cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1427406
title: Reinforced Angle-Based Multicategory Support Vector Machines

description: The support vector machine (SVM) is a very popular classification tool with many successful applications. It was originally designed for binary problems with desirable theoretical properties. Although there exist various multicategory SVM (MSVM) extensions in the literature, some challenges remain. In particular, most existing MSVMs make use of <i>k</i> classification functions for a <i>k</i>-class problem, and the corresponding optimization problems are typically handled by existing quadratic programming solvers. In this article, we propose a new group of MSVMs, namely, the reinforced angle-based MSVMs (RAMSVMs), using an angle-based prediction rule with <i>k</i> − 1 functions directly. We prove that RAMSVMs can enjoy Fisher consistency. Moreover, we show that the RAMSVM can be implemented using the very efficient coordinate descent algorithm on its dual problem. Numerical experiments demonstrate that our method is highly competitive in terms of computational speed, as well as classification prediction performance. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.1427406.v2
title: Reinforced Angle-Based Multicategory Support Vector Machines

description: The support vector machine (SVM) is a very popular classification tool with many successful applications. It was originally designed for binary problems with desirable theoretical properties. Although there exist various multicategory SVM (MSVM) extensions in the literature, some challenges remain. In particular, most existing MSVMs make use of <i>k</i> classification functions for a <i>k</i>-class problem, and the corresponding optimization problems are typically handled by existing quadratic programming solvers. In this article, we propose a new group of MSVMs, namely, the reinforced angle-based MSVMs (RAMSVMs), using an angle-based prediction rule with <i>k</i> − 1 functions directly. We prove that RAMSVMs can enjoy Fisher consistency. Moreover, we show that the RAMSVM can be implemented using the very efficient coordinate descent algorithm on its dual problem. Numerical experiments demonstrate that our method is highly competitive in terms of computational speed, as well as classification prediction performance. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.1427406.v1
title: Reinforced Angle-based Multicategory Support Vector Machines

description: The Support Vector Machine (SVM) is a very popular classification tool with many successful applications. It was originally designed for binary problems with desirable theoretical properties. Although there exist various Multicategory SVM (MSVM) extensions in the literature, some challenges remain. In particular, most existing MSVMs make use of <i>k</i> classification functions for a <i>k</i>-class problem, and the corresponding optimization problems are typically handled by existing quadratic programming solvers. In this paper, we propose a new group of MSVMs, namely the Reinforced Angle-based MSVMs (RAMSVMs), using an angle-based prediction rule with <i>k</i> − 1 functions directly. We prove that RAMSVMs can enjoy Fisher consistency. Moreover, we show that the RAMSVM can be implemented using the very efficient coordinate descent algorithm on its dual problem. Numerical experiments demonstrate that our method is highly competitive in terms of computational speed, as well as classification prediction performance. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.1430498
title: Identification of Methylation sites on pUC19 using Oxford Nanopore Sequencing

description: Nanopore sequencing allows direct sequencing of single-stranded DNA molecules in real time. To explore whether Nanopore sequencing can discriminate methylated bases, we sequenced two plasmids with and without methylation at the dam and dcm methylation sites (GmeATC and CmeCWGG motifs respectively). By analyzing the resistance of 5-mers occupying a pore we observed significant differences between methylated and unmethylated sequences at the sites of both types of methylation, presumably due to the difference in the obstruction of current flow across the pore by the methyl groups. This finding indicates that Nanopore sequencing has the potential to robustly detect methylated bases, and that the current basecalling model would be improved by incorporating models of modified bases. Additionally, we observed a large fraction of 5-mers that significantly deviate from the default METRICHOR basecalling models, indicating that re-calibration is necessary to correct systematic biases in those models and improve overall sequencing accuracy.
DOI: 10.6084/m9.figshare.1431902
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v1
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signalling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v2
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v3
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v4
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v5
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v6
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v8
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1431902.v7
title: The PRKAA1/AMPKα1 pathway triggers autophagy during CSF1-induced human monocyte differentiation and is a potential target in CMML

