cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7376090
title: Occurrence and characterization of lipofuscin and ceroid in human atherosclerotic plaque

description: Atherosclerotic plaque formation starts early in life, develops silently over decades, and often displays clear evidence of accelerated biological aging. Lipofuscin has been classically defined as “the most consistent and phylogenetically conserved cellular morphologic change of aging,” however, despite this traditional view different lines of evidence have recently demonstrated that, besides aging, various noxious influences can engeder its accumulation in cells and also that specific experimental conditions can revert this effect. Lipofuscin has been also proven to interact with disease-related factors to enhance cell loss. Along with lipofuscin, ceroid, another autofluorescent lipopigment usually produced under various pathological conditions unrelated to aging, has been suggested to jeopardize cell performance and viability by inducing membrane fragility, mitochondrial dysfunction, DNA damage, and oxidative stress-induced apoptosis. With regard to atherosclerosis, very few investigations have been conducted to assess whether a link could exist between lipofuscin/ceroid accumulation and the progression of the disease and no information still exist regarding the anatomy and the ultrastructural diversification of lipofuscin and ceroid in the lesional vascular tissue. At the same time, data concerning their potential toxicity at the cellular level are fragmentary, dated, and scarce. The present study investigates the occurrence and distribution of lipofuscin and ceroid in human atherosclerotic plaque and adjacent healthy tissues and analyzes the ultrastructural changes associated with their accumulation within the cell.
DOI: 10.6084/m9.figshare.7376090.v1
title: Occurrence and characterization of lipofuscin and ceroid in human atherosclerotic plaque

description: Atherosclerotic plaque formation starts early in life, develops silently over decades, and often displays clear evidence of accelerated biological aging. Lipofuscin has been classically defined as “the most consistent and phylogenetically conserved cellular morphologic change of aging,” however, despite this traditional view different lines of evidence have recently demonstrated that, besides aging, various noxious influences can engeder its accumulation in cells and also that specific experimental conditions can revert this effect. Lipofuscin has been also proven to interact with disease-related factors to enhance cell loss. Along with lipofuscin, ceroid, another autofluorescent lipopigment usually produced under various pathological conditions unrelated to aging, has been suggested to jeopardize cell performance and viability by inducing membrane fragility, mitochondrial dysfunction, DNA damage, and oxidative stress-induced apoptosis. With regard to atherosclerosis, very few investigations have been conducted to assess whether a link could exist between lipofuscin/ceroid accumulation and the progression of the disease and no information still exist regarding the anatomy and the ultrastructural diversification of lipofuscin and ceroid in the lesional vascular tissue. At the same time, data concerning their potential toxicity at the cellular level are fragmentary, dated, and scarce. The present study investigates the occurrence and distribution of lipofuscin and ceroid in human atherosclerotic plaque and adjacent healthy tissues and analyzes the ultrastructural changes associated with their accumulation within the cell.
DOI: 10.7284/129913
title: GNSS (Global Navigation Satellite System) data collected during research cruise OC1802B using a Ashtech ADU5 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376069
title: Supplementary Material for: Itraconazole Attenuates Peritoneal Fibrosis Through Its Effect on the Sonic Hedgehog Signaling Pathway in Mice

