cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5938003
title: MOESM3 of H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

description: Additional file 3. Results of in silico analysis of experimental data and â optimalâ growth predictions with the GEM iCLAU786. Table S3. Summary of results; Table S4. Complete results.
DOI: 10.6084/m9.figshare.5938003.v1
title: MOESM3 of H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

description: Additional file 3. Results of in silico analysis of experimental data and â optimalâ growth predictions with the GEM iCLAU786. Table S3. Summary of results; Table S4. Complete results.
DOI: 10.6084/m9.figshare.5937997
title: Additional file 7: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S4. Ca. P. polyenzymogenes-affiliated ORFs detected via HTP metaproteomic analysis of rumen microbiome samples. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5937997.v1
title: Additional file 7: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S4. Ca. P. polyenzymogenes-affiliated ORFs detected via HTP metaproteomic analysis of rumen microbiome samples. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.5937988
title: MOESM2 of H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

description: Additional file 2. Results of intracellular metabolome analysis. Table S1. Intracellular metabolite concentrations in high biomass cultures; Table S2. Metabolite abbreviations.
DOI: 10.6084/m9.figshare.5937988.v1
title: MOESM2 of H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum

description: Additional file 2. Results of intracellular metabolome analysis. Table S1. Intracellular metabolite concentrations in high biomass cultures; Table S2. Metabolite abbreviations.
DOI: 10.6084/m9.figshare.5937979
title: Additional file 6: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S3. Open reading frame coordinates and CAZyme annotation for UBA genomes affiliated to Ca. MH11. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.5937979.v1
title: Additional file 6: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S3. Open reading frame coordinates and CAZyme annotation for UBA genomes affiliated to Ca. MH11. (XLSX 182 kb)
DOI: 10.6084/m9.figshare.5937961
title: Additional file 3: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: Dutch medical screening questionnaire for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (XLSX 67 kb)
DOI: 10.6084/m9.figshare.5937961.v1
title: Additional file 3: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: Dutch medical screening questionnaire for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (XLSX 67 kb)
DOI: 10.6084/m9.figshare.5937949
title: Additional file 2: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: Data collected for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (XLSX 62 kb)
DOI: 10.6084/m9.figshare.5937949.v1
title: Additional file 2: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: Data collected for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (XLSX 62 kb)
DOI: 10.6084/m9.figshare.5937928
title: Additional file 1: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: READ ME â medical screening questionnaireÂ for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (ZIP 32 kb)
DOI: 10.6084/m9.figshare.5937928.v1
title: Additional file 1: of A Benefit of Being Heavier Is Being Strong: a Cross-Sectional Study in Young Adults

description: READ ME â medical screening questionnaireÂ for the study "A benefit of being heavier is being strong: a cross-sectional study in young adults". (ZIP 32 kb)
DOI: 10.6084/m9.figshare.5937925
title: Additional file 3: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S2. CAZyme profiles for the seven Ca. MH11 affiliated genomes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5937925.v1
title: Additional file 3: of “Candidatus Paraporphyromonas polyenzymogenes” encodes multi-modular cellulases linked to the type IX secretion system

description: Table S2. CAZyme profiles for the seven Ca. MH11 affiliated genomes. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.5937877
title: Additional file 4: of CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival

description: Table S1. Table showing differentially methylated CpGs between BM of NSCLC with a highly functional immune response, defined as CD74high and TILhigh tumors (CD74 TIL high) and tumors not showing both of these features (CD74 TIL low). (CSV 1 kb)
DOI: 10.6084/m9.figshare.5937877.v1
title: Additional file 4: of CD74 regulates complexity of tumor cell HLA class II peptidome in brain metastasis and is a positive prognostic marker for patient survival

