cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/vvt585gp9n.1
title: Replication Data for: Crisis Adaptation in a Thai Community-Based Tourism Setting during the COVID-19 Pandemic: A Qualitative Phenomenological Approach

description: This dataset includes replication data for the paper "Sann, R.; Lai, P.-C.; Chen, C.-T. Crisis Adaptation in a Thai Community-Based Tourism Setting during the COVID-19 Pandemic: A Qualitative Phenomenological Approach. Sustainability 2023, 15, 340. https://doi.org/10.3390/su15010340."
DOI: 10.6084/m9.figshare.19745855
title: Fibrinogen A α-chain amyloidosis associated with a rare frameshift pathogenic variant p.Arg547GlyfsTer21

description: Fibrinogen A α-chain amyloidosis associated with a rare frameshift pathogenic variant p.Arg547GlyfsTer21
DOI: 10.6084/m9.figshare.19745855.v1
title: Fibrinogen A α-chain amyloidosis associated with a rare frameshift pathogenic variant p.Arg547GlyfsTer21

description: Fibrinogen A α-chain amyloidosis associated with a rare frameshift pathogenic variant p.Arg547GlyfsTer21
DOI: 10.6084/m9.figshare.21790189
title: Detection of semenogelin 1 amyloidosis through immunohistochemical staining with novel antiserum developed based on mass spectrometric peptide mapping analysis

description: Detection of semenogelin 1 amyloidosis through immunohistochemical staining with novel antiserum developed based on mass spectrometric peptide mapping analysis
DOI: 10.6084/m9.figshare.21790189.v1
title: Detection of semenogelin 1 amyloidosis through immunohistochemical staining with novel antiserum developed based on mass spectrometric peptide mapping analysis

description: Detection of semenogelin 1 amyloidosis through immunohistochemical staining with novel antiserum developed based on mass spectrometric peptide mapping analysis
DOI: 10.5281/zenodo.5744196
title: Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"

description: This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; doi:10.3389/fcell.2021.746359. If you have used the code for your research, please cite the original publication. Thank you very much.
DOI: 10.5281/zenodo.5744195
title: Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"

description: This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; doi:10.3389/fcell.2021.746359. If you have used the code for your research, please cite the original publication. Thank you very much.
DOI: 10.25318/2310029901-fra
title: Mouvements itinérants, par règles de vol et piste 88, dans les aéroports offrant des services de NAV CANADA et d’autres aéroports sélectionnés, mensuel

description: Mouvements itinérants mensuels par règles de vol aux instruments (IFR), règles de vol à vue (VFR) et piste 88, dans les aéroports dotés d’une tour de contrôle ou d’une station d’information de vol de NAV CANADA et certains aéroports autres que NAV CANADA.
DOI: 10.25318/2310029901-eng
title: Itinerant movements, by flight rules and runway 88, at airports with NAV CANADA services and other selected airports, monthly

description: Monthly itinerant movements by instrument flight rules (IFR), visual flight rules (VFR) and runway 88 movements, for airports with NAV CANADA towers or flight service stations and other selected non-NAV CANADA airports.
DOI: 10.25318/2310030001-eng
title: Itinerant movements, by type of power plant, at airports with NAV CANADA services and other selected airports, monthly

description: Monthly itinerant movements by type of power plant (jet, turbo-propellers, piston, helicopters and gliders), for airports with NAV CANADA towers or flight service stations and other selected non-NAV CANADA airports.
DOI: 10.25318/2310030001-fra
title: Mouvements itinérants, par groupe motopropulseur, dans les aéroports offrant des services de NAV CANADA et d’autres aéroports sélectionnés, mensuel

description: Mouvements itinérants mensuels par groupe motopropulseur (à réaction, turbo-propulseurs, à pistons, hélicoptères et planeurs), dans les aéroports dotés d’une tour de contrôle ou d’une station d’information de vol de NAV CANADA et certains aéroports autres que NAV CANADA.
DOI: 10.5281/zenodo.7235995
title: rDNA 18S V4 metabarcoding tables (Swarm) for Tara Oceans Expedition (2009-2013), including Tara Polar Circle Expedition (2013)

description: Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011).<br> Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).
DOI: 10.5281/zenodo.4043756
title: rDNA 18S V4 metabarcoding tables (Swarm) for Tara Oceans Expedition (2009-2013), including Tara Polar Circle Expedition (2013)

