cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1488640.v6
title: Stratigraphic records of the dynamic uplift of the Emeishan large igneous province

description: Fluid dynamical and numerical modelling predicts a large-scale regional domal uplift prior to basalt eruptions in large igneous provinces, which can be readily measured when a plume head rises below a shallow marine sedimentary basin. Research on the sedimentology, biostratigraphy, and isotopic chronology of the Emeishan large igneous province demonstrates that the sedimentary environment in the Maokou stage is not uniform carbonate platform facies, but rather sedimentary facies with a north–south linear alignment and west–east different distribution controlled by the syn-depositional normal faulting of the Changhai and Xiaojiang faults, which are the result of underwater dynamic uplift induced by deep mantle activity. The dynamic uplift started in the Maokou stage. Thus, thinning of the Maokou limestone was the product of the difference in the initial depositional thickness caused by the underwater uplift and post-depositional surface uplift and erosion, but post-depositional uplift was much less than kilometre scale. Sedimentary facies differentiation and tectonic–sedimentary evolution in the Maokou stage provide a constraint for the time of the initial eruption and eruption environment before and during the Emeishan basalt eruption. Small-scale magmatic activity might have already begun in the middle of the Maokou stage, whereas submarine and terrestrial sedimentary environments coexisted before and during Emeishan basalt eruption.
DOI: 10.6084/m9.figshare.1488640.v7
title: Stratigraphic records of the dynamic uplift of the Emeishan large igneous province

description: Fluid dynamical and numerical modelling predicts a large-scale regional domal uplift prior to basalt eruptions in large igneous provinces, which can be readily measured when a plume head rises below a shallow marine sedimentary basin. Research on the sedimentology, biostratigraphy, and isotopic chronology of the Emeishan large igneous province demonstrates that the sedimentary environment in the Maokou stage is not uniform carbonate platform facies, but rather sedimentary facies with a north–south linear alignment and west–east different distribution controlled by the syn-depositional normal faulting of the Changhai and Xiaojiang faults, which are the result of underwater dynamic uplift induced by deep mantle activity. The dynamic uplift started in the Maokou stage. Thus, thinning of the Maokou limestone was the product of the difference in the initial depositional thickness caused by the underwater uplift and post-depositional surface uplift and erosion, but post-depositional uplift was much less than kilometre scale. Sedimentary facies differentiation and tectonic–sedimentary evolution in the Maokou stage provide a constraint for the time of the initial eruption and eruption environment before and during the Emeishan basalt eruption. Small-scale magmatic activity might have already begun in the middle of the Maokou stage, whereas submarine and terrestrial sedimentary environments coexisted before and during Emeishan basalt eruption.
DOI: 10.6084/m9.figshare.1491380.v1
title: Expression of imprinted genes in placenta is associated with infant neurobehavioral development

description: Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified ten genes (<i>DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2</i>, and <i>COPG2IT1</i>) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
DOI: 10.6084/m9.figshare.1491380
title: Expression of imprinted genes in placenta is associated with infant neurobehavioral development

description: Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified 10 genes (<i>DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2</i>, and <i>COPG2IT1</i>) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
DOI: 10.6084/m9.figshare.1491380.v2
title: Expression of imprinted genes in placenta is associated with infant neurobehavioral development

description: Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified 10 genes (<i>DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2</i>, and <i>COPG2IT1</i>) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
DOI: 10.6084/m9.figshare.1491380.v4
title: Expression of imprinted genes in placenta is associated with infant neurobehavioral development

description: Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified 10 genes (<i>DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2</i>, and <i>COPG2IT1</i>) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
DOI: 10.6084/m9.figshare.1491380.v3
title: Expression of imprinted genes in placenta is associated with infant neurobehavioral development

