cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5656933.v1
title: Additional file 1: of Evaluation of an accelerated hydrogen peroxide disinfectant to inactivate porcine epidemic diarrhea virus in swine feces on aluminum surfaces under freezing conditions

description: Results of PEDV N-gene RT-qPCR tests on environmental samples from coupons and rectal swabs from pigs used for bioassay. Results from all diagnostic tests conducted for the study are reported for each replicate, one row for each replicate. Test results, Ct value and genomic copies are reported for PCR tests on pre and post treatment environmental samples from coupons. Test result and Ct values are reported for PCR tests on rectal swabs from pigs 3 and 7Â days post inoculation for the bioassay. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.5657308
title: Association between TPMT<i>*</i>3C and decreased thiopurine S-methyltransferase activity in patients with neuromyelitis optica spectrum disorders in China

description: <b>Aim of the study:</b> Thiopurines are effective drugs in treating neuromyelitis optica spectrum disorders and other diseases. Thiopurines’ toxicity is mainly imputed to thiopurine S-methyltransferase activity. In Chinese population, the most common and important variation of thiopurine S-methyltransferase is TPMT<i>*</i>3C (rs1142345). This study aims to reveal the association between thiopurine S-methyltransferase activity and genetic polymorphisms of thiopurine S-methyltransferase in patients with neuromyelitis optica spectrum disorders in China. <b>Material and methods:</b> A liquid chromatography tandem mass/mass method was used to evaluate the thiopurine S-methyltransferase activity by using 6-mercapthioprine as the substrate in human erythrocyte haemolysate via 1 h incubation at 37 °C to form its methylated product 6-methylmercaptopurine. The amount of 6-methylmercaptopurine was adjusted by haematocrit and normalized to 8 × 10<sup>8</sup> erythrocytes. The selected polymorphisms of thiopurine S-methyltransferase were identified using MassARRAY system (Sequenom) and multiple SNaPshot technique. <b>Results:</b> In 69 patients with neuromyelitis optica spectrum disorders, thiopurine S-methyltransferase activity was 80.29–154.53 (127.51 ± 16.83) pmol/h/8 × 10<sup>8</sup> erythrocytes. TPMT<i>*</i>3C (rs1142345) was associated with lower thiopurine S-methyltransferase activity (BETA = −25.37, <i>P</i> = 0.011). Other selected variants were not associated with thiopurine S-methyltransferase activity. <b>Conclusions:</b> TPMT*3C affects TPMT activity in Chinese patients with neuromyelitis optica spectrum disorders. Further studies are warranted to confirm the results. <b>Abbreviations:</b><i>TPRs</i> = thiopurines; <i>NMOSD</i> = neuromyelitis optica spectrum disorders; <i>TPMT</i> = thiopurine S-methyltransferase; <i>LC-MS/MS</i> = liquid chromatography tandem mass/mass; <i>6-MMP</i> = 6-methylmercaptopurine; <i>IS</i> = internal standard; <i>SNP</i> = single nucleotide polymorphism; <i>MAF</i> = minor allele frequency; <i>HWE</i> = Hardy–Weinberg equilibrium; <i>BETA</i> = regression coefficients; <i>UTR-3</i> = untranslated region 3
DOI: 10.6084/m9.figshare.5657308.v1
title: Association between TPMT<i>*</i>3C and decreased thiopurine S-methyltransferase activity in patients with neuromyelitis optica spectrum disorders in China

