cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8796953.v1
title: Assessment of tonsil grade classification by measuring actual tonsil size during surgery

description: Adenotonsillar enlargement is a common cause of substantial pediatric illnesses, including obstructive respiratory disease and recurrent airway infection. The current tonsil grading systems in use allows clinicians to evaluate tonsil size, but the correlation with actual tonsillar size in a clinical setting has not been established.
DOI: 10.6084/m9.figshare.8796944.v1
title: FosSahul 2.0 database and R code

description: <i>FosSahul</i> 2.0 database and R code accompanying manuscript "<i>FosSahul </i>2.0, an updated database for the Late Quaternary fossil records of Sahul" submitted to <i>Scientific Data</i>. Excel files: FosSahul2.0.csv: <i>FosSahul</i> database collating non-human vertebrate megafauna fossil records for the Sahul region. Note that location data have been rounded to one degree decimal and might not reflect the exact location of the fossil record. For more information on precise locations, contact the authors.FosSahul2.0_metadata.xlsx: Column description and further detail on the <i>FosSahul</i> 2.0 database.CalibratedC14Dates_FosSahul.csv: Calibrated radiocarbon dates for <i>FosSahul</i> 2.0. Needed for the calculation of the biodiversity index.TimeBins.csv: Time bins needed for the calculation of the biodiversity index. R-scripts: FosSahul_Rating.R: Quality-rating algorithm for the <i>FosSahul</i> database.FosSahul_Data import.R: Data import script necessary for the calculation of the biodiversity index.FosSahul_Biodiversity_index_calculation.R: Code for the calculation of the biodiversity index.
DOI: 10.6084/m9.figshare.8796899
title: Word2vec Convolutional Neural Networks for Classification of News Articles and Tweets

description: This data is intended to reproduce the performance evaluation of the word2vec CNN classification model.<br>It consists of news+CBOW, news+Skipgram, news+random vector, Twitter+CBOW, Twitter+Skipgram, Twitter+random vector.<br>Each file contains values of acuracy, determination, recall, f1 score, and training volume is 4K for the random vector and 10K for the rest.<br><br>
DOI: 10.6084/m9.figshare.8796875
title: Additional data concerning closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands

description: Supplementary data on 122 Salmonella Heidelberg isolates, recovered from poultry meat imported into the Netherlands from Brazil.This includes both epidemiological information on the source of the isolates, as well as biological characteristics of the isolates themselves.<br>
DOI: 10.6084/m9.figshare.8796854
title: Data supplement for paper "Multiple sources of variation in human stool microbiome from a population-based randomized controlled trial"

description: De-identified microbiome sequence data from samples collected in a trial conducted in rural Niger, 2015. Includes metadata on children's consumption of solid food and randomization to placebo or antibiotics. Verbal consent was obtained from the guardians of the children. Ethical clearance was obtained from the institutional review board at the University of California San Francisco (UCSF) (10-01036), and by the Ministère de la Santé Publique of Niger, Deliberation N004/2013/CCNE, Comité Consultatif National d’Éthique.
DOI: 10.6084/m9.figshare.8796854.v1
title: Data supplement for paper "Multiple sources of variation in human stool microbiome from a population-based randomized controlled trial"

description: De-identified microbiome sequence data from samples collected in a trial conducted in rural Niger, 2015. Includes metadata on children's consumption of solid food and randomization to placebo or antibiotics. Verbal consent was obtained from the guardians of the children. Ethical clearance was obtained from the institutional review board at the University of California San Francisco (UCSF) (10-01036), and by the Ministère de la Santé Publique of Niger, Deliberation N004/2013/CCNE, Comité Consultatif National d’Éthique.
DOI: 10.6084/m9.figshare.8796848
title: Selected data from the French Sentence Corpus for analyses of saccades' overall landing positions, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of saccades' overall landing positions relative to the center of the next word on the line (N+1), whether or not saccades landed on this word, as a function of the length and frequency of Word N+1 and saccades' launch-site distance to the beginning of Word N+1.<br>
DOI: 10.6084/m9.figshare.8796839
title: Selected data from the French Sentence Corpus for analysis of initial eye landing positions in the target words

