cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.2069379
title: DataFile: "Predation alters disturbance resistance"

description: Data set with metadata and morphospecies list for:<br><b><i>"Prior predation alters community resistance to an extreme climate disturbance"</i></b>Jurgens, Freestone, Ruiz, and Torchin<br>Ecosphere Article DOI: 10.1002/ecs2.1986<br>
DOI: 10.6084/m9.figshare.2069385
title: Dabase_EEGfMRI_children_study.xlsx

description: Database containing the following information:Clinic and demographic data of the subjects (Clinical)Movement inside the scanner per sessionInterictal epileptiform discharges per sessionConcordance of EEG-fMRI maps per session and accumulated across sessionsSubjects are labelled C1-20 for controls 1-20 and P1-46 for patients 1 to 46
DOI: 10.6084/m9.figshare.2069403.v1
title: Data Access FigShare Links

description: This is a description and links to data and commands run in Needham and Fuhrman, in press.
DOI: 10.6084/m9.figshare.2069376
title: Highly Sensitive Search String for Systematic Reviews and Meta-analyses Published in the top 20 Pregnancy and Childbirth Journals

description: This search string was designed to retrieve Systematic Reviews and Meta-analyses published in the top 20 Pregnancy and Childbirth Journals between January 1, 2007 and December 31st, 2015.
DOI: 10.6084/m9.figshare.2069385.v1
title: Dabase_EEGfMRI_children_study.xlsx

description: Database containing the following information:Clinic and demographic data of the subjects (Clinical)Movement inside the scanner per sessionInterictal epileptiform discharges per sessionConcordance of EEG-fMRI maps per session and accumulated across sessionsSubjects are labelled C1-20 for controls 1-20 and P1-46 for patients 1 to 46
DOI: 10.6084/m9.figshare.2069388.v1
title: GSE10320

description: TBA.
DOI: 10.6084/m9.figshare.2069376.v1
title: Highly Sensitive Search String for Systematic Reviews and Meta-analyses Published in the top 20 Pregnancy and Childbirth Journals

description: This search string was designed to retrieve Systematic Reviews and Meta-analyses published in the top 20 Pregnancy and Childbirth Journals between January 1, 2007 and December 31st, 2015.
DOI: 10.6084/m9.figshare.2069379.v2
title: DataFile: "Predation alters disturbance resistance"

description: Data set with metadata and morphospecies list for:<br><b><i>"Prior predation alters community resistance to an extreme climate disturbance"</i></b>Jurgens, Freestone, Ruiz, and Torchin<br>Ecosphere Article DOI: 10.1002/ecs2.1986<br>
DOI: 10.6084/m9.figshare.2069379.v1
title: DataFile: "Predation alters disturbance resistance"

description: Data set with metadata and morphospecies list for:<br><b><i>"Predation during initial assembly alters resistance to disturbance in a tropical invertebrate community"</i></b>Jurgens, Freestone, Torchin and Ruiz<br>
DOI: 10.6084/m9.figshare.2069388.v2
title: GSE10320

description: We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069334
title: Isomorphism tables

description: Monte Carlo results for isomorphism and homology study
DOI: 10.6084/m9.figshare.2069328
title: Taxonomic and functional divergence of tree assemblages in a fragmented tropical forest

description: We provide the data we used for the main analyses and the R function to calculate the β-diversity between pair of plots. In species x plots.csv, C1-C20 are the Reference plots, whereas E1-E10 and FR1-FR18 are Edge and Fragments plots, respectively. In species X traits.csv: Specific leaf area = cm²/g, Leaf area = cm², Wood density = g/cm<sup>3</sup>, Seed size = cm, Maximum height = m. beta2a2.R is a function to construct a matrix containing β-diversity values of each pairwise comparison.
DOI: 10.6084/m9.figshare.2069388.v3
title: Biomarker Benchmark - Gene expression data from Gene Expression Omnibus - GSE10320