description: Genomic imprinting disorders often exhibit delayed neurobehavioral development, suggesting this unique mechanism of epigenetic regulation plays a role in mental and neurological health. While major errors in imprinting have been linked to adverse health outcomes, there has been little research conducted on how moderate variability in imprinted gene expression within a population contributes to differences in neurobehavioral outcomes, particularly at birth. Here, we profiled the expression of 108 known and putative imprinted genes in human placenta samples from 615 infants assessed by the Neonatal Intensive Care Unit (NICU) Network Neurobehavioral Scales (NNNS). Data reduction identified 10 genes (<i>DLX5, DHCR24, VTRNA2-1, PHLDA2, NPAP1, FAM50B, GNAS-AS1, PAX8-AS1, SHANK2</i>, and <i>COPG2IT1</i>) whose expression could distinguish between newborn neurobehavioral profiles derived from the NNNS. Clustering infants based on the expression pattern of these genes identified 2 groups of infants characterized by reduced quality of movement, increased signs of asymmetrical and non-optimal reflexes, and increased odds of demonstrating increased signs of physiologic stress and abstinence. Overall, these results suggest that common variation in placental imprinted gene expression is linked to suboptimal performance on scales of neurological functioning as well as with increased signs of physiologic stress, highlighting the central importance of the control of expression of these genes in the placenta for neurobehavioral development.
DOI: 10.6084/m9.figshare.1495494.v3
title: Efficient <i>PRNP</i> deletion in bovine genome using gene-editing technologies in bovine cells

description: Even though prion (encoded by the <i>PRNP</i> gene) diseases like bovine spongiform encephalopathy (BSE) are fatal neurodegenerative diseases in cattle, their study via gene deletion has been limited due to the absence of cell lines or mutant models. In this study, we aim to develop an immortalized fibroblast cell line in which genome-engineering technology can be readily applied to create gene-modified clones for studies. To this end, this study is designed to 1) investigate the induction of primary fibroblasts to immortalization by introducing <i>Bmi-1</i> and <i>hTert</i> genes; 2) investigate the disruption of the <i>PRNP</i> in those cells; and 3) evaluate the gene expression and embryonic development using knockout (KO) cell lines. Primary cells from a male neonate were immortalized with <i>Bmi-1</i>and <i>hTert</i>. Immortalized cells were cultured for more than 180 days without any changes in their doubling time and morphology. Furthermore, to knockout the <i>PRNP</i> gene, plasmids that encode transcription activator-like effector nuclease (TALEN) pairs were transfected into the cells, and transfected single cells were propagated. Mutated clonal cell lines were confirmed by T7 endonuclease I assay and sequencing. Four knockout cell lines were used for somatic cell nuclear transfer (SCNT), and the resulting embryos were developed to the blastocyst stage. The genes (<i>CSNK2A1, FAM64A, MPG and PRND</i>) were affected after <i>PRNP</i> disruption in immortalized cells. In conclusion, we established immortalized cattle fibroblasts using <i>Bmi-1</i> and <i>hTert</i> genes, and used TALENs to knockout the <i>PRNP</i> gene in these immortalized cells. The efficient <i>PRNP</i> KO is expected to be a useful technology to develop our understanding of <i>in vitro</i> prion protein functions in cattle.
DOI: 10.6084/m9.figshare.1495494.v2
title: Efficient <i>PRNP</i> deletion in bovine genome using gene-editing technologies in bovine cells