description: Selected data from the French Sentence Corpus (FSC) for analysis of initial eye landing positions in the test words as a function of the test words' length, frequency and predictability, as well as the saccades' launch-site distance to the beginning of the test words.<br>
DOI: 10.6084/m9.figshare.8796845
title: Selected data from the French Sentence Corpus for analyses of within-word initial eye landing positions, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of within-word landing positions as a function of the words' length and frequency, as well as saccades' launch-site distance to the beginning of words.<br>
DOI: 10.6084/m9.figshare.8796848.v1
title: Selected data from the French Sentence Corpus for analyses of saccades' overall landing positions, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of saccades' overall landing positions relative to the center of the next word on the line (N+1), whether or not saccades landed on this word, as a function of the length and frequency of Word N+1 and saccades' launch-site distance to the beginning of Word N+1.<br>
DOI: 10.6084/m9.figshare.8796839.v1
title: Selected data from the French Sentence Corpus for analysis of initial eye landing positions in the target words

description: Selected data from the French Sentence Corpus (FSC) for analysis of initial eye landing positions in the test words as a function of the test words' length, frequency and predictability, as well as the saccades' launch-site distance to the beginning of the test words.<br>
DOI: 10.6084/m9.figshare.8796845.v1
title: Selected data from the French Sentence Corpus for analyses of within-word initial eye landing positions, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of within-word landing positions as a function of the words' length and frequency, as well as saccades' launch-site distance to the beginning of words.<br>
DOI: 10.6084/m9.figshare.8796830
title: Selected data from the French Sentence Corpus for analyses of word skipping, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of the likelihood of word skipping as a function of the words' length and frequency, as well as saccades' launch-site distance to the beginning of words.<br>
DOI: 10.6084/m9.figshare.8796791
title: Selected data from the French Sentence Corpus for analyses of target-word skipping.

description: Selected data from the French Sentence Corpus (FSC) for analysis of the likelihood of skipping the test words as a function of the test words' length, frequency and predictability, as well as saccades' launch-site distance to the beginning of the test word.<br>
DOI: 10.6084/m9.figshare.8796830.v1
title: Selected data from the French Sentence Corpus for analyses of word skipping, using all words in the sentences that responded to our selection criteria.

description: Selected data from the French Sentence Corpus (FSC) for analysis of the likelihood of word skipping as a function of the words' length and frequency, as well as saccades' launch-site distance to the beginning of words.<br>
DOI: 10.6084/m9.figshare.8796791.v2
title: Selected data from the French Sentence Corpus for analyses of target-word skipping.

description: Selected data from the French Sentence Corpus (FSC) for analysis of the likelihood of skipping the test words as a function of the test words' length, frequency and predictability, as well as saccades' launch-site distance to the beginning of the test word.<br>
DOI: 10.6084/m9.figshare.8796791.v1
title: Selected data from the French Sentence Corpus for analysis of target-word skipping.

description: Selected data from the French Sentence Corpus (FSC) for analysis of the likelihood of skipping the test words as a function of the test words' length, frequency and predictability, as well as saccades' launch-site distance to the beginning of the test word.<br>
DOI: 10.6084/m9.figshare.8796698
title: The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element