description: "The gene expression patterns of favorable histology Wilms tumors (FHWT) that relapsed were compared with those that did not relapse using oligonucleotide arrays<br>Description: 250 FHWT of all stages enriched for relapses treated on National Wilms Tumor Study 5 passed quality parameters and were suitable for analysis using oligonucleotide arrays. Relapse risk stratification utilized Support Vector Machine; two and ten fold cross-validation was applied. The number of genes associated with relapse was less than that predicted by chance alone for 106 patients (32 relapses) with stages I and II FHWT and no further analyses were performed. This number was greater than expected by chance for 76 local stage III patients. Cross validation including an additional 68 local stage III patients (total 144 patients, 53 relapses) demonstrated that classifiers for relapse composed of 50 genes were associated with a median sensitivity of 47%, specificity 70%, and total error rate of 38%. Analysis of genes differentially expressed in relapse patients revealed apoptosis, Wnt signaling, IGF pathway, and epigenetic modification to be mechanisms important in relapse. Potential therapeutic targets include FRAP/MTOR and CD40.<br>Keywords: Classification by microarray analysis"<br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10320<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069328.v1
title: Taxonomic and functional divergence of tree assemblages in a fragmented tropical forest

description: We provide the data we used for the main analyses and the R function to calculate the β-diversity between pair of plots. In species x plots.csv, C1-C20 are the Reference plots, whereas E1-E10 and FR1-FR18 are Edge and Fragments plots, respectively. In species X traits.csv: Specific leaf area = cm²/g, Leaf area = cm², Wood density = g/cm<sup>3</sup>, Seed size = cm, Maximum height = m. beta2a2.R is a function to construct a matrix containing β-diversity values of each pairwise comparison.
DOI: 10.6084/m9.figshare.2069388.v5
title: Biomarker Benchmark - GSE10320

description: <b><br>[NOTICE: This data set has been deprecated. Please see our new version of the data (and additional data sets) here: https://osf.io/mhk93 ]</b><br><b><br></b>"The gene expression patterns of favorable histology Wilms tumors (FHWT) that relapsed were compared with those that did not relapse using oligonucleotide arrays<br>Description: 250 FHWT of all stages enriched for relapses treated on National Wilms Tumor Study 5 passed quality parameters and were suitable for analysis using oligonucleotide arrays. Relapse risk stratification utilized Support Vector Machine; two and ten fold cross-validation was applied. The number of genes associated with relapse was less than that predicted by chance alone for 106 patients (32 relapses) with stages I and II FHWT and no further analyses were performed. This number was greater than expected by chance for 76 local stage III patients. Cross validation including an additional 68 local stage III patients (total 144 patients, 53 relapses) demonstrated that classifiers for relapse composed of 50 genes were associated with a median sensitivity of 47%, specificity 70%, and total error rate of 38%. Analysis of genes differentially expressed in relapse patients revealed apoptosis, Wnt signaling, IGF pathway, and epigenetic modification to be mechanisms important in relapse. Potential therapeutic targets include FRAP/MTOR and CD40.<br>Keywords: Classification by microarray analysis"<br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10320<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069388.v4
title: Biomarker Benchmark - Gene expression data from Gene Expression Omnibus - GSE10320

description: "The gene expression patterns of favorable histology Wilms tumors (FHWT) that relapsed were compared with those that did not relapse using oligonucleotide arrays<br>Description: 250 FHWT of all stages enriched for relapses treated on National Wilms Tumor Study 5 passed quality parameters and were suitable for analysis using oligonucleotide arrays. Relapse risk stratification utilized Support Vector Machine; two and ten fold cross-validation was applied. The number of genes associated with relapse was less than that predicted by chance alone for 106 patients (32 relapses) with stages I and II FHWT and no further analyses were performed. This number was greater than expected by chance for 76 local stage III patients. Cross validation including an additional 68 local stage III patients (total 144 patients, 53 relapses) demonstrated that classifiers for relapse composed of 50 genes were associated with a median sensitivity of 47%, specificity 70%, and total error rate of 38%. Analysis of genes differentially expressed in relapse patients revealed apoptosis, Wnt signaling, IGF pathway, and epigenetic modification to be mechanisms important in relapse. Potential therapeutic targets include FRAP/MTOR and CD40.<br>Keywords: Classification by microarray analysis"<br>http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10320<br>We have included gene-expression data, the outcome (class) being predicted, and any clinical covariates. When gene-expression data were processed in multiple batches, we have provided batch information. Each data set is organized into a file set, where each contains all pertinent files for an individual dataset. The gene expression files have been normalized using both the SCAN and UPC methods using the SCAN.UPC package in Bioconductor (https://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html). We summarized the data at the gene level using the BrainArray resource (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/20.0.0/ensg.asp). We used Ensembl identifiers. The class, clinical, and batch data were hand curated to ensure consistency ("tidy data" formatting). In addition, the data files have been formatted to be imported easily into the ML-Flex machine learning package (http://mlflex.sourceforge.net/).
DOI: 10.6084/m9.figshare.2069274
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069265
title: Prasiolales (Trebouxiophyceae, Chlorophyta) of the Svalbard Archipelago: diversity, biogeography and description of the new genera <i>Prasionella</i> and <i>Prasionema</i>

