cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5649106.v1
title: MOESM2 of Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan

description: Additional file 2: Table S1. Data for Clostridium difficile strain NCKUH-21 genes. The columns are as follows: locus_tag, length in amino acids (Laa), G+C content at the third codon positions (GC3), binary number (1 or 0) indicating whether the gene is NCKUH-21 strain-specific (StrainSpecific), gene and product names, and the most similar sequence annotation in the UniRef90 database (FASTA header and organism name).
DOI: 10.6084/m9.figshare.5649100
title: Additional file 2: Table S6. of Correction to: FLAGS, frequently mutated genes in public exomes

description: A list of variants, in variant call format (VCF), showing the mutations that were observed more than 10 times in our in-house database consisting of 150 exomes and 13 whole genomes, after they were filtered by allelic frequencies according to the annotations from dbSNP and Exome variant server (refer to methodology section for more details). (VCF 207Â kb)
DOI: 10.6084/m9.figshare.5649100.v1
title: Additional file 2: Table S6. of Correction to: FLAGS, frequently mutated genes in public exomes

description: A list of variants, in variant call format (VCF), showing the mutations that were observed more than 10 times in our in-house database consisting of 150 exomes and 13 whole genomes, after they were filtered by allelic frequencies according to the annotations from dbSNP and Exome variant server (refer to methodology section for more details). (VCF 207Â kb)
DOI: 10.6084/m9.figshare.12283760
title: Slovenian Building Cadastre

description: Polygons representing footprints of buildings from Slovenian Building Cadastre. Format: Shapefile<br>Available under Slovenian license Creative Commons 2.5.https://creativecommons.org/licenses/by/2.5/si/legalcode<br>Source: Geodetska uprava Republike Slovenije, Grafični podatki katastra stavb, 11.5.2020<br>
DOI: 10.6084/m9.figshare.5649073
title: Additional file 1: Table S1. of Correction to: FLAGS, frequently mutated genes in public exomes

description: This table lists the five datasets used in this study, and the genes that made up each dataset. The first row in the table shows the names of the datasets referred throughout the manuscript, and each column contains the list of genes, referred to by their official gene symbol (TXT 220Â kb)
DOI: 10.6084/m9.figshare.5649073.v1
title: Additional file 1: Table S1. of Correction to: FLAGS, frequently mutated genes in public exomes

description: This table lists the five datasets used in this study, and the genes that made up each dataset. The first row in the table shows the names of the datasets referred throughout the manuscript, and each column contains the list of genes, referred to by their official gene symbol (TXT 220Â kb)
DOI: 10.6084/m9.figshare.5649013
title: MOESM5 of Urine cell-free microRNA as biomarkers for transitional cell carcinoma

description: Additional file 5. Differentially expressed miRNA in urine of TCC patients vs. healthy controls by SAMseq and DESeqÂ 2 analyses.
DOI: 10.6084/m9.figshare.5649010
title: Additional file 2: Table S2. of Metabolomic effects of CeO2, SiO2 and CuO metal oxide nanomaterials on HepG2 cells

description: Large excel Metabolon data sheet (heat map) with all results. (XLSX 533Â kb)
DOI: 10.6084/m9.figshare.5649013.v1
title: MOESM5 of Urine cell-free microRNA as biomarkers for transitional cell carcinoma

description: Additional file 5. Differentially expressed miRNA in urine of TCC patients vs. healthy controls by SAMseq and DESeqÂ 2 analyses.
DOI: 10.6084/m9.figshare.5649010.v1
title: Additional file 2: Table S2. of Metabolomic effects of CeO2, SiO2 and CuO metal oxide nanomaterials on HepG2 cells

description: Large excel Metabolon data sheet (heat map) with all results. (XLSX 533Â kb)
DOI: 10.6084/m9.figshare.5649004
title: Additional file 10: Table S8. of Correction to: FLAGS, frequently mutated genes in public exomes

description: A table of number of exomes from TIDEX project that lists out the number of rare functional variants for each protein-coding gene captured in the exome capture kits. Please refer to methodology section for how ‘rare’ and ‘functional’ descriptors were defined. (TXT 81 kb)
DOI: 10.6084/m9.figshare.5649004.v1
title: Additional file 10: Table S8. of Correction to: FLAGS, frequently mutated genes in public exomes