description: In this study we report here on a detailed characterization of the standby site in <i>tisB</i> mRNA. 30S subunits bind to a single-stranded region and a 5'- stem loop structure, as shown by fluorescence anisotropy experiments and footprint mapping by CLIP experiments. <br>The data presented in figshare includes raw and processed RNA reads obtained from our in vitro CLIP experiment. Briefly, purified tisB mRNA was incubated with sub-stoichiometric concentrations of either purified 30S subunits (carrying S1-3xFLAG) or S1-3xFLAG only, followed by UV-crosslinking (250 mJ/cm2). 30S, S1 and cross-linked RNAs were isolated by immuno-precipitation using Anti-FLAG coupled magnetic beads. RNA footprints were generated on the beads with benzonase. Proteins were digested with proteinase K, and, after labeling with radioactive gamma-ATP, labeled RNA footprints (25-50 nt) were gel-purified. Eluted RNAs were converted into cDNA using the CATS RNA-Seq kit v2 (diagenode) and sequenced on an Illumina Miseq device. Reads were then aligned either to the tisB sequence or the 16S rRNA sequence (as control). <br>The files available comprised: - The raw data from the 30S and S1 CLIP experiments (Romilly_30S.fa and Romilly_S1.fa) - Bam/bai files of reads mapped to the tisB mRNA or the 16S rRNA, from the 30S and S1 pulldown assay (30S_tisB.bam/bai, 30S_16S.bam.bai, S1_tisB.bam/bai, S1_16S.bam/bai) - The sequence file containing the tisB sequence and 16S rRNA, respectively (tisB_sequence.fa, 16S_sequence.fa) - A gff files containing the postions of the CDS and the standby site for the tisB sequence (tisB_annotation.gff) - Files with bowtie 2 summary and stats for each of the processing step (Bowtie2 sumary, stats.30S.tabular, stats.S1.tabular, stats.30Svs16SrRNA.tabular, stats.S1vs16SrRNA.tabular)<br> The figure representing the data in the paper was generated using the visualization tool IGV 2.3.68<br> For more information on data processing, please refer to the paper SI, or contact romilly.cedric@icm.uu.se or gerhart.wagner@icm.uu.se.
DOI: 10.6084/m9.figshare.8796659
title: 程度词语列表

description: adverb list of sentiment analysis
DOI: 10.6084/m9.figshare.8796656
title: hCINAP WT U2OS RNA-seq

description: RNA-seq analysis was performed by ANNOROAD. Briefly, the total RNA from wild-type and knockout hCINAP U2OS cells was extracted, and sequences were performed with Illumina Solexa Ultrasequencing.HISTORY
DOI: 10.6084/m9.figshare.8796659.v1
title: 程度词语列表

description: adverb list of sentiment analysis
DOI: 10.6084/m9.figshare.8796647
title: hCINAP KO U2OS RNA-seq

description: RNA-seq analysis was performed by ANNOROAD. Briefly, the total RNA from wild-type and knockout hCINAP U2OS cells was extracted, and sequences were performed with Illumina Solexa Ultrasequencing.
DOI: 10.6084/m9.figshare.8796653
title: 餐厅类自定义情感词典

description: sentiment dictionary based on catering industry.
DOI: 10.6084/m9.figshare.8796656.v1
title: hCINAP WT U2OS RNA-seq

description: RNA-seq analysis was performed by ANNOROAD. Briefly, the total RNA from wild-type and knockout hCINAP U2OS cells was extracted, and sequences were performed with Illumina Solexa Ultrasequencing.HISTORY
DOI: 10.6084/m9.figshare.8796641
title: DATA for "Kinetic exchange of remobilized phosphorus concerned with phosphorus-iron-sulfur biogeochemical coupling in coastal sediment"

description: phosphorus-iron-sulfur biogeochemistry
DOI: 10.6084/m9.figshare.8796647.v1
title: hCINAP KO U2OS RNA-seq

description: RNA-seq analysis was performed by ANNOROAD. Briefly, the total RNA from wild-type and knockout hCINAP U2OS cells was extracted, and sequences were performed with Illumina Solexa Ultrasequencing.
DOI: 10.6084/m9.figshare.8796653.v1
title: 餐厅类自定义情感词典

description: sentiment dictionary based on catering industry.
DOI: 10.6084/m9.figshare.8796545
title: Data from: Cold temperature improves tannin tolerance in a granivorous rodent.xlsx

