cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1497885.v1
title: Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features

description: <b>Objective</b>: To study epigenetic alterations in fibrolamellar hepatocellular carcinoma (FLC) and establish an associated DNA methylation signature. <b>Design</b>: 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. <b>Results</b>: <i>LINE-1</i> methylation correlates with shorter recurrence-free survival and overall survival in resected pure-FLC patients. Unsupervised clustering using CG sites located in islands distinguishes 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 (ie, <i>SMARCA4, RXRA</i>). Partially methylated domains were the regions found to be more prone to DNA methylation changes. Furthermore, we identified several putative tumor suppressor genes (i.e. <i>DLEU7</i>) and oncogenes (i.e. <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 validate it in an independent dataset. <b>Conclusions</b>: Our analysis reveals 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.
DOI: 10.6084/m9.figshare.1497885.v3
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.
DOI: 10.6084/m9.figshare.1497885.v2
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.
DOI: 10.6084/m9.figshare.1501494
title: Biodegradation of Phenol from Wastewater by Microorganism Immobilized in Bentonite and Carboxymethyl Cellulose Gel

description: This study presents a microbial process for phenol degradation in coking wastewater. The optimum immobilized condition of the strain for degrading phenol was determined through orthogonal experiment. The free and immobilized microorganisms were examined for their capabilities on degrading phenol. Results indicated that the optimum immobilized conditions were 20% microorganism suspension, 5% bentonite, 3% sodium carboxymethyl cellulose content, and 1 h of crosslinking time. The biodegradation rate was optimized at 35°C and 0.23 gmL<sup>−1</sup> of immobilized microorganism bead. The degrading rate for the immobilized microorganism bead was up to 95.96% at an initial phenol concentration of 100 mgL<sup>−1</sup>; however, the immobilized microorganism considerably took more time (288 h) to reach 94.6% removal efficiency at a much higher concentration of 1000 mgL<sup>−1</sup>. The batch experiment demonstrated that 94.50% of phenol was removed using the beads with the immobilized microorganism at an initial concentration of 500 mgL<sup>−1</sup>. By contrast, only 24.60% and 33.88% of phenol were degraded using the gel beads without and with free microorganisms, respectively. The immobilized microorganism beads can used reused for up to nine cycles at the same initial phenol concentration (50 mgL<sup>−1</sup>) and can be stored up to 40 d without loss of its degradation capacity.
DOI: 10.6084/m9.figshare.1501494.v2
title: Biodegradation of Phenol from Wastewater by Microorganism Immobilized in Bentonite and Carboxymethyl Cellulose Gel

description: This study presents a microbial process for phenol degradation in coking wastewater. The optimum immobilized condition of the strain for degrading phenol was determined through orthogonal experiment. The free and immobilized microorganisms were examined for their capabilities on degrading phenol. Results indicated that the optimum immobilized conditions were 20% microorganism suspension, 5% bentonite, 3% sodium carboxymethyl cellulose content, and 1 h of crosslinking time. The biodegradation rate was optimized at 35°C and 0.23 gmL<sup>−1</sup> of immobilized microorganism bead. The degrading rate for the immobilized microorganism bead was up to 95.96% at an initial phenol concentration of 100 mgL<sup>−1</sup>; however, the immobilized microorganism considerably took more time (288 h) to reach 94.6% removal efficiency at a much higher concentration of 1000 mgL<sup>−1</sup>. The batch experiment demonstrated that 94.50% of phenol was removed using the beads with the immobilized microorganism at an initial concentration of 500 mgL<sup>−1</sup>. By contrast, only 24.60% and 33.88% of phenol were degraded using the gel beads without and with free microorganisms, respectively. The immobilized microorganism beads can used reused for up to nine cycles at the same initial phenol concentration (50 mgL<sup>−1</sup>) and can be stored up to 40 d without loss of its degradation capacity.
DOI: 10.6084/m9.figshare.1504087
title: Table 2. Heart functional recovery parameters by E2 and in presence of MEK1/2, PKC translocation and PI-3K inhibitors in WT mice.

description: Cardiac functional parameters in WT male mice. Left ventricular systolic pressure (LVSP); left ventricular end-diastolic pressure (LVEDP); left ventricular developed pressure (LVDP) and heart rate (HR) before ischemia (Basal) and at different times of reperfusion after I/R in control, E2-treated, and E2+Inhibitors (U0126, LY294002 and CC: chelerythrine chloride). Values are mean±SEM. * P&lt;0.05 control versus E2 group (n=6-7/ group); + P&lt;0.05 E2+CC versus E2 group (n=4-6/ group); and # P&lt;0.05 E2+U0126 versus E2 group (n=4-6 hearts/ group).
DOI: 10.6084/m9.figshare.1504087.v1
title: Table 2. Heart functional recovery parameters by E2 and in presence of MEK1/2, PKC translocation and PI-3K inhibitors in WT mice.