description: <b><i>Background:</i></b> Peritoneal fibrosis is a devastating complication of peritoneal dialysis. However, its precise mechanism is unclear, and specific treatments have not yet been established. Recent evidence suggests that the sonic hedgehog (SHH) signaling pathway is involved in tissue fibrogenesis. Drugs that inhibit this pathway are emerging in the field of anti-fibrosis therapy. Itraconazole, an anti-fungal agent, was also recently recognized as an inhibitor of the SHH signaling pathway. In this study, we used a mouse model to investigate whether the SHH signaling pathway is involved in the development of peritoneal fibrosis and the effects of itraconazole on peritoneal fibrosis. <b><i>Methods:</i></b> Peritoneal fibrosis was induced by intraperitoneal (IP) injection of 0.1% chlorhexidine gluconate (CG) solution every other day for 4 weeks, with or without itraconazole treatment (20 mg/kg, IP injection on a daily basis). Male C57BL/6 mice were divided into 4 groups: saline group, saline plus itraconazole group, CG group, and CG plus itraconazole group. Isotonic saline was administered intraperitoneally to the control group. The peritoneal tissues were evaluated for histological changes, expression of fibrosis markers, and the main components of the SHH signaling pathway. <b><i>Results:</i></b> Peritoneal thickening was evident in the CG group and was significantly decreased by itraconazole administration (80.4 ± 7.7 vs. 28.2 ± 3.8 µm, <i>p</i> &lt; 0.001). The expression of the following SHH signaling pathway components was upregulated in the CG group and suppressed by itraconazole treatment: SHH, patched, smoothened, and glioma-associated oncogene transcription factor 1. The IP injection of CG solution increased the expression of fibrosis markers such as α-smooth muscle actin and transforming growth factor-β1 in the peritoneal tissues. Itraconazole treatment significantly decreased the expression of these markers. <b><i>Conclusion:</i></b> Our study provides the first evidence that the SHH signaling pathway may be implicated in peritoneal fibrosis. It also demonstrates that itraconazole treatment has protective effects on peritoneal fibrosis through the regulation of the SHH signaling pathway. These findings suggest that blockage of the SHH signaling pathway is a potential therapeutic strategy for peritoneal fibrosis.
DOI: 10.7284/129900
title: Gyrocompass data collected during research cruise OC1802B using a Sperry MK-37 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376057
title: Supplementary Material for: Antibodies against M-Type Phospholipase A2 Receptor May Predict Treatment Response and Outcome in Membranous Nephropathy

description: <b><i>Background:</i></b> Anti-phospholipase A<sub>2</sub> receptor (PLA2R) antibodies are specific to the diagnosis of primary membranous nephropathy (pMN). The prevalence of positive antibodies varies among different cohorts. Still there is discrepancy in regard to the association between antibody levels and clinical courses, and the prognostic value of antibodies to treatment responses and kidney outcomes. <b><i>Methods:</i></b> Three hundred fifty-nine consecutive kidney biopsy-proven pMN patients were enrolled. Anti-PLA2R antibodies were detected by immunofluorescence assay (IFA) and enzyme-linked immunosorbent assay (ELISA). <b><i>Results:</i></b> The positive rate of anti-PLA2R antibodies in pMN was 65.2% (234/359) by IFA and 56.3% (202/359) by ELISA. The antibody level presented positive correlation with urinary protein excretion (r = 0.164, <i>p</i> = 0.002). Detectable antibodies and a higher level of proteinuria were independent risk factors to no-remission after treatments (OR 3.15, <i>p</i> = 0.004; OR 1.11, <i>p</i> = 0.006) and were independent risk factors to no-spontaneous remission (OR 2.20, <i>p</i> = 0.011; OR 1.36, <i>p</i> &lt; 0.001). A higher level of antibodies (hazard ratio 1.002, <i>p</i> = 0.019) was the independent risk factor to kidney dysfunction during follow-up. The antibodies turned negative in 42 out of 52 (80.8%) patients who achieved clinical remission, while they remained positive in all patients of the no-response category (<i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> We documented correlations between anti-PLA2R antibody levels and clinical severity in this large Chinese pMN cohort. Antibody positivity and higher antibody level might predict treatment responses and kidney outcomes of pMN.
DOI: 10.7284/129901
title: PTU (Pressure, Temperature, Humidity) data collected during research cruise OC1802B using a Vaisala PTU300 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376057.v1
title: Supplementary Material for: Antibodies against M-Type Phospholipase A2 Receptor May Predict Treatment Response and Outcome in Membranous Nephropathy

