cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6875522
title: Raw 16S rRNA fastq data files for herbivore microbiome study

description: This repository contains the <b>RAW</b> sequencing data for the herbivorous reef fish microbiome study. Trimmed reads (with primers removed) were deposited at the European Nucleotide Archive, study accession number <b>PRJEB28397 (ERP110594)</b>.<br><br>Raw fastq data files are named using the root format RunQ_GnSpe000_G, where Q is the run number (1, 2, or 3), GnSpe is the host genus and species, 00 is a unique host ID number, and G is the gut segment (F = foregut; M = midgut; H = hind). So the file name Run1_SpVir11_M_S147_L001_R2_001.fastq corresponds to: the R2 reads; midgut sample; Sparisoma viride; individual 11; Run01.<br> <b>Raw fastq files are deposited here by Run.</b><b><br> </b>To process please use the scripts in the <b>Pipeline for 16S rRNA processing using DADA2 </b>directory.<br><b>DNA Extraction & Sequencing Methods</b><br>For all samples, we homogenized material from each gut segment (fore, mid, hind) separately in 50mL conical tubes for 2 minutes on a Vortex Genie 2. We collected 200 mg (wet weight) of homogenate for DNA extraction following the Human Microbiome Project Core Microbiome Sampling Protocol A (v12.0, HMP Protocol # 07-001) for stool samples. Prior to extraction, we heat treated each sample, first at 65℃ f or 10 minutes, followed by 95℃ for 10 minutes. We then used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's protocol to extract community DNA from each sample.<br> Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome Resource at the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University).<br> We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA) and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 53 individual fish encompassing seven species and three genera. Two species—Sparisoma chrysopterum and Scarus vetula—were only represented by 1 and 2 individuals, respectively. Though we chose to omit these samples from the final analysis, these samples were sequenced and analyzed along with the rest of the samples and made the data available for analysis.<br>We generate sequence data for all 159 sample—three gut segments (fore, mid, and hind) from 53 individuals. Sequencing was conducted across three runs. In the first run (Run01), 144 samples were sequenced and, due to lower than average yield, were re-sequenced (Run02). The remaining 15 samples (5 individuals) were sequenced on a separate run (Run03).<br>
DOI: 10.6084/m9.figshare.6875525.v1
title: TESS Perigee Times

description: Perigee passage times for the Transiting Exoplanet Survey Satellite (TESS). This was calculated by using the JPL Horizons website (https://ssd.jpl.nasa.gov/horizons.cgi), with the target body as TESS(spacecraft) [-95] and the observer as Geocentric [500]. The times given are the minimum orbital distance from Earth and are good to 10 minutes. <br>The emphemeris is from June 21, 2018.<br><br>
DOI: 10.6084/m9.figshare.6875525.v3
title: TESS Perigee Times

description: Perigee passage times for the Transiting Exoplanet Survey Satellite (TESS). This was calculated by using the JPL Horizons website (https://ssd.jpl.nasa.gov/horizons.cgi), with the target body as TESS(spacecraft) [-95] and the observer as Geocentric [500]. The times given are the minimum orbital distance from Earth and are good to 15 minutes. <br>The emphemeris is from June 16, 2019.<br><br>
DOI: 10.6084/m9.figshare.6875525.v2
title: TESS Perigee Times

description: Perigee passage times for the Transiting Exoplanet Survey Satellite (TESS). This was calculated by using the JPL Horizons website (https://ssd.jpl.nasa.gov/horizons.cgi), with the target body as TESS(spacecraft) [-95] and the observer as Geocentric [500]. The times given are the minimum orbital distance from Earth and are good to 15 minutes. <br>The emphemeris is from June 16, 2019.<br><br>
DOI: 10.6084/m9.figshare.6875522.v1
title: Raw 16S rRNA fastq data files for herbivore microbiome study

