cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6350390.v1
title: Additional file 1: of The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

description: General characteristics of the reported species in this repertoire along with its classification based on oxygen tolerance (0 being able to tolerate oxygen and 1 strictly anaerobic), risk group, potential pathogenicity, and the PMID of the article. A: New species isolated by culturomics approach but not in the gut. B: Species isolated without culturomics approach and not isolated in the gut. C: New species isolated not using culturomics approach. D: Species isolated by routine culture in our laboratory. E: Species isolated in the human gut by culturomics. F: New species isolated in the human gut by culturomics. G: Species isolated in the human gut and without using culturomics. (XLSX 40 kb)
DOI: 10.6084/m9.figshare.6350378
title: Additional file 1: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

description: ASV counts and number of ASVs detected in all samples. Tables providing total read counts, read counts for each ASV with assigned taxonomy, and the number of ASVs detected for each sample. (XLSX 119Â kb)
DOI: 10.6084/m9.figshare.6350375
title: Additional file 2: of Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota

description: Supplementary Data. (XLSX 75.6 kb)
DOI: 10.6084/m9.figshare.6350378.v1
title: Additional file 1: of Gut microbes contribute to variation in solid organ transplant outcomes in mice

description: ASV counts and number of ASVs detected in all samples. Tables providing total read counts, read counts for each ASV with assigned taxonomy, and the number of ASVs detected for each sample. (XLSX 119Â kb)
DOI: 10.6084/m9.figshare.6350375.v1
title: Additional file 2: of Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota

description: Supplementary Data. (XLSX 75.6 kb)
DOI: 10.6084/m9.figshare.6350345
title: Additional file 2: of Predictive equation of metastasis in patients with malignant ovarian epithelial tumors with the Ca-125 marker

description: Database in Excel format. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6350345.v1
title: Additional file 2: of Predictive equation of metastasis in patients with malignant ovarian epithelial tumors with the Ca-125 marker

description: Database in Excel format. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.6350333
title: Additional file 1: of Predictive equation of metastasis in patients with malignant ovarian epithelial tumors with the Ca-125 marker

description: Excel sheet for calculating the probability of ovarian cancer metastasis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6350333.v1
title: Additional file 1: of Predictive equation of metastasis in patients with malignant ovarian epithelial tumors with the Ca-125 marker

description: Excel sheet for calculating the probability of ovarian cancer metastasis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.6350282
title: Additional file 2: of Integrating rare genetic variants into pharmacogenetic drug response predictions

description: Genes and variants not considered in current drug response predictions. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.6350282.v1
title: Additional file 2: of Integrating rare genetic variants into pharmacogenetic drug response predictions

description: Genes and variants not considered in current drug response predictions. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.6350267
title: Additional file 1: of Integrating rare genetic variants into pharmacogenetic drug response predictions

description: Overview of NGS-based analyses of pharmacogenes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.6350267.v1
title: Additional file 1: of Integrating rare genetic variants into pharmacogenetic drug response predictions

description: Overview of NGS-based analyses of pharmacogenes. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.6350261
title: Additional file 2: of Comorbidities and co-medications in populations with and without chronic hepatitis C virus infection in Japan between 2015 and 2016

description: Table S2. Non-HCV-related medications prescribed at least once during the study period by age group. Description of data: The proportions of patients who received non-HCV-related medications at least once during the study period are summarised by age for both chronic HCV patients and non-HCV patients. (XLSX 184Â kb)
DOI: 10.6084/m9.figshare.6350261.v1
title: Additional file 2: of Comorbidities and co-medications in populations with and without chronic hepatitis C virus infection in Japan between 2015 and 2016

description: Table S2. Non-HCV-related medications prescribed at least once during the study period by age group. Description of data: The proportions of patients who received non-HCV-related medications at least once during the study period are summarised by age for both chronic HCV patients and non-HCV patients. (XLSX 184Â kb)
DOI: 10.6084/m9.figshare.6350201
title: Additional file 3: of Prevalence of anemia among school-age children in Ethiopia: a systematic review and meta-analysis