description: Cardiac functional parameters in WT male mice. Left ventricular systolic pressure (LVSP); left ventricular end-diastolic pressure (LVEDP); left ventricular developed pressure (LVDP) and heart rate (HR) before ischemia (Basal) and at different times of reperfusion after I/R in control, E2-treated, and E2+Inhibitors (U0126, LY294002 and CC: chelerythrine chloride). Values are mean±SEM. * P&lt;0.05 control versus E2 group (n=6-7/ group); + P&lt;0.05 E2+CC versus E2 group (n=4-6/ group); and # P&lt;0.05 E2+U0126 versus E2 group (n=4-6 hearts/ group).
DOI: 10.6084/m9.figshare.1504089
title: Table 1. Heart recovery parameters by E2 in WT, Esr1-/-, Esr2-/- and Gper1-/-

description: Cardiac functional parameters, left ventricular systolic pressure (LVSP); left ventricular end-diastolic pressure (LVEDP); left ventricular developed pressure (LVDP) and heart rate (HR) before ischemia (Basal) and at different times of reperfusion after ischemia with and without E2 treatment in WT, Esr1-/-, Esr2-/- and Gper1. Values are mean±SEM.; * P&lt;0.05 WT-control versus WT+E2-treated group (n=4-6 hearts/ group). # P&lt;0.05 Esr2-/--control versus Esr1-/-+E2-treated group (n=4-6 hearts/ group), + P&lt;0.05 Esr2-/--control versus Esr2-/-+E2-treated group (n=4-6 hearts/ group).
DOI: 10.6084/m9.figshare.1504089.v1
title: Table 1. Heart recovery parameters by E2 in WT, Esr1-/-, Esr2-/- and Gper1-/-

description: Cardiac functional parameters, left ventricular systolic pressure (LVSP); left ventricular end-diastolic pressure (LVEDP); left ventricular developed pressure (LVDP) and heart rate (HR) before ischemia (Basal) and at different times of reperfusion after ischemia with and without E2 treatment in WT, Esr1-/-, Esr2-/- and Gper1. Values are mean±SEM.; * P&lt;0.05 WT-control versus WT+E2-treated group (n=4-6 hearts/ group). # P&lt;0.05 Esr2-/--control versus Esr1-/-+E2-treated group (n=4-6 hearts/ group), + P&lt;0.05 Esr2-/--control versus Esr2-/-+E2-treated group (n=4-6 hearts/ group).
DOI: 10.6084/m9.figshare.1506863
title: Mitochondrial Calcium Retention Capacity

description: Gper1 activation is required for E2-mediated increase in mitochondrial Ca2+ retention capacity.
DOI: 10.6084/m9.figshare.1506863.v1
title: Mitochondrial Calcium Retention Capacity

description: Gper1 activation is required for E2-mediated increase in mitochondrial Ca2+ retention capacity.
DOI: 10.6084/m9.figshare.1506864
title: ERs transcripts

description: Gper1 mRNAs are the most abundant ER transcripts in male mouse ventricle.
DOI: 10.6084/m9.figshare.1506864.v1
title: ERs transcripts

description: Gper1 mRNAs are the most abundant ER transcripts in male mouse ventricle.
DOI: 10.6084/m9.figshare.1506865
title: Myocardial Infaction analysis

description: We also examined whether Gper1 expression is required for acute E2-induced improvement of heart viability by determining the myocardial infarct size in sham or hearts subjected to I/R. 3A. Hearts were sectioned and analyzed at the end of the perfusion  or reperfusion periods. As expected, acute E2 treatment reduced myocardial infarct size significantly in WT animals. Supporting the functional data, acute E2 treatment had the same protective action (as in the WT animals) when hearts from Esr1and Esr2 knockouts were used  but lost its protective effect in the absence of Gper1 as hearts from Gper1-/- animals displayed a robust infarcted area regardless of E2 treatment.
DOI: 10.6084/m9.figshare.1506865.v1
title: Myocardial Infaction analysis

description: We also examined whether Gper1 expression is required for acute E2-induced improvement of heart viability by determining the myocardial infarct size in sham or hearts subjected to I/R. 3A. Hearts were sectioned and analyzed at the end of the perfusion  or reperfusion periods. As expected, acute E2 treatment reduced myocardial infarct size significantly in WT animals. Supporting the functional data, acute E2 treatment had the same protective action (as in the WT animals) when hearts from Esr1and Esr2 knockouts were used  but lost its protective effect in the absence of Gper1 as hearts from Gper1-/- animals displayed a robust infarcted area regardless of E2 treatment.
DOI: 10.6084/m9.figshare.1506866
title: ER Western Analysis

