cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6960083
title: An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in <i>Enterobacteriaceae</i>

description: The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of <i>Enterobacter cloacae, Klebsiella pneumoniae</i> and <i>Escherichia coli</i> isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species <i>E. cloacae, K. pneumoniae</i> and <i>E. coli</i> emerged from their common ancestry. A representative MGI from <i>E. cloacae</i> was named MIR17-GI, because it harbors the novel β-lactamase gene variant <i>bla</i><sub>MIR17</sub>. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective <i>E. cloacae</i> isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst <i>Enterobacteriaceae</i>. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.
DOI: 10.6084/m9.figshare.6960083.v1
title: An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in <i>Enterobacteriaceae</i>

description: The exchange of mobile genomic islands (MGIs) between microorganisms is often mediated by phages, which may provide benefits to the phage’s host. The present study started with the identification of <i>Enterobacter cloacae, Klebsiella pneumoniae</i> and <i>Escherichia coli</i> isolates with exceptional cephalosporin and carbapenem resistance phenotypes from patients in a neonatal ward. To identify possible molecular connections between these isolates and their β-lactam resistance phenotypes, the respective bacterial genome sequences were compared. This unveiled the existence of a family of ancient MGIs that were probably exchanged before the species <i>E. cloacae, K. pneumoniae</i> and <i>E. coli</i> emerged from their common ancestry. A representative MGI from <i>E. cloacae</i> was named MIR17-GI, because it harbors the novel β-lactamase gene variant <i>bla</i><sub>MIR17</sub>. Importantly, our observations show that the MIR17-GI-like MGIs harbor genes associated with high-level resistance to cephalosporins. Among them, MIR17-GI stands out because MIR17 also displays carbapenemase activity. As shown by mass spectrometry, the MIR17 carbapenemase is among the most abundantly expressed proteins of the respective <i>E. cloacae</i> isolate. Further, we show that MIR17-GI-like islands are associated with integrated P4-like prophages. This implicates phages in the spread of cephalosporin and carbapenem resistance amongst <i>Enterobacteriaceae</i>. The discovery of an ancient family of MGIs, mediating the spread of cephalosporinase and carbapenemase genes, is of high clinical relevance, because high-level cephalosporin and carbapenem resistance have serious implications for the treatment of patients with enterobacteriaceal infections.
DOI: 10.6084/m9.figshare.8003573.v1
title: Attachment 1.csv

description: Experimental results
DOI: 10.6084/m9.figshare.7479410
title: Assembly of polyoxometalate-templated metal-organic framework with effective peroxidase-like catalytic activity

description: A new polyoxometalate (POM)-templated 3-D copper(II)-triazole framework [Cu<sub>10</sub>(trz)<sub>10</sub>(OH)<sub>6</sub>(Cl)<sub>4</sub>][H<sub>3</sub>PW<sub>12</sub>O<sub>40</sub>]·2H<sub>2</sub>O (trz = 1,2,3-triazole) has been synthesized and characterized by single crystal X-ray diffraction and other routine methods. The 3-D POM/copper(II)-triazole hybrid framework with a 1-D channel possesses a <i>pcu</i> topology under the template of bulk Keggin-type phosphotungstate. As a new kind of peroxidase mimetic, the new compound effectively catalyzed oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of H<sub>2</sub>O<sub>2</sub>. The electrostatic interactions and hydrogen bonds/π-π stacking interactions among TMB, trz, and phosphotungstate are responsible for the enhancement of peroxidase-like activity. In addition, application for colorimetric sensing of H<sub>2</sub>O<sub>2</sub> is also explored; the new compound exhibits a wide linear range (1–80 μM), low detection limit (0.21 μM), and fast response (2 min).
DOI: 10.6084/m9.figshare.7479410.v2
title: Assembly of polyoxometalate-templated metal-organic framework with effective peroxidase-like catalytic activity