description: This repository contains the <b>RAW</b> sequencing data for the herbivorous reef fish microbiome study. Trimmed reads (with primers removed) were deposited at the European Nucleotide Archive, study accession number <b>PRJEB28397 (ERP110594)</b>.<br><br>Raw fastq data files are named using the root format RunQ_GnSpe000_G, where Q is the run number (1, 2, or 3), GnSpe is the host genus and species, 00 is a unique host ID number, and G is the gut segment (F = foregut; M = midgut; H = hind). So the file name Run1_SpVir11_M_S147_L001_R2_001.fastq corresponds to: the R2 reads; midgut sample; Sparisoma viride; individual 11; Run01.<br> <b>Raw fastq files are deposited here by Run.</b><b><br> </b>To process please use the scripts in the <b>Pipeline for 16S rRNA processing using DADA2 </b>directory.<br><b>DNA Extraction & Sequencing Methods</b><br>For all samples, we homogenized material from each gut segment (fore, mid, hind) separately in 50mL conical tubes for 2 minutes on a Vortex Genie 2. We collected 200 mg (wet weight) of homogenate for DNA extraction following the Human Microbiome Project Core Microbiome Sampling Protocol A (v12.0, HMP Protocol # 07-001) for stool samples. Prior to extraction, we heat treated each sample, first at 65℃ f or 10 minutes, followed by 95℃ for 10 minutes. We then used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's protocol to extract community DNA from each sample.<br> Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome Resource at the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University).<br> We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA) and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 53 individual fish encompassing seven species and three genera. Two species—Sparisoma chrysopterum and Scarus vetula—were only represented by 1 and 2 individuals, respectively. Though we chose to omit these samples from the final analysis, these samples were sequenced and analyzed along with the rest of the samples and made the data available for analysis.<br>We generate sequence data for all 159 sample—three gut segments (fore, mid, and hind) from 53 individuals. Sequencing was conducted across three runs. In the first run (Run01), 144 samples were sequenced and, due to lower than average yield, were re-sequenced (Run02). The remaining 15 samples (5 individuals) were sequenced on a separate run (Run03).<br>
DOI: 10.6084/m9.figshare.6875522.v2
title: Raw 16S rRNA fastq data files for herbivore microbiome study

description: This repository contains the <b>RAW</b> sequencing data for the herbivorous reef fish microbiome study. Trimmed reads (with primers removed) were deposited at the European Nucleotide Archive, study accession number <b>PRJEB28397 (ERP110594)</b>.<br><br>Raw fastq data files are named using the root format RunQ_GnSpe000_G, where Q is the run number (1, 2, or 3), GnSpe is the host genus and species, 00 is a unique host ID number, and G is the gut segment (F = foregut; M = midgut; H = hind). So the file name Run1_SpVir11_M_S147_L001_R2_001.fastq corresponds to: the R2 reads; midgut sample; Sparisoma viride; individual 11; Run01.<br> <b>Raw fastq files are deposited here by Run.</b><b><br> </b>To process please use the scripts in the <b>Pipeline for 16S rRNA processing using DADA2 </b>directory.<br><b>DNA Extraction & Sequencing Methods</b><br>For all samples, we homogenized material from each gut segment (fore, mid, hind) separately in 50mL conical tubes for 2 minutes on a Vortex Genie 2. We collected 200 mg (wet weight) of homogenate for DNA extraction following the Human Microbiome Project Core Microbiome Sampling Protocol A (v12.0, HMP Protocol # 07-001) for stool samples. Prior to extraction, we heat treated each sample, first at 65℃ f or 10 minutes, followed by 95℃ for 10 minutes. We then used the PowerSoil® DNA Isolation Kit (MoBio) following the manufacturer's protocol to extract community DNA from each sample.<br> Extracted DNA was sequenced on an Illumina MiSeq by Integrated Microbiome Resource at the Centre for Comparative Genomics and Evolutionary Bioinformatics (Dalhousie University).<br> We targeted the V4-V5 hypervariable region using 515F (5′-GTGYCAGCMGCCGCGGTA) and 926R (5′-CCGYCAATTYMTTTRAGT). We collected 53 individual fish encompassing seven species and three genera. Two species—Sparisoma chrysopterum and Scarus vetula—were only represented by 1 and 2 individuals, respectively. Though we chose to omit these samples from the final analysis, these samples were sequenced and analyzed along with the rest of the samples and made the data available for analysis.<br>We generate sequence data for all 159 sample—three gut segments (fore, mid, and hind) from 53 individuals. Sequencing was conducted across three runs. In the first run (Run01), 144 samples were sequenced and, due to lower than average yield, were re-sequenced (Run02). The remaining 15 samples (5 individuals) were sequenced on a separate run (Run03).<br>
DOI: 10.6084/m9.figshare.6875462
title: FE model for IH gear pair model