description: Reads were grouped into OTUs using the following swarm-based pipeline: paired-end reads were merged with vsearch’s --fastq_mergepairs command (version 2.15.1, allowing for staggered reads; Rognes et al., 2016), and trimmed with cutadapt (version 3.0; Martin, 2011), keeping only reads containing both forward and reverse primers. After trimming, the expected error per read was estimated with vsearch’s command --fastq_filter and the option --eeout. Each sample was then de-replicated, i.e. strictly identical reads were merged, using vsearch’s command --derep_fulllength, and converted into fasta format. Clustering was performed at the sample level with swarm 3.0 using default parameters (Mahé et al., 2015). Prior to global clustering, individual fasta files (one per sample) were pooled and further dereplicated with vsearch. Files containing per-read expected error values were also dereplicated to retain only the lowest expected error for each unique sequence. Global clustering was performed with swarm (using the fastidious option). Cluster representative sequences were then searched for chimeras with vsearch’s command --uchime_denovo using default parameters (Edgar et al., 2011).<br> Clustering results, expected error values, taxonomic assignments, and chimera detection results were used to build a “raw” occurrence table. Reads without primers, reads shorter than 32 nucleotides and reads with uncalled bases (“N”) were discarded. For a “filtered” occurrence table, non-chimeric sequences, sequences with an expected error per nucleotide below 0.0002, and clusters containing at least 2 reads were retained. Since primer trimming is not perfect, some sequences can still contain primer fragments or be excessively trimmed. These sub- or super-sequences were identified using vsearch and merged with their closest, most abundant perfectly trimmed sequence. Finally, occurrence patterns throughout our sample collection were used to further refine the occurrence table. Clusters that contain sub-clusters with only a single-nucleotide difference but with different ecological patterns (defined here as uncorrelated abundance values in at least 5% of the samples) were turned into distinct clusters (https://github.com/frederic-mahe/fred-metabarcoding-pipeline). On the other hand, clusters with similar sequences that had correlated abundance values in at least 95% of the samples, were merged using a re-implementation of lulu's method (Frøslev et al. 2017; https://github.com/frederic-mahe/mumu).
DOI: 10.25318/2310030101-eng
title: Itinerant movements, by aircraft maximum take-off weight, at airports with NAV CANADA services and other selected airports, monthly

description: Monthly itinerant movements by aircraft weight group, broken down by maximum take-off weight categories ranging from under 2,000kgs to over 136,000kgs, for airports with NAV CANADA towers or flight service stations and other selected non-NAV CANADA airports.
DOI: 10.25318/2310030101-fra
title: Mouvements itinérants, par poids maximum au décollage des aéronefs, dans les aéroports offrant des services de NAV CANADA et d’autres aéroports sélectionnés, mensuel

description: Mouvements itinérants mensuels par groupe de poids d’aéronefs, ventilés selon le poids maximum au décollage variant de moins de 2 000 kg à plus de 136 000 kg, dans les aéroports dotés d’une tour de contrôle ou d’une station d’information de vol de NAV CANADA et certains aéroports autres que NAV CANADA.
DOI: 10.25318/2310030201-eng
title: Domestic and international itinerant movements, by type of operation, at airports with NAV CANADA services and other selected airports, monthly

description: Monthly itinerant movements (domestic, transborder and other international) by type of operation, (Level I-III and foreign air carriers, Level IV-VI, other commercial, private, government civil and government military), for airports with NAV CANADA towers or flight service stations and other selected non-NAV CANADA airports.
DOI: 10.25318/2310030201-fra
title: Mouvements itinérants intérieurs et internationaux, par type d’exploitation, dans les aéroports offrant des services de NAV CANADA et d’autres aéroports sélectionnés, mensuel

description: Mouvements itinérants mensuels (intérieurs, transfrontaliers et internationaux), par type d’exploitation (transporteurs aériens de niveau I à III et étrangers, de niveau IV à VI, autres commerciaux, privés, officiels civils et officiels militaires), dans les aéroports dotés d’une tour de contrôle ou d’une station d’information de vol de NAV CANADA et certains aéroports autres que NAV CANADA.
DOI: 10.6084/m9.figshare.15168973
title: IL-1<i>β</i>-mediated TGFβ/SMAD signaling pathway inactivation impaired <i>ex vivo</i> osteogenic activity of human bone marrow-derived stromal cells

