cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4539844
title: Supplementary Material for: MicroRNA-126 Reduces Blood-Retina Barrier Breakdown via the Regulation of VCAM-1 and BCL2L11 in Ischemic Retinopathy

description: To evaluate the role of microRNA-126 (miR-126) in maintaining the integrity of the blood-retina barrier (BRB), we established a mouse model of oxygen-induced retinopathy (OIR) and measured the retinal levels of miR-126 using recombinant plasmid pCMV-MIR or pCMV-MIR-126 intravitreal injections. We also detected VCAM-1 and BCL2L11 levels. Retinal vaso-obliteration, VCAM-1 localization on retinal endothelial cells, the blood-retina vascular permeability or albumin leakage in retinas, TUNEL histology, Evans blue assays, or Western blotting for detecting albumin or tight junction levels in the retina was performed. We also detected the effect of miR-126 on the survival of Müller cells in a mouse model using vimentin fluorescence staining. Our results suggested that miR-126 may not only regulate the overexpression of VCAM-1 or BCL2L11 and lead to the reduction of retinal endothelial cell apoptosis, retinal vascular leakage, or retinal permeability in the OIR mouse model, but may also protect hypoxic retinal Müller cells via the STAT3 signaling pathway. We believe that miR-126 could also be a potential therapeutic agent to maintain the stability of the BRB in ischemic retinopathy.
DOI: 10.6084/m9.figshare.4539856.v1
title: Supplementary Material for: Adverse Renal Effects of Immune Checkpoint Inhibitors: A Narrative Review

description: <b><i>Background:</i></b> Cancer immunotherapy, such as anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and anti-programmed death 1 (PD-1), has revolutionized the treatment of malignancies by engaging the patient's own immune system against the tumor rather than targeting the cancer directly. These therapies have demonstrated a significant benefit in the treatment of melanomas and other cancers. <b><i>Summary:</i></b> In order to provide an extensive overview of the renal toxicities induced by these agents, a Medline search was conducted of published literature related to ipilimumab-, pembrolizumab-, and nivolumab-induced kidney toxicity. In addition, primary data from the initial clinical trials of these agents and the FDA adverse reporting system database were also reviewed to determine renal adverse events. Acute interstitial nephritis (AIN), podocytopathy, and hyponatremia were toxicities caused by ipilimumab. The main adverse effect associated with both the PD-1 inhibitors was AIN. The onset of kidney injury seen with PD-1 inhibitors is usually late (3-10 months) compared to CTLA-4 antagonists related renal injury, which happens earlier (2-3 months). PD-1 as opposed to CTLA-4 inhibitors has been associated with kidney rejection in transplantation. Steroids appear to be effective in treating the immune-related adverse effects noted with these agents. <b><i>Key Message:</i></b> Although initially thought to be rare, the incidence rates of renal toxicities might be higher (9.9-29%) as identified by recent studies. As a result, obtaining knowledge about renal toxicities of immune checkpoint inhibitors is extremely important.
DOI: 10.6084/m9.figshare.4539149
title: EMIRGE-reconstructed-SSU-rRNA-genes-from-1362A-1362B-metagenomes.fasta

description: FASTA file containing 1951 (U1362A) and 1434 (U1362B) SSU rRNA genes reconstructed from the two metagenomes.
DOI: 10.6084/m9.figshare.4539164
title: Public datasets - Endothelial Cell Loss in Penetrating Keratoplasty, Endothelial Keratoplasty, and Deep Anterior Lamellar Keratoplasty .xlsx

description: This is the raw data of the endothelial cell density in three keratoplastic procedures which performed in National Taiwan University Hospital(NTUH). We wants to evaluate the natural course of endothelial cell density loss rate of these three procedures.
DOI: 10.6084/m9.figshare.4539149.v1
title: EMIRGE-reconstructed-SSU-rRNA-genes-from-1362A-1362B-metagenomes.fasta

description: FASTA file containing 1951 (U1362A) and 1434 (U1362B) SSU rRNA genes reconstructed from the two metagenomes.
DOI: 10.6084/m9.figshare.4539164.v2
title: Public datasets - Endothelial Cell Loss in Penetrating Keratoplasty, Endothelial Keratoplasty, and Deep Anterior Lamellar Keratoplasty .xlsx