description: abstractEven though prion (encoded by the <i>PRNP</i> gene) diseases like bovine spongiform encephalopathy (BSE) are fatal neurodegenerative diseases in cattle, their study via gene deletion has been limited due to the absence of cell lines or mutant models. In this study, we aim to develop an immortalized fibroblast cell line in which genome-engineering technology can be readily applied to create gene-modified clones for studies. To this end, this study is designed to 1) investigate the induction of primary fibroblasts to immortalization by introducing <i>Bmi-1</i> and <i>hTert</i> genes; 2) investigate the disruption of the <i>PRNP</i> in those cells; and 3) evaluate the gene expression and embryonic development using knockout (KO) cell lines. Primary cells from a male neonate were immortalized with <i>Bmi-1</i>and <i>hTert</i>. Immortalized cells were cultured for more than 180 days without any changes in their doubling time and morphology. Furthermore, to knockout the <i>PRNP</i> gene, plasmids that encode transcription activator-like effector nuclease (TALEN) pairs were transfected into the cells, and transfected single cells were propagated. Mutated clonal cell lines were confirmed by T7 endonuclease I assay and sequencing. Four knockout cell lines were used for somatic cell nuclear transfer (SCNT), and the resulting embryos were developed to the blastocyst stage. The genes (<i>CSNK2A1, FAM64A, MPG and PRND</i>) were affected after <i>PRNP</i> disruption in immortalized cells. In conclusion, we established immortalized cattle fibroblasts using <i>Bmi-1</i> and <i>hTert</i> genes, and used TALENs to knockout the <i>PRNP</i> gene in these immortalized cells. The efficient <i>PRNP</i> KO is expected to be a useful technology to develop our understanding of <i>in vitro</i> prion protein functions in cattle.
DOI: 10.6084/m9.figshare.1495557
title: Preparation and certification of two freshwater sediments certified reference materials for polycyclic aromatic hydrocarbons

description: Two freshwater sediments certified reference materials (CRMs) for 16 polycyclic aromatic hydrocarbons (PAHs) have been developed by the Institute for Environmental Reference Materials (IERM) of Ministry of Environmental Protection (MEP) in China. The methodology for preparing the CRMs of PAHs in sediments is described in this paper. The collected natural sediment samples were air-dried, ground, homogenised, packed, sterilised and tested on stability and homogeneity. Homogeneity results showed that the between-unit variation was confirmed to be below 4.5% for each compound. Stability was assessed after storage of samples for 16 months at temperature less than 30°C and in shade. The certification of the natural sediment matrix CRMs for PAHs was based on the agreement of results using different analytical techniques including gas chromatography/mass spectrometry (GC/MS) and reversed-phase liquid chromatography (LC) by no less than eight collaborating laboratories including IERM. Results of the homogeneity showed that the calculated <i>u</i><sub>bb</sub>′ was 0.9–2.5% for environmental river standard-4 (ERS-4) and 9–2.3% for environmental lake standard-1 (ELS-1), whereas stability results of total 16 PAHs indicated that the calculated <i>u</i><sub>rel,lts</sub> was 4.2% for ERS-4 and 2.2% for ELS-1. Certified values of 16 PAHs in ERS-4 varied from 8.5 to 167 μg/kg and ranged from 0.036 to 2.8 mg/kg in ELS-1.The good comparability, together with the independent confirmation of the assigned mass fraction by using different methods, confirmed that the CRMs are suitable for the method validation and quality control in soil or sediments analysis.
DOI: 10.6084/m9.figshare.1495557.v1
title: Preparation and certification of two freshwater sediments certified reference materials for polycyclic aromatic hydrocarbons

description: Two freshwater sediments certified reference materials (CRMs) for 16 polycyclic aromatic hydrocarbons (PAHs) have been developed by the Institute for Environmental Reference Materials (IERM) of Ministry of Environmental Protection (MEP) in China. The methodology for preparing the CRMs of PAHs in sediments is described in this paper. The collected natural sediment samples were air-dried, ground, homogenised, packed, sterilised and tested on stability and homogeneity. Homogeneity results showed that the between-unit variation was confirmed to be below 4.5% for each compound. Stability was assessed after storage of samples for 16 months at temperature less than 30°C and in shade. The certification of the natural sediment matrix CRMs for PAHs was based on the agreement of results using different analytical techniques including gas chromatography/mass spectrometry (GC/MS) and reversed-phase liquid chromatography (LC) by no less than eight collaborating laboratories including IERM. Results of the homogeneity showed that the calculated <i>u</i><sub>bb</sub>′ was 0.9–2.5% for environmental river standard-4 (ERS-4) and 9–2.3% for environmental lake standard-1 (ELS-1), whereas stability results of total 16 PAHs indicated that the calculated <i>u</i><sub>rel,lts</sub> was 4.2% for ERS-4 and 2.2% for ELS-1. Certified values of 16 PAHs in ERS-4 varied from 8.5 to 167 μg/kg and ranged from 0.036 to 2.8 mg/kg in ELS-1.The good comparability, together with the independent confirmation of the assigned mass fraction by using different methods, confirmed that the CRMs are suitable for the method validation and quality control in soil or sediments analysis.
DOI: 10.6084/m9.figshare.1495557.v2
title: Preparation and certification of two freshwater sediments certified reference materials for polycyclic aromatic hydrocarbons