description: Bone loss is caused by inflammation and is mediated by pro-inflammatory cytokines that control bone formation and bone resorption. The study aimed to determine the effect of secreted factors from human bone marrow-derived stromal cells (hBMSC) of no-heterotopic bone-forming capacity (hBMSC<sup>–Bone</sup>) cells on the differentiation potential of hBMSC which capable of creating bone <i>in-vivo</i> (hBMSC<sup>+Bone</sup>) and dissect the molecular signature of these cells for understanding the complicated relationship of stem cells and microenvironment. hBMSC cultures are heterogenous with respect to differentiation and function. However, the nature of interaction between different cell populations within hBMSC cultures is poorly investigated. We employed two clonal hBMSC lines which exhibit different functional phenotypes based on the presence of either high or low osteoblastic differentiation capacity, bone forming (hBMSC<sup>+Bone</sup>) and non-bone forming (hBMSC<sup>−Bone</sup>), and examined their biological interaction. Adding conditioned media (CM) of hBMSC<sup>−Bone</sup> cultures resulted in suppression of cell proliferation and osteoblasts differentiation of hBMSC<sup>+Bone</sup>. Microarray analysis of CM-treated hBMSC<sup>+Bone</sup> revealed significant enrichment of several pathways, including TGFβ signaling. Follow-up experiments corroborated the inhibitory effects on TGFβ signaling as evidenced by decreased SMAD2 phosphorylation and TGFβ-responsive genes (<i>TAGLN</i>, <i>ACTA2</i> and <i>TPM1</i>). Interestingly, IL1β is highly expressed in hBMSC<sup>−Bone</sup> and is present in its CM. Incubating hBMSC<sup>−Bone</sup> with rhIL-1RI rescued the functional phenotype of hBMSC<sup>−Bone</sup> with respect to cell proliferation and differentiation into osteoblasts, and upregulated TGFβ-responsive genes. These data demonstrated that IL1β-TGFβ signaling is part of the intercellular communication within the heterogenous population of hBMSCs and regulates their commitment to osteoblastic fate. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1939784 .
DOI: 10.6084/m9.figshare.15168973.v2
title: IL-1<i>β</i>-mediated TGFβ/SMAD signaling pathway inactivation impaired <i>ex vivo</i> osteogenic activity of human bone marrow-derived stromal cells

description: Bone loss is caused by inflammation and is mediated by pro-inflammatory cytokines that control bone formation and bone resorption. The study aimed to determine the effect of secreted factors from human bone marrow-derived stromal cells (hBMSC) of no-heterotopic bone-forming capacity (hBMSC<sup>–Bone</sup>) cells on the differentiation potential of hBMSC which capable of creating bone <i>in-vivo</i> (hBMSC<sup>+Bone</sup>) and dissect the molecular signature of these cells for understanding the complicated relationship of stem cells and microenvironment. hBMSC cultures are heterogenous with respect to differentiation and function. However, the nature of interaction between different cell populations within hBMSC cultures is poorly investigated. We employed two clonal hBMSC lines which exhibit different functional phenotypes based on the presence of either high or low osteoblastic differentiation capacity, bone forming (hBMSC<sup>+Bone</sup>) and non-bone forming (hBMSC<sup>−Bone</sup>), and examined their biological interaction. Adding conditioned media (CM) of hBMSC<sup>−Bone</sup> cultures resulted in suppression of cell proliferation and osteoblasts differentiation of hBMSC<sup>+Bone</sup>. Microarray analysis of CM-treated hBMSC<sup>+Bone</sup> revealed significant enrichment of several pathways, including TGFβ signaling. Follow-up experiments corroborated the inhibitory effects on TGFβ signaling as evidenced by decreased SMAD2 phosphorylation and TGFβ-responsive genes (<i>TAGLN</i>, <i>ACTA2</i> and <i>TPM1</i>). Interestingly, IL1β is highly expressed in hBMSC<sup>−Bone</sup> and is present in its CM. Incubating hBMSC<sup>−Bone</sup> with rhIL-1RI rescued the functional phenotype of hBMSC<sup>−Bone</sup> with respect to cell proliferation and differentiation into osteoblasts, and upregulated TGFβ-responsive genes. These data demonstrated that IL1β-TGFβ signaling is part of the intercellular communication within the heterogenous population of hBMSCs and regulates their commitment to osteoblastic fate. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1939784 .
DOI: 10.6084/m9.figshare.15168973.v1
title: IL-1<i>β</i>-mediated TGFβ/SMAD signaling pathway inactivation impaired <i>ex vivo</i> osteogenic activity of human bone marrow-derived stromal cells

