cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11376285
title: Supplementary Material for: Risk Stratification for Ischemic Cerebrovascular Events and Mortality among Intracerebral Hemorrhage Patients with and without Atrial Fibrillation: A Nationwide Cohort Study

description: <b><i>Background:</i></b> Intracerebral hemorrhage is a devastating clinical event, and secondary prevention is pivotal to avoid further cerebral complications, but no clear guidance exist for selecting high-risk patients. The CHA<sub>2</sub>DS<sub>2</sub>-VASc score is a widespread tool to assess the risk of stroke among patients with atrial fibrillation (AF). <b><i>Objectives:</i></b> We investigated the ability of the CHA<sub>2</sub>DS<sub>2</sub>-VASc score for estimating cerebrovascular ischemic events in patients with recent intracerebral hemorrhage with or without comorbid AF. <b><i>Methods:</i></b> Patients with a diagnosis of intracerebral hemorrhage between 2003 and 2018 were considered for inclusion. Four registries were linked to obtain individual-level information, and included patients were followed for the occurrence of cerebrovascular ischemic events and all-cause mortality. We report absolute risks at 5 years stratified by baseline CHA<sub>2</sub>DS<sub>2</sub>-VASc score and AF prevalence. <b><i>Results:</i></b> The study included 12,245 patients (46.4% females) of whom 19% had prevalent AF. Patients without AF were younger (mean age: 70 vs. 78 years) and had a lower CHA<sub>2</sub>DS<sub>2</sub>-VASc score (2.5 vs. 3.6). The overall 5-year risk of cerebrovascular ischemic events was 5.2% (95% CI 4.7–5.6) for patients without AF and 7.3% (95% CI 6.0–8.5) for AF patients; all-cause mortality was higher than 30 and 50% in patients without or with AF, respectively. The predictive performance of the CHA<sub>2</sub>DS<sub>2</sub>-VASc score was poor with c-statistics around 0.56 regardless of AF status. Among patients without AF, a score ≥6 was associated with a 7.0% risk of cerebrovascular ischemic events. In patients with AF, the associated risk was lowest for patients with a CHA<sub>2</sub>DS<sub>2</sub>-VASc score of 1 (4.1%) and highest among those with a score of 5 (11.9%). <b><i>Conclusion:</i></b> In this nationwide cohort of intracerebral hemorrhage patients with or without AF, the risk of cerebrovascular ischemic events and mortality was substantial. The CHA<sub>2</sub>DS<sub>2</sub>-VASc score may be used for the estimation of stroke risk in patients sustaining an intracerebral hemorrhage, although its discriminative performance was poor.
DOI: 10.6084/m9.figshare.11376048
title: Supplementary Material for: Molecular Barcode Sequencing for Highly Sensitive Detection of Circulating Tumor DNA in Patients with Esophageal Squamous Cell Carcinoma

description: <b><i>Introduction:</i></b>Next-generation sequencing (NGS) with molecular barcodes (MB) is a novel method that enables the highly sensitive detection of circulating tumor DNA (ctDNA) in a relatively wide range of genes. <b><i>Objective:</i></b>The aim of this study was to examine the utility of NGS with MB for detecting ctDNA in patients with esophageal squamous cell carcinoma (ESCC). <b><i>Methods:</i></b>Five patients with ESCC who underwent preoperative treatment followed by esophagectomy were examined. The frequency of <i>TP53</i> mutations in DNA extracted from tumor tissue and plasma at each time point during the treatment course was analyzed using NGS without MB. In 1 patient, additional analysis using NGS with MB was conducted to compare the sensitivities and to evaluate the clinical utility of this novel method. <b><i>Results:</i></b><i>TP53</i> mutations in tumor tissue were identified in 3 of 5 patients with ESCC. In 1 patient, the mutational allele frequency in plasma was 1.97% before preoperative treatment, and decreased to 0.09% after preoperative treatment. As the maximum frequency of background errors were 3.22% using NGS without MB and 0.08% with MB, which indicated that the sensitivity of ctDNA detection using NGS with MB was much higher than without MB. In 1 patient who had recurrence half a year after surgery, only NGS with MB could detect ctDNA even at 4 weeks after surgery, at a frequency of 0.20%. <b><i>Conclusions:</i></b>NGS with MB enabled comprehensive and highly sensitive detection of ctDNA in a patient with ESCC. This novel method may be useful for the clinical diagnosis of ESCC.
DOI: 10.6084/m9.figshare.11376051
title: Supplementary Material for: Expression of c-Met in Primary and Recurrent Hepatocellular Carcinoma