description: Species of Prasiolales (Trebouxiophyceae, Chlorophyta) are among the most common terrestrial and freshwater algae in polar regions. Comprehensive molecular studies of this group are available for Antarctica, but not yet for Arctic regions. We examined the diversity of the Prasiolales in the Svalbard Archipelago combining morphological observations of field-collected material, culture studies, molecular data (plastid <i>rbc</i>L and <i>tuf</i>A sequences) and literature records. We confirmed the widespread occurrence of <i>Prasiola crispa</i> and <i>P. fluviatilis</i>, species recorded from Spitsbergen since the 19th century. Molecular phylogenetic analyses led to the discovery of two new genera of Prasiolales. <i>Prasionema payeri</i> is morphologically identical to filamentous stages of <i>P. crispa</i>, but represents an early-diverging lineage in the order. <i>Prasionella wendyae</i> is a colonial alga reproducing by aplanospores; its phylogenetic position is among the basal lineages of the order, but it could not be reliably reconstructed due to weak statistical support. The inclusion of <i>P. wendyae</i> in the prasiolalean phylogeny determined the paraphyly of <i>Rosenvingiella</i>, requiring the establishment of the new genus <i>Rosenvingiellopsis</i> for <i>R. constricta</i>. A poorly known species described from Spitsbergen, <i>Ulothrix discifera</i>, is transferred here to <i>Rosenvingiella</i>. Whereas some species of Prasiolales have bipolar distribution (<i>P. crispa</i>), others appear to be restricted to one or other of the poles. Our results suggest that polar regions are still a major repository of unknown algal diversity and highlight the importance of continued field surveys and the use of molecular data.
DOI: 10.6084/m9.figshare.2069265.v1
title: Prasiolales (Trebouxiophyceae, Chlorophyta) of the Svalbard Archipelago: diversity, biogeography and description of the new genera <i>Prasionella</i> and <i>Prasionema</i>

description: Species of Prasiolales (Trebouxiophyceae, Chlorophyta) are among the most common terrestrial and freshwater algae in polar regions. Comprehensive molecular studies of this group are available for Antarctica, but not yet for Arctic regions. We examined the diversity of the Prasiolales in the Svalbard Archipelago combining morphological observations of field-collected material, culture studies, molecular data (plastid <i>rbc</i>L and <i>tuf</i>A sequences) and literature records. We confirmed the widespread occurrence of <i>Prasiola crispa</i> and <i>P. fluviatilis</i>, species recorded from Spitsbergen since the 19th century. Molecular phylogenetic analyses led to the discovery of two new genera of Prasiolales. <i>Prasionema payeri</i> is morphologically identical to filamentous stages of <i>P. crispa</i>, but represents an early-diverging lineage in the order. <i>Prasionella wendyae</i> is a colonial alga reproducing by aplanospores; its phylogenetic position is among the basal lineages of the order, but it could not be reliably reconstructed due to weak statistical support. The inclusion of <i>P. wendyae</i> in the prasiolalean phylogeny determined the paraphyly of <i>Rosenvingiella</i>, requiring the establishment of the new genus <i>Rosenvingiellopsis</i> for <i>R. constricta</i>. A poorly known species described from Spitsbergen, <i>Ulothrix discifera</i>, is transferred here to <i>Rosenvingiella</i>. Whereas some species of Prasiolales have bipolar distribution (<i>P. crispa</i>), others appear to be restricted to one or other of the poles. Our results suggest that polar regions are still a major repository of unknown algal diversity and highlight the importance of continued field surveys and the use of molecular data.
DOI: 10.6084/m9.figshare.2069274.v1
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069274.v2
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069274.v3
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069274.v4
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069274.v5
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069190
title: Mum was sick: Umama wagula.mov

description: This video narrative was created in November 2013 in a digital storytelling workshop in an under-resourced, rural community of high HIV prevalence of South Africa. The aim of this study is to employ community stories to explore community perceptions of HIV, ART adherence and adherence to other chronic medications in this setting. The workshop was facilitated by professional facilitator Pam Sykes and hosted by Africa Centre for Population Health.
DOI: 10.6084/m9.figshare.2069274.v6
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069190.v3
title: Mum was sick: Umama wagula.mov

description: This video narrative was created in November 2013 in a digital storytelling workshop in an under-resourced, rural community of high HIV prevalence of South Africa. The aim of this study is to employ community stories to explore community perceptions of HIV, ART adherence and adherence to other chronic medications in this setting. The workshop was facilitated by professional facilitator Pam Sykes and hosted by Africa Centre for Population Health.
DOI: 10.6084/m9.figshare.2069274.v7
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069184.v1
title: Isifo samathambo.mov

description: This video narrative was created in November 2013 in a digital storytelling workshop in an under-resourced, rural community of high HIV prevalence of South Africa. It is a product of the ‘Adherence Stories project that was funded by the Wellcome Trust (PI: Astrid Treffry-Goatley; WT 106852AIA). The aim of this study is to employ community stories to explore community perceptions of HIV, ART adherence and adherence to other chronic medications in this setting. The workshop was facilitated by professional facilitator Pam Sykes and hosted by Africa Centre for Population Health.
DOI: 10.6084/m9.figshare.2069274.v8
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069178.v1
title: YSB book

description: The files contained are the chapters for a book project (tentatively) called <i>On an Even Keel: Silver Risk, Trade Insurance and Hedging Strategies around the Turn of the Twentieth Century</i>. The book revisits literature on silver risk in the second half of the nineteenth century and argues that if the latter existed for sovereign debt, there should be an equivalent for trade finance as well. Using contemporary accounting manuals, the archives of the Yokohama Specie Bank (preserved at the University of Tokyo), contemporary journalistic sources etc., I demonstrate that 19th century exchange bankers did have a strong understanding of ways to hedge risk. The book demonstrates the latter in a quantitative manner, and uses network theoretical visualizations to show how these strategies evolved over time, especially in the context of Japan's expanding imperialist ambitions in the region.
DOI: 10.6084/m9.figshare.2069274.v9
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.
DOI: 10.6084/m9.figshare.2069169.v1
title: 6 March 2015 Field Notes

description: Field notes including image and/or video records.<br>
DOI: 10.6084/m9.figshare.2069178.v2
title: YSB book

description: The files contained are the chapters for a book project (tentatively) called <i>On an Even Keel: Silver Risk, Trade Insurance and Hedging Strategies around the Turn of the Twentieth Century</i>. The book revisits literature on silver risk in the second half of the nineteenth century and argues that if the latter existed for sovereign debt, there should be an equivalent for trade finance as well. Using contemporary accounting manuals, the archives of the Yokohama Specie Bank (preserved at the University of Tokyo), contemporary journalistic sources etc., I demonstrate that 19th century exchange bankers did have a strong understanding of ways to hedge risk. The book demonstrates the latter in a quantitative manner, and uses network theoretical visualizations to show how these strategies evolved over time, especially in the context of Japan's expanding imperialist ambitions in the region.
DOI: 10.6084/m9.figshare.2069274.v10
title: Bruna et al. A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell, 2016

description: Normalised tables for molecular features of the patient-derived tumour xenograft models (PDTXs) from Bruna et al.