description: Figure S3. Funnel plot of 13 studies on prevalence of anemia among school-age children in Ethiopia, 2003â 2016. (WMF 2Â kb)
DOI: 10.6084/m9.figshare.6350201.v1
title: Additional file 3: of Prevalence of anemia among school-age children in Ethiopia: a systematic review and meta-analysis

description: Figure S3. Funnel plot of 13 studies on prevalence of anemia among school-age children in Ethiopia, 2003â 2016. (WMF 2Â kb)
DOI: 10.6084/m9.figshare.6350186
title: Additional file 2: of Prevalence of anemia among school-age children in Ethiopia: a systematic review and meta-analysis

description: Table S2. Risk of bias assessment of included studies using the Hoy 2012 tool. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6350186.v1
title: Additional file 2: of Prevalence of anemia among school-age children in Ethiopia: a systematic review and meta-analysis

description: Table S2. Risk of bias assessment of included studies using the Hoy 2012 tool. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.6350171
title: Additional file 5: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S5. Enzyme Classification (EC) analysis of the transcriptome of H. dromdarii. Distribution of EC subClasses number in general EC terms compared to the number of specific transcripts in male, female and in common. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6350171.v1
title: Additional file 5: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S5. Enzyme Classification (EC) analysis of the transcriptome of H. dromdarii. Distribution of EC subClasses number in general EC terms compared to the number of specific transcripts in male, female and in common. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6350153
title: Additional file 4: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S4. Distribution of putative transcripts in KEGG pathways. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6350153.v1
title: Additional file 4: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S4. Distribution of putative transcripts in KEGG pathways. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.6350135
title: Additional file 3: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S3.Transposable elements transcripts and their annotations. (XLS 2170 kb)
DOI: 10.6084/m9.figshare.6350135.v1
title: Additional file 3: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S3.Transposable elements transcripts and their annotations. (XLS 2170 kb)
DOI: 10.6084/m9.figshare.6350123
title: Additional file 2: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S2. Housekeeping class transcripts and their annotations. (XLSX 775 kb)
DOI: 10.6084/m9.figshare.6350123.v1
title: Additional file 2: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S2. Housekeeping class transcripts and their annotations. (XLSX 775 kb)
DOI: 10.6084/m9.figshare.6350102
title: Additional file 1: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S1. Annotated transcripts of H. dromedarii salivary glands. (XLSX 17611 kb)
DOI: 10.6084/m9.figshare.6350102.v1
title: Additional file 1: of De novo assembly and annotation of Hyalomma dromedarii tick (Acari: Ixodidae) sialotranscriptome with regard to gender differences in gene expression

description: Table S1. Annotated transcripts of H. dromedarii salivary glands. (XLSX 17611 kb)
DOI: 10.6084/m9.figshare.6349562
title: Incorporated Synechococcus Genomes

description: Fasta files of the genomes incorporated in the study.
DOI: 10.6084/m9.figshare.6349562.v1
title: Incorporated Synechococcus Genomes

description: Fasta files of the genomes incorporated in the study.
DOI: 10.6084/m9.figshare.6349529
title: LondonCalling2018poster

description: Poster for 2018 London Calling Nanopore conference describing the fun (work?) we've done incorporating MinION and EPI2ME platforms in high school and college courses.
DOI: 10.6084/m9.figshare.6349529.v2
title: LondonCalling2018poster

description: Poster for 2018 London Calling Nanopore conference describing the fun (work?) we've done incorporating MinION and EPI2ME platforms in high school and college courses.
DOI: 10.6084/m9.figshare.6349529.v1
title: LondonCalling2018poster

description: Poster for 2018 London Calling Nanopore conference describing the fun (work?) we've done incorporating MinION and EPI2ME platforms in high school and college courses.
DOI: 10.17608/k6.auckland.6349496
title: Selective Raster Graphics