description: FE model catalysts of the IH condition for carburizded gear pair
DOI: 10.6084/m9.figshare.6875477
title: The experiment catalysts data of the hardness gradient of carburized gear pair

description: The experiment catalysts data of the hardness gradient of carburized gear pair
DOI: 10.6084/m9.figshare.6875450
title: EH_gear transmission_strengh.inp

description: FE model catalysts of the EH condition for carburizded gear pair
DOI: 10.6084/m9.figshare.6875456
title: FE model of HH condition grat pair

description: FE model catalysts of the HH condition for carburizded gear pair<br>
DOI: 10.6084/m9.figshare.6875309
title: Supplementary_Table_1.xlsx

description: <b>Data of all the subjects on tumor type and scores for SWM and DMVs.</b>Data are stored in an Excel file. MT, metastatic tumor; DA, diffuse astrocytoma; GB, glioblastoma; SWM, superficial white matter; DMV, deep medullary vein.<br>
DOI: 10.6084/m9.figshare.6875285
title: Additional file 9: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Coverage plots and read counts for annotated ncRNAs regions of NEM316 strain. X axis on images are annotated region and Y axis are coverage per base. (ZIP 272 kb)
DOI: 10.6084/m9.figshare.6875285.v1
title: Additional file 9: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Coverage plots and read counts for annotated ncRNAs regions of NEM316 strain. X axis on images are annotated region and Y axis are coverage per base. (ZIP 272 kb)
DOI: 10.6084/m9.figshare.6875258
title: Additional file 7: of Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes

description: Circos plots for all individual GBS genomes analyzed. All Additional file 4 information is plotted over genome extension. The tracks and the color code follow the same pattern as in Fig. 1. (ZIP 10957 kb)
DOI: 10.6084/m9.figshare.6875258.v1
title: Additional file 7: of Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes

description: Circos plots for all individual GBS genomes analyzed. All Additional file 4 information is plotted over genome extension. The tracks and the color code follow the same pattern as in Fig. 1. (ZIP 10957 kb)
DOI: 10.6084/m9.figshare.6875228
title: Additional file 5: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: RNA families group, function and conservation information. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6875228.v1
title: Additional file 5: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: RNA families group, function and conservation information. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6875213
title: Additional file 4: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: GFF3 annotations for all classified Regions and ncRNAs. (ZIP 1638 kb)
DOI: 10.6084/m9.figshare.6875213.v1
title: Additional file 4: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: GFF3 annotations for all classified Regions and ncRNAs. (ZIP 1638 kb)
DOI: 10.6084/m9.figshare.6875201
title: Additional file 3: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Curated ncRNA count. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6875201.v1
title: Additional file 3: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Curated ncRNA count. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.6875180
title: Additional file 2: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Rfam entries only found in Lactobacillales order, used to annotation of ncRNAs with Infernal software. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6875180.v1
title: Additional file 2: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Rfam entries only found in Lactobacillales order, used to annotation of ncRNAs with Infernal software. (TXT 1 kb)
DOI: 10.6084/m9.figshare.6875171
title: Additional file 1: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Strain Information Table. (XLS 37 kb)
DOI: 10.6084/m9.figshare.6875171.v1
title: Additional file 1: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Strain Information Table. (XLS 37 kb)
DOI: 10.6084/m9.figshare.6875141
title: Additional file 10: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Coverage plots for surrounding region of detected RNA families. (ZIP 2654 kb)
DOI: 10.6084/m9.figshare.6875141.v1
title: Additional file 10: of Functional annotation and distribution overview of RNA families in 27Â Streptococcus agalactiae genomes

description: Coverage plots for surrounding region of detected RNA families. (ZIP 2654 kb)
DOI: 10.6084/m9.figshare.6875129
title: Additional file 1: of Effects of sex on response of the bovine preimplantation embryo to insulin-like growth factor 1, activin A, and WNT7A