description: A new polyoxometalate (POM)-templated 3-D copper(II)-triazole framework [Cu<sub>10</sub>(trz)<sub>10</sub>(OH)<sub>6</sub>(Cl)<sub>4</sub>][H<sub>3</sub>PW<sub>12</sub>O<sub>40</sub>]·2H<sub>2</sub>O (trz = 1,2,3-triazole) has been synthesized and characterized by single crystal X-ray diffraction and other routine methods. The 3-D POM/copper(II)-triazole hybrid framework with a 1-D channel possesses a <i>pcu</i> topology under the template of bulk Keggin-type phosphotungstate. As a new kind of peroxidase mimetic, the new compound effectively catalyzed oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of H<sub>2</sub>O<sub>2</sub>. The electrostatic interactions and hydrogen bonds/π-π stacking interactions among TMB, trz, and phosphotungstate are responsible for the enhancement of peroxidase-like activity. In addition, application for colorimetric sensing of H<sub>2</sub>O<sub>2</sub> is also explored; the new compound exhibits a wide linear range (1–80 μM), low detection limit (0.21 μM), and fast response (2 min).
DOI: 10.4121/df349dfc-9668-4169-a7d6-9852d68b4adf
title: Data underlying the publication: Building a Mycenaean chamber tomb catalogue from terrestrial laser scan data

description: The Aidonia cemetery is an archeological site on the Peleponnese Peninsula in Greece. It was constructed in the Late Bronze Age and consists of chamber tombs dug into rock outcrops. In August 2019, a team of researchers from TU Delft and University of Stavanger acquired detailed 3D scan data of the Aidonia site using a Leica P40 laser scanner. The team scanned the site from 51 scan positions. 29 positions were focusing on the chamber tombs while the other 22 positions sampled the overall cemetery setting. The scans were combined in a common coordinate system providing a point cloud consisting of ~5.9 billion points. Analysis of the point cloud notably provided insight in the architectural setting and current status of the different tombs. The data set in this repository consist of the raw, aligned point cloud. A detailed description of the point cloud data and its application in documenting the status of the Aidoinia cemetery can be found in the corresponding publication, at https://doi.org/10.1016/j.daach.2024.e00319.<br>
DOI: 10.6084/m9.figshare.7484516.v1
title: LncRNA MIAT overexpression reduced neuron apoptosis in a neonatal rat model of hypoxic-ischemic injury through miR-211/GDNF

description: <b>Objective</b>: To investigate the underlying mechanism of lncRNA myocardial infarction-associated transcript (MIAT) in hypoxic-ischemic (HI)-induced neonatal cerebral palsy. <b>Materials and methods</b>: Neonatal rat model of HI injury was established to detect the motor function. LncRNA MIAT, miR-211, glial cell line-derived neurotrophic factor (GDNF) and caspase-3 expressions were measured by qRT-PCR or western blot. The apoptosis of Neuro2A cells was detected by flow cytometry. RNA immunoprecipitation (RIP) and RNA pull-down assays were performed to confirm the interaction between MIAT and miR-211. <b>Results</b>: Compared with control group, lncRNA MIAT and GDNF were downregulated in striatal tissues of neonatal rats in HI group and oxygen glucose deprivation (OGD)-induced ischemic injury of Neuro2A cells, whereas miR-211 was up-regulated in striatal tissues of HI group and OGD-induced ischemic injury of Neuro2A cells. LncRNA MIAT interacted with miR-211, and lncRNA MIAT overexpression reduced neuron apoptosis through miR-211. Besides, GDNF expression was positively regulated by lncRNA MIAT and negatively regulated by miR-211 in Neuro2A cells. <i>In vivo</i> experiment proved MIAT promoted motor function and relieved HI injury. <b>Conclusion</b>: MIAT overexpression reduced apoptosis of Neuro2A cells through miR-211/GDNF, which relieved HI injury of neonatal rats.
DOI: 10.6084/m9.figshare.22679503
title: Additional file 6 of Knockdown of heat shock protein family D member 1 (HSPD1) promotes proliferation and migration of ovarian cancer cells via disrupting the stability of mitochondrial 3-oxoacyl-ACP synthase (OXSM)