description: Table S1. Table showing differentially methylated CpGs between BM of NSCLC with a highly functional immune response, defined as CD74high and TILhigh tumors (CD74 TIL high) and tumors not showing both of these features (CD74 TIL low). (CSV 1 kb)
DOI: 10.6084/m9.figshare.5937760
title: Additional file 9: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: Examples of AS estimates for two- and three-group data. The procedures for analyzing Nakai’s MAS-quantified data consisting of 31,099 probesets × 24 samples are provided. Example 1 compares three-group data with four BRs, 4 BAT_fed samples vs. 4 WAT_fed samples vs. 4 LIV_fed samples, with AS = 0.460. Example 2 compares three-group data with two BRs, “BAT_fed1 and 2” vs. “WAT_fed1 and 2” vs. “LIV_fed1 and 2,” with AS = 0.438. Example 3 compares three-group data with two BRs, “BAT_fed1 and BAT_fas1” vs. “BAT_fed2 and BAT_fas2” vs. “BAT_fed3 and BAT_fas3,” with AS = − 0.185. Example 4 compares two-group data with four BRs, 4 BAT_fed samples vs. 4 WAT_fed samples, with AS = 0.374. Example 5 compares two-group data with four BRs, 4 BAT_fed samples vs. 4 LIV_fed samples, with AS = 0.657. (R 3 kb)
DOI: 10.6084/m9.figshare.5937760.v1
title: Additional file 9: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: Examples of AS estimates for two- and three-group data. The procedures for analyzing Nakai’s MAS-quantified data consisting of 31,099 probesets × 24 samples are provided. Example 1 compares three-group data with four BRs, 4 BAT_fed samples vs. 4 WAT_fed samples vs. 4 LIV_fed samples, with AS = 0.460. Example 2 compares three-group data with two BRs, “BAT_fed1 and 2” vs. “WAT_fed1 and 2” vs. “LIV_fed1 and 2,” with AS = 0.438. Example 3 compares three-group data with two BRs, “BAT_fed1 and BAT_fas1” vs. “BAT_fed2 and BAT_fas2” vs. “BAT_fed3 and BAT_fas3,” with AS = − 0.185. Example 4 compares two-group data with four BRs, 4 BAT_fed samples vs. 4 WAT_fed samples, with AS = 0.374. Example 5 compares two-group data with four BRs, 4 BAT_fed samples vs. 4 LIV_fed samples, with AS = 0.657. (R 3 kb)
DOI: 10.6084/m9.figshare.5937709
title: MOESM1 of Current applications of antibody microarrays

description: Additional file 1. Detailed information about the home-made and commercially available antibody microarrays.
DOI: 10.6084/m9.figshare.5937709.v1
title: MOESM1 of Current applications of antibody microarrays

description: Additional file 1. Detailed information about the home-made and commercially available antibody microarrays.
DOI: 10.6084/m9.figshare.5937643
title: Additional file 2: of South-south collaboration on HIV/AIDS prevention and treatment research: when birds of a feather rarely flock together

description: VOSviewer map file, depicted in Figure 4. (ZIP 8919Â kb)
DOI: 10.6084/m9.figshare.5937643.v1
title: Additional file 2: of South-south collaboration on HIV/AIDS prevention and treatment research: when birds of a feather rarely flock together

description: VOSviewer map file, depicted in Figure 4. (ZIP 8919Â kb)
DOI: 10.6084/m9.figshare.5937625
title: Additional file 1: of South-south collaboration on HIV/AIDS prevention and treatment research: when birds of a feather rarely flock together

description: List of articles involving at least one author based on a low- or middle-income country (LMIC). (XLSX 17149Â kb)
DOI: 10.6084/m9.figshare.5937625.v1
title: Additional file 1: of South-south collaboration on HIV/AIDS prevention and treatment research: when birds of a feather rarely flock together

description: List of articles involving at least one author based on a low- or middle-income country (LMIC). (XLSX 17149Â kb)
DOI: 10.6084/m9.figshare.5937616
title: Additional file 1: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: Detailed results for Blekhman’s RNA-seq count data. (a) Silhouette indices (s i ) for each sample i and the average (AS). The sample names (A1, A2, A3, B1, B2, or B3) for i correspond to those shown in Fig. 1b. (b) PDEG values at various FDR thresholds (1%, 5%, 10%, 20%, 30%, and 40% FDR). The values at 10% FDR were the same as those shown in Fig. 1b. (c) Percentages of true DEGs (PtrueDEG), defined as PDEG × (1 − FDR threshold), at corresponding FDR thresholds shown in (b). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.5937616.v1
title: Additional file 1: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: Detailed results for Blekhman’s RNA-seq count data. (a) Silhouette indices (s i ) for each sample i and the average (AS). The sample names (A1, A2, A3, B1, B2, or B3) for i correspond to those shown in Fig. 1b. (b) PDEG values at various FDR thresholds (1%, 5%, 10%, 20%, 30%, and 40% FDR). The values at 10% FDR were the same as those shown in Fig. 1b. (c) Percentages of true DEGs (PtrueDEG), defined as PDEG × (1 − FDR threshold), at corresponding FDR thresholds shown in (b). (XLSX 19 kb)
DOI: 10.6084/m9.figshare.5937601
title: MOESM2 of Large-scale genomic prediction using singular value decomposition of the genotype matrix

description: Additional file 2. Combining reduced-dimension genomic data from multiple chromosomes in computation of an inverse approximated genomic relationship matrix.
DOI: 10.6084/m9.figshare.5937601.v1
title: MOESM2 of Large-scale genomic prediction using singular value decomposition of the genotype matrix