description: Least-squares means of the fold-chage value for each gene examined, by treatment (control vs IGF1), sex (female vs male), and the interaction (P-values from dCT analyses). Tab 1: Genes measured only in Experiment 1. Tab 2: Genes measured only in Experiment 2. Tab 3: Genes measured in both Experiments 1 & 2. (XLS 95 kb)
DOI: 10.6084/m9.figshare.6875129.v1
title: Additional file 1: of Effects of sex on response of the bovine preimplantation embryo to insulin-like growth factor 1, activin A, and WNT7A

description: Least-squares means of the fold-chage value for each gene examined, by treatment (control vs IGF1), sex (female vs male), and the interaction (P-values from dCT analyses). Tab 1: Genes measured only in Experiment 1. Tab 2: Genes measured only in Experiment 2. Tab 3: Genes measured in both Experiments 1 & 2. (XLS 95 kb)
DOI: 10.6084/m9.figshare.6875117
title: Additional file 2: of Prognosis of ovarian cancer in women with type 2 diabetes using metformin and other forms of antidiabetic medication or statins: a retrospective cohort study

description: ATC codes for different types of oral ADM and statins. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6875117.v1
title: Additional file 2: of Prognosis of ovarian cancer in women with type 2 diabetes using metformin and other forms of antidiabetic medication or statins: a retrospective cohort study

description: ATC codes for different types of oral ADM and statins. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6875108
title: Additional file 1: of Panoramic radiographs and quantitative ultrasound of the radius and phalanx III to assess bone mineral status in postmenopausal women

description: Osteoporosis. Raw data. Individual values of all parameters analyzed are provided in Excel. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.6875102
title: Additional file 1: of Prognosis of ovarian cancer in women with type 2 diabetes using metformin and other forms of antidiabetic medication or statins: a retrospective cohort study

description: ICD-10 and ICD-O-3 codes for epithelial ovarian cancer and different histological types. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6875102.v1
title: Additional file 1: of Prognosis of ovarian cancer in women with type 2 diabetes using metformin and other forms of antidiabetic medication or statins: a retrospective cohort study

description: ICD-10 and ICD-O-3 codes for epithelial ovarian cancer and different histological types. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.6875045
title: Additional file 2: of Association of malalignment, muscular dysfunction, proprioception, laxity and abnormal joint loading with tibiofemoral knee osteoarthritis - a systematic review and meta-analysis

description: Forest plots of data pooling for skeletal malalignment, muscular dysfunction, impaired proprioception, laxity and abnormal loading, and the presence of knee osteoarthritis (ZIP 1272 kb).
DOI: 10.6084/m9.figshare.6875045.v1
title: Additional file 2: of Association of malalignment, muscular dysfunction, proprioception, laxity and abnormal joint loading with tibiofemoral knee osteoarthritis - a systematic review and meta-analysis

description: Forest plots of data pooling for skeletal malalignment, muscular dysfunction, impaired proprioception, laxity and abnormal loading, and the presence of knee osteoarthritis (ZIP 1272 kb).
DOI: 10.6084/m9.figshare.6874955
title: supplemental data.zip

description: Figure S1-5; Table S1-14; Language service certificate
DOI: 10.6084/m9.figshare.6874955.v1
title: supplemental data.zip

description: Figure S1-5; Table S1-14; Language service certificate
DOI: 10.6084/m9.figshare.6874940
title: KEGG pathways including their raw copy number in two hot springs of the Uzon Caldera, Kamchatka, Russia

description: An exhaustive list of 222 predicted KEGG pathways including their raw copy number in two hot springs of the Uzon Caldera, Kamchatka, Russia, and KEGG pathway maps can be found here. <br>Gene calls were annotated during this workflow with NCBI’s Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies downloaded from GhostKOALA following the workflow for anvi’o by Elaina Graham (as described in http://merenlab.org/2018/01/17/importing-ghostkoala-annotations/).<br>
DOI: 10.6084/m9.figshare.6874940.v1
title: KEGG pathways including their raw copy number in two hot springs of the Uzon Caldera, Kamchatka, Russia

description: An exhaustive list of 222 predicted KEGG pathways including their raw copy number in two hot springs of the Uzon Caldera, Kamchatka, Russia, and KEGG pathway maps can be found here. <br>Gene calls were annotated during this workflow with NCBI’s Clusters of Orthologous Groups (COGs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies downloaded from GhostKOALA following the workflow for anvi’o by Elaina Graham (as described in http://merenlab.org/2018/01/17/importing-ghostkoala-annotations/).<br>
DOI: 10.6084/m9.figshare.6874928
title: Tree in Fig.2 - Archaeal and bacterial genomes used by Hug et al. in 2016 to construct a microbial tree of life; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all genomes of taxa analyzed in Burgess et al. (2012) with one representative genome on NCBI (Newick file)