description: <b>This data supports the article "Cold temperature improves tannin tolerance in a granivorous rodent", H.R. Windley & T. Shimada, 2019, Journal of Animal Ecology.</b>
DOI: 10.6084/m9.figshare.8796536
title: Additional file 2: of Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

description: Supplemental Tables S1-S7. (XLSX 313 kb)
DOI: 10.6084/m9.figshare.8796641.v1
title: DATA for "Kinetic exchange of remobilized phosphorus concerned with phosphorus-iron-sulfur biogeochemical coupling in coastal sediment"

description: phosphorus-iron-sulfur biogeochemistry
DOI: 10.6084/m9.figshare.8796545.v1
title: Data from: Cold temperature improves tannin tolerance in a granivorous rodent.xlsx

description: <b>This data supports the article "Cold temperature improves tannin tolerance in a granivorous rodent", H.R. Windley & T. Shimada, 2019, Journal of Animal Ecology.</b>
DOI: 10.6084/m9.figshare.8796536.v1
title: Additional file 2: of Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

description: Supplemental Tables S1-S7. (XLSX 313 kb)
DOI: 10.6084/m9.figshare.8796488
title: Additional file 1: of Cryopreservation in 95% serum with 5% DMSO maintains colony formation and chondrogenic abilities in human synovial mesenchymal stem cells

description: Figure S1. Donor specific analysis of colony formation. (a) Colony number/dish. (b) Cell number/dish. (c) Cell number/colony number. (ZIP 507 kb)
DOI: 10.6084/m9.figshare.8796488.v1
title: Additional file 1: of Cryopreservation in 95% serum with 5% DMSO maintains colony formation and chondrogenic abilities in human synovial mesenchymal stem cells

description: Figure S1. Donor specific analysis of colony formation. (a) Colony number/dish. (b) Cell number/dish. (c) Cell number/colony number. (ZIP 507 kb)
DOI: 10.6084/m9.figshare.8796449
title: Table S1. Expression of wheat NLR-ID alternative splicing candidate genes available in Wheat Gene Expression Atlas and NCBI databases.

description: The 54 transcripts shown in <b>Figure 3</b> were acquired from the GSE106397 dataset in NCBI and the Wheat Gene Expression Atlas. Cells are colored by expression level, showing differential expression between alternative transcripts of the same gene.
DOI: 10.6084/m9.figshare.8796419
title: Supplementary Data for Kogay et al. (2019)

description: This dataset contains supplementary figures and tables, sequence alignments, phylogenetic trees and outlier removal calculations used in the bioinformatic analyses presented in:<br> <br> Roman Kogay, Taylor B. Neely, Daniel P. Birnbaum, Camille R. Hankel, Migun Shakya, and Olga Zhaxybayeva. “Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents”, BioRxiv, 2019. (BIORXIV/2019/697243; available at https://www.biorxiv.org/content/10.1101/697243v1)<br><br> <b>File Contents:</b><b><br></b> <b>Supplementary_Figures.pdf: </b>Supplementary Figures S1 and S2 in the manuscript.<br><br> <b>Supplementary_Tables.zip:</b> Supplementary Tables S1-S15 in the manuscript. <b><br> Alignments_for_weight_assignment_GTAs.zip:</b> Alignments of 'true GTA' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_weight_assignment_viruses.zip:</b> Alignments of 'true virus' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_removal_of_outliers.zip:</b> Alignments of ‘true GTA’ and ‘true virus’ sequences in the training datasets. Pairwise phylogenetic distances calculated from these alignments were used to remove GTA homologs that are more closely related to viruses than to other GTAs, as well as to investigate obtained lower accuracies for g6 and g12 (<b>Supplementary Table S11)</b>. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Outlier_removal.xlsx</b>: Calculations to identify GTAs that are more closely related to viruses than to other GTAs. The removed sequences are highlighted. <b><br></b><b>Reference_phylogenetic_tree_reconstruction.zip:</b> Concatenated alignment of 83 marker genes in 1,423 taxa in PHYLIP format (concatenated_83markers.phy); information about partitions and substitution models used in phylogenetic reconstruction (partitions.txt); and phylogenetic tree in Newick format (1423_alphaproteobacteria_reference_tree.newick).
DOI: 10.6084/m9.figshare.8796359
title: BASELINE RASs DATASET_Figshare.xlsx