description: This report explores ways to render specific components of an R plot in raster format, when the overall format of the plot is vector. For example, we demonstrate ways to draw raster data symbols within a PDF scatter plot. A general solution is provided by the grid.rasterize function from the R package ‘rasterize’.
DOI: 10.17608/k6.auckland.6349496.v1
title: Selective Raster Graphics

description: This report explores ways to render specific components of an R plot in raster format, when the overall format of the plot is vector. For example, we demonstrate ways to draw raster data symbols within a PDF scatter plot. A general solution is provided by the grid.rasterize function from the R package ‘rasterize’.
DOI: 10.6084/m9.figshare.6349469
title: Soil Structural Degradation during Low-severity Burns

description: This dataset contains raw data and processing R codes that document a research on the effect of low-severity fire on soil structure. There are two different soils analyzed.
DOI: 10.6084/m9.figshare.6349469.v1
title: Soil Structural Degradation during Low-severity Burns

description: This dataset contains raw data and processing R codes that document a research on the effect of low-severity fire on soil structure. There are two different soils analyzed.
DOI: 10.6084/m9.figshare.6349424
title: Appendix 2:Nexus formatted alignments

description: Separate nexus files for each of 19 focal bird species<br>
DOI: 10.6084/m9.figshare.6349415
title: Appendix 1: Sampling table, voucher specimens

description: Museum voucher numbers and provinence for each genetic sample.<br>
DOI: 10.6084/m9.figshare.6349205
title: Data & Analysis Code

description: AUTHORS: <br>Lena R. Bartell, Lisa A. Fortier, Lawrence J. Bonassar, Hazel H. Szeto, Itai Cohen, and Michelle L. Delco. <br><br>ABSTRACT: <br>Post-traumatic osteoarthritis (PTOA) involves the mechanical and biological deterioration of articular cartilage that occurs following joint injury. PTOA is a growing problem in healthcare due to the lack of effective therapies combined with an aging population with high activity levels. Recently, acute mitochondrial dysfunction and altered cellular respiration have been associated with cartilage degeneration after injury. This finding is particularly important because recently-developed mitoprotective drugs, including SS-peptides, can preserve mitochondrial structure and function after acute injury in other tissues. It is not known, however, if cartilage injury induces peracute structural changes in mitochondria, to what degree mitochondrial dysfunction in cartilage depends on the mechanics of injury, or the time frame over which such dysfunction develops. Similarly, it is unknown if SS peptide treatment can preserve mitochondrial structure and function after cartilage injury. Here, we combined fast-camera elastography, longitudinal fluorescence assays, and computer vision techniques to track the fates of thousands of individual cells. Our results show that impact induces mechanically-dependent mitochondrial depolarization within a few minutes after injury. Using electron microscopy, we further showed that impact induces rapid structural changes in mitochondria that are related to reduced mitochondrial function, namely fission and loss of cristae structure. Remarkably, we find that SS-peptide treatment prior to impact protects mitochondrial structure and preserves mitochondrial function at levels comparable to that of unimpacted control samples. Overall, this study reveals the vital role of mitochondria in mediating cartilage’s peracute response to traumatic injury and demonstrates mitoprotection as a promising therapeutic target for injury-induced cartilage damage.
DOI: 10.6084/m9.figshare.6349205.v1
title: Data & Analysis Code