description: Additional file 2. Combining reduced-dimension genomic data from multiple chromosomes in computation of an inverse approximated genomic relationship matrix.
DOI: 10.6084/m9.figshare.5937598
title: Additional file 10: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: R-codes for analyses. This zipped file includes a total of 23 R-code files. Results can be obtained by executing scripts in the order of the serial numbers XX in the filename “rcode_XX_...” Note that two files (“rcode_08_Add6_pre.R” and “rcode_10_Add7_pre.R”) must be executed using R ver. 3.1.3 (affy ver. 1.44.0) instead of R ver. 3.3.2 (affy ver. 1.52.0). (ZIP 33 kb)
DOI: 10.6084/m9.figshare.5937598.v1
title: Additional file 10: of Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

description: R-codes for analyses. This zipped file includes a total of 23 R-code files. Results can be obtained by executing scripts in the order of the serial numbers XX in the filename “rcode_XX_...” Note that two files (“rcode_08_Add6_pre.R” and “rcode_10_Add7_pre.R”) must be executed using R ver. 3.1.3 (affy ver. 1.44.0) instead of R ver. 3.3.2 (affy ver. 1.52.0). (ZIP 33 kb)
DOI: 10.6084/m9.figshare.5937586
title: MOESM1 of Large-scale genomic prediction using singular value decomposition of the genotype matrix

description: Additional file 1. How to do reduced-dimension approximation of a larger genomic data set from a specific chromosome, using SVD of data on the same chromosome in a smaller core sample.
DOI: 10.6084/m9.figshare.5937586.v1
title: MOESM1 of Large-scale genomic prediction using singular value decomposition of the genotype matrix

description: Additional file 1. How to do reduced-dimension approximation of a larger genomic data set from a specific chromosome, using SVD of data on the same chromosome in a smaller core sample.
DOI: 10.6084/m9.figshare.5937541
title: MOESM1 of Transcriptome of Russet Norkotah and its clonal selection, TXNS278

description: Additional file 1: Table S1. Overview of the mapping results.
DOI: 10.6084/m9.figshare.5937541.v1
title: MOESM1 of Transcriptome of Russet Norkotah and its clonal selection, TXNS278

description: Additional file 1: Table S1. Overview of the mapping results.
DOI: 10.6084/m9.figshare.5937535
title: Additional file 5: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: Location of gaps and their distances in the merged data set. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5937535.v1
title: Additional file 5: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: Location of gaps and their distances in the merged data set. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5937526
title: Additional file 4: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: Location of gaps and their distances in the genotyping-by-sequencing data set. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5937526.v1
title: Additional file 4: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: Location of gaps and their distances in the genotyping-by-sequencing data set. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5937511
title: Additional file 7: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: Table of primers used in this study. (XLSX 295Â kb)
DOI: 10.6084/m9.figshare.5937511.v1
title: Additional file 7: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: Table of primers used in this study. (XLSX 295Â kb)
DOI: 10.6084/m9.figshare.5937508
title: Additional file 4: of The effects of interventions targeting multiple health behaviors on smoking cessation outcomes: a rapid realist review protocol

description: Excel spreadseet. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.5937508.v1
title: Additional file 4: of The effects of interventions targeting multiple health behaviors on smoking cessation outcomes: a rapid realist review protocol

description: Excel spreadseet. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.5937481
title: Additional file 1: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: List of 86 lines used in the GWA analyses, along with their corresponding maturity group and fastStructure group. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.5937481.v1
title: Additional file 1: of Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

description: List of 86 lines used in the GWA analyses, along with their corresponding maturity group and fastStructure group. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.5937460
title: Additional file 4: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: SNPs in predicted regulatory binding sites of validated genes. Detected SNPs in the 1000-bp upstream region of evaluated target genes that affect binding motifs for regulatory proteins as predicted with YEASTRACT [66]. Comparison of the strains MTF2621 and MTF2622 with the S. cerevisiae reference strain S288C. (XLSX 242Â kb)
DOI: 10.6084/m9.figshare.5937460.v1
title: Additional file 4: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: SNPs in predicted regulatory binding sites of validated genes. Detected SNPs in the 1000-bp upstream region of evaluated target genes that affect binding motifs for regulatory proteins as predicted with YEASTRACT [66]. Comparison of the strains MTF2621 and MTF2622 with the S. cerevisiae reference strain S288C. (XLSX 242Â kb)
DOI: 10.6084/m9.figshare.5937400
title: Additional file 1: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: Additional phenotypic information. Concentrations of determined secondary metabolites produced by the parental strains used in this study with trait variety among the segregant population given as interquartile range (IQR) and heritability of evaluated traits. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.5937400.v1
title: Additional file 1: of QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation

description: Additional phenotypic information. Concentrations of determined secondary metabolites produced by the parental strains used in this study with trait variety among the segregant population given as interquartile range (IQR) and heritability of evaluated traits. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.5937388
title: SupportingInformation.zipComputational pharmacogenetics of P-glycoprotein in antiepileptic drug resistance

description: To accompany manuscript: "Computational pharmacogenetics of P-glycoprotein mediated antiepileptic drug resistance." Includes:<br>1. alignment with conservation scores<br>2. modelled structures of wildtype and mutant human PGP<br>3. Complex structures of docked receptor-drug<br>4. Best pose analysis<br>5. Clustering of docked conformations<br><br>
DOI: 10.6084/m9.figshare.5937388.v1
title: SupportingInformation.zip

description: To accompany manuscript: "Computational pharmacogenetics of P-glycoprotein mediated antiepileptic drug resistance." Includes:<br>1. alignment with conservation scores<br>2. modelled structures of wildtype and mutant human PGP<br>3. Complex structures of docked receptor-drug<br>4. Best pose analysis<br>5. Clustering of docked conformations<br><br>
DOI: 10.5281/zenodo.4008379
title: mthK.double.pdb

description: mthK.double.pdb
DOI: 10.5281/zenodo.4008378
title: mthK.double.pdb

description: mthK.double.pdb
DOI: 10.6084/m9.figshare.5937355
title: Online resources for Acoustic perturbation of breathing - a newly discovered response to soft sounds in rats using an approach of image analysis

description: all online resources for Acoustic perturbation of breathing - a newly discovered response to soft sounds in rats using an approach of image analysis, published in <i>Journal of Medical and Biological Engineering</i><b> <br></b>
DOI: 10.6084/m9.figshare.5937355.v1
title: Online resources for Acoustic perturbation of breathing - a newly discovered response to soft sounds in rats using an approach of image analysis

description: all online resources for Acoustic perturbation of breathing - a newly discovered response to soft sounds in rats using an approach of image analysis, published in <i>Journal of Medical and Biological Engineering</i><b> <br></b>
DOI: 10.6084/m9.figshare.5937280
title: Interpreting the Tinnitus Questionnaire (German version): what individual differences are clinically important?

description: <i>Objective</i>: Reporting of clinical significance is recommended because findings can be statistically significant without being relevant to patients. For aiding clinical interpretation of the Tinnitus Questionnaire (TQ), many investigators use a 5-point change cut-off as a minimal clinically important difference (MCID). But there are shortcomings in how this value was originally determined. <i>Design</i>: The MCID was evaluated by analysing retrospective clinical data on the TQ (German version). Following recommended standards, multiple estimates were computed using anchor- and distribution-based statistical methods. These took into account not only patients’ experience of clinical improvement, but also measurement reliability. <i>Study sample</i>: Pre- and post-intervention scores were assessed for 202 patients. <i>Results</i>: Our six estimates ranged from 5 to 21 points in TQ change score from pre- to post- intervention. The 5-point TQ change score was obtained using a method that considered change between groups, and did not account for measurement error or bias. The size of the measurement error was considerable, and this comprises interpretation of individual patient change scores. <i>Conclusions</i>: To enhance confidence that a TQ change over time in individual patients is clinically meaningful, we advise at least the median MCID of 12 points.
DOI: 10.6084/m9.figshare.5937280.v1
title: Interpreting the Tinnitus Questionnaire (German version): what individual differences are clinically important?

description: <i>Objective</i>: Reporting of clinical significance is recommended because findings can be statistically significant without being relevant to patients. For aiding clinical interpretation of the Tinnitus Questionnaire (TQ), many investigators use a 5-point change cut-off as a minimal clinically important difference (MCID). But there are shortcomings in how this value was originally determined. <i>Design</i>: The MCID was evaluated by analysing retrospective clinical data on the TQ (German version). Following recommended standards, multiple estimates were computed using anchor- and distribution-based statistical methods. These took into account not only patients’ experience of clinical improvement, but also measurement reliability. <i>Study sample</i>: Pre- and post-intervention scores were assessed for 202 patients. <i>Results</i>: Our six estimates ranged from 5 to 21 points in TQ change score from pre- to post- intervention. The 5-point TQ change score was obtained using a method that considered change between groups, and did not account for measurement error or bias. The size of the measurement error was considerable, and this comprises interpretation of individual patient change scores. <i>Conclusions</i>: To enhance confidence that a TQ change over time in individual patients is clinically meaningful, we advise at least the median MCID of 12 points.
DOI: 10.6084/m9.figshare.5937274
title: Matlab codes

description: The raw data and Matlab code to predict the Zika transmission dynamics
DOI: 10.6084/m9.figshare.5937274.v1
title: Matlab codes

description: The raw data and Matlab code to predict the Zika transmission dynamics