description: E2 triggers ERK1/2 and Akt parallel pathways but only ERK1/2 pathway converges on GSK-3β.
DOI: 10.6084/m9.figshare.1506866.v1
title: ER Western Analysis

description: E2 triggers ERK1/2 and Akt parallel pathways but only ERK1/2 pathway converges on GSK-3β.
DOI: 10.6084/m9.figshare.1506867
title: Heart Function

description: Gper1-but not Esr1 nor Esr2- activation is essential for acute E2-mediated heart protection from ischemic/reperfusion (I/R) injury.
DOI: 10.6084/m9.figshare.1506868
title: ERs-Western Blot Analysis

description: Signaling mechanisms involved in E2-mediated Gper1 activation: role of Akt, ERK1/2and GSK-3β phosphorylation.
DOI: 10.6084/m9.figshare.1506868.v1
title: ERs-Western Blot Analysis

description: Signaling mechanisms involved in E2-mediated Gper1 activation: role of Akt, ERK1/2and GSK-3β phosphorylation.
DOI: 10.6084/m9.figshare.1509877
title: OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

description: We've included here the scripts of OTG-snpcaller, which was published previously (DOI:10.1371/journal.pone.0097507).
DOI: 10.6084/m9.figshare.1509877.v1
title: OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data

description: We've included here the scripts of OTG-snpcaller, which was published previously (DOI:10.1371/journal.pone.0097507).
DOI: 10.6084/m9.figshare.1512409
title: brainTumorDataPublic_1-766.zip

description: The first part of the whole dataset including file numbers from 1 to 766. The whole dataset contains 3064 slices.
DOI: 10.6084/m9.figshare.1512413
title: brainTumorDataPublic_1533-2298.zip

description: The third part of the whole dataset including file numbers from 1533 to 2298. The whole dataset contains 3064 slices.
DOI: 10.6084/m9.figshare.1512413.v1
title: brainTumorDataPublic_1533-2298.zip

description: The third part of the whole dataset including file numbers from 1533 to 2298. The whole dataset contains 3064 slices.
DOI: 10.6084/m9.figshare.1512414
title: brainTumorDataPublic_767-1532.zip

description: The second part of the whole dataset including file numbers from 767 to 1532. The whole dataset contains 3064 slices.
DOI: 10.6084/m9.figshare.1512415
title: brainTumorDataPublic_2299-3064.zip

description: The fourth part of the whole dataset including file numbers from 2299 to 3064. The whole dataset contains 3064 slices.
DOI: 10.6084/m9.figshare.1512426
title: readme

description: a readme file to describe dataset features.
DOI: 10.6084/m9.figshare.1533283
title: The effects of Twitter sentiment on stock price returns

description: The data files consist of the DJIA30 financial data (daily prices) and Twitter sentiment data (the number of negative, neutral and positive tweets) for the period of June 1, 2013 until September 18, 2014. The data analysis is described in the following paper: G. Ranco, D. Aleksovski, G. Caldarelli, M. Grčar, I. Mozetič, The effects of Twitter sentiment on stock price returns, PLoS ONE 10(9): e0138441, http://dx.doi.org/10.1371/journal.pone.0138441, 2015.
DOI: 10.6084/m9.figshare.1540066
title: origin software data

description: Fig 1 Effect of dietary vitamin A supplemental levels(0, 1500, 6000, and 12000 IU/kg) on the serum IgA concentration
Fig 2 Effect of dietary vitamin A supplemental levels on the mucin and IgA concentrations in BALF
Fig 4 Effect of the dietary vitamin A supplemental levels on the IgA (A), MUC2 (B), and MUC5AC (C) mRNA expression levels in the trachea and lung tissue
Fig 5 Effect of the dietary vitamin A supplemental levels on the TNF-α (A), IL-6 (B), IL-13 (C), TGF-α (D), TGF-β (E), and EGFR (F) mRNA expression levels in the trachea and lung tissue
DOI: 10.6084/m9.figshare.1540066.v1
title: origin software data

description: Fig 1 Effect of dietary vitamin A supplemental levels(0, 1500, 6000, and 12000 IU/kg) on the serum IgA concentration
Fig 2 Effect of dietary vitamin A supplemental levels on the mucin and IgA concentrations in BALF
Fig 4 Effect of the dietary vitamin A supplemental levels on the IgA (A), MUC2 (B), and MUC5AC (C) mRNA expression levels in the trachea and lung tissue
Fig 5 Effect of the dietary vitamin A supplemental levels on the TNF-α (A), IL-6 (B), IL-13 (C), TGF-α (D), TGF-β (E), and EGFR (F) mRNA expression levels in the trachea and lung tissue
DOI: 10.6084/m9.figshare.1548193
title: Are Structural Changes Induced By Lithium In The HIV Brain Accompanied By Changes In Functional Connectivity?