description: Taxonomy of our MAGs was refined by placing MAGs in a phylogenetic context using PhyloSift v. 1.0.1 with the updated PhyloSift markers database (version 4; 2018-02-12; https://figshare.com/articles/PhyloSift_markers_database/5755404/4). For this purpose, MAGs, all taxa previously identified by Burgess et al. (2012) with complete genomes available on NCBI (downloaded 2017-09-06) and all archaeal and bacterial genomes previously used in Hug et al. (2016) were placed in a phylogenetic tree. All genomes used in this tree and a mapping file can be found on figshare (https://doi.org/10.6084/m9.figshare.6863594.v1; https://doi.org/10.6084/m9.figshare.6863744.v2; https://doi.org/10.6084/m9.figshare.6863798.v1; https://doi.org/10.6084/m9.figshare.6863813.v1). For more information about the available core marker gene sets see Darling et al. 2014 (updated last on 2018-02-12). We used 37 of these single-copy marker genes (ribosomal protein S2 rpsB, S10 rpsJ, L1 rplA, L22, L4/L1e rplD, L2 rplB, S9 rpsl, L3 rplC, L14b/L23e rplN, S5, S19 rpsS, S7, L16/L10E rplP, S13 rpsM, L15, L25/L23, L6 rplF, L11 rplK, L5 rplE, S12/S23, L29, S3 rpsC, S11 rpsK, L10, S8, L18P/L5E, S15P/S13e, S17, S13 rplM, L24; and translation initiation factor IF-2, metalloendopeptidase, phenylalanyl-tRNA synthetase beta subunit, phenylalanyl-tRNA synthetase alpha subunit, tRNA pseudouridine synthase B, Porphobilinogen deaminase, and ribonuclease HII; i.e., PhyloSift markers DNGNGWU00001 - DNGNGWU00040 without DNGNGWU00004, DNGNGWU00008 and DNGNGWU00038). The amino acid alignment of these 37 concatenated genes was trimmed using trimAl v.1.2. Columns with gaps in more than 5% of the sequences were removed, as well as taxa with with less than 75% of the concatenated sequences. MAGs from ARK and ZAV that did not meet this threshold were manually kept in the alignment. The final alignment comprised 3,240 taxa (make a supplementary table) and 5,459 amino acid positions. This alignment was then used to build a new phylogenetic tree in RAxML v. 8.2.10 on the CIPRES Science Gateway web server. First, we searched for the best protein substitution model of the alignment with its empirical base frequencies using the Bayesian Information Criterion (BIC) within RAxML. Then, this substitution model; i.e, LG plus CAT (after Le and Gascuel), was used to infer a phylogenetic tree. We chose the rapid bootstrapping algorithm (flag -f a) to find the best scoring maximum likelihood tree with 10 starting trees in one run with the number of bootstraps automatically determined (MRE-based bootstopping criterion). One hundred fifty bootstrap replicates were conducted. The full tree inference required 2,236 computational hours on the CIPRES supercomputer.<br>--&gt; I added bootstraps later (check latest version)!
DOI: 10.6084/m9.figshare.6874934
title: Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI.

description: Table with all the taxa names and NCBI IDs that can be found in this tree: https://doi.org/10.6084/m9.figshare.6874928.v1
DOI: 10.6084/m9.figshare.6874934.v1
title: Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016, and MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia (tre file)

description: Table with all the taxa names and NCBI IDs that can be found in this tree: https://doi.org/10.6084/m9.figshare.6874928.v1
DOI: 10.6084/m9.figshare.6874934.v3
title: Table with taxa we used for the tree of life - archaea and bacteria from Hug et al.'s tree of life in 2016; MAGs isolated from two hot springs in the Uzon Caldera, Kamchatka, Russia; and all taxa from Burgess et al. (2012) with one representative genome on NCBI.

description: Table with all the taxa names and NCBI IDs that can be found in this tree: https://doi.org/10.6084/m9.figshare.6874928.v1