cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11369025.v1
title: Stromal-associated cytokines bias the interplay between gene expression and DNA methylation in human breast cancers

description: In human tumours, the crosstalk between cancer cells and their microenvironment is involved in tumour progression, metastasis and resistance to anti-cancer therapies. Among the factors involved in this exchange of information pro-inflammatory cytokines seem to play a crucial role. We observed that a group of pro-inflammatory cytokines, interleukin 6 (IL6), interleukin 1-beta (IL1b), and tumour necrosis factor-alpha (TNFa), preferentially activated genes exhibiting a high basal methylation level at their transcription start sites, in the human breast cancer cell line MCF7. In human breast tumours, these responding genes were also hypermethylated, and some of them (N = 104) were differentially methylated across human breast tumour samples (The Cancer Genome Atlas cohort). While their expression was positively correlated with the stromal content of the tumours and the expression of stromal-associated pro-inflammatory cytokines, the expression of this subset of genes was negatively correlated with their methylation level at their 5ʹ end. Nevertheless, while the methylation level of this subset of genes was not correlated with the stromal cell content of the tumours, this negative correlation was partially lost in tumours with high stromal cell content. Consistently, we observed that the methylation level in this subset of genes influenced the correlation between gene expression and stromal cell content. Thus, these data indicated that the stromal component of breast tumours should be taken into account for DNA methylation and gene expression studies and suggest an additional pathway, via DNA methylation, in the cross-talk between cancer cells and their microenvironment in human breast cancers.
DOI: 10.6084/m9.figshare.11368851
title: supplemental data AJP-renal.pdf

description: <b>S1. </b>V-ATPase E1 subunit (red, arrows) expression to localize ICs and Aqp2 (green) expression to localize collecting ducts. WT<sup>kidney&gt;</sup>WT<sup>recipient </sup>kidneys (<b>A</b>) appeared to have similar number of intercalated cells (red cells, arrows) compared to WT native kidneys (<b>B</b>). <i>Car2<sup>-/-</sup></i><sup>kidney&gt;</sup>WT<sup>recipient </sup>kidneys (<b>C)</b>appeared to have similarly diminished numbers of ICs (red cells, arrows) compared to <i>Car2</i><sup>-/-</sup>native kidneys (<b>D</b>). On A, the cells were stained with the inverse secondary colored and were pseudocolored red or green for consistency with the other images. <b></b> <b><br></b><b>S2. </b>Transplant hydronephrosis in excluded mouse<b></b><b> </b><b><br></b><b>S3. </b>Murine<b></b>VCUG demonstrating no vesicoureteral reflux status post renal transplant <b><br></b><b>S4</b>. Complete results of RT<sup>2 </sup>Profiler Bacterial Response PCR Arrays evaluating acetazolamide vs. no acetazolamide in the kidney at baseline. <b><br></b><b>S5</b>. Complete results of RT<sup>2 </sup>Profiler Bacterial Response PCR Arrays evaluating acetazolamide vs. no acetazolamide in the kidney during UTI at 6-hrs post transurethral UPEC inoculation. <b><br></b><b>S6</b>. Primer sequences for RT-PCR.
DOI: 10.6084/m9.figshare.11368668
title: Australian Senate Simulated Election Results 2010 - 2019

description: Datasets measuring the proportionality of Australian Senate election results from 2010, 2013, 2016, and 2019, using the Gallagher Index. The Gallagher Index is also used to measure the implications of the D'Hondt method, with and without boundaries, and the national remainder method, on the proportionality of each election.
DOI: 10.6084/m9.figshare.11368603
title: Figure 5 Raw Data

description: Figure 5 Raw data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368606
title: Figure 6 Raw Data

description: Figure 6 raw data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368597
title: The original data

description: The original data in our study were shown here, including the lipid biomarkers compostions (i.e., n-alkanes and free fatty acid), OTU (<i>pmoA</i> gene) abundance and quantified gene copy numbers.<br>
DOI: 10.6084/m9.figshare.11368603.v1
title: Figure 5 Raw Data

description: Figure 5 Raw data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368606.v1
title: Figure 6 Raw Data

description: Figure 6 raw data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368595
title: Figure 4 Raw data

description: Fig 4 Raw Data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368597.v1
title: The original data

description: The original data in our study were shown here, including the lipid biomarkers compostions (i.e., n-alkanes and free fatty acid), OTU (<i>pmoA</i> gene) abundance and quantified gene copy numbers.<br>
DOI: 10.6084/m9.figshare.11368586
title: Figure 3 Raw Data