description: <b><i>Background:</i></b>The clinical course of hepatocellular carcinoma (HCC) is complicated, because it often recurs and shows multiple lesions, some of which progress to a more malignant form, shortening the life of the patient. The hepatocyte growth factor receptor c-Met has been shown to play an important role in the pathogenesis of HCC, but the influence of c-Met expression on the clinical course of HCC remains to be fully elucidated. <b><i>Methods:</i></b>We randomly selected and included 600 tumor specimens obtained from the primary and recurrent lesions of 319 HCC cases between 1995 and 2007. The expression of c-Met was determined by immunohistochemistry using archived formalin-fixed paraffin-embedded samples. We analyzed the correlation between c-Met expression and clinical parameters, including survival. In addition, we examined c-Met expression in the malignant transition of HCC in all cases including recurrent lesions. <b><i>Results:</i></b>Survival analysis using the multivariate Cox proportional-regression model revealed that the prognosis was significantly better in the primary cases with high c-Met expression than in those with low c-Met expression (hazard ratio 0.159, 95% confidence interval 0.065–0.391; <i>p</i> &lt; 0.001). During the course of recurrence, some cases with high c-Met expression returned to low c-Met expression. Among 40 cases with high c-Met expression, 29 survived more than 2 years after detecting the high c-Met expression. <b><i>Conclusion:</i></b>High expression of c-Met may be a prognostic factor for a good, rather than a poor, HCC prognosis. The involvement of c-Met expression in the malignant transition of recurrent HCC is obscure.
DOI: 10.6084/m9.figshare.11376048.v1
title: Supplementary Material for: Molecular Barcode Sequencing for Highly Sensitive Detection of Circulating Tumor DNA in Patients with Esophageal Squamous Cell Carcinoma

description: <b><i>Introduction:</i></b>Next-generation sequencing (NGS) with molecular barcodes (MB) is a novel method that enables the highly sensitive detection of circulating tumor DNA (ctDNA) in a relatively wide range of genes. <b><i>Objective:</i></b>The aim of this study was to examine the utility of NGS with MB for detecting ctDNA in patients with esophageal squamous cell carcinoma (ESCC). <b><i>Methods:</i></b>Five patients with ESCC who underwent preoperative treatment followed by esophagectomy were examined. The frequency of <i>TP53</i> mutations in DNA extracted from tumor tissue and plasma at each time point during the treatment course was analyzed using NGS without MB. In 1 patient, additional analysis using NGS with MB was conducted to compare the sensitivities and to evaluate the clinical utility of this novel method. <b><i>Results:</i></b><i>TP53</i> mutations in tumor tissue were identified in 3 of 5 patients with ESCC. In 1 patient, the mutational allele frequency in plasma was 1.97% before preoperative treatment, and decreased to 0.09% after preoperative treatment. As the maximum frequency of background errors were 3.22% using NGS without MB and 0.08% with MB, which indicated that the sensitivity of ctDNA detection using NGS with MB was much higher than without MB. In 1 patient who had recurrence half a year after surgery, only NGS with MB could detect ctDNA even at 4 weeks after surgery, at a frequency of 0.20%. <b><i>Conclusions:</i></b>NGS with MB enabled comprehensive and highly sensitive detection of ctDNA in a patient with ESCC. This novel method may be useful for the clinical diagnosis of ESCC.
DOI: 10.6084/m9.figshare.11376051.v1
title: Supplementary Material for: Expression of c-Met in Primary and Recurrent Hepatocellular Carcinoma