description: This is the raw data of the endothelial cell density in three keratoplastic procedures which performed in National Taiwan University Hospital(NTUH). We wants to evaluate the natural course of endothelial cell density loss rate of these three procedures.
DOI: 10.6084/m9.figshare.4539164.v1
title: Public datasets - Endothelial Cell Loss in Penetrating Keratoplasty, Endothelial Keratoplasty, and Deep Anterior Lamellar Keratoplasty .xlsx

description: This is the raw data of the endothelial cell density in three keratoplastic procedures which performed in National Taiwan University Hospital(NTUH). We wants to evaluate the natural course of endothelial cell density loss rate of these three procedures.
DOI: 10.6084/m9.figshare.4539143
title: Russian Wiktionary thesaurus in Gephi format (20160210) with screenshots

description: Russian Wiktionary thesaurus in Gephi format (dump ruwikt20160210).<br><br>There are 4 parts of speech (POS): noun, adjective, verb, adverb. There is one graph in .gexf format for each POS.<br><br>These POS data files are accompanied with several screenshots taken in the program Gephi.<br>
DOI: 10.6084/m9.figshare.4539143.v1
title: Russian Wiktionary thesaurus in Gephi format (20160210) with screenshots

description: Russian Wiktionary thesaurus in Gephi format (dump ruwikt20160210).<br><br>There are 4 parts of speech (POS): noun, adjective, verb, adverb. There is one graph in .gexf format for each POS.<br><br>These POS data files are accompanied with several screenshots taken in the program Gephi.<br>
DOI: 10.6084/m9.figshare.4538906.v1
title: Demographic information

description: The demographic information about subjects used in the manuscript
DOI: 10.6084/m9.figshare.4538906.v2
title: The demographic information

description: The demographic information about subjects used in the manuscript
DOI: 10.6084/m9.figshare.4538270.v1
title: Supplemental_File_S1.bb

description: Supplementary files for "Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach".
DOI: 10.6084/m9.figshare.4537922
title: A global assessment of climatic niche shifts and human influence in insect invasions

description: This file contains descriptions of all the distribution data we used in our study. It includes sources for the distribution data, and maps of the geographic extents employed in the study.<br>See the supplementary 1 PDF file for details.<br>Will add link to paper upon publication.
DOI: 10.6084/m9.figshare.4537922.v1
title: A global assessment of climatic niche shifts, and human influence, in insect invasions: Supplementary 1

description: This file contains descriptions of all the distribution data we used in our study. It includes sources for the distribution data, and maps of the geographic extents employed in the study.<br>See the supplementary PDF file for details.<br>Will add link to paper upon publication.
DOI: 10.6084/m9.figshare.4536626
title: 16-12-16 - full data matrix.zip

description: The data here were used to model human West Nile virus (WNV) cases in South Dakota, USA, 2004-2016. Each combination of county and week is associated with a meteorological history and a measure of how quickly mosquito infections appeared to rise in the early WNV season.<br><br>Due to a data sharing agreement, certain columns are not present in the file. The associated paper, with contact information for the owners of the human case data, will be linked here if accepted.
DOI: 10.6084/m9.figshare.4536626.v1
title: 16-12-16 - full data matrix.zip

description: The data here were used to model human West Nile virus (WNV) cases in South Dakota, USA, 2004-2016. Each combination of county and week is associated with a meteorological history and a measure of how quickly mosquito infections appeared to rise in the early WNV season.<br><br>Due to a data sharing agreement, certain columns are not present in the file. The associated paper, with contact information for the owners of the human case data, will be linked here if accepted.
DOI: 10.6084/m9.figshare.4536275
title: 6_9_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4536098
title: D. occidentalis 16S rRNA OTU filtered and rarefied OTU table

description: D. occidentalis 16S rRNA OTUs after filtering for samples with at least 150 OTUs, no single OTUs, OTUs occur in at least 10 samples and rarefied to 1500 even sampling depth.
DOI: 10.6084/m9.figshare.4536275.v1
title: 6_9_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4536101
title: Orion Regions

description: A BED file that contains the hg19 coordinates of the Orion regions.
DOI: 10.6084/m9.figshare.4536095
title: Coordinates of Defined Orion Scores