description: <b><i>Background:</i></b> Anti-phospholipase A<sub>2</sub> receptor (PLA2R) antibodies are specific to the diagnosis of primary membranous nephropathy (pMN). The prevalence of positive antibodies varies among different cohorts. Still there is discrepancy in regard to the association between antibody levels and clinical courses, and the prognostic value of antibodies to treatment responses and kidney outcomes. <b><i>Methods:</i></b> Three hundred fifty-nine consecutive kidney biopsy-proven pMN patients were enrolled. Anti-PLA2R antibodies were detected by immunofluorescence assay (IFA) and enzyme-linked immunosorbent assay (ELISA). <b><i>Results:</i></b> The positive rate of anti-PLA2R antibodies in pMN was 65.2% (234/359) by IFA and 56.3% (202/359) by ELISA. The antibody level presented positive correlation with urinary protein excretion (r = 0.164, <i>p</i> = 0.002). Detectable antibodies and a higher level of proteinuria were independent risk factors to no-remission after treatments (OR 3.15, <i>p</i> = 0.004; OR 1.11, <i>p</i> = 0.006) and were independent risk factors to no-spontaneous remission (OR 2.20, <i>p</i> = 0.011; OR 1.36, <i>p</i> &lt; 0.001). A higher level of antibodies (hazard ratio 1.002, <i>p</i> = 0.019) was the independent risk factor to kidney dysfunction during follow-up. The antibodies turned negative in 42 out of 52 (80.8%) patients who achieved clinical remission, while they remained positive in all patients of the no-response category (<i>p</i> &lt; 0.001). <b><i>Conclusion:</i></b> We documented correlations between anti-PLA2R antibody levels and clinical severity in this large Chinese pMN cohort. Antibody positivity and higher antibody level might predict treatment responses and kidney outcomes of pMN.
DOI: 10.7284/129904
title: Radiometer data collected during research cruise OC1802B using a RMR Co. PRP instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376048
title: Gene expression data for trophoblast development in the horse

description: This dataset contains two <b>.xlsx</b> Excel spreadsheets holding gene expression analysis data for equine chorionic girdle trophoblast cells from matched mare and stallion pairs.<br>The related study identified genes and signalling pathways in vivo, in a 7-day window, obtaining placental tissue between days 27 and 34 of pregnancy from matched mare and stallion pairs. Whole transcriptome profiling was used to measure and compare gene expression in chorionic girdle trophoblast and adjacent regressing chorion at pregnancy day 27 (initiation of proliferation and prior to differentiation), day 30 (initiation of differentiation), day 31 (consolidation of differentiation and movement of cells) and day 34 (when the majority of the trophoblast cells have terminally differentiated into binucleate eCG-secreting trophoblast and have started to obtain invasive qualities and immunomodulatory capacities). Differentially-expressed genes were then identified to determine functions and signalling pathways whose activity was modulated over this critical period of trophoblast development. A selection of genes and pathways were subsequently validated.<br><br>The late implantation of the equine conceptus offers unique accessibility opportunities for the study of cellular processes around trophoblast development into placental cells. These cellular processes are difficult to study in humans due to the limited availability of tissues at key consecutive developmental stages, but the processes are similar across mammalian species (despite differences in the final anatomical structure).<br><br>Data were analysed using R packages limma and maSigPro, Ingenuity Pathway Analysis and DAVID and verified using qRT-PCR, promoter analysis, western blotting and migration assays<br><br><b>Supplementary Table 3.xlsx:</b> lists all differentially-expressed genes across tissues and gestation <br><br>Each row reports <b>Probe name, Gene name, Gene Symbol, Systematic Name, Gene Description</b> and differential expression in terms of False Discovery Rate (FDR)-adjusted <i>p</i>-values and Absolute log fold changes for the comparisons across days 27-34 and tissues CH: chorion and CG: chorionic girdle. e.g. CH_27vsCG_27_LogFC - Log Fold change in chorion versus chorionic girdle at 27 days.<br><br><b>Supplementary Table 4.xlsx:</b> lists genes that clustered together with similar expression across tissue and time. <br><br>Each row reports <b>Probe ID, Gene Symbol, Gene Name, GenBank ID, R</b><sup>2 </sup>and <b>p-value</b>. <br><br>The related array data can be found in the NCBI Gene Expression Omnibus (GSE113072)
DOI: 10.6084/m9.figshare.7376048.v1
title: Gene expression data for trophoblast development in the horse