description: Two freshwater sediments certified reference materials (CRMs) for 16 polycyclic aromatic hydrocarbons (PAHs) have been developed by the Institute for Environmental Reference Materials (IERM) of Ministry of Environmental Protection (MEP) in China. The methodology for preparing the CRMs of PAHs in sediments is described in this paper. The collected natural sediment samples were air-dried, ground, homogenised, packed, sterilised and tested on stability and homogeneity. Homogeneity results showed that the between-unit variation was confirmed to be below 4.5% for each compound. Stability was assessed after storage of samples for 16 months at temperature less than 30°C and in shade. The certification of the natural sediment matrix CRMs for PAHs was based on the agreement of results using different analytical techniques including gas chromatography/mass spectrometry (GC/MS) and reversed-phase liquid chromatography (LC) by no less than eight collaborating laboratories including IERM. Results of the homogeneity showed that the calculated <i>u</i><sub>bb</sub>′ was 0.9–2.5% for environmental river standard-4 (ERS-4) and 9–2.3% for environmental lake standard-1 (ELS-1), whereas stability results of total 16 PAHs indicated that the calculated <i>u</i><sub>rel,lts</sub> was 4.2% for ERS-4 and 2.2% for ELS-1. Certified values of 16 PAHs in ERS-4 varied from 8.5 to 167 μg/kg and ranged from 0.036 to 2.8 mg/kg in ELS-1.The good comparability, together with the independent confirmation of the assigned mass fraction by using different methods, confirmed that the CRMs are suitable for the method validation and quality control in soil or sediments analysis.
DOI: 10.6084/m9.figshare.1497885
title: Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features

description: With the goal of studying epigenetic alterations in fibrolamellar hepatocellular carcinoma (FLC) and establish an associated DNA methylation signature, we analyzed <i>LINE-1</i> methylation in a cohort of FLC and performed next-generation sequencing of DNA methylation in a training set of pure-FLCs and non-cirrhotic hepatocellular carcinomas (nc-HCC). DNA methylation was correlated with gene expression. Furthermore, we established and validated an epigenetic signature differentiating pure-FLC from other HCCs. <i>LINE-1</i> methylation correlated with shorter recurrence-free survival and overall survival in resected pure-FLC patients. Unsupervised clustering using CG sites located in islands distinguished pure-FLC from nc-HCC. Major DNA methylation changes occurred outside promoters, mainly in gene bodies and intergenic regions located in the vicinity of liver developmental genes (i.e., <i>SMARCA4</i> and <i>RXRA</i>). Partially methylated domains were more prone to DNA methylation changes. Furthermore, we identified several putative tumor suppressor genes (e.g., <i>DLEU7</i>) and oncogenes (e.g., <i>DUSP4</i>). While ∼70% of identified gene promoters gaining methylation were marked by bivalent histone marks (H3K4me3/H3K27me3) in embryonic stem cells, ∼70% of those losing methylation were marked by H3K4me3. Finally, we established a pure FLC DNA methylation signature and validated it in an independent dataset. Our analysis reveals a distinct epigenetic signature of pure FLC as compared to nc-HCC, with DNA methylation changes occurring in the vicinity of liver developmental genes. These data suggest new options for targeting FLC based on cancer epigenome aberrations.