description: <b>Aim of the study:</b> Thiopurines are effective drugs in treating neuromyelitis optica spectrum disorders and other diseases. Thiopurines’ toxicity is mainly imputed to thiopurine S-methyltransferase activity. In Chinese population, the most common and important variation of thiopurine S-methyltransferase is TPMT<i>*</i>3C (rs1142345). This study aims to reveal the association between thiopurine S-methyltransferase activity and genetic polymorphisms of thiopurine S-methyltransferase in patients with neuromyelitis optica spectrum disorders in China. <b>Material and methods:</b> A liquid chromatography tandem mass/mass method was used to evaluate the thiopurine S-methyltransferase activity by using 6-mercapthioprine as the substrate in human erythrocyte haemolysate via 1 h incubation at 37 °C to form its methylated product 6-methylmercaptopurine. The amount of 6-methylmercaptopurine was adjusted by haematocrit and normalized to 8 × 10<sup>8</sup> erythrocytes. The selected polymorphisms of thiopurine S-methyltransferase were identified using MassARRAY system (Sequenom) and multiple SNaPshot technique. <b>Results:</b> In 69 patients with neuromyelitis optica spectrum disorders, thiopurine S-methyltransferase activity was 80.29–154.53 (127.51 ± 16.83) pmol/h/8 × 10<sup>8</sup> erythrocytes. TPMT<i>*</i>3C (rs1142345) was associated with lower thiopurine S-methyltransferase activity (BETA = −25.37, <i>P</i> = 0.011). Other selected variants were not associated with thiopurine S-methyltransferase activity. <b>Conclusions:</b> TPMT*3C affects TPMT activity in Chinese patients with neuromyelitis optica spectrum disorders. Further studies are warranted to confirm the results. <b>Abbreviations:</b><i>TPRs</i> = thiopurines; <i>NMOSD</i> = neuromyelitis optica spectrum disorders; <i>TPMT</i> = thiopurine S-methyltransferase; <i>LC-MS/MS</i> = liquid chromatography tandem mass/mass; <i>6-MMP</i> = 6-methylmercaptopurine; <i>IS</i> = internal standard; <i>SNP</i> = single nucleotide polymorphism; <i>MAF</i> = minor allele frequency; <i>HWE</i> = Hardy–Weinberg equilibrium; <i>BETA</i> = regression coefficients; <i>UTR-3</i> = untranslated region 3
DOI: 10.6084/m9.figshare.5657332
title: Fupplementary file: The list of the genes which were mapped to Go terms from The muscle development transcriptome landscape of ovariectomized goat

description: Table S4 GO analysis result
DOI: 10.6084/m9.figshare.5657335
title: Fupplementary file: The list of the 1612 differently expressed genes from The muscle development transcriptome landscape of ovariectomized goat

description: Table S3 The differently expressed genes
DOI: 10.6084/m9.figshare.5657335.v1
title: Fupplementary file: The list of the 1612 differently expressed genes from The muscle development transcriptome landscape of ovariectomized goat

description: Table S3 The differently expressed genes
DOI: 10.6084/m9.figshare.5657338
title: Fupplementary file: The list of the genes which were enriched to specific KEGG pathway from The muscle development transcriptome landscape of ovariectomized goat

description: Table S5 KEGG analysis result
DOI: 10.6084/m9.figshare.5657338.v1
title: Fupplementary file: The list of the genes which were enriched to specific KEGG pathway from The muscle development transcriptome landscape of ovariectomized goat

description: Table S5 KEGG analysis result
DOI: 10.6084/m9.figshare.5658934
title: Bacterial endotoxin (lipopolysaccharide) binds to the surface of gold nanoparticles, interferes with biocorona formation and induces human monocyte inflammatory activation

description: Nanoparticles (NPs) are easily contaminated by bacterial endotoxin (lipopolysaccharide [LPS]). The presence of LPS can be responsible for many immune/inflammatory effects attributed to NPs. In this study, we examined the effects of LPS adsorption on the NP surface on the formation of a biocorona in biological fluids and on the subsequent inflammation-inducing activity of NPs. Different gold (Au) NPs with sizes ranging from 10 to 80 nm and with different surface functionalization (sodium citrate, lipoic acid, and branched polyethyleneimine (BPEI), or polyethylene glycol (PEG)) were exposed to <i>E. coli</i> LPS under different conditions. The binding capacity of LPS to the surface of AuNPs was dose- and time-dependent. LPS attached to sodium citrate and lipoic acid coatings, but did not adhere to BPEI- or PEG-coated NPs. By computational simulation, the binding of LPS to AuNPs seems to follow the Langmuir absorption isotherm. The presence of LPS on AuNP surface interfered and caused a decrease in the formation of the expected biomolecular corona upon incubation in human plasma. LPS-coated AuNPs, but not the LPS-free NPs, induced significant inflammatory responses <i>in vitro</i>. Notably, while free LPS did also induce an anti-inflammatory response, LPS bound to NPs appeared unable to do so. In conclusion, the unintentional adsorption of LPS onto the NP surface can affect the biocorona formation and the inflammatory properties of NPs. Thus, for an accurate interpretation of NP interactions with cells, it is extremely important to be able to distinguish the intrinsic NP biological effects from those caused by biologically active contaminants such as endotoxin.
DOI: 10.6084/m9.figshare.5658934.v2
title: Bacterial endotoxin (lipopolysaccharide) binds to the surface of gold nanoparticles, interferes with biocorona formation and induces human monocyte inflammatory activation

