cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1482037.v2
title: The Zn(II)2Cys6 putative transcription factor is involved in the regulation of leucinostatin production and pathogenicity of the nematophagous fungus <i>Paecilomyces lilacinus</i>

description: Zn(II)2Cys6 transcription factor genes encode transcription regulators that manage the infection potential and production of secondary metabolites such as toxins in fungi. In this study, a gene named <i>rolP</i> that encodes a putative Zn(II)2Cys6 transcription factor regulating leucinostatin production in the ﬁlamentous fungus <i>Paecilomyces lilacinus</i> was characterized by a gene knockout approach. The deduced proprotein consists of 705 amino acids and is highly homologous to the Zn(II)2Cys6 transcription factor of the entomopathogenic fungus <i>Metarhizium brunneum</i>. Predictive analysis of the secondary structure of the proportion showed that it has two domains. <i>Paecilomyces lilacinus</i> can produce nematotoxins leucinostatins A and B. Deletion of <i>rolP</i> from the <i>P. lilacinus</i> wild-type strain Pl36-1 leads to the absence of leucinostatin A, while a large increase in the leucinostatin A level was achieved in the <i>rolP</i> overexpression strain Ov-Pl36-1. During the process of nematode infection, <i>rolP</i> showed high expression levels at 48–72 h and peaked at 48 h. Bioassay tests confirmed the requirement of <i>rolP</i> for leucinostatin production. However, the root-knot second-stage juvenile-toxicity was minimized to 35.3% in Δ<i>rolP</i>; toxicity was 97.2% with Ov-Pl36-1 compared with 68.4% with the wild type strain Pl36-1. Interestingly, neither knockout nor overexpression of the <i>rolP</i> gene affected the growth or sporulation of <i>P. lilacinus</i>. Additionally, fungal nutrition and acidic media might stimulate the <i>rolP</i> activity of the wild type strain against nematodes. These findings suggested that the <i>rolP</i> gene is required for the induction and production of leucinostatins and is considered a leucinostatin regulatory gene in <i>P. lilacinus</i>.
DOI: 10.6084/m9.figshare.1483478
title: Controlled Vocabularies for Scientific Data: Users and Desired Functionalities

description: The data was collected through a web survey conducted by the Metadata Research Center at UNC-Chapel Hill (now at Drexel). The survey link was distributed to the DataNet community. The web survey targeted DataNet partners affiliated with DataONE (Data Observation Network for Earth), DFC, SEAD (Sustainable Environment Actionable Data), and TerraPop (Terra Populus). Scientists, curators, administrators, and repository developers who were involved in the deposit or management of scientific research data in repositories could participate in this study. The survey was open for response from May 17, 2013 to July 15, 2013. In total, there were 243 participants involved in the survey who answered questions about their duties, usage of data repositories and controlled vocabularies, and future desired tools of controlled vocabularies.
DOI: 10.6084/m9.figshare.1483478.v1
title: Controlled Vocabularies for Scientific Data: Users and Desired Functionalities

description: The data was collected through a web survey conducted by the Metadata Research Center at UNC-Chapel Hill (now at Drexel). The survey link was distributed to the DataNet community. The web survey targeted DataNet partners affiliated with DataONE (Data Observation Network for Earth), DFC, SEAD (Sustainable Environment Actionable Data), and TerraPop (Terra Populus). Scientists, curators, administrators, and repository developers who were involved in the deposit or management of scientific research data in repositories could participate in this study. The survey was open for response from May 17, 2013 to July 15, 2013. In total, there were 243 participants involved in the survey who answered questions about their duties, usage of data repositories and controlled vocabularies, and future desired tools of controlled vocabularies.
DOI: 10.6084/m9.figshare.1485315.v1
title: Characterization of CpG sites that escape methylation on the inactive human X-chromosome

description: In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming <i>de novo</i> methylated. To test this, we treated four female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from <i>de novo</i> methylation on the Xi.
DOI: 10.6084/m9.figshare.1485315
title: Characterization of CpG sites that escape methylation on the inactive human X-chromosome

description: In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming <i>de novo</i> methylated. To test this, we treated 4 female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from <i>de novo</i> methylation on the Xi.
DOI: 10.6084/m9.figshare.1485315.v2
title: Characterization of CpG sites that escape methylation on the inactive human X-chromosome

description: In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming <i>de novo</i> methylated. To test this, we treated 4 female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from <i>de novo</i> methylation on the Xi.
DOI: 10.6084/m9.figshare.1485315.v4
title: Characterization of CpG sites that escape methylation on the inactive human X-chromosome

description: In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming <i>de novo</i> methylated. To test this, we treated 4 female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from <i>de novo</i> methylation on the Xi.
DOI: 10.6084/m9.figshare.1485315.v3
title: Characterization of CpG sites that escape methylation on the inactive human X-chromosome

description: In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming <i>de novo</i> methylated. To test this, we treated 4 female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from <i>de novo</i> methylation on the Xi.
DOI: 10.6084/m9.figshare.1486462
title: RAPTT: An Exact Two-Sample Test in High Dimensions Using Random Projections

description: In high dimensions, the classical Hotelling’s <i>T</i><sup>2</sup> test tends to have low power or becomes undefined due to singularity of the sample covariance matrix. In this article, this problem is overcome by projecting the data matrix onto lower dimensional subspaces through multiplication by random matrices. We propose RAPTT (RAndom Projection T<sup>2</sup>-Test), an exact test for equality of means of two normal populations based on projected lower dimensional data. RAPTT does not require any constraints on the dimension of the data or the sample size. A simulation study indicates that in high dimensions the power of this test is often greater than that of competing tests. The advantages of RAPTT are illustrated on a high-dimensional gene expression dataset involving the discrimination of tumor and normal colon tissues.
DOI: 10.6084/m9.figshare.1486462.v1
title: RAPTT: An Exact Two-Sample Test in High Dimensions Using Random Projections

description: In high dimensions, the classical Hotelling’s <i>T</i><sup>2</sup> test tends to have low power or becomes undefined due to singularity of the sample covariance matrix. In this article, this problem is overcome by projecting the data matrix onto lower dimensional subspaces through multiplication by random matrices. We propose RAPTT (RAndom Projection T<sup>2</sup>-Test), an exact test for equality of means of two normal populations based on projected lower dimensional data. RAPTT does not require any constraints on the dimension of the data or the sample size. A simulation study indicates that in high dimensions the power of this test is often greater than that of competing tests. The advantages of RAPTT are illustrated on a high-dimensional gene expression dataset involving the discrimination of tumor and normal colon tissues.
DOI: 10.6084/m9.figshare.1488640
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.v1
title: Stratigraphic records of the dynamic uplift of the Emeishan large igneous province

description: ABSTRACTFluid 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.v2
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.v4
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.v5
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.