description: <b><i>Background:</i></b>The clinical course of hepatocellular carcinoma (HCC) is complicated, because it often recurs and shows multiple lesions, some of which progress to a more malignant form, shortening the life of the patient. The hepatocyte growth factor receptor c-Met has been shown to play an important role in the pathogenesis of HCC, but the influence of c-Met expression on the clinical course of HCC remains to be fully elucidated. <b><i>Methods:</i></b>We randomly selected and included 600 tumor specimens obtained from the primary and recurrent lesions of 319 HCC cases between 1995 and 2007. The expression of c-Met was determined by immunohistochemistry using archived formalin-fixed paraffin-embedded samples. We analyzed the correlation between c-Met expression and clinical parameters, including survival. In addition, we examined c-Met expression in the malignant transition of HCC in all cases including recurrent lesions. <b><i>Results:</i></b>Survival analysis using the multivariate Cox proportional-regression model revealed that the prognosis was significantly better in the primary cases with high c-Met expression than in those with low c-Met expression (hazard ratio 0.159, 95% confidence interval 0.065–0.391; <i>p</i> &lt; 0.001). During the course of recurrence, some cases with high c-Met expression returned to low c-Met expression. Among 40 cases with high c-Met expression, 29 survived more than 2 years after detecting the high c-Met expression. <b><i>Conclusion:</i></b>High expression of c-Met may be a prognostic factor for a good, rather than a poor, HCC prognosis. The involvement of c-Met expression in the malignant transition of recurrent HCC is obscure.
DOI: 10.6084/m9.figshare.11376015
title: MS data for "The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes"

description: Raw data for "The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes"
DOI: 10.6084/m9.figshare.11376015.v1
title: MS data for "The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes"

description: Raw data for "The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes"
DOI: 10.6084/m9.figshare.11375826
title: GNNWR Code and Simulated Data.zip

description: GNNWR Code and Simulated Data
DOI: 10.6084/m9.figshare.11375754
title: Simple stochastic simulation of time irreversible and reversible processes

description: As time irreversibility of streamflow is marked for time scales up to several days, while common stochastic generation methods are good only for time-symmetric processes, the need for new methods to handle irreversibility, particularly in flood simulations, has been recently highlighted. From an investigation of the historical evolution of existing stochastic generation methods, which is a useful step before proposing new methods, the strengths and weaknesses of current approaches are located. Following this investigation, a generic solution to the stochastic generation problem is proposed. This is an analytical exact method based on an asymmetric moving-average scheme, capable of handling time irreversibility in addition to preserving the second-order stochastic structure, as well as higher-order marginal statistics, of a process. The method is studied theoretically in its general setting, as well as in its most interesting special cases, and is successfully applied to streamflow generation at an hourly scale.
DOI: 10.6084/m9.figshare.11375754.v1
title: Simple stochastic simulation of time irreversible and reversible processes

description: As time irreversibility of streamflow is marked for time scales up to several days, while common stochastic generation methods are good only for time-symmetric processes, the need for new methods to handle irreversibility, particularly in flood simulations, has been recently highlighted. From an investigation of the historical evolution of existing stochastic generation methods, which is a useful step before proposing new methods, the strengths and weaknesses of current approaches are located. Following this investigation, a generic solution to the stochastic generation problem is proposed. This is an analytical exact method based on an asymmetric moving-average scheme, capable of handling time irreversibility in addition to preserving the second-order stochastic structure, as well as higher-order marginal statistics, of a process. The method is studied theoretically in its general setting, as well as in its most interesting special cases, and is successfully applied to streamflow generation at an hourly scale.
DOI: 10.6084/m9.figshare.11375694
title: Hypophysitis induced by immune checkpoint inhibitors: a 10-year assessment