description: Nanoparticles (NPs) are easily contaminated by bacterial endotoxin (lipopolysaccharide [LPS]). The presence of LPS can be responsible for many immune/inflammatory effects attributed to NPs. In this study, we examined the effects of LPS adsorption on the NP surface on the formation of a biocorona in biological fluids and on the subsequent inflammation-inducing activity of NPs. Different gold (Au) NPs with sizes ranging from 10 to 80 nm and with different surface functionalization (sodium citrate, lipoic acid, and branched polyethyleneimine (BPEI), or polyethylene glycol (PEG)) were exposed to <i>E. coli</i> LPS under different conditions. The binding capacity of LPS to the surface of AuNPs was dose- and time-dependent. LPS attached to sodium citrate and lipoic acid coatings, but did not adhere to BPEI- or PEG-coated NPs. By computational simulation, the binding of LPS to AuNPs seems to follow the Langmuir absorption isotherm. The presence of LPS on AuNP surface interfered and caused a decrease in the formation of the expected biomolecular corona upon incubation in human plasma. LPS-coated AuNPs, but not the LPS-free NPs, induced significant inflammatory responses <i>in vitro</i>. Notably, while free LPS did also induce an anti-inflammatory response, LPS bound to NPs appeared unable to do so. In conclusion, the unintentional adsorption of LPS onto the NP surface can affect the biocorona formation and the inflammatory properties of NPs. Thus, for an accurate interpretation of NP interactions with cells, it is extremely important to be able to distinguish the intrinsic NP biological effects from those caused by biologically active contaminants such as endotoxin.
DOI: 10.6084/m9.figshare.5658934.v1
title: Bacterial endotoxin (lipopolysaccharide) binds to the surface of gold nanoparticles, interferes with biocorona formation and induces human monocyte inflammatory activation

description: Nanoparticles (NPs) are easily contaminated by bacterial endotoxin (lipopolysaccharide [LPS]). The presence of LPS can be responsible for many immune/inflammatory effects attributed to NPs. In this study, we examined the effects of LPS adsorption on the NP surface on the formation of a biocorona in biological fluids and on the subsequent inflammation-inducing activity of NPs. Different gold (Au) NPs with sizes ranging from 10 to 80 nm and with different surface functionalization (sodium citrate, lipoic acid, and branched polyethyleneimine (BPEI), or polyethylene glycol (PEG)) were exposed to <i>E. coli</i> LPS under different conditions. The binding capacity of LPS to the surface of AuNPs was dose- and time-dependent. LPS attached to sodium citrate and lipoic acid coatings, but did not adhere to BPEI- or PEG-coated NPs. By computational simulation, the binding of LPS to AuNPs seems to follow the Langmuir absorption isotherm. The presence of LPS on AuNP surface interfered and caused a decrease in the formation of the expected biomolecular corona upon incubation in human plasma. LPS-coated AuNPs, but not the LPS-free NPs, induced significant inflammatory responses <i>in vitro</i>. Notably, while free LPS did also induce an anti-inflammatory response, LPS bound to NPs appeared unable to do so. In conclusion, the unintentional adsorption of LPS onto the NP surface can affect the biocorona formation and the inflammatory properties of NPs. Thus, for an accurate interpretation of NP interactions with cells, it is extremely important to be able to distinguish the intrinsic NP biological effects from those caused by biologically active contaminants such as endotoxin.
DOI: 10.6084/m9.figshare.5659159
title: Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China