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.22679503.v1
title: Additional file 6 of Knockdown of heat shock protein family D member 1 (HSPD1) promotes proliferation and migration of ovarian cancer cells via disrupting the stability of mitochondrial 3-oxoacyl-ACP synthase (OXSM)

description: Supplementary Material 6
DOI: 10.6084/m9.figshare.22681092
title: Additional file 1 of Toosendanin targeting eEF2 impedes Topoisomerase I & II protein translation to suppress esophageal squamous cell carcinoma growth

description: Additional file 1. MS identified proteins which Toosendanin potentially bond with.
DOI: 10.6084/m9.figshare.23265015.v1
title: Additional file 4 of MPC-n (IgG) improves long-term cognitive impairment in the mouse model of repetitive mild traumatic brain injury

description: Additional file 4: Table S2. All differentially expressed genes between the rmTBI group and the sham group.
DOI: 10.6084/m9.figshare.22681095
title: Additional file 2 of Toosendanin targeting eEF2 impedes Topoisomerase I & II protein translation to suppress esophageal squamous cell carcinoma growth

description: Additional file 2. Enriched mRNA list by RIP-sequencing when conducted with DMSO or TSN.
DOI: 10.6084/m9.figshare.22681092.v1
title: Additional file 1 of Toosendanin targeting eEF2 impedes Topoisomerase I & II protein translation to suppress esophageal squamous cell carcinoma growth

description: Additional file 1. MS identified proteins which Toosendanin potentially bond with.
DOI: 10.6084/m9.figshare.22681094.v1
title: Additional file 1 of The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22681095.v1
title: Additional file 2 of Toosendanin targeting eEF2 impedes Topoisomerase I & II protein translation to suppress esophageal squamous cell carcinoma growth

description: Additional file 2. Enriched mRNA list by RIP-sequencing when conducted with DMSO or TSN.
DOI: 10.6084/m9.figshare.14677127
title: Additional file 8 of Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

description: Additional file 8: Table S13
DOI: 10.15161/oar.it/143163
title: Carta Geologica d'Italia alla scala 1:50.000, F. 154 Susa

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:25.000 (eseguiti tra il 1995 e il 1998) comprensivo di legenda, schemi a cornice, sezioni geologiche.
DOI: 10.15161/oar.it/143164
title: Carta Geologica d'Italia alla scala 1:50.000, F. 154 Susa

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:25.000 (eseguiti tra il 1995 e il 1998) comprensivo di legenda, schemi a cornice, sezioni geologiche.
DOI: 10.6084/m9.figshare.22681094
title: Additional file 1 of The pan-plastome of tartary buckwheat (fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.23730796.v1
title: Additional file 7 of H3K27me3 of Rnf19a promotes neuroinflammatory response during Japanese encephalitis virus infection

description: Additional file 7: S7.
DOI: 10.15161/oar.it/143168
title: Carta Geologica d'Italia alla scala 1:50.000, F. 156 Torino Est

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:10.000 (eseguiti tra il 2001 e il 2005) comprensivo di legenda, schemi a cornice, sezioni geologiche.
DOI: 10.15161/oar.it/143169
title: Carta Geologica d'Italia alla scala 1:50.000, F. 156 Torino Est

description: Foglio geologico alla scala 1:50.000 basato su rilevamenti alla scala 1:10.000 (eseguiti tra il 2001 e il 2005) comprensivo di legenda, schemi a cornice, sezioni geologiche.
DOI: 10.6084/m9.figshare.23730850
title: Additional file 3 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 3: Table S2. sQTL mapping summary.
DOI: 10.6084/m9.figshare.23730889.v1
title: Additional file 3 of Identification and analysis of lipid metabolism-related genes in allergic rhinitis