description: Bone loss is caused by inflammation and is mediated by pro-inflammatory cytokines that control bone formation and bone resorption. The study aimed to determine the effect of secreted factors from human bone marrow-derived stromal cells (hBMSC) of no-heterotopic bone-forming capacity (hBMSC<sup>–Bone</sup>) cells on the differentiation potential of hBMSC which capable of creating bone <i>in-vivo</i> (hBMSC<sup>+Bone</sup>) and dissect the molecular signature of these cells for understanding the complicated relationship of stem cells and microenvironment. hBMSC cultures are heterogenous with respect to differentiation and function. However, the nature of interaction between different cell populations within hBMSC cultures is poorly investigated. We employed two clonal hBMSC lines which exhibit different functional phenotypes based on the presence of either high or low osteoblastic differentiation capacity, bone forming (hBMSC<sup>+Bone</sup>) and non-bone forming (hBMSC<sup>−Bone</sup>), and examined their biological interaction. Adding conditioned media (CM) of hBMSC<sup>−Bone</sup> cultures resulted in suppression of cell proliferation and osteoblasts differentiation of hBMSC<sup>+Bone</sup>. Microarray analysis of CM-treated hBMSC<sup>+Bone</sup> revealed significant enrichment of several pathways, including TGFβ signaling. Follow-up experiments corroborated the inhibitory effects on TGFβ signaling as evidenced by decreased SMAD2 phosphorylation and TGFβ-responsive genes (<i>TAGLN</i>, <i>ACTA2</i> and <i>TPM1</i>). Interestingly, IL1β is highly expressed in hBMSC<sup>−Bone</sup> and is present in its CM. Incubating hBMSC<sup>−Bone</sup> with rhIL-1RI rescued the functional phenotype of hBMSC<sup>−Bone</sup> with respect to cell proliferation and differentiation into osteoblasts, and upregulated TGFβ-responsive genes. These data demonstrated that IL1β-TGFβ signaling is part of the intercellular communication within the heterogenous population of hBMSCs and regulates their commitment to osteoblastic fate. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1939784 .
DOI: 10.6084/m9.figshare.16990096.v1
title: Morphological variation, genetic diversity and phylogenetic relationships of <i>Hypericum triquetrifolium</i> Turra populations from Tunisia

description: <i>Hypericum triquetrifolium</i> Turra is an ecologically, medicinally and economically important species in Tunisia. Thirty-six <i>Hypericum</i> individuals sampled from 6 northern Tunisian locations were investigated for their diversity and relationships using 10 inter-simple sequence repeats (ISSR) markers and 10 morphological features at vegetative stage. The phylogenetic analysis, using 308 bp of sequenced ITS1 region, identified the <i>Hypericum</i> individuals as <i>H. triquetrifolium</i> that clustered with members of genus <i>Hypericum</i> section 9, 9a, 9b and 27, in agreement with the previous molecular classification of the genus. Among the 10 ISSR markers tested, 7 were scorable and yielded 91 loci with 94.5% of polymorphism. UBC848 and UBC836 were the most polymorphic ISSR markers. The level of genetic diversity (HT = 0.247) and gene flow between the six populations (<i>N</i><sub>m</sub> = 1.169) were moderate. The structure analysis revealed three genetic subpopulations: individuals of Le Krib location formed a subpopulation divergent from two other subpopulations, probably due to its northwestern and high-altitude geographic barriers, and its sub-humid microclimate. Zaghouan, northeastern location in the lower semi-arid, with the highest genetic (<i>I</i> = 0.370) and morphological (<i>I</i> = 0.631) Shannon’s information indices and, regrouping two out of the three genetic subpopulations, is the most probable zone of origin for <i>H. triquetrifolium.</i> In addition, morphological data showed higher diversity than ISSR data; however, no evidence of correlation between genetic and morphologic traits could be suggested in this study. These results on the genetic diversity and phylogenetic analysis will contribute to the conservation of the gene pool of <i>H. triquetrifolium</i> in Tunisia.
DOI: 10.6084/m9.figshare.14157109
title: Transcriptome analysis of ionic-liquid tolerant <i>Bacillus amyloliquefaciens</i> CMW1 and identification of a novel efflux pump

description: Bacteria that exhibit ionic-liquid (IL) tolerance are useful in chemical industries using renewable carbon sources pre-treated by ILs to produce biofuels and fine chemicals. An IL, 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), has a remarkable ability to solubilize wood components, whereas [BMIM]Cl inhibits the growth of various bacterial hosts useful for bioconversion. We previously isolated a 10% [BMIM]Cl-tolerant bacterium <i>Bacillus amyloliquefaciens</i> CMW1. Here we report novel mechanisms of tolerance to [BMIM]Cl in strain CMW1 and a novel major facilitator superfamily transporter coded by an ionic-liquid tolerance (ILT) gene. First, using CMW1 cells grown in the presence or absence of 10% [BMIM]Cl, whole-transcriptome analysis and differentially expressed gene analysis were performed. Probable mechanisms of tolerance to [BMIM]Cl include the uptake of osmoprotectants from the culture medium toward CMW1 cells and the export of [BMIM] cations that accumulated in CMW1 cells. The finding represents a first step in elucidation of the mechanisms of IL resistance in Gram-positive bacteria. Second, we conferred tolerance to 5% [BMIM]Cl on [BMIM]Cl-susceptible <i>Brevibacillus choshinensis</i> using ILT gene. This finding provides a notable basis for engineering IL-tolerant bacterial hosts that are applicable for the effective and sustainable production of industrially important chemicals.