description: A table of number of exomes from TIDEX project that lists out the number of rare functional variants for each protein-coding gene captured in the exome capture kits. Please refer to methodology section for how ‘rare’ and ‘functional’ descriptors were defined. (TXT 81 kb)
DOI: 10.5281/zenodo.4009105
title: Table S1 and S2

description: Table S1. RNAseq for HCT116CSC vs HCT116. Table S2. HT29CSC vs HT29.
DOI: 10.5281/zenodo.4009104
title: Table S1 and S2

description: Table S1. RNAseq for HCT116CSC vs HCT116. Table S2. HT29CSC vs HT29.
DOI: 10.6084/m9.figshare.5648959
title: Additional file 1: of Genotypic characterization of gentamicin and cephalosporin resistant Escherichia coli isolates from blood cultures in a Norwegian university hospital 2011â 2015

description: Overview of all 255 E. coli isolates from bacteremia with regards to antibiotic resistance profiles, MLVA type, and bla CTX-M and bla ampC. (XLS 82 kb)
DOI: 10.6084/m9.figshare.5648959.v1
title: Additional file 1: of Genotypic characterization of gentamicin and cephalosporin resistant Escherichia coli isolates from blood cultures in a Norwegian university hospital 2011â 2015

description: Overview of all 255 E. coli isolates from bacteremia with regards to antibiotic resistance profiles, MLVA type, and bla CTX-M and bla ampC. (XLS 82 kb)
DOI: 10.6084/m9.figshare.5648956
title: Additional file 4: of DBNorm: normalizing high-density oligonucleotide microarray data based on distributions

description: DBNorm installation. Describes how to install DBNorm via devtools in R. (TXT 4Â kb)
DOI: 10.6084/m9.figshare.5648956.v1
title: Additional file 4: of DBNorm: normalizing high-density oligonucleotide microarray data based on distributions

description: DBNorm installation. Describes how to install DBNorm via devtools in R. (TXT 4Â kb)
DOI: 10.5281/zenodo.4002055
title: Data supplement for "Adaptive stochastic continuation with a modified lifting procedure applied to complex systems"

description: This dataset contains the data and source files for the diagrams of the following preprint: <em>Clemens Willers, Uwe Thiele, Andrew J. Archer, David J. B. Lloyd, and Oliver Kamps<br> Adaptive stochastic continuation with a modified lifting procedure applied to complex systems<br> arXiv preprint arXiv:2002.01705, 2020 </em> Please follow the instructions given in 'Readme.txt'.
DOI: 10.5281/zenodo.4002054
title: Data supplement for "Adaptive stochastic continuation with a modified lifting procedure applied to complex systems"

description: This dataset contains the data and source files for the diagrams of the following preprint: <em>Clemens Willers, Uwe Thiele, Andrew J. Archer, David J. B. Lloyd, and Oliver Kamps<br> Adaptive stochastic continuation with a modified lifting procedure applied to complex systems<br> arXiv preprint arXiv:2002.01705, 2020 </em> Please follow the instructions given in 'Readme.txt'.
DOI: 10.6084/m9.figshare.5648938
title: Additional file 2:Table S1. of Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations

description: List of Y-chromosomal DNA compound haplotypes (YDNA haplotype), Y-chromosomal haplotypes based on only the 3.1Â kb data set (YSNP_haplotype), Y-linked SNPs in the 3.1Â kb data set, fragment sizes of six Y-linked microsatellites markers, and the number of individuals from each geographical regions having each Y-chromosomal DNA compound haplotypes. Table S2. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. Table S3. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. Table S4. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. (ZIP 63 kb)
DOI: 10.6084/m9.figshare.5648938.v1
title: Additional file 2:Table S1. of Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations

description: List of Y-chromosomal DNA compound haplotypes (YDNA haplotype), Y-chromosomal haplotypes based on only the 3.1Â kb data set (YSNP_haplotype), Y-linked SNPs in the 3.1Â kb data set, fragment sizes of six Y-linked microsatellites markers, and the number of individuals from each geographical regions having each Y-chromosomal DNA compound haplotypes. Table S2. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. Table S3. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. Table S4. Analysis of molecular variance (AMOVA) for brown bear Y-chromosomal polymorphisms in various geographical partitions. (ZIP 63 kb)
DOI: 10.6084/m9.figshare.5648932
title: Additional file 3: of DBNorm: normalizing high-density oligonucleotide microarray data based on distributions

description: DBNorm test script. Code of how we test DBNorm package. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.5648932.v1
title: Additional file 3: of DBNorm: normalizing high-density oligonucleotide microarray data based on distributions