description: Autophagy is induced during differentiation of human monocytes into macrophages that is mediated by CSF1/CSF-1/M-CSF (colony stimulating factor 1 [macrophage]). However, little is known about the molecular mechanisms that link CSF1 receptor engagement to the induction of autophagy. Here we show that the CAMKK2-PRKAA1-ULK1 pathway is required for CSF1-induced autophagy and human monocyte differentiation. We reveal that this pathway links P2RY6 to the induction of autophagy, and we decipher the signaling network that links the CSF1 receptor to P2RY6-mediated autophagy and monocyte differentiation. In addition, we show that the physiological P2RY6 ligand UDP and the specific P2RY6 agonist MRS2693 can restore normal monocyte differentiation through reinduction of autophagy in primary myeloid cells from some but not all chronic myelomonocytic leukemia (CMML) patients. Collectively, our findings highlight an essential role for PRKAA1-mediated autophagy during differentiation of human monocytes and pave the way for future therapeutic interventions for CMML.
DOI: 10.6084/m9.figshare.1434067
title: MiR-2 family targets <i>awd</i> and <i>fng</i> to regulate wing morphogenesis in <i>Bombyx mori</i>

description: MicroRNAs (miRNAs) are post-transcriptional regulators that target specific mRNAs for repression and thus play key roles in many biological processes, including insect wing morphogenesis. <i>miR-2</i> is an invertebrate-specific miRNA family that has been predicted in the fruit fly, <i>Drosophila melanogaster</i>, to be involved in regulating the Notch signaling pathway. We show here that <i>miR-2</i> plays a critical role in wing morphogenesis in the silkworm, <i>Bombyx mori</i>, a lepidopteran model insect. Transgenic over-expression of a <i>miR-2</i> cluster using a Gal4/UAS system results in deformed adult wings, supporting the conclusion that <i>miR-2</i> regulates functions essential for normal wing morphogenesis. Two genes, <i>abnormal wing disc</i> (<i>awd</i>) and <i>fringe</i> (<i>fng</i>), which are positive regulators in Notch signaling, are identified as <i>miR-2</i> targets and validated by a dual-luciferase reporter assay. The relative abundance of both <i>awd</i> and <i>fng</i> expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. Furthermore, somatic mutagenesis analysis of <i>awd</i> and <i>fng</i> using the CRISPR/Cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the <i>miR-2</i> overexpression transgenic animals. The critical role of <i>miR-2</i> in <i>Bombyx</i> wing morphogenesis may provide a potential target in future lepidopteran pest control.
DOI: 10.6084/m9.figshare.1434067.v1
title: MiR-2 family targets <i>awd</i> and <i>fng</i> to regulate wing morphogenesis in <i>Bombyx mori</i>

description: MicroRNAs (miRNAs) are post-transcriptional regulators that target specific mRNAs for repression and thus play key roles in many biological processes, including insect wing morphogenesis. <i>miR-2</i> is an invertebrate-specific miRNA family that has been predicted in the fruit fly, <i>Drosophila melanogaster</i>, to be involved in regulating the Notch signaling pathway. We show here that <i>miR-2</i> plays a critical role in wing morphogenesis in the silkworm, <i>Bombyx mori,</i> a lepidopteran model insect. Transgenic over-expression of a <i>miR-2</i> cluster using a Gal4/UAS system results in deformed adult wings, supporting the conclusion that <i>miR-2</i> regulates functions essential for normal wing morphogenesis. Two genes, <i>abnormal wing disc</i> (<i>awd</i>) and <i>fringe</i> (<i>fng</i>), which are positive regulators in Notch signaling, are identified as <i>miR-2</i> targets and validated by a dual-luciferase reporter assay. The relative abundance of both <i>awd</i> and <i>fng</i> expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. Furthermore, somatic mutagenesis analysis of <i>awd</i> and <i>fng</i> using the CRISPR/Cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the <i>miR-2</i> over-expression transgenic animals. The critical role of <i>miR-2</i> in <i>Bombyx</i> wing morphogenesis may provide a potential target in future lepidopteran pest control.
DOI: 10.6084/m9.figshare.1434067.v3
title: MiR-2 family targets <i>awd</i> and <i>fng</i> to regulate wing morphogenesis in <i>Bombyx mori</i>