description: <pre>Study of baseline resistance to direct-acting antivirals against hepatitis C virus, resistance-guided treatment, therapeutic follow-up and efficacy.</pre>
DOI: 10.6084/m9.figshare.8796419.v1
title: Supplementary Data for Kogay et al. (2019)

description: This dataset contains supplementary figures and tables, sequence alignments, phylogenetic trees and outlier removal calculations used in the bioinformatic analyses presented in:<br> <br> Roman Kogay, Taylor B. Neely, Daniel P. Birnbaum, Camille R. Hankel, Migun Shakya, and Olga Zhaxybayeva. “Machine-learning classification suggests that many alphaproteobacterial prophages may instead be gene transfer agents”, BioRxiv, 2019. (BIORXIV/2019/697243; available at https://www.biorxiv.org/content/10.1101/697243v1)<br><br> <b>File Contents:</b><b><br></b> <b>Supplementary_Figures.pdf: </b>Supplementary Figures S1 and S2 in the manuscript.<br><br> <b>Supplementary_Tables.zip:</b> Supplementary Tables S1-S15 in the manuscript. <b><br> Alignments_for_weight_assignment_GTAs.zip:</b> Alignments of 'true GTA' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_weight_assignment_viruses.zip:</b> Alignments of 'true virus' sequences in the training dataset. These alignments were used to generate pairwise phylogenetic distances for the weighting scheme. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Alignments_for_removal_of_outliers.zip:</b> Alignments of ‘true GTA’ and ‘true virus’ sequences in the training datasets. Pairwise phylogenetic distances calculated from these alignments were used to remove GTA homologs that are more closely related to viruses than to other GTAs, as well as to investigate obtained lower accuracies for g6 and g12 (<b>Supplementary Table S11)</b>. The alignments are in FASTA format. The filename prefix (g2, …, g15) refers to the RcGTA gene name (see <b>Supplementary Table S1</b>). <b><br></b><b>Outlier_removal.xlsx</b>: Calculations to identify GTAs that are more closely related to viruses than to other GTAs. The removed sequences are highlighted. <b><br></b><b>Reference_phylogenetic_tree_reconstruction.zip:</b> Concatenated alignment of 83 marker genes in 1,423 taxa in PHYLIP format (concatenated_83markers.phy); information about partitions and substitution models used in phylogenetic reconstruction (partitions.txt); and phylogenetic tree in Newick format (1423_alphaproteobacteria_reference_tree.newick).
DOI: 10.6084/m9.figshare.8796356
title: Intraoperative lidocaine infusion in laparoscopic bariatric surgery

description: Approval was obtained from University of California, San Francisco Institutional Review Board (IRB) to perform a retrospective cohort study by review of electronic medical records, with waiver of requirement for informed consent.<br><br> <br>
DOI: 10.6084/m9.figshare.8796359.v2
title: BASELINE RASs DATASET_Figshare.xlsx

description: <pre>Study of baseline resistance to direct-acting antivirals against hepatitis C virus, resistance-guided treatment, therapeutic follow-up and efficacy.</pre>
DOI: 10.6084/m9.figshare.8796344
title: Thermal-hydro coupling model of immiscible two-phase flow in heterogeneous porous structures at high temperature

description: This file includes the figures, tables and equations that underlie the conclusions of our paper.
DOI: 10.6084/m9.figshare.8796356.v1
title: Intraoperative lidocaine infusion in laparoscopic bariatric surgery

description: Approval was obtained from University of California, San Francisco Institutional Review Board (IRB) to perform a retrospective cohort study by review of electronic medical records, with waiver of requirement for informed consent.<br><br> <br>