description: This dataset contains two <b>.xlsx</b> Excel spreadsheets holding gene expression analysis data for equine chorionic girdle trophoblast cells from matched mare and stallion pairs.<br>The related study identified genes and signalling pathways in vivo, in a 7-day window, obtaining placental tissue between days 27 and 34 of pregnancy from matched mare and stallion pairs. Whole transcriptome profiling was used to measure and compare gene expression in chorionic girdle trophoblast and adjacent regressing chorion at pregnancy day 27 (initiation of proliferation and prior to differentiation), day 30 (initiation of differentiation), day 31 (consolidation of differentiation and movement of cells) and day 34 (when the majority of the trophoblast cells have terminally differentiated into binucleate eCG-secreting trophoblast and have started to obtain invasive qualities and immunomodulatory capacities). Differentially-expressed genes were then identified to determine functions and signalling pathways whose activity was modulated over this critical period of trophoblast development. A selection of genes and pathways were subsequently validated.<br><br>The late implantation of the equine conceptus offers unique accessibility opportunities for the study of cellular processes around trophoblast development into placental cells. These cellular processes are difficult to study in humans due to the limited availability of tissues at key consecutive developmental stages, but the processes are similar across mammalian species (despite differences in the final anatomical structure).<br><br>Data were analysed using R packages limma and maSigPro, Ingenuity Pathway Analysis and DAVID and verified using qRT-PCR, promoter analysis, western blotting and migration assays<br><br><b>Supplementary Table 3.xlsx:</b> lists all differentially-expressed genes across tissues and gestation <br><br>Each row reports <b>Probe name, Gene name, Gene Symbol, Systematic Name, Gene Description</b> and differential expression in terms of False Discovery Rate (FDR)-adjusted <i>p</i>-values and Absolute log fold changes for the comparisons across days 27-34 and tissues CH: chorion and CG: chorionic girdle. e.g. CH_27vsCG_27_LogFC - Log Fold change in chorion versus chorionic girdle at 27 days.<br><br><b>Supplementary Table 4.xlsx:</b> lists genes that clustered together with similar expression across tissue and time. <br><br>Each row reports <b>Probe ID, Gene Symbol, Gene Name, GenBank ID, R</b><sup>2 </sup>and <b>p-value</b>. <br><br>The related array data can be found in the NCBI Gene Expression Omnibus (GSE113072)
DOI: 10.6084/m9.figshare.7376024
title: PAPER3_DOI.zip

description: Data used in "The impact of interactive visualization on geospatial decision-making based on trade-off thinking"
DOI: 10.6084/m9.figshare.7376042
title: Supplementary Material for: Prognostic Value of microRNA-133a Expression and Its Clinicopathologic Significance in Non-Small Cell Lung Cancer: A Comprehensive Study Based on Meta-Analysis and the TCGA Database

description: <b><i>Background:</i></b> The role of microRNA-133a (miR-133a) in non-small cell lung cancers (NSCLCs) is controversial. Thus, we conducted a comprehensive study based on meta-analysis and The Cancer Genome Atlas (TCGA) database. <b><i>Methods:</i></b> Publications were searched in both English and Chinese databases, and meta-analysis was performed using Stata 12.0. The clinical value of miR-133a in NSCLC was investigated by collecting and calculating data from the TCGA database, and the statistical analysis was performed in R 3.5.0. <b><i>Results:</i></b> 5 studies with 364 cases were included in this meta-analysis. The combined pooled result showed that high expression of miR-133a was associated with a favorable survival outcome in NSCLC patients (hazard ratio 0.561, 95% confidence interval 0.396-0.794, p = 0.001). Meanwhile, a total of 984 NSCLC patients were extracted from the TCGA database. Results showed an area under the ROC curve value for miR-133a-3p of 0.902, and the expression of miR-133a-3p was linked with clinicopathologic parameters of NSCLC (p &lt; 0.05), including sex, age, social status, and lymph node metastasis. <b><i>Conclusion:</i></b> Our study indicated that miR-133a might act as a tumor suppressor and be a valuable independent prognostic and diagnostic biomarker for NSCLC, and NSCLC patients with high expression of miR-133 might have a better prognosis.
DOI: 10.7284/129905
title: Water Temperature data collected during research cruise OC1802B using a Sea-Bird SBE-38 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376024.v1
title: PAPER3_DOI.zip

description: Data used in "The impact of interactive visualization on geospatial decision-making based on trade-off thinking"
DOI: 10.6084/m9.figshare.7376012
title: WikiConv - Chinese

description: WikiConv (Chinese): A Corpus of the Complete Conversational History of a Large Online Collaborative Community<br><br>This directory contains the WikiConv Corpus which encompasses the full history of conversations on Wikipedia Talk Pages.<br>The project webpage for this work is at: https://github.com/conversationai/wikidetox/tree/master/wikiconv<br>The dataset and reconstruction process for this corpus has been published in the paper [WikiConv: A Corpus of the Complete Conversational History of a Large OnlineCollaborative Community](https://arxiv.org/abs/1810.13181), presented at [EMNLP 2018](http://EMNLP2018.org).<br>The work has also been presented at [the June 2018 Wikipedia researchshowcase](https://www.mediawiki.org/wiki/Wikimedia_Research/Showcase#June_2018) (the first half describes our work, using an earlier version of this dataset to predict [conversations going awry](https://arxiv.org/abs/1805.05345).<br>The meta-data in this corpus is governed by the [CC0 license v1.0](http://creativecommons.org/publicdomain/zero/1.0/), and the content of the comments is governed by the [CC-SA license v3.0](https://creativecommons.org/licenses/by-sa/3.0/).
DOI: 10.6084/m9.figshare.7376015
title: WikiConv - Russian