description: DBNorm test script. Code of how we test DBNorm package. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.5648914
title: Additional file 1: Figure S1. of Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations

description: Median-joining haplotype network for brown, polar, and American black bears, based on the 3.1Â kb Y-linked data set. Figure S2. Median-joining haplotype network for brown, polar, and American black bears, based on the 5.3Â kb Y-linked data set. Figure S3. Median-joining haplotype network for brown bears, based on Y-chromosomal compound haplotypes combined with Y-linked SNPs from a 3.1Â kb data set and Y-linked microsatellites. Haplotypes enclosed by a dashed line are from Hokkaido (including one Kunashiri brown bear). Figure S4. Map of Eurasia showing the geographical distribution of brown bear Y-chromosomal compound haplotypes. Each symbol represents one individual. Figure S5. Enlargement of the larger boxed area in Fig. S4, showing the geographical distribution of brown bear Y-chromosomal compound haplotypes around the Ural Mountains. (ZIP 4.95 mb)
DOI: 10.6084/m9.figshare.5648914.v1
title: Additional file 1: Figure S1. of Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations

description: Median-joining haplotype network for brown, polar, and American black bears, based on the 3.1Â kb Y-linked data set. Figure S2. Median-joining haplotype network for brown, polar, and American black bears, based on the 5.3Â kb Y-linked data set. Figure S3. Median-joining haplotype network for brown bears, based on Y-chromosomal compound haplotypes combined with Y-linked SNPs from a 3.1Â kb data set and Y-linked microsatellites. Haplotypes enclosed by a dashed line are from Hokkaido (including one Kunashiri brown bear). Figure S4. Map of Eurasia showing the geographical distribution of brown bear Y-chromosomal compound haplotypes. Each symbol represents one individual. Figure S5. Enlargement of the larger boxed area in Fig. S4, showing the geographical distribution of brown bear Y-chromosomal compound haplotypes around the Ural Mountains. (ZIP 4.95 mb)
DOI: 10.6084/m9.figshare.5648842
title: Additional file 1: of Genome-wide analysis of miRNAs in Carya cathayensis

description: Table S1. Cloning of hickory miRNA precursors primers. Table S2. Real-Time PCR of hickory miRNA primers. Table S3. Real-Time PCR of hickory miRNA targets primers and target sequencses. Table S4. Hickory miRNA sequences. Table S5. Conserved and Novel different expression miRNAs identified in Carya cathayensis. (XLS 259Â kb)
DOI: 10.6084/m9.figshare.5648842.v1
title: Additional file 1: of Genome-wide analysis of miRNAs in Carya cathayensis

description: Table S1. Cloning of hickory miRNA precursors primers. Table S2. Real-Time PCR of hickory miRNA primers. Table S3. Real-Time PCR of hickory miRNA targets primers and target sequencses. Table S4. Hickory miRNA sequences. Table S5. Conserved and Novel different expression miRNAs identified in Carya cathayensis. (XLS 259Â kb)
DOI: 10.6084/m9.figshare.5648836
title: MOESM1 of Avian introgression in the genomic era

description: Additional file 1: Table S1. Result of literature search published between 1987 and 2017.
DOI: 10.6084/m9.figshare.5648836.v1
title: MOESM1 of Avian introgression in the genomic era

description: Additional file 1: Table S1. Result of literature search published between 1987 and 2017.
DOI: 10.6084/m9.figshare.5648806
title: Additional file 1 of ImageJ2: ImageJ for the next generation of scientific image data