description: Supplementary Materials 3: Table S3. Results of the 256 Gene Ontology (GO) enriched terms using gene set enrichment analysis (GSEA)
DOI: 10.6084/m9.figshare.23730853
title: Additional file 4 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 4: Table S3. Summary for cis-sQTL colocalizing with trait associations.
DOI: 10.6084/m9.figshare.23730886.v1
title: Additional file 2 of Identification and analysis of lipid metabolism-related genes in allergic rhinitis

description: Supplementary Materials 2: Table S2. List of 73 lipid metabolism-related differentially expressed genes (LMR DEGs)
DOI: 10.6084/m9.figshare.12720304
title: Additional file 7 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 7: Table S2. Relative amounts of microbiota in small intestine samples after FMT.
DOI: 10.6084/m9.figshare.12720307
title: Additional file 8 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 8: Table S3. The commonly changed blood metabolites in Sa vs. A10-FMT and A100-FMT.
DOI: 10.6084/m9.figshare.12720307.v1
title: Additional file 8 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 8: Table S3. The commonly changed blood metabolites in Sa vs. A10-FMT and A100-FMT.
DOI: 10.6084/m9.figshare.23730892
title: Additional file 4 of Identification and analysis of lipid metabolism-related genes in allergic rhinitis

description: Supplementary Materials 4: Table S4. Results of the 33 Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched terms using GSEA
DOI: 10.5281/zenodo.10325096
title: Monia Federica Lombardo Ph.D. Thesis Supplementary Data

description: Supplementary data Monia Federica Lombardo Ph.D. Thesis Chapter IV and APPENDIX
DOI: 10.5281/zenodo.10325097
title: Monia Federica Lombardo Ph.D. Thesis Supplementary Data

description: Supplementary data Monia Federica Lombardo Ph.D. Thesis Chapter IV and APPENDIX
DOI: 10.5281/zenodo.10611071
title: Monia Federica Lombardo Ph.D. Thesis Supplementary Data

description: Supplementary data Monia Federica Lombardo Ph.D. Thesis Chapter IV and APPENDIX
DOI: 10.6084/m9.figshare.12720304.v1
title: Additional file 7 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 7: Table S2. Relative amounts of microbiota in small intestine samples after FMT.
DOI: 10.6084/m9.figshare.23730847.v1
title: Additional file 2 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 2: Table S1. Accessions used in this study.
DOI: 10.6084/m9.figshare.23730856.v1
title: Additional file 5 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 5: Table S4. Indentified cis-sQTL are affective to transcription factors.
DOI: 10.6084/m9.figshare.23730935
title: Additional file 1 of Downregulation of MAL2 inhibits breast cancer progression through regulating β-catenin/c-Myc axis

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.23730836.v1
title: Additional file 4 of Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus

description: Additional file 4: Table S1. Primer sequences of genes in qRT-PCR.
DOI: 10.6084/m9.figshare.12720298
title: Additional file 5 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 5: Data file 1. Metabolite changes for mouse blood samples in the following comparisons: Sa vs. Con-FMT, Sa vs. A10-FMT, and Sa vs. A100-FMT.
DOI: 10.6084/m9.figshare.12720298.v1
title: Additional file 5 of Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis

description: Additional file 5: Data file 1. Metabolite changes for mouse blood samples in the following comparisons: Sa vs. Con-FMT, Sa vs. A10-FMT, and Sa vs. A100-FMT.
DOI: 10.6084/m9.figshare.23730868
title: Additional file 1 of Causal effects of serum lipid biomarkers on early age-related macular degeneration using Mendelian randomization

description: Additional file 1: Table S1. Reciprocal causation.
DOI: 10.6084/m9.figshare.6955166
title: DNA methylation biomarkers for head and neck squamous cell carcinoma

