
title: Additional file 3: of Saving Lives at Birth; development of a retrospective theory of change, impact framework and prioritised metrics

description: Theory of change description and assumptions. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.5834496.v1
title: Additional file 3: of Saving Lives at Birth; development of a retrospective theory of change, impact framework and prioritised metrics

description: Theory of change description and assumptions. (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.5834484
title: Additional file 2: of Are CONSORT checklists submitted by authors adequately reflecting what information is actually reported in published papers?

description: Summary of evaluations. (XLSX 77 kb)