description: A gzipped BED file that contains the hg19 coordinates for which the Orion scores are defined – non-repeat autosomal regions that were covered in our sample.
DOI: 10.6084/m9.figshare.4536098.v1
title: D. occidentalis 16S rRNA OTU filtered and rarefied OTU table

description: D. occidentalis 16S rRNA OTUs after filtering for samples with at least 150 OTUs, no single OTUs, OTUs occur in at least 10 samples and rarefied to 1500 even sampling depth.
DOI: 10.6084/m9.figshare.4536095.v1
title: Coordinates of Defined Orion Scores

description: A gzipped BED file that contains the hg19 coordinates for which the Orion scores are defined – non-repeat autosomal regions that were covered in our sample.
DOI: 10.6084/m9.figshare.4536059
title: Runoff response to rainfall variance in managed and unmanaged lands in Mo'orea, French Polynesia

description: <b>Background. </b>Increased precipitation variance is a predicted effect of climate change, with the highest variance expected in tropical areas. Increased rainfall can lead to increased runoff, which can cause soil erosion, eutrophication, and other forms of environmental degradations, in both terrestrial and marine environments. Mo’orea, a small volcanic island in French Polynesia with an extremely rugged mountainous landscape, is likely to be affected by increased rainfall in coming decades. This puts the island’s surrounding coral reef at risk of stress from increased runoff. This study was designed to compare the responses of soil from differently managed lands when subjected to different amounts of rainfall. <b>Methods. </b>Fieldwork consisted of sampling soil from three differently managed areas in the ‘Opunohu Valley in Mo’orea: rangeland, grassland, and forest. Soil was measured for bulk density and water content. The soil was then used in a simulated rainfall experiment to test for time it took for water to flow off of the soil surface and amount of runoff collected. <b>Results. </b>Results showed the grassland soil to have the highest bulk density and water content. The grassland soil took the longest for water to runoff in the rainfall experiments. A strong positive relationship between increasing soil bulk density and increasing time in seconds for the simulated rainfall to runoff the soil samples was found. All other differences tested were found to be insignificant. <b>Discussion. </b>The differences in bulk density and water content found in soil between study sites suggest that the way land is used and managed affects soil physical properties, which in turn affects soil response to different amounts of rain. Insignificant results may reveal differences with further experimental trials. Additionally, the soil water content results from this study support previous findings that the soil in ‘Opunohu Valley are loose, moist alluvial deposits.
DOI: 10.6084/m9.figshare.4536059.v1
title: Runoff response to rainfall variance in managed and unmanaged lands in Mo'orea, French Polynesia

description: <b>Background. </b>Increased precipitation variance is a predicted effect of climate change, with the highest variance expected in tropical areas. Increased rainfall can lead to increased runoff, which can cause soil erosion, eutrophication, and other forms of environmental degradations, in both terrestrial and marine environments. Mo’orea, a small volcanic island in French Polynesia with an extremely rugged mountainous landscape, is likely to be affected by increased rainfall in coming decades. This puts the island’s surrounding coral reef at risk of stress from increased runoff. This study was designed to compare the responses of soil from differently managed lands when subjected to different amounts of rainfall. <b>Methods. </b>Fieldwork consisted of sampling soil from three differently managed areas in the ‘Opunohu Valley in Mo’orea: rangeland, grassland, and forest. Soil was measured for bulk density and water content. The soil was then used in a simulated rainfall experiment to test for time it took for water to flow off of the soil surface and amount of runoff collected. <b>Results. </b>Results showed the grassland soil to have the highest bulk density and water content. The grassland soil took the longest for water to runoff in the rainfall experiments. A strong positive relationship between increasing soil bulk density and increasing time in seconds for the simulated rainfall to runoff the soil samples was found. All other differences tested were found to be insignificant. <b>Discussion. </b>The differences in bulk density and water content found in soil between study sites suggest that the way land is used and managed affects soil physical properties, which in turn affects soil response to different amounts of rain. Insignificant results may reveal differences with further experimental trials. Additionally, the soil water content results from this study support previous findings that the soil in ‘Opunohu Valley are loose, moist alluvial deposits.
DOI: 10.6084/m9.figshare.4535684
title: Particulate matter-mediated release of long pentraxin 3 (PTX3) and vascular endothelial growth factor (VEGF) in vitro: Limited importance of endotoxin and organic content