description: <b>Introduction</b>: Hypophysitis caused by immune checkpoint inhibitors (ICIs) has risen to the medical attention during the past decade. ICIs are monoclonal antibodies that block the interaction between molecules that normally inhibit the function of effector T cells, ultimately increasing their ability to destroy cancer cells but also causing immune-related adverse events, such as hypophysitis. Ipilimumab, a CTLA-4 blocker, was the first ICI approved from the Food and Drug Administration for advanced melanoma patients in 2011. Several additional ICIs targeting CTLA-4, PD-1, or PD-L1 are now used in many clinical trials, making it important for physicians to recognize and treat hypophysitis adequately. <b>Areas covered</b>: This review will provide insights into the mechanisms of pituitary toxicity, highlight the complexity of clinical phenotypes of ICI hypophysitis, and offer practical recommendations. <b>Expert opinion</b>: ICI hypophysitis differs in many respects from primary hypophysitis, and also according to the type of ICI that caused it. Its pathogenesis remains unknown, although the expression of CTLA-4 and PD-1 on pituitary cells could play a role. The diagnosis is mainly clinical since there are no specific serological markers and MRI findings are subtle. The treatment is based on long-term hormone replacement and does not typically require discontinuation of immunotherapy
DOI: 10.6084/m9.figshare.11375736.v1
title: typhoon jgr

description: typhoon caused saltwater intrusion
DOI: 10.6084/m9.figshare.11375736.v2
title: typhoon jgr

description: typhoon caused saltwater intrusion
DOI: 10.6084/m9.figshare.11375655
title: Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

description: Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
DOI: 10.6084/m9.figshare.11375655.v1
title: Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue

description: Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
DOI: 10.6084/m9.figshare.11375736.v3
title: typhoon_wrr

description: typhoon caused saltwater intrusion
DOI: 10.6084/m9.figshare.11375580
title: MODIS

description: Derived MODIS data files containing NDVI, NPP, GPP, and EVI values for all 1218 USHCN sites used in the DroughtNet study. See the Ecology Letters publication or the "Code and documentation" repository in this Figshare collection for details on the source and processing of this data.<br>
DOI: 10.6084/m9.figshare.11375736.v4
title: typhoon_wrr

description: typhoon caused saltwater intrusion
DOI: 10.6084/m9.figshare.11375580.v1
title: MODIS

description: Derived MODIS data files containing NDVI, NPP, GPP, and EVI values for all 1218 USHCN sites used in the DroughtNet study. See the Ecology Letters publication or the "Code and documentation" repository in this Figshare collection for details on the source and processing of this data.<br>
DOI: 10.6084/m9.figshare.11375364
title: USHCN_derived

description: Derived USHCN data files containing long-term climate, climate indices, summary data, and calculated statistics. Raw data from the USHCN_raw dataset in this Figshare collection was processed and reduced in several ways using R code in the "Code and documentation repository" (droughtnet_precipsens_ecolets). The resulting derived data products are collected in files in this dataset.
DOI: 10.6084/m9.figshare.11375736.v5
title: typhoon_wrr

description: typhoon caused saltwater intrusion
DOI: 10.6084/m9.figshare.11375736.v6
title: typhoon

description: typhoon caused saltwater intrusion
DOI: 10.5281/zenodo.3999218
title: Diploid VCF files used for publication "Haplotype Threading: Accurate Polyploid Phasing from Long Reads"

description: Diploid VCF files for three human samples, from which polyploid datasets were generated as evaluation data for the publication given in the title. Files contain gold standard haplotypes, which have been conducted by trio phasing from the samples themselves and their respective parents.
description: Publication has been accepted for being published in Genome Biology in the near future. Therefore there is no proper reference yet.
DOI: 10.5281/zenodo.3999217
title: Diploid VCF files used for publication "Haplotype Threading: Accurate Polyploid Phasing from Long Reads"