description: Raw data for figure 3 of "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368466
title: Curvilinear Homophily and Heterophily Mechanisms in Online Political Discussion: A Relational Event Modeling of Content and Process

description: Anonymized behavioral dataset of online political discussion
DOI: 10.6084/m9.figshare.11368466.v1
title: Curvilinear Homophily and Heterophily Mechanisms in Online Political Discussion: A Relational Event Modeling of Content and Process

description: Anonymized behavioral dataset of online political discussion
DOI: 10.6084/m9.figshare.11368586.v1
title: Figure 3 Raw Data

description: Raw data for figure 3 of "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368595.v1
title: Figure 4 Raw data

description: Fig 4 Raw Data for "Optimization of a Plasmodium Falciparum Circumsporozoite Protein Repeat Vaccine using the Tobacco Mosaic Virus Platform"
DOI: 10.6084/m9.figshare.11368307
title: Fig4 exp3

description: fluorescence images of GFP expressing cells
DOI: 10.6084/m9.figshare.11368313
title: Fig7 and 8 tumor images

description: fluorescence images of GFP expressing cells
DOI: 10.6084/m9.figshare.11368313.v1
title: Fig7 and 8 tumor images

description: fluorescence images of GFP expressing cells
DOI: 10.6084/m9.figshare.11368295
title: Fig4 exp 1

description: images of cell culture infected with AAV-GFP
DOI: 10.6084/m9.figshare.11368298
title: Fig4 exp 2

description: data set of replicate experiment
DOI: 10.6084/m9.figshare.11368289
title: Fig6 M+104 and CBA vector Tumor images

description: images of tumor tissue infected with AAV -GFP
DOI: 10.6084/m9.figshare.11368289.v1
title: Fig6 M+104 and CBA vector Tumor images

description: images of tumor tissue infected with AAV -GFP
DOI: 10.6084/m9.figshare.11368295.v1
title: Fig4 exp 1

description: images of cell culture infected with AAV-GFP
DOI: 10.6084/m9.figshare.11368226
title: Levy PLoS One Min Data Excel.xlsx

description: data in excel
DOI: 10.6084/m9.figshare.11368136
title: Supplementary Table 2-5

description: Supplementary Table 2-5 of <i>DIP2B</i>
DOI: 10.6084/m9.figshare.11368160
title: Spacer sequence for targeting rpoH gene in Pseudomonas aeruginosa PAO1 via CRISPR-Cas9 genome editing

description: <i>rpoH </i>encodes a RNA polymerase sigma factor that coordinates the expression of heat shock genes in <i>Pseudomonas aeruginosa</i> PAO1. Thus, <i>rpoH </i>is a useful target for modulating the expression of heat shock genes in the versatile environmental bacterium in studies ranging from understanding the heat shock response of the species to determining the effect of the regulon on the cellular physiology of the organism. One approach for deleting <i>rpoH</i> is through the CRISPR-Cas9 genome editing technique that requires a guide RNA encoding a spacer sequence specific for the gene of interest to be designed. Using an in-house MATLAB software, the spacer sequences able to target the sense and antisense DNA strands of <i>rpoH </i>gene in <i>P. aeruginosa</i> PAO1 were designed, and archived as an Excel file for ease of access and storage. Overall, the spacer sequences presented in this work should find use in targeting the <i>rpoH </i>gene in <i>P. aeruginosa</i> PAO1 for a range of applications such as gene deletion and gene activation through the CRISPR-Cas9 system.<br><br>
DOI: 10.6084/m9.figshare.11368163
title: Sequencing data

description: Transcriptome sequencing data
DOI: 10.6084/m9.figshare.11368136.v1
title: Supplementary Table 2-5

description: Supplementary Table 2-5 of <i>DIP2B</i>
DOI: 10.6084/m9.figshare.11368163.v1
title: Sequencing data

description: Transcriptome sequencing data
DOI: 10.6084/m9.figshare.11368133
title: Raw reads — five fresh specimens

description: HTS raw reads obtained with Sequel platform (Pacific Biosciences)
DOI: 10.6084/m9.figshare.11368160.v1
title: Spacer sequence for targeting rpoH gene in Pseudomonas aeruginosa PAO1 via CRISPR-Cas9 genome editing