description: Exposure to particulate matter (PM) is associated with adverse health effects, but it is still relatively unknown which role PM sources and physicochemical properties play in the observed effects. It was postulated that PM in vitro induces release of long pentraxin 3 (PTX3) and vascular endothelial growth factor (VEGF) and that endotoxin and organic compounds present in the PM regulate this release. A contact coculture of THP-1 human leukemia monocytes and A549 human adenocarcinoma alveolar pneumocytes was exposed to PM from Traffic, Wood, Diesel, and Quartz (10–40 µg/cm<sup>2</sup>) for 12–64 h to determine release of PTX3 and VEGF. The role of endotoxin and the organic fraction in the mediator release was assessed using polymyxin B sulfate and organic extracts, respectively. Finally, antagonists were used to investigate whether the early proinflammatory cytokines interleukin (IL)-1 and tumor necrosis factor (TNF)-α affected the PTX3 and VEGF release. All PM samples induced a time-dependent release of both PTX3 and VEGF. Traffic mediated the greatest release of PTX3, whereas Wood and Diesel were more potent inducers of VEGF. The endotoxin content did not markedly affect release of either mediator, while the organic fraction exerted no significant effect on VEGF release and limited influence on PTX3 release. In addition, the IL-1 and TNF-α agonists affected PTX3 release more strongly than VEGF release. In conclusion, the current data show a limited impact of endotoxin and organic compounds on PTX3 and VEGF release. Further, the observed differences in response patterns may point toward differential regulation of PM-mediated release of PTX3 and VEGF.
DOI: 10.6084/m9.figshare.4535666
title: 6_6_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4535684.v1
title: Particulate matter-mediated release of long pentraxin 3 (PTX3) and vascular endothelial growth factor (VEGF) in vitro: Limited importance of endotoxin and organic content

description: Exposure to particulate matter (PM) is associated with adverse health effects, but it is still relatively unknown which role PM sources and physicochemical properties play in the observed effects. It was postulated that PM in vitro induces release of long pentraxin 3 (PTX3) and vascular endothelial growth factor (VEGF) and that endotoxin and organic compounds present in the PM regulate this release. A contact coculture of THP-1 human leukemia monocytes and A549 human adenocarcinoma alveolar pneumocytes was exposed to PM from Traffic, Wood, Diesel, and Quartz (10–40 µg/cm<sup>2</sup>) for 12–64 h to determine release of PTX3 and VEGF. The role of endotoxin and the organic fraction in the mediator release was assessed using polymyxin B sulfate and organic extracts, respectively. Finally, antagonists were used to investigate whether the early proinflammatory cytokines interleukin (IL)-1 and tumor necrosis factor (TNF)-α affected the PTX3 and VEGF release. All PM samples induced a time-dependent release of both PTX3 and VEGF. Traffic mediated the greatest release of PTX3, whereas Wood and Diesel were more potent inducers of VEGF. The endotoxin content did not markedly affect release of either mediator, while the organic fraction exerted no significant effect on VEGF release and limited influence on PTX3 release. In addition, the IL-1 and TNF-α agonists affected PTX3 release more strongly than VEGF release. In conclusion, the current data show a limited impact of endotoxin and organic compounds on PTX3 and VEGF release. Further, the observed differences in response patterns may point toward differential regulation of PM-mediated release of PTX3 and VEGF.
DOI: 10.6084/m9.figshare.4535666.v1
title: 6_6_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.
DOI: 10.6084/m9.figshare.4535657
title: Table S2 from Methylation of <i>avpr1a</i> in the cortex of wild prairie voles: effects of CpG position and polymorphism

description: Position and sequence polymorphism at polyCpG sites across the avpr1a locus. SNP positions are based on avpr1a reference AF069304.2 (NCBI) and abbreviations are as follow: CpGi = CpG island, CDS = coding sequence, UTR = untranslated region.
DOI: 10.6084/m9.figshare.4535660
title: Tianyi_microbiome