description: Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China, as published in<em> Microbial Genomics.</em> DOI: 10.1099/mgen.0.000149
DOI: 10.6084/m9.figshare.5659159.v1
title: Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China

description: Genome analysis of Clinical Multilocus Sequence Type 11 Klebsiella pneumoniae from China, as published in<em> Microbial Genomics.</em> DOI: 10.1099/mgen.0.000149
DOI: 10.6084/m9.figshare.5660782
title: Additional file 2 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: SV lists from the CEU (Northern Europeans from Utah) trio. This file provides the SVs identified by OMSV from the CEU trio. The first three sheets list the indels identified from NA12878, NA12891, and NA12892, respectively. The fourth sheet lists the union of these three lists. The fifth sheet lists all the sites with multiple indels called at the same site (two insertions, two deletions, or one insertion and one deletion). The sixth sheet lists the high-confidence indels and non-indels for evaluating Mendelian concordance. The last sheet lists the complex SVs. (XLSX 570 kb)
DOI: 10.6084/m9.figshare.5660782.v1
title: Additional file 2 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: SV lists from the CEU (Northern Europeans from Utah) trio. This file provides the SVs identified by OMSV from the CEU trio. The first three sheets list the indels identified from NA12878, NA12891, and NA12892, respectively. The fourth sheet lists the union of these three lists. The fifth sheet lists all the sites with multiple indels called at the same site (two insertions, two deletions, or one insertion and one deletion). The sixth sheet lists the high-confidence indels and non-indels for evaluating Mendelian concordance. The last sheet lists the complex SVs. (XLSX 570 kb)
DOI: 10.6084/m9.figshare.5660785
title: Additional file 3 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: SV list from the C666-1 cell line. This file provides the SVs identified by OMSV from the C666-1 cell line. The first sheet lists the indels identified. The second sheet lists all the sites with multiple indels called at the same site (two insertions, two deletions, or one insertion and one deletion). The third sheet lists the complex SVs. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.5660785.v1
title: Additional file 3 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: SV list from the C666-1 cell line. This file provides the SVs identified by OMSV from the C666-1 cell line. The first sheet lists the indels identified. The second sheet lists all the sites with multiple indels called at the same site (two insertions, two deletions, or one insertion and one deletion). The third sheet lists the complex SVs. (XLSX 110 kb)
DOI: 10.6084/m9.figshare.5660788
title: Additional file 4 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Overlapping of C666-1 indels with segmental duplications. This file provides the overlap of C666-1 indels identified by OMSV with human segmental duplications. The first three columns show the genomic location of the SVs. The fourth column shows the SV type. The fifth and sixth columns show the overlapping segmental duplications (if any) and the genes of which the exons overlap the segmental duplications (if any). (XLSX 72 kb)
DOI: 10.6084/m9.figshare.5660788.v1
title: Additional file 4 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Overlapping of C666-1 indels with segmental duplications. This file provides the overlap of C666-1 indels identified by OMSV with human segmental duplications. The first three columns show the genomic location of the SVs. The fourth column shows the SV type. The fifth and sixth columns show the overlapping segmental duplications (if any) and the genes of which the exons overlap the segmental duplications (if any). (XLSX 72 kb)
DOI: 10.6084/m9.figshare.5660794
title: Additional file 6 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Fragile sites in the in silico map based on hg38. This file provides the locations of fragile sites in the human reference genome hg38. (BED 90 kb)
DOI: 10.6084/m9.figshare.5660794.v1
title: Additional file 6 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Fragile sites in the in silico map based on hg38. This file provides the locations of fragile sites in the human reference genome hg38. (BED 90 kb)
DOI: 10.6084/m9.figshare.5660797
title: Additional file 7 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Gaps in hg38. This file provides the locations of unspecified nucleotides (Nâ s) in the human reference genome hg38. (BED 18 kb)
DOI: 10.6084/m9.figshare.5660800
title: Additional file 8 of OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