description: <i>rpoH </i>encodes a RNA polymerase sigma factor that coordinates the expression of heat shock genes in <i>Pseudomonas aeruginosa</i> PAO1. Thus, <i>rpoH </i>is a useful target for modulating the expression of heat shock genes in the versatile environmental bacterium in studies ranging from understanding the heat shock response of the species to determining the effect of the regulon on the cellular physiology of the organism. One approach for deleting <i>rpoH</i> is through the CRISPR-Cas9 genome editing technique that requires a guide RNA encoding a spacer sequence specific for the gene of interest to be designed. Using an in-house MATLAB software, the spacer sequences able to target the sense and antisense DNA strands of <i>rpoH </i>gene in <i>P. aeruginosa</i> PAO1 were designed, and archived as an Excel file for ease of access and storage. Overall, the spacer sequences presented in this work should find use in targeting the <i>rpoH </i>gene in <i>P. aeruginosa</i> PAO1 for a range of applications such as gene deletion and gene activation through the CRISPR-Cas9 system.<br><br>
DOI: 10.6084/m9.figshare.11368088
title: Supplementary Table 1.docx

description: Supplementary Table 1. Information of the six SNPs of <i>DIP2B</i><br><br><i></i>
DOI: 10.6084/m9.figshare.11368124
title: Dataset for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media"

description: The dataset includes the input data for simulation (i.e. basic parameters for simulation, relative permeability and capillary pressure curves, and coordinates for 2D fracture and vug networks) and calculation results.
DOI: 10.6084/m9.figshare.11368088.v2
title: Supplementary Table 1.docx

description: Supplementary Table 1. Information of the six SNPs of <i>DIP2B</i><br><br><i></i>
DOI: 10.6084/m9.figshare.11368124.v1
title: Dataset for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media"

description: Calculation results for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media".
DOI: 10.6084/m9.figshare.11368133.v2
title: Raw reads — five fresh specimens

description: HTS raw reads obtained with Sequel platform (Pacific Biosciences)
DOI: 10.23641/asha.11368073
title: Language in 3-year-olds born preterm and term (Sanchez et al., 2019)

description: <b>Purpose: </b>Language difficulties are prevalent among children born preterm. Existing studies have largely used standardized language tests, providing limited scope for detailed descriptive examination of preterm language. This study aimed to examine differences in conversational language between children born &lt; 30 weeks and at term as well as correlations between language sample analysis (LSA) and a standardized language tool.<b>Method:</b> Two hundred four 3-year-olds (103 born &lt; 30 weeks, 101 born at term) recruited at birth provided a 10-min language sample and completed the Preschool Language Scales–Fifth Edition (I. Zimmerman, Steiner, & Pond, 2011). LSA was conducted using the Systematic Analysis of Language Transcripts and Index of Productive Syntax. Group differences were analyzed using linear regression, and Pearson correlation coefficient (coef) was used to determine correlations between measures.<b>Results:</b> Children born &lt; 30 weeks scored lower than term-born peers on multiple metrics when controlled for confounding factors (sex, high social risk, multilingualism, and diagnosed neurodevelopmental disorders), including mean length of utterance in morphemes (coef = –0.28, 95% confidence interval [CI] [–0.56, 0.01]) and words (coef = –0.29, 95% CI [–0.53, –0.05]), number of different word roots (coef = –10.04, 95% CI [–17.93, –2.14]), and Index of Productive Syntax sentence structures (coef = –1.81, 95% CI [–3.10, –0.52]). Other variables (e.g., number of utterances, number of nouns and adjectives) were not significantly different between groups. LSA and the Preschool Language Scales–Fifth Edition were at most moderately correlated (≤ .45).<b>Conclusions: </b>Three-year-old children born preterm demonstrated poorer conversational language than children born at term, with some specific areas of deficit emerging. Furthermore, formal assessment and LSA appear to provide relatively distinct and yet complementary data to guide diagnostic and intervention decisions.<br><b>Supplemental Material S1. </b>Comparison between participants with &lt; 50 versus ≥ 50 utterances.<br><b>Supplemental Material S2. </b>Interrater reliability. <br>Sanchez, K., Spittle, A. J., Boyce, J. O., Leembruggen, L., Mantelos, A., Mills, S., Mitchell, N., Neil, E., St John, M., Treloar, J., & Morgan, A. T. (2019). Conversational language in 3-year-old children born very preterm and at term. <i>Journal of Speech, Language, and Hearing Research. </i>Advance online publication. https://doi.org/10.1044/2019_JSLHR-19-00153
DOI: 10.6084/m9.figshare.11368088.v1
title: Supplementary Tables.docx

description: Supplementary Tables of <i>DIP2B </i><br><i></i>
DOI: 10.6084/m9.figshare.11368124.v3
title: Dataset for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media"