description: Diploid VCF files for three human samples, from which polyploid datasets were generated as evaluation data for the publication given in the title. Files contain gold standard haplotypes, which have been conducted by trio phasing from the samples themselves and their respective parents.
description: Publication has been accepted for being published in Genome Biology in the near future. Therefore there is no proper reference yet.
DOI: 10.6084/m9.figshare.11374647
title: Supplementary Tables for submission JGR2019JB019238.zip

description: The zip. file includs four .xlsx files, which are Supplementary Tables for our submission JGR2019JB019238. We are glad the data could attract interest of researchers. Everyone should get our grant before using these data.
DOI: 10.6084/m9.figshare.11374572
title: Data001 .xlsx

description: Reproduce the heat transfer mechanism in metal under short pulse laser based on the fractional thermal wave model.
DOI: 10.6084/m9.figshare.11374647.v2
title: Supplementary Tables for submission JGR2019JB019238.zip

description: The zip. file includs four .xlsx files, which are Supplementary Tables for our submission JGR2019JB019238. We are glad the data could attract interest of researchers. Everyone should get our grant before using these data.
DOI: 10.6084/m9.figshare.11374461
title: Sample Data for Accelerated Longitudinal Design

description: These are sample data from three subjects who are from a primary, middle and high school, respectively. The data only contains neuroimaging samples including T1/T2/REST images.
DOI: 10.6084/m9.figshare.11374572.v1
title: Data001 .xlsx

description: Reproduce the heat transfer mechanism in metal under short pulse laser based on the fractional thermal wave model.
DOI: 10.6084/m9.figshare.11374455
title: Input Data for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media"

description: Input Data for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media". The dataset includes basic parameters for simulation, relative permeability and capillary pressure curves, and coordinates for 2D fracture and vug networks.
DOI: 10.6084/m9.figshare.11374458
title: Single Cell RNA-Seq data for Cancer Stem Like Reversal Project

description: scRNA-Seq data for the CSL reversal project.
DOI: 10.6084/m9.figshare.11374461.v1
title: Sample Data for Accelerated Longitudinal Design

description: These are sample data from three subjects who are from a primary, middle and high school, respectively. The data only contains neuroimaging samples including T1/T2/REST images.
DOI: 10.6084/m9.figshare.11374452
title: GCCAAT_S1_R1_001.fastq.gz

description: test data for nature protocol
DOI: 10.6084/m9.figshare.11374449
title: Dataset_Reproducibility

description: Dataset of CCT, Ishihara and Lanthony.
DOI: 10.6084/m9.figshare.11374452.v1
title: GCCAAT_S1_R1_001.fastq.gz

description: test data for nature protocol
DOI: 10.6084/m9.figshare.11374272
title: AA_hepatocyte_baseline_FastQTL_significant_exon_eQTL

description: column 1: snpidcolumn 2: chrcolumn 3: poscolumn 4: refcolumn 5: altcolumn 6: exon_idcolumn 7: exon_startcolumn 8: exon_end<br>column 9: betacolumn 10: p-value
DOI: 10.6084/m9.figshare.11374275
title: AA_hepatocyte_baseline_MatrixEQTL_significant_eQTLs

description: eQTL mapping summary statistics using 60 primary hepatocytes of AA ancestry with MatrixEQTL adjusting for sex, platform, batch, 1st PC and 10 PEER variables estimated from normalized expression values.<br>column 1: snpidcolumn 2: chrcolumn 3: poscolumn 4: refcolumn 5: altcolumn 6: geneidcolumn 7: betacolumn 8: t-statcolumn 9: p-value<br><br>
DOI: 10.6084/m9.figshare.11374272.v1
title: AA_hepatocyte_baseline_FastQTL_significant_exon_eQTL

description: column 1: snpidcolumn 2: chrcolumn 3: poscolumn 4: refcolumn 5: altcolumn 6: exon_idcolumn 7: exon_startcolumn 8: exon_end<br>column 9: betacolumn 10: p-value