description: Pseudo-autosomal regions in hg38. This file provides the locations of pseudo-autosomal regions in the human reference genome hg38. (BED 0.078 kb)
DOI: 10.6084/m9.figshare.5660869
title: Supplementary Table S2 from Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll

description: Abundances of major (wt%) and trace (ppm) elements. Previously reported composition of rocks dredged from Yaeyama knoll are shown for comparison.
DOI: 10.6084/m9.figshare.5660869.v1
title: Supplementary Table S2 from Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll

description: Abundances of major (wt%) and trace (ppm) elements. Previously reported composition of rocks dredged from Yaeyama knoll are shown for comparison.
DOI: 10.6084/m9.figshare.5660872
title: Supplementary Table S1 from Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll

description: All measurements of fluids from the Yokosuka field.
DOI: 10.6084/m9.figshare.5660872.v1
title: Supplementary Table S1 from Deepest and hottest hydrothermal activity in the Okinawa Trough: the Yokosuka site at Yaeyama Knoll

description: All measurements of fluids from the Yokosuka field.
DOI: 10.6084/m9.figshare.5661319
title: Additional file 4: Figure S3 and S4. of Direct inhibition of ACTN4 by ellagic acid limits breast cancer metastasis via regulation of Î˛-catenin stabilization in cancer stem cells

description: The wound healing and chamber invasive assay revealed that breast cancer cell migration and invasion were inhibited by EA in a time- and dose-dependent manner. (ZIP 2039Â kb)
DOI: 10.6084/m9.figshare.5661319.v1
title: Additional file 4: Figure S3 and S4. of Direct inhibition of ACTN4 by ellagic acid limits breast cancer metastasis via regulation of Î˛-catenin stabilization in cancer stem cells

description: The wound healing and chamber invasive assay revealed that breast cancer cell migration and invasion were inhibited by EA in a time- and dose-dependent manner. (ZIP 2039Â kb)
DOI: 10.6084/m9.figshare.5661388
title: MOESM1 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 1. Detailed information about metabolic model iYL_2.0.
DOI: 10.6084/m9.figshare.5661388.v1
title: MOESM1 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 1. Detailed information about metabolic model iYL_2.0.
DOI: 10.6084/m9.figshare.5661400
title: MOESM2 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 2. Gene essentiality analysis in minimal growth medium and yeast extract medium by flux balance analysis.
DOI: 10.6084/m9.figshare.5661400.v1
title: MOESM2 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 2. Gene essentiality analysis in minimal growth medium and yeast extract medium by flux balance analysis.
DOI: 10.6084/m9.figshare.5661424
title: MOESM3 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 3. Potential gene-level targets identified by OptGeneKnock, Idealknock and APGC to improve TAG production.
DOI: 10.6084/m9.figshare.5661424.v1
title: MOESM3 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 3. Potential gene-level targets identified by OptGeneKnock, Idealknock and APGC to improve TAG production.
DOI: 10.6084/m9.figshare.5661445
title: MOESM4 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 4. Simulation results of amino acid supplementation for TAG production.
DOI: 10.6084/m9.figshare.5661445.v1
title: MOESM4 of Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol

description: Additional file 4. Simulation results of amino acid supplementation for TAG production.
DOI: 10.6084/m9.figshare.5661490
title: Additional file 6: Table S2. of Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice

description: Differentially expressed genes in four comparison groups. (XLSX 191Â kb)
DOI: 10.6084/m9.figshare.5661490.v1
title: Additional file 6: Table S2. of Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice

description: Differentially expressed genes in four comparison groups. (XLSX 191Â kb)
DOI: 10.6084/m9.figshare.5661508
title: Additional file 7: Table S3. of Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice

description: Specific differentially expressed genes in four comparison groups. (XLSX 87Â kb)
DOI: 10.6084/m9.figshare.5661508.v1
title: Additional file 7: Table S3. of Pervasive interactions of Sa and Sb loci cause high pollen sterility and abrupt changes in gene expression during meiosis that could be overcome by double neutral genes in autotetraploid rice

description: Specific differentially expressed genes in four comparison groups. (XLSX 87Â kb)