description: The dataset includes the input data for simulation (i.e. basic parameters for simulation, relative permeability and capillary pressure curves, and coordinates for 2D fracture and vug networks) and calculation results.
DOI: 10.6084/m9.figshare.11368133.v1
title: Raw reads — five fresh specimens

description: HTS raw reads obtained with Sequel platform (Pacific Biosciences)
DOI: 10.23641/asha.11368073.v1
title: Language in 3-year-olds born preterm and term (Sanchez et al., 2019)

description: <b>Purpose: </b>Language difficulties are prevalent among children born preterm. Existing studies have largely used standardized language tests, providing limited scope for detailed descriptive examination of preterm language. This study aimed to examine differences in conversational language between children born &lt; 30 weeks and at term as well as correlations between language sample analysis (LSA) and a standardized language tool.<b>Method:</b> Two hundred four 3-year-olds (103 born &lt; 30 weeks, 101 born at term) recruited at birth provided a 10-min language sample and completed the Preschool Language Scales–Fifth Edition (I. Zimmerman, Steiner, & Pond, 2011). LSA was conducted using the Systematic Analysis of Language Transcripts and Index of Productive Syntax. Group differences were analyzed using linear regression, and Pearson correlation coefficient (coef) was used to determine correlations between measures.<b>Results:</b> Children born &lt; 30 weeks scored lower than term-born peers on multiple metrics when controlled for confounding factors (sex, high social risk, multilingualism, and diagnosed neurodevelopmental disorders), including mean length of utterance in morphemes (coef = –0.28, 95% confidence interval [CI] [–0.56, 0.01]) and words (coef = –0.29, 95% CI [–0.53, –0.05]), number of different word roots (coef = –10.04, 95% CI [–17.93, –2.14]), and Index of Productive Syntax sentence structures (coef = –1.81, 95% CI [–3.10, –0.52]). Other variables (e.g., number of utterances, number of nouns and adjectives) were not significantly different between groups. LSA and the Preschool Language Scales–Fifth Edition were at most moderately correlated (≤ .45).<b>Conclusions: </b>Three-year-old children born preterm demonstrated poorer conversational language than children born at term, with some specific areas of deficit emerging. Furthermore, formal assessment and LSA appear to provide relatively distinct and yet complementary data to guide diagnostic and intervention decisions.<br><b>Supplemental Material S1. </b>Comparison between participants with &lt; 50 versus ≥ 50 utterances.<br><b>Supplemental Material S2. </b>Interrater reliability. <br>Sanchez, K., Spittle, A. J., Boyce, J. O., Leembruggen, L., Mantelos, A., Mills, S., Mitchell, N., Neil, E., St John, M., Treloar, J., & Morgan, A. T. (2019). Conversational language in 3-year-old children born very preterm and at term. <i>Journal of Speech, Language, and Hearing Research. </i>Advance online publication. https://doi.org/10.1044/2019_JSLHR-19-00153
DOI: 10.6084/m9.figshare.11368124.v2
title: Dataset for "A Novel Coupled Hydro-Mechanical Model for Two-Phase Flow in Fractured Karst Porous Media"

description: The dataset includes the input data for simulation (i.e. basic parameters for simulation, relative permeability and capillary pressure curves, and coordinates for 2D fracture and vug networks) and calculation results.
DOI: 10.6084/m9.figshare.11368019
title: Fetal abdominal aortas in ultrasound images

description: <b>Supporting data for article "Real-time diameter of the fetal aorta from ultrasound"</b><b></b><br>Annotated collection of ultrasound images of the fetal aorta, together with the code and examples of synthetic images, used to train and evaluate a deep learning solution that extracts the diameter of the aorta in the image.<br><b>Annotation</b>Clinicians used a semi-automated tool: they were presented with a proposed separation for all boundaries (upper media/adventitia, upper lumen/intima, lower media/adventitia, lower lumen/intima), which they manually reviewed and corrected.<br>
DOI: 10.6084/m9.figshare.11368025
title: Salinity affects topsoil organic carbon concentrations through regulating vegetation structure and productivity

