cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.25917628
title: snRNA-seq, Primary-Recurrent GBM (Mikolajewicz Cohort)

description: <b>Summary.</b><br>10 primary GBM and 8 recurrent GBM samples (14/18 matched) profiled using single nucleus RNA- sequencing (sci-RNA-seq3 protocol).<br><b>Data Format.</b><br>Data is provided as preprocessed dataset, stored in Seurat Object.<br><b>Sample processing, sci-RNA-seq3 library generation, and sequencing</b><br>Snap-frozen patient pGBM and rGBM tissues were chopped with a razor blade or scissors before nucleus isolation. Nuclei extraction and fixation were performed as previously described (Cao 2019), except for the use of a modified CST lysis buffer50 plus 1% of SUPERase-In RNase Inhibitor (Invitrogen, #AM2696). Lysis time and washing steps were further optimized based on human GBM tissue. Nuclei quality was checked with DAPI and Wheat Germ Agglutinin (WGA) staining. Sci-RNA-seq3 libraries were generated as previously described49 using three-level combinatorial indexing. The final libraries were sequenced on Illumina NovaSeq as follows: read 1: 34bp, read 2: &gt;=69bp, index 1: 10bp, index 2: 10bp.<br><b>Demultiplexing and read alignments.</b><br>Raw sequencing reads were first demultiplexed based on i5/i7 PCR barcodes. FASTQ files were then processed using the sci-RNA-Seq3 pipeline. After barcodes and unique molecular identifiers (UMIs) were extracted from the read1 of FASTQ files, read alignment was performed using STAR short-read aligner (v2.5.2b) with the human genome (hg19) and Gencode v24 gene annotations. After removing duplicate reads based on UMI, barcode, chromosome and alignment position, reads were summarized into a count matrix of M genes × N nuclei.<br><b>Filtering, normalization, integration, and dimensional reduction.</b><br>Raw count matrices were loaded into a Seurat object (version 4.0.1) and filtered to retain cells with (i) 200 – 9000 recovered genes per cell, (ii) less than 60% mitochondrial content, and (iii) unmatched rate within 3 median absolute deviations of the median. To normalize count matrix, we adopted the modeling framework previously described and implemented in sctransform (R Package, version 0.3.2). In brief, count data were modelled by regularized negative binomial regression, using sequencing depth as a model covariate to regress out the influence of technical effects, and Pearson residuals were used as the normalized and variance stabilized biological signal for downstream analysis. Data from each patient were integrated with the reciprocal PCA method (Seurat) using the top 2000 variable features. PCA was performed on the integrated dataset, and the top N components that accounted for 90% of the observed variance were used for UMAP embedding, RunUMAP(max_components = 2, n_neighbours = 50, min_dist = 01, metric = cosine).<br><b>Contact.</b><br>Contact Dr. Nicholas Mikolajewicz regarding any questions about the data or analysis (n.mikolajewicz@utoronto.ca)
DOI: 10.6084/m9.figshare.25970653
title: Dataset ninis

description: Project: Smartphone dependence and addiction and bruxism in “NEET” young people in two coastal cities in Peru
DOI: 10.6084/m9.figshare.26305429
title: A new model of endotracheal tube biofilm identifies combinations of matrix-degrading enzymes and antimicrobials able to eradicate biofilms of pathogens that cause ventilator-associated pneumonia

description: <b>Supplementary Material for '</b><b>A new model of endotracheal tube biofilm identifies combinations of matrix-degrading enzymes and antimicrobials able to eradicate biofilms of pathogens that cause ventilator-associated pneumonia' </b><br><b><i>Abstract: </i></b>Defined as a pneumonia occurring after more than 48 hours of mechanical ventilation via an endotracheal tube, ventilator-associated pneumonia results from biofilm formation on the indwelling tube, seeding the patient’s lower airways with pathogenic microbes such as <i>Pseudomonas aeruginosa, Klebsiella pneumoniae, </i>and <i>Candida albicans.</i> Currently there is a lack of accurate <i>in vitro </i>models of ventilator-associated pneumonia development. This greatly limits our understanding of how the in-host environment alters pathogen physiology and the efficacy of ventilator-associated pneumonia prevention or treatment strategies. Here, we showcase a reproducible model that simulates biofilm formation of these pathogens in a host-mimicking environment, and demonstrate that the biofilm matrix produced differs from that observed in standard laboratory growth medium. In our model, pathogens are grown on endotracheal tube segments in the presence of a novel synthetic ventilator airway mucus (SVAM) medium that simulates the in-host environment. Matrix-degrading enzymes and cryo-SEM were employed to characterise the system in terms of biofilm matrix composition and structure, as compared to standard laboratory growth medium. As seen in patients, the biofilms of ventilator-associated pneumonia pathogens in our model either required very high concentrations of antimicrobials for eradication, or could not be eradicated. However, combining matrix-degrading enzymes with antimicrobials greatly improved biofilm eradication of all pathogens. Our <i>in vitro</i> endotracheal tube (IVETT) model informs on fundamental microbiology in the ventilator-associated pneumonia context, and has broad applicability as a screening platform for antibiofilm measures including the use of matrix-degrading enzymes as antimicrobial adjuvants.
DOI: 10.6084/m9.figshare.5313643
title: v1.2 3D files.zip

description: 3D design file for printing
DOI: 10.15468/dl.bztotw
title: Occurrence Download

description: A dataset containing 1996 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "TaxonKey is Troglodytes troglodytes (Linnaeus, 1758)",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1996 records from 57 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0103016-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/v9p8pm3fd7.1
title: CRISPR array-mediated imaging of non-repetitive and multiplex genomic loci in living cells