description: WikiConv (Russian): A Corpus of the Complete Conversational History of a Large Online Collaborative Community<br><br>This directory contains the WikiConv Corpus which encompasses the full history of conversations on Wikipedia Talk Pages.<br>The project webpage for this work is at: https://github.com/conversationai/wikidetox/tree/master/wikiconv<br>The dataset and reconstruction process for this corpus has been published in the paper [WikiConv: A Corpus of the Complete Conversational History of a Large OnlineCollaborative Community](https://arxiv.org/abs/1810.13181), presented at [EMNLP 2018](http://EMNLP2018.org).<br>The work has also been presented at [the June 2018 Wikipedia researchshowcase](https://www.mediawiki.org/wiki/Wikimedia_Research/Showcase#June_2018) (the first half describes our work, using an earlier version of this dataset to predict [conversations going awry](https://arxiv.org/abs/1805.05345).<br>The meta-data in this corpus is governed by the [CC0 license v1.0](http://creativecommons.org/publicdomain/zero/1.0/), and the content of the comments is governed by the [CC-SA license v3.0](https://creativecommons.org/licenses/by-sa/3.0/).<br>
DOI: 10.7284/129911
title: Water Temperature data collected during research cruise OC1802B using a Sea-Bird SBE-48 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376009
title: WikiConv - German

description: WikiConv (German): A Corpus of the Complete Conversational History of a Large Online Collaborative Community<br><br>This directory contains the WikiConv Corpus which encompasses the full history of conversations on Wikipedia Talk Pages.<br>The project webpage for this work is at: https://github.com/conversationai/wikidetox/tree/master/wikiconv<br>The dataset and reconstruction process for this corpus has been published in the paper [WikiConv: A Corpus of the Complete Conversational History of a Large OnlineCollaborative Community](https://arxiv.org/abs/1810.13181), presented at [EMNLP 2018](http://EMNLP2018.org).<br>The work has also been presented at [the June 2018 Wikipedia researchshowcase](https://www.mediawiki.org/wiki/Wikimedia_Research/Showcase#June_2018) (the first half describes our work, using an earlier version of this dataset to predict [conversations going awry](https://arxiv.org/abs/1805.05345).<br>The meta-data in this corpus is governed by the [CC0 license v1.0](http://creativecommons.org/publicdomain/zero/1.0/), and the content of the comments is governed by the [CC-SA license v3.0](https://creativecommons.org/licenses/by-sa/3.0/).<br>
DOI: 10.7284/129910
title: Timeserver data collected during research cruise OC1802B using a Microsemi SyncServer S350 instrument system onboard the platform RV Oceanus

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7376003
title: WikiConv - English

description: WikiConv: A Corpus of the Complete Conversational History of a Large Online Collaborative Community<br><br>This directory contains the WikiConv Corpus which encompasses the full history of conversations on Wikipedia Talk Pages.<br>The project webpage for this work is at: https://github.com/conversationai/wikidetox/tree/master/wikiconv<br>The dataset and reconstruction process for this corpus has been published in the paper [WikiConv: A Corpus of the Complete Conversational History of a Large OnlineCollaborative Community](https://arxiv.org/abs/1810.13181), presented at [EMNLP 2018](http://EMNLP2018.org).<br>The work has also been presented at [the June 2018 Wikipedia researchshowcase](https://www.mediawiki.org/wiki/Wikimedia_Research/Showcase#June_2018) (the first half describes our work, using an earlier version of this dataset to predict [conversations going awry](https://arxiv.org/abs/1805.05345).<br>The meta-data in this corpus is governed by the [CC0 license v1.0](http://creativecommons.org/publicdomain/zero/1.0/), and the content of the comments is governed by the [CC-SA license v3.0](https://creativecommons.org/licenses/by-sa/3.0/).<br>