description: AUTHORS: <br>Lena R. Bartell, Lisa A. Fortier, Lawrence J. Bonassar, Hazel H. Szeto, Itai Cohen, and Michelle L. Delco. <br><br>ABSTRACT: <br>Post-traumatic osteoarthritis (PTOA) involves the mechanical and biological deterioration of articular cartilage that occurs following joint injury. PTOA is a growing problem in healthcare due to the lack of effective therapies combined with an aging population with high activity levels. Recently, acute mitochondrial dysfunction and altered cellular respiration have been associated with cartilage degeneration after injury. This finding is particularly important because recently-developed mitoprotective drugs, including SS-peptides, can preserve mitochondrial structure and function after acute injury in other tissues. It is not known, however, if cartilage injury induces peracute structural changes in mitochondria, to what degree mitochondrial dysfunction in cartilage depends on the mechanics of injury, or the time frame over which such dysfunction develops. Similarly, it is unknown if SS peptide treatment can preserve mitochondrial structure and function after cartilage injury. Here, we combined fast-camera elastography, longitudinal fluorescence assays, and computer vision techniques to track the fates of thousands of individual cells. Our results show that impact induces mechanically-dependent mitochondrial depolarization within a few minutes after injury. Using electron microscopy, we further showed that impact induces rapid structural changes in mitochondria that are related to reduced mitochondrial function, namely fission and loss of cristae structure. Remarkably, we find that SS-peptide treatment prior to impact protects mitochondrial structure and preserves mitochondrial function at levels comparable to that of unimpacted control samples. Overall, this study reveals the vital role of mitochondria in mediating cartilage’s peracute response to traumatic injury and demonstrates mitoprotection as a promising therapeutic target for injury-induced cartilage damage.
DOI: 10.6084/m9.figshare.6347741
title: warmed_biocrusts_nine_years

description: <b>Abstract.</b> Biological soil crusts (biocrusts) are predicted to be sensitive to the increased temperature and altered precipitation associated with climate change. We assessed the effects of these factors on soil carbon dioxide (CO<sub>2</sub>) balance in biocrusted soils using a sequence of manipulations over a nine-year period. We warmed biocrusted soils by 2 and, later, by 4 °C to better capture updated forecasts of future temperature at a site on the Colorado Plateau, USA. We also watered soils to alter monsoon-season precipitation amount and frequency, and had plots that received both warming and altered precipitation treatments. Within treatment plots, we used 20 automated flux chambers to monitor net soil exchange (NSE) of CO<sub>2</sub> hourly, first in 2006-2007 and then again in 2013-2014, for a total of 39 months. Net CO<sub>2</sub> efflux from biocrusted soils in the warming treatment increased a year after the experiment began (2006-2007). However, after 9 years and even greater warming (4 °C), results were more mixed, with a reversal of the increase in 2013 (i.e., controls showed higher net CO<sub>2</sub> efflux than treatment plots) and with similarly high rates in all treatments during 2014, a wet year. Over the longer-term, we saw evidence of reduced photosynthetic capacity of the biocrusts in response to both the temperature and altered precipitation treatments. Patterns in biocrusted soil CO<sub>2</sub> exchange under experimentally altered climate suggest that (1) warming stimulation of CO<sub>2</sub> efflux was diminished later in the experiment, even in the face of greater warming and (2) treatment effects on CO<sub>2</sub> flux patterns were likely driven by changes in biocrust species composition and by changes in root respiration due to vascular plant responses.<b><br> </b>
DOI: 10.6084/m9.figshare.6347741.v2
title: warmed_biocrusts_nine_years

description: <b>Abstract.</b> Biological soil crusts (biocrusts) are predicted to be sensitive to the increased temperature and altered precipitation associated with climate change. We assessed the effects of these factors on soil carbon dioxide (CO<sub>2</sub>) balance in biocrusted soils using a sequence of manipulations over a nine-year period. We warmed biocrusted soils by 2 and, later, by 4 °C to better capture updated forecasts of future temperature at a site on the Colorado Plateau, USA. We also watered soils to alter monsoon-season precipitation amount and frequency, and had plots that received both warming and altered precipitation treatments. Within treatment plots, we used 20 automated flux chambers to monitor net soil exchange (NSE) of CO<sub>2</sub> hourly, first in 2006-2007 and then again in 2013-2014, for a total of 39 months. Net CO<sub>2</sub> efflux from biocrusted soils in the warming treatment increased a year after the experiment began (2006-2007). However, after 9 years and even greater warming (4 °C), results were more mixed, with a reversal of the increase in 2013 (i.e., controls showed higher net CO<sub>2</sub> efflux than treatment plots) and with similarly high rates in all treatments during 2014, a wet year. Over the longer-term, we saw evidence of reduced photosynthetic capacity of the biocrusts in response to both the temperature and altered precipitation treatments. Patterns in biocrusted soil CO<sub>2</sub> exchange under experimentally altered climate suggest that (1) warming stimulation of CO<sub>2</sub> efflux was diminished later in the experiment, even in the face of greater warming and (2) treatment effects on CO<sub>2</sub> flux patterns were likely driven by changes in biocrust species composition and by changes in root respiration due to vascular plant responses.<b><br> </b>
DOI: 10.6084/m9.figshare.6345065
title: Data file for Figures 3,4,5,7,8 from Base-catalysed decomposition of polychlorinated biphenyls in transformer oils by mixture of sodium hydroxide, glycerol and iron