description: Estuarine salt marshes have been recognized as one of the most efficient carbon sinks in the biosphere, with considerable potential for climate change mitigation. However, there are still uncertainties about the response of soil carbon stocks to enhanced soil salinization caused by accelerated sea-level rises and aggravated saltwater intrusion. We therefore conducted both field investigations in the Chongming Dongtan salt marsh of the Yangtze River Estuary, China, and manipulative experiments on marsh soils occupied respectively by the invasive Spartina alterniflora, and the native Phragmites australis and Scirpus mariqueter, to identify the effects of elevated soil salinity on top soil organic carbon concentration. This dataset consists of two tables listed below. Table S1: Sampling data for invasive (<i>Spartina alterniflora</i>) and native (<i>Phragmites australis</i> and <i>Scirpus mariqueter</i>) species in the Chongming Dongtan salt marsh of the Yangtze River Estuary, China. Table S2 : Responses of invasive (<i>Spartina alterniflora</i>) and native (<i>Phragmites australis</i> and <i>Scirpus mariqueter</i>) species to six flooding salinity treatments (0, 5, 10, 15, 25 and 35 ppt).
DOI: 10.6084/m9.figshare.11368025.v1
title: Salinity affects topsoil organic carbon concentrations through regulating vegetation structure and productivity

description: Estuarine salt marshes have been recognized as one of the most efficient carbon sinks in the biosphere, with considerable potential for climate change mitigation. However, there are still uncertainties about the response of soil carbon stocks to enhanced soil salinization caused by accelerated sea-level rises and aggravated saltwater intrusion. We therefore conducted both field investigations in the Chongming Dongtan salt marsh of the Yangtze River Estuary, China, and manipulative experiments on marsh soils occupied respectively by the invasive Spartina alterniflora, and the native Phragmites australis and Scirpus mariqueter, to identify the effects of elevated soil salinity on top soil organic carbon concentration. This dataset consists of two tables listed below. Table S1: Sampling data for invasive (<i>Spartina alterniflora</i>) and native (<i>Phragmites australis</i> and <i>Scirpus mariqueter</i>) species in the Chongming Dongtan salt marsh of the Yangtze River Estuary, China. Table S2 : Responses of invasive (<i>Spartina alterniflora</i>) and native (<i>Phragmites australis</i> and <i>Scirpus mariqueter</i>) species to six flooding salinity treatments (0, 5, 10, 15, 25 and 35 ppt).
DOI: 10.6084/m9.figshare.11367755
title: sub-01_task-deterministicclassification_run-01_bold.npy

description: This is a copy of the data array in the file 'sub-01_task-deterministicclassification_run-01_bold.nii.gz' from https://openneuro.org/datasets/ds000002/versions/57fecec2cce88d000bc17549, stored in the numpy .npy format
DOI: 10.6084/m9.figshare.11367800
title: Data from: Differential monovalent anion selectivity in narrow diameter carbon nanotube porins. http://dx.doi.org/10.1021/acsnano.0c02423

description: Data from: <b><br></b><b>Differential monovalent anion selectivity in narrow diameter carbon nanotube porins</b><b><br></b> <b>Figure 1. Anion permeability assay.</b> (a) Schematics of the lucigenin-based assay for halide anions transport. (b,c) Representative stopped-flow kinetic traces recorded for control LUVs (b) and CNTP-LUVs (c) after exposure to Br− gradient (as indicated on the legend) at pH 7.5. The average density of CNTP channels in CNTP-LUVs was ca. 5 per vesicle. <br> <b>Figure 2. Anion transport in 0.8 nm CNTPs.</b> Plots of anion flux as a function of anion concentration gradient for CNTP-LUVs measured at pH 7.5 and pH 3.0 for (a) Cl− ions; (b) Br− ions; (c) I− ions; and (d) SCN− ions. Error bars were obtained from at least three separate experiments. The corresponding stopped- flow traces (Fig. S3 for pH 7.5) and (Fig. S4 for pH 3.0) and anion flux in control LUVs (Fig. S5) are shown in the Supplementary Materials.<br> <b>Figure 3. Anion permeability of CNTPs.</b> (a) Anion permeabilities measured at two pH values. (b) Measured anion permeabilities plotted as a function of the first solvation shell hydration energies calculated from the first principle simulations. <br><br> <br>
DOI: 10.6084/m9.figshare.11367704
title: Table S2. Primers used for site-directed mutagenesis

description: <b>Table S2. </b>Primers used for site-directed mutagenesis
DOI: 10.6084/m9.figshare.11367704.v1
title: Table S2. Primers used for site-directed mutagenesis

description: <b>Table S2. </b>Primers used for site-directed mutagenesis
DOI: 10.6084/m9.figshare.11367755.v1
title: sub-01_task-deterministicclassification_run-01_bold.npy

description: This is a copy of the data array in the file 'sub-01_task-deterministicclassification_run-01_bold.nii.gz' from https://openneuro.org/datasets/ds000002/versions/57fecec2cce88d000bc17549, stored in the numpy .npy format