description: This repository contains the final code, count table, metadata, and precomputed data files for "The gut microbiota of healthy aged Chinese is similar to the healthy young".<br>tianyi_results.Rnw builds cleanlytianyi_supplement.Rnw builds cleanly<br>tianyi_results.Rnw file contains the knitr document and minimal code for figures 1-3 of the papertianyi_supplement.Rnw file contians the code and figures for the supplement<br>chunk/ contains actual R commands used for all figures and analyses. These are referenced in the results and supplement documents<br>data/ contains the raw (count tables, metadata) and precomputed data for the figures<br>figure/ contains the figures only<br>to build the documents, download this entire repository, then in a terminal on a UNIX type machine run:<br>./build_results.sh<br>and then<br>./build_supplement.sh<br>
DOI: 10.6084/m9.figshare.4535657.v1
title: Table S2 from Methylation of <i>avpr1a</i> in the cortex of wild prairie voles: effects of CpG position and polymorphism

description: Position and sequence polymorphism at polyCpG sites across the avpr1a locus. SNP positions are based on avpr1a reference AF069304.2 (NCBI) and abbreviations are as follow: CpGi = CpG island, CDS = coding sequence, UTR = untranslated region.
DOI: 10.6084/m9.figshare.4535648
title: Code S1. from Growth overshoot and seasonal size changes in the skulls of two weasel species

description: Program R code for executing bootstrapping of t-tests to compare skull metrics between age, sex, species, and origin groupings.
DOI: 10.6084/m9.figshare.4535648.v1
title: Code S1. from Growth overshoot and seasonal size changes in the skulls of two weasel species

description: Program R code for executing bootstrapping of t-tests to compare skull metrics between age, sex, species, and origin groupings.
DOI: 10.6084/m9.figshare.4535660.v1
title: Tianyi_microbiome

description: This repository contains the final code, count table, metadata, and precomputed data files for "The gut microbiota of healthy aged Chinese is similar to the healthy young".<br>tianyi_results.Rnw builds cleanlytianyi_supplement.Rnw builds cleanly<br>tianyi_results.Rnw file contains the knitr document and minimal code for figures 1-3 of the papertianyi_supplement.Rnw file contians the code and figures for the supplement<br>chunk/ contains actual R commands used for all figures and analyses. These are referenced in the results and supplement documents<br>data/ contains the raw (count tables, metadata) and precomputed data for the figures<br>figure/ contains the figures only<br>to build the documents, download this entire repository, then in a terminal on a UNIX type machine run:<br>./build_results.sh<br>and then<br>./build_supplement.sh<br>
DOI: 10.6084/m9.figshare.4535660.v2
title: Tianyi_microbiome

description: This repository contains the final code, count table, metadata, and precomputed data files for "The gut microbiota of healthy aged Chinese is similar to the healthy young".<br>tianyi_results.Rnw builds cleanlytianyi_supplement.Rnw builds cleanly<br>tianyi_results.Rnw file contains the knitr document and minimal code for figures 1-3 of the papertianyi_supplement.Rnw file contians the code and figures for the supplement<br>chunk/ contains actual R commands used for all figures and analyses. These are referenced in the results and supplement documents<br>data/ contains the raw (count tables, metadata) and precomputed data for the figures<br>figure/ contains the figures only<br>to build the documents, download this entire repository, then in a terminal on a UNIX type machine run:<br>./build_results.sh<br>and then<br>./build_supplement.sh<br>
DOI: 10.6084/m9.figshare.4535660.v3
title: Tianyi_microbiome

description: This repository contains the final code, count table, metadata, and precomputed data files for "The gut microbiota of healthy aged Chinese is similar to the healthy young".<br>tianyi_results.Rnw builds cleanlytianyi_supplement.Rnw builds cleanly<br>tianyi_results.Rnw file contains the knitr document and minimal code for figures 1-3 of the papertianyi_supplement.Rnw file contians the code and figures for the supplement<br>chunk/ contains actual R commands used for all figures and analyses. These are referenced in the results and supplement documents<br>data/ contains the raw (count tables, metadata) and precomputed data for the figures<br>figure/ contains the figures only<br>to build the documents, download this entire repository, then in a terminal on a UNIX type machine run:<br>./build_results.sh<br>and then<br>./build_supplement.sh<br>
DOI: 10.6084/m9.figshare.4535603
title: 6_4_2016 (IL 50)

description: Acoustic data recorded in an intertidal zone in Wilmington, North Carolina over summer 2016. See attached R script for calibration instructions.