description: MicroRNAs (miRNAs) are post-transcriptional regulators that target specific mRNAs for repression and thus play key roles in many biological processes, including insect wing morphogenesis. <i>miR-2</i> is an invertebrate-specific miRNA family that has been predicted in the fruit fly, <i>Drosophila melanogaster</i>, to be involved in regulating the Notch signaling pathway. We show here that <i>miR-2</i> plays a critical role in wing morphogenesis in the silkworm, <i>Bombyx mori</i>, a lepidopteran model insect. Transgenic over-expression of a <i>miR-2</i> cluster using a Gal4/UAS system results in deformed adult wings, supporting the conclusion that <i>miR-2</i> regulates functions essential for normal wing morphogenesis. Two genes, <i>abnormal wing disc</i> (<i>awd</i>) and <i>fringe</i> (<i>fng</i>), which are positive regulators in Notch signaling, are identified as <i>miR-2</i> targets and validated by a dual-luciferase reporter assay. The relative abundance of both <i>awd</i> and <i>fng</i> expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. Furthermore, somatic mutagenesis analysis of <i>awd</i> and <i>fng</i> using the CRISPR/Cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the <i>miR-2</i> overexpression transgenic animals. The critical role of <i>miR-2</i> in <i>Bombyx</i> wing morphogenesis may provide a potential target in future lepidopteran pest control.
DOI: 10.6084/m9.figshare.1434067.v2
title: MiR-2 family targets <i>awd</i> and <i>fng</i> to regulate wing morphogenesis in <i>Bombyx mori</i>

description: MicroRNAs (miRNAs) are post-transcriptional regulators that target specific mRNAs for repression and thus play key roles in many biological processes, including insect wing morphogenesis. <i>miR-2</i> is an invertebrate-specific miRNA family that has been predicted in the fruit fly, <i>Drosophila melanogaster</i>, to be involved in regulating the Notch signaling pathway. We show here that <i>miR-2</i> plays a critical role in wing morphogenesis in the silkworm, <i>Bombyx mori</i>, a lepidopteran model insect. Transgenic over-expression of a <i>miR-2</i> cluster using a Gal4/UAS system results in deformed adult wings, supporting the conclusion that <i>miR-2</i> regulates functions essential for normal wing morphogenesis. Two genes, <i>abnormal wing disc</i> (<i>awd</i>) and <i>fringe</i> (<i>fng</i>), which are positive regulators in Notch signaling, are identified as <i>miR-2</i> targets and validated by a dual-luciferase reporter assay. The relative abundance of both <i>awd</i> and <i>fng</i> expression products was reduced significantly in transgenic animals, implicating them in the abnormal wing phenotype. Furthermore, somatic mutagenesis analysis of <i>awd</i> and <i>fng</i> using the CRISPR/Cas9 system and knock-out mutants also resulted in deformed wings similar to those observed in the <i>miR-2</i> overexpression transgenic animals. The critical role of <i>miR-2</i> in <i>Bombyx</i> wing morphogenesis may provide a potential target in future lepidopteran pest control.
DOI: 10.6084/m9.figshare.1435919
title: Theoretical investigation on H abstraction reaction mechanisms and rate constants of Isoflurane with the OH radical

description: The mechanism of H abstraction reactions for Isoflurane with the OH radical was investigated using density functional theory and G3(MP2) duel theory methods. The geometrical structures of all the species were fully optimised at B3LYP/6-311++G** level of theory. Thermochemistry data were obtained by utilising the high accurate model chemistry method G3(MP2) combined with the standard statistical thermodynamic calculations. Gibbs free energies were used for the reaction channels analysis. All the reaction channels were confirmed throughout the intrinsic reaction coordinate analysis. The results show that two channels were obtained, which correspond to <b>P(1)</b> and <b>P(2)</b> with the respective activation barriers of 63.03 and 54.82 kJ/mol. The rate constants for the two channels over a wide temperature range of 298.15–2000 K were predicted and the calculated data are in agreement with the experimental one. The results show that <b>P(2)</b> is the dominant reaction channel under 800 K and above 800 K, it can be found that <b>P(1)</b> will be more preferable reaction channel.