description: Data underlying the findings described in
"Are Structural Changes Induced By Lithium In The HIV Brain Accompanied By Changes In Functional Connectivity?" published in PLOSOne.
The set includes raw fMRI data and gPDC results.
DOI: 10.6084/m9.figshare.1562452
title: Association of SNPs in EGR3 and ARC with Schizophrenia Supports a Biological Pathway for Schizophrenia Risk

description: Genotyping ped/map files & metadata.
DOI: 10.6084/m9.figshare.1568096
title: Neoarchaean quartz diorites in the Jiefangyingzi area, Central Asian Orogenic Belt: geological and tectonic significance

description: Quartz diorite intrusions in the Jiefangyingzi area associated with deformed Palaeozoic rocks of the Palaeozoic Bainaimiao arc magmatic belt on the northern margin of the North China Craton (NCC) were studied to determine their age, chemical composition, and isotopic characteristics. U–Pb dating of magmatic zircons indicates that the quartz diorites formed in Neoarchaean time between 2502.6 ± 9.1 Ma and 2551 ± 7.3 Ma. The quartz diorites have high Al<sub>2</sub>O<sub>3</sub> and low K<sub>2</sub>O contents, A/CNK = 0.75–0.97, and belong to the low-K tholeiitic series. The quartz diorites are enriched in light rare earth elements (LREEs) with high (La/Yb)<sub>N</sub> ratios and exhibit weak positive or no Eu anomalies, characteristics of high-alumina tonalite–trondhjemite–granodiorite (TTG) igneous rocks. Zircon <i>ε</i><sub>Hf</sub>(<i>t</i>) value for the quartz diorites ranges from +1.6 to +8.7, and the two-stage Hf-depleted mantle model age (T<sub>DM</sub>) ranges from 2705 to 2744 Ma, suggesting that the quartz diorite was derived from melting juvenile Neoarchaean crust formed from partial melting of the mantle at 2.7 Ga. Amphibolite xenoliths have low REE concentrations and are moderately depleted in LREE with (La/Yb)<sub>N</sub> ratios of 0.46–1.09. The trace element characteristics of the amphibolites are consistent with a mid-ocean-ridge basalt (MORB)-like protolith. This is the first time that Archaean rocks have been identified in the Bainaimiao arc magmatic belt and the age and nature of Jiefangyingzi quartz diorites suggest that they belonged to the NCC. The Early Palaeozoic Bainaimiao arc thus appears to represent an Andean-type continental arc on the northern margin of the NCC.
DOI: 10.6084/m9.figshare.1568096.v1
title: Neoarchaean quartz diorites in the Jiefangyingzi area, Central Asian Orogenic Belt: geological and tectonic significance

description: Quartz diorite intrusions in the Jiefangyingzi area associated with deformed Palaeozoic rocks of the Palaeozoic Bainaimiao arc magmatic belt on the northern margin of the North China Craton (NCC) were studied to determine their age, chemical composition, and isotopic characteristics. U–Pb dating of magmatic zircons indicates that the quartz diorites formed in Neoarchaean time between 2502.6 ± 9.1 Ma and 2551 ± 7.3 Ma. The quartz diorites have high Al<sub>2</sub>O<sub>3</sub> and low K<sub>2</sub>O contents, A/CNK = 0.75–0.97, and belong to the low-K tholeiitic series. The quartz diorites are enriched in light rare earth elements (LREEs) with high (La/Yb)<sub>N</sub> ratios and exhibit weak positive or no Eu anomalies, characteristics of high-alumina tonalite–trondhjemite–granodiorite (TTG) igneous rocks. Zircon <i>ε</i><sub>Hf</sub>(<i>t</i>) value for the quartz diorites ranges from +1.6 to +8.7, and the two-stage Hf-depleted mantle model age (T<sub>DM</sub>) ranges from 2705 to 2744 Ma, suggesting that the quartz diorite was derived from melting juvenile Neoarchaean crust formed from partial melting of the mantle at 2.7 Ga. Amphibolite xenoliths have low REE concentrations and are moderately depleted in LREE with (La/Yb)<sub>N</sub> ratios of 0.46–1.09. The trace element characteristics of the amphibolites are consistent with a mid-ocean-ridge basalt (MORB)-like protolith. This is the first time that Archaean rocks have been identified in the Bainaimiao arc magmatic belt and the age and nature of Jiefangyingzi quartz diorites suggest that they belonged to the NCC. The Early Palaeozoic Bainaimiao arc thus appears to represent an Andean-type continental arc on the northern margin of the NCC.