description: Figures and illustrations. Figure S1: Module execution in different contexts. When running a parameterized script (panel B) from the ImageJ user interface (panel A), a pop-up dialog box (panel C) enables the user to enter the name and age values; when running the script headless from the command line (panel D), input values are passed as arguments and output values echoed to the standard output stream. Figure S2: Comparison of time performance across ImageJ 1.x and ImgLib2 data structures. For ten iterations, we ran a “cheap” per-pixel operation and an “expensive” operation on a 25 Mpx image stored in the ImageJ 1.x container, various ImgLib2 containers, and raw byte arrays. Panel A (left) shows the time (ms) it took to complete a “cheap” operations versus the loop iteration for each container. Panel B (right) shows the same information but for the time (ms) it took to complete the expensive operation. Figure S3: Sample ImageJ plugin usage of ImageJ 1.x and ImageJ2. This plot displays a select few ImageJ plugins in varying stages of transition, from ImageJ 1.x to ImageJ2, as of 11 Aug 2017 2:35 PM CDT. The ratio of ImageJ 1.x to ImageJ2 usage was computed by counting the number of imports each plugin uses from relevant Java packages: "ImageJ 1.x plugins" is ij.plugin.*, "ImageJ 1.x data structures" is ij.* excluding the plugin subpackage, "SciJava framework" is org.scijava.*, and "ImageJ2 data structures" is net.imagej.* and net.imglib2.*. References for plugins shown: TrackMate [67], MaMuT [150], Multiview Reconstruction [70, 71], MotherMachine Analyzer (MoMA) [151, 152], Sholl Analysis [74], Kymograph Builder [153], Z-Spacing Correction [154], Trainable Weka Segmentation [155], Pendent Drop [156], SciView [157], BigDataViewer [66], Image Stitching [158], Coloc 2 [159], MorphoLibJ [100]. Table S1: Built-in SciJava input widgets. Table S2: Kinds and arities of special ops. Table S3: Image types supported by ImageJ. (ZIP 549 kb)
DOI: 10.6084/m9.figshare.5648806.v1
title: Additional file 1 of ImageJ2: ImageJ for the next generation of scientific image data

description: Figures and illustrations. Figure S1: Module execution in different contexts. When running a parameterized script (panel B) from the ImageJ user interface (panel A), a pop-up dialog box (panel C) enables the user to enter the name and age values; when running the script headless from the command line (panel D), input values are passed as arguments and output values echoed to the standard output stream. Figure S2: Comparison of time performance across ImageJ 1.x and ImgLib2 data structures. For ten iterations, we ran a “cheap” per-pixel operation and an “expensive” operation on a 25 Mpx image stored in the ImageJ 1.x container, various ImgLib2 containers, and raw byte arrays. Panel A (left) shows the time (ms) it took to complete a “cheap” operations versus the loop iteration for each container. Panel B (right) shows the same information but for the time (ms) it took to complete the expensive operation. Figure S3: Sample ImageJ plugin usage of ImageJ 1.x and ImageJ2. This plot displays a select few ImageJ plugins in varying stages of transition, from ImageJ 1.x to ImageJ2, as of 11 Aug 2017 2:35 PM CDT. The ratio of ImageJ 1.x to ImageJ2 usage was computed by counting the number of imports each plugin uses from relevant Java packages: "ImageJ 1.x plugins" is ij.plugin.*, "ImageJ 1.x data structures" is ij.* excluding the plugin subpackage, "SciJava framework" is org.scijava.*, and "ImageJ2 data structures" is net.imagej.* and net.imglib2.*. References for plugins shown: TrackMate [67], MaMuT [150], Multiview Reconstruction [70, 71], MotherMachine Analyzer (MoMA) [151, 152], Sholl Analysis [74], Kymograph Builder [153], Z-Spacing Correction [154], Trainable Weka Segmentation [155], Pendent Drop [156], SciView [157], BigDataViewer [66], Image Stitching [158], Coloc 2 [159], MorphoLibJ [100]. Table S1: Built-in SciJava input widgets. Table S2: Kinds and arities of special ops. Table S3: Image types supported by ImageJ. (ZIP 549 kb)
DOI: 10.6084/m9.figshare.5648785
title: Additional file 1: Table S1. of Treatment effects of renin-angiotensin aldosterone system blockade on kidney failure and mortality in chronic kidney disease patients

description: Estimation of average treatment model for ESRD in diabetic patients. Table S2. Estimation of average treatment model for ESRD in non-diabetic patients (RTF 343Â kb)
DOI: 10.6084/m9.figshare.5648785.v1
title: Additional file 1: Table S1. of Treatment effects of renin-angiotensin aldosterone system blockade on kidney failure and mortality in chronic kidney disease patients

description: Estimation of average treatment model for ESRD in diabetic patients. Table S2. Estimation of average treatment model for ESRD in non-diabetic patients (RTF 343Â kb)
DOI: 10.6084/m9.figshare.12895994.v1
title: Baseline characteristics

description: An analysis of the demographic characteristics, baseline metabolic measures and hormonal levels
DOI: 10.6084/m9.figshare.12895994
title: Baseline characteristics

description: An analysis of the demographic characteristics, baseline metabolic measures and hormonal levels
DOI: 10.6084/m9.figshare.5648725
title: Additional file 1: Table S1. of A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA

description: LAMP test selectivity by in silico analysis using Nc-5 gene DNA. This file provides information regarding all the sequences found of Nc-5 gene from different isolates available in databases. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5648725.v1
title: Additional file 1: Table S1. of A novel loop-mediated isothermal amplification-based test for detecting Neospora caninum DNA

description: LAMP test selectivity by in silico analysis using Nc-5 gene DNA. This file provides information regarding all the sequences found of Nc-5 gene from different isolates available in databases. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.5648707
title: Additional file 8: of Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)

description: P-values of the pairwise comparisons among lifestyle categories. Excel workbook containing two worksheets, one for the traditional (non-phylogenetic) comparisons between each pair of category for each ROI and parameter, and the other for the phylogenetically informed comparisons (given only when the latter are warranted). Abbreviations: Av.Br.Len, averageÂ branch length; BS, bone surface; BV, bone volume; Conn.D, connectivity density; DA, degree of anisotropy; Tb.Th, trabecular mean thickness; Tb.Sp, trabecular mean spacing; NU, no units. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5648707.v1
title: Additional file 8: of Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)

description: P-values of the pairwise comparisons among lifestyle categories. Excel workbook containing two worksheets, one for the traditional (non-phylogenetic) comparisons between each pair of category for each ROI and parameter, and the other for the phylogenetically informed comparisons (given only when the latter are warranted). Abbreviations: Av.Br.Len, averageÂ branch length; BS, bone surface; BV, bone volume; Conn.D, connectivity density; DA, degree of anisotropy; Tb.Th, trabecular mean thickness; Tb.Sp, trabecular mean spacing; NU, no units. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5648695
title: Additional file 7: of Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)

description: Summary of the non-directional trabecular parameters values among xenarthrans for each region of interest. Excel workbook containing three worksheets, for the mean, minimum, and maximum values respectively of the non-directional trabecular parameters among xenarthrans for each region of interest. Abbreviations: Av.Br.Len, averageÂ branch length; BS, bone surface; BV, bone volume; Conn.D, connectivity density; DA, degree of anisotropy; Tb.Th, trabecular mean thickness; Tb.Sp, trabecular mean spacing; NU, no units. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.5648683
title: Additional file 1: Tables S1, S2 and S3. of COGcollator: a web server for analysis of distant relationships between homologous protein families

description: Representative list of 124 genomes sampled from the 711 genomes of the current COG database release [2]. Table S2. Representative list of 27 eukaryotic genomes sampled manually. Table S3. Results of the similarity assessment for the homologs of catalytic β-subunit of the bacterial FOF1-type ATP synthase by applying the HHpred algorithm [19]. The top hits for the α- and β-subunits of the F-type ATP synthase of E.coli and the B- and A- subunits of the A-type ATP synthase of Methanosarcina mazei (cf with Table 1) are colored red. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5648683.v1
title: Additional file 1: Tables S1, S2 and S3. of COGcollator: a web server for analysis of distant relationships between homologous protein families

description: Representative list of 124 genomes sampled from the 711 genomes of the current COG database release [2]. Table S2. Representative list of 27 eukaryotic genomes sampled manually. Table S3. Results of the similarity assessment for the homologs of catalytic β-subunit of the bacterial FOF1-type ATP synthase by applying the HHpred algorithm [19]. The top hits for the α- and β-subunits of the F-type ATP synthase of E.coli and the B- and A- subunits of the A-type ATP synthase of Methanosarcina mazei (cf with Table 1) are colored red. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.5648680
title: Additional file 2: of The learning environment of paediatric interns in South Africa

description: Appendix B: Modified PHEEM for Intern-superviors in South Africa. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5648680.v1
title: Additional file 2: of The learning environment of paediatric interns in South Africa

description: Appendix B: Modified PHEEM for Intern-superviors in South Africa. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.5648665
title: Additional file 5: of Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)

description: R script to convert eigenvector cosines (as outputted by BoneJ [61]) into azimuth and plunge. Made under R version 3.4.1 [66]. (R 1Â kb)
DOI: 10.6084/m9.figshare.5648665.v1
title: Additional file 5: of Trabecular architecture in the forelimb epiphyses of extant xenarthrans (Mammalia)

description: R script to convert eigenvector cosines (as outputted by BoneJ [61]) into azimuth and plunge. Made under R version 3.4.1 [66]. (R 1Â kb)
DOI: 10.6084/m9.figshare.5648656
title: MOESM3 of Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol

description: Additional file 3: Table S3. Primers used in this study.