description: DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (<i>FAM135B</i> and <i>ZNF610</i>) and 2 hypomethylated-high-expression genes (<i>HOXA9</i> and <i>DCC</i>) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that <i>FAM135B</i> methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.
DOI: 10.6084/m9.figshare.6955166.v1
title: DNA methylation biomarkers for head and neck squamous cell carcinoma

description: DNA methylation plays an important role in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). The current study aimed to identify aberrantly methylated-differentially expressed genes (DEGs) by a comprehensive bioinformatics analysis. In addition, we screened for DEGs affected by DNA methylation modification and further investigated their prognostic values for HNSCC. We included microarray data of DNA methylation (GSE25093 and GSE33202) and gene expression (GSE23036 and GSE58911) from Gene Expression Omnibus. Aberrantly methylated-DEGs were analyzed with R software. The Cancer Genome Atlas (TCGA) RNA sequencing and DNA methylation (Illumina HumanMethylation450) databases were utilized for validation. In total, 27 aberrantly methylated genes accompanied by altered expression were identified. After confirmation by The Cancer Genome Atlas (TCGA) database, 2 hypermethylated-low-expression genes (<i>FAM135B</i> and <i>ZNF610</i>) and 2 hypomethylated-high-expression genes (<i>HOXA9</i> and <i>DCC</i>) were identified. A receiver operating characteristic (ROC) curve confirmed the diagnostic value of these four methylated genes for HNSCC. Multivariate Cox proportional hazards analysis showed that <i>FAM135B</i> methylation was a favorable independent prognostic biomarker for overall survival of HNSCC patients.
DOI: 10.6084/m9.figshare.13246934.v3
title: MoSec61β, the beta subunit of Sec61, is involved in fungal development and pathogenicity, plant immunity, and ER-phagy in <i>Magnaporthe oryzae</i>

description: The process of protein translocation into the endoplasmic reticulum (ER) is the initial and decisive step in the biosynthesis of all secretory proteins and many soluble organelle proteins. In this process, the Sec61 complex is the protein-conducting channel for transport. In this study, we identified and characterized the β subunit of the Sec61 complex in <i>Magnaporthe oryzae</i> (MoSec61β). Compared with the wild-type strain Guy11, the Δ<i>Mosec61β</i> mutant exhibited highly branched mycelial morphology, reduced conidiation, high sensitivity to cell wall integrity stress, severely reduced virulence to rice and barley, and restricted biotrophic invasion. The turgor pressure of Δ<i>Mosec61β</i> was notably reduced, which affected the function of appressoria. Moreover, Δ<i>Mosec61β</i> was also sensitive to oxidative stress and exhibited a reduced ability to overcome plant immunity. Further examination demonstrated that MoSec61β affected the normal secretion of the apoplastic effectors Bas4 and Slp1. In addition, Δ<i>Mosec61β</i> upregulated the level of ER-phagy. In conclusion, our results demonstrate the importance of the roles played by MoSec61β in the fungal development and pathogenesis of <i>M. oryzae</i>.
DOI: 10.6084/m9.figshare.23730862.v1
title: Additional file 7 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 7: Table S6. Summary for cis-sQTL coupled miRNA.
DOI: 10.6084/m9.figshare.23730868.v1
title: Additional file 1 of Causal effects of serum lipid biomarkers on early age-related macular degeneration using Mendelian randomization

description: Additional file 1: Table S1. Reciprocal causation.
DOI: 10.6084/m9.figshare.23730845.v1
title: Additional file 7 of Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus

description: Additional file 7: Table S4. Degree of transcription factors in the co-expression network.
DOI: 10.6084/m9.figshare.23730859
title: Additional file 6 of Mapping intron retention events contributing to complex traits using splice quantitative trait locus

description: Additional file 6: Table S5. Summary of primer sequences used in the study.
DOI: 10.18112/openneuro.ds003338.v1.0.0
title: bball