description: Detailed images and statistics of genomic loci labeling using CRISPRdelight.
DOI: 10.18126/xqiz-hzc2
title: Dataset for Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

description: This dataset contains 186 molecular dynamics simulation trajectories of coarse-grained pi-conjugated peptides in the Asp-X-X-X-(oligophenylenevinylene)3-X-X-X-Asp (DXXX-OPV3-XXXD) family, where X denotes one of the 20 natural amino acids. The oligopeptide wings are constrained to be mirror-symmetric both in the identity of the amino acids and the N-to-C directionality such that each molecule possesses two C-termini. These trajectories were generated during an active learning search for the peptide sequences that yield structurally optimal self-assembled pseudo-1D nanoaggregates with good stacking between the pi-cores. Directories containing the trajectories are named "dxxx" where each "x" corresponds to an amino acid in the DXXX-OPV3-XXXD sequence (e.g. 'dfag' corresponds to the structure DFAG-OPV3-GAFD). Each trajectory itself is a 3,000 nanosecond simulation of 96 identical pi-conjugated peptides in water (/solvent), and the same trajectories where the water has been removed (/no-solvent).
DOI: 10.18170/dvn/qkqhtg
title: Tornado Database in China (2007~2016)

description: This tornado databse includes the tornado information in contiguous China from 2007 to 2016. These data were obtained from various sources with cross checking: the Yearbook of Meteorological Disasters in China (China Meteorological Administration, 2005–2017), the tornado dataset in contiguous China during the period 1948–2012 compiled by Chen et al. (2018), almost all the published papers on tornadoes in China, the damage surveys conducted by local meteorological agencies and the reports archived through web searches. With the availability of widely-covering China New Generation Weather Radar network after 2006, we performed quality control on tornado records by reviewing the national and regional radar reflectivity mosaic images, and some tornado records that were not associated with a convective storm were removed. In the high-incidence area of tornadoes (e.g., Jiangsu Province), the reported locations and times of most tornado reports in JS were further manually verified and corrected, based on the track of parent storms and the cyclonic rotational signature at the lowest two levels in the radial velocity field from the available Doppler radar base data.
DOI: 10.25318/3710000901-fra
title: Nombre d'élèves dans les programmes de langues officielles, écoles primaires et secondaires publiques, selon le type de programme, l'année d'études et le sexe

description: Effectifs dans les programmes de langues officielles offerts dans les écoles publiques primaires et secondaires, selon le type de programme, l'année d'études et le sexe, dernières cinq années scolaires.
DOI: 10.5066/p9i22z24
title: Public-Supply Water Service Areas Within the Conterminous United States, 2017

description: This data release describes water service areas (WSA) for community water systems (CWS) within the conterminous United States, representing areas of active service between 2010 and 2020. A WSA is defined by a delineated polygon that contains all customers served by a water system. WSAs are represented by an ArcGIS shapefile. The U.S. Safe Drinking Water Act defines a CWS as a type of public-water system that serves at least 15 service connections used by year-round residents or regularly serves at least 25 year-round residents. Water may be used for several purposes (such as for commercial, industrial, and residential uses) or may be used only for one specific purpose (such as for residential use). This data release includes CWS that operate their own infrastructure and furnish water through their own water sources, purchase water from a neighboring water system, or are diversified in that they serve water from a combination of their own sources and purchases. This dataset also includes communities that do not operate a water system but receive water services by way of contract; in other words, an adjacent water system?s infrastructure extends their waterlines across boundaries from which residents connect to, are supplied, and directly billed from this neighboring water system. This data release includes two shapefiles, five tables, a data dictionary, and four metadata documents which are described below. PublicSupplyWaterServiceAreas_metadata.xml -�Public-supply water service areas main page metadata.� v1_GU_wWS.zip� Zipped folder which contains the shapefile�of�the individual geographic units that were used to build the water service area (WSA) dataset for public-supply systems,�and the metadata document for this shapefile. WSA_v1.zip Zipped folder which contains the shapefile of the�the aggregated geographic units (GU) that were used to represent the water service areas (WSA) for public-supply water systems, and the metadata document for this shapefile. DataTables.zip - Zipped folder of all five tables used in comparisons to water service areas, the data dictionary which is a quick reference guide for all attributes in the five tables, and the metadata document for the tables �
DOI: 10.5281/zenodo.11082703
title: Dataset: Stable oxygen and carbon isotopes in freshwater pearl mussels from ultrastructurally distinct shell portions

description: Oxygen isotopes in stream water can serve as natural tracers of watershed dynamics. Freshwater pearl mussels provide δ18Owater estimates that overcome temporal and spatial limitations of instrumental records. The reliability of shell‑based δ18Owater reconstructions depends on understanding which shell layer biomineralizes closer to oxygen isotopic equilibrium with ambient water.

This dataset contains isotope data obtained from freshwater pearl mussel shells, as discussed in the article titled "Biologically driven isotope fractionation in ultrastructurally different shell portions of freshwater pearl mussels (Margaritifera margaritifera): Implications for stream water δ18O reconstructions".

The dataset includes δ18O and δ13C values from field-collected and tank-reared bivalve shells, complemented by in-situ δ18Owater measurements from the tanks and shell growth rates of the tank-reared specimens.
DOI: 10.5281/zenodo.12200393
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-2

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12251706
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-3

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12251770
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-4

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12251824
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-5

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12251892
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-6

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12251936
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-7

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12290707
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-8

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12290785
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-9

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12291751
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-10

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12291819
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-11

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12291915
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-12

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.
DOI: 10.5281/zenodo.12291977
title: The natural variance of Arabidopsis secondary metabolism on extended darkness-13

description: In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0- and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the MetaboLights database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.