description: Excel file containing the data for figures 3,4,5, 7, and 8 each in a separate sheet
DOI: 10.6084/m9.figshare.6345065.v1
title: Data file for Figures 3,4,5,7,8 from Base-catalysed decomposition of polychlorinated biphenyls in transformer oils by mixture of sodium hydroxide, glycerol and iron

description: Excel file containing the data for figures 3,4,5, 7, and 8 each in a separate sheet
DOI: 10.6084/m9.figshare.6345062
title: Data file for Figure-2 from Base-catalysed decomposition of polychlorinated biphenyls in transformer oils by mixture of sodium hydroxide, glycerol and iron

description: Data for chromatogram of detected PCBs in untreated used transformer oil, and treated oil after 1 and 4 h using iron catalyst.
DOI: 10.6084/m9.figshare.6345059
title: Cytochrome oxidase I (cox1) sequences from Natural hybridization between divergent lineages in a selfing hermaphroditic fish

description: Sequences of cytochrome oxidase I (cox1) gene in mangrove rivulus
DOI: 10.6084/m9.figshare.6345062.v1
title: Data file for Figure-2 from Base-catalysed decomposition of polychlorinated biphenyls in transformer oils by mixture of sodium hydroxide, glycerol and iron

description: Data for chromatogram of detected PCBs in untreated used transformer oil, and treated oil after 1 and 4 h using iron catalyst.
DOI: 10.6084/m9.figshare.6345059.v1
title: Cytochrome oxidase I (cox1) sequences from Natural hybridization between divergent lineages in a selfing hermaphroditic fish

description: Sequences of cytochrome oxidase I (cox1) gene in mangrove rivulus
DOI: 10.6084/m9.figshare.6345056
title: Microsatellite genotypes from Natural hybridization between divergent lineages in a selfing hermaphroditic fish

description: Genotypes of 33 microsatellite loci in mangrove rivulus
DOI: 10.6084/m9.figshare.6345056.v1
title: Microsatellite genotypes from Natural hybridization between divergent lineages in a selfing hermaphroditic fish

description: Genotypes of 33 microsatellite loci in mangrove rivulus
DOI: 10.6084/m9.figshare.6344948
title: Appendix from Forward and inverse problems in the mechanics of soft filaments

description: Additional mathematical derivations and validation test cases.
DOI: 10.6084/m9.figshare.6344948.v1
title: Appendix from Forward and inverse problems in the mechanics of soft filaments

description: Additional mathematical derivations and validation test cases.
DOI: 10.6084/m9.figshare.6344888
title: Fecal source identification using random forest

description: Script_RF_V6.R: Code to perform the source identification using random forest classification (creation/training of the classifiers + prediction of new samples).<br>RF_SourceIdentification_v6.RData: R-objects that contains the training/testing V6-databases used in the publication. <br>ClostridialesBacteroiales_v6.fa: File containing the sequences of the V6- Clostridiales/Bacteroidales amplicon sequence variants.<br><br>RF_training_outputs.zip: Folder containing the outputs of the random forest classifications performed to train the V6-classifiers.<br>Confusion_Matrix_V6.xlsx: Excel spreadsheet containing the confusion matrix for each V6-classifiers.<br><br>Comparison_V4V5_V6.zip (not peer-reviewed): Folder containing the files used to